diff --git a/package/MDAnalysis/analysis/encore/clustering/affinityprop.c b/package/MDAnalysis/analysis/encore/clustering/affinityprop.c index 6d9ae915199..b282110f633 100644 --- a/package/MDAnalysis/analysis/encore/clustering/affinityprop.c +++ b/package/MDAnalysis/analysis/encore/clustering/affinityprop.c @@ -1,11 +1,11 @@ -/* Generated by Cython 0.28.2 */ +/* Generated by Cython 0.28.5 */ /* BEGIN: Cython Metadata { "distutils": { "depends": [ - "/home/richard/miniconda2/envs/mda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h", - "/home/richard/miniconda2/envs/mda3/lib/python3.6/site-packages/numpy/core/include/numpy/ufuncobject.h", + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h", + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include/numpy/ufuncobject.h", "MDAnalysis/analysis/encore/clustering/include/ap.h" ], "extra_compile_args": [ @@ -15,7 +15,7 @@ "-funroll-loops" ], "include_dirs": [ - "/home/richard/miniconda2/envs/mda3/lib/python3.6/site-packages/numpy/core/include", + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include", "MDAnalysis/analysis/encore/clustering/include" ], "libraries": [ @@ -38,7 +38,7 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) #error Cython requires Python 2.6+ or Python 3.3+. #else -#define CYTHON_ABI "0_28_2" +#define CYTHON_ABI "0_28_5" #define CYTHON_FUTURE_DIVISION 0 #include #ifndef offsetof @@ -484,6 +484,7 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact + #define PyObject_Unicode PyObject_Str #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) @@ -681,7 +682,7 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); #define __Pyx_PySequence_Tuple(obj)\ @@ -789,7 +790,7 @@ static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } static PyObject *__pyx_m = NULL; static PyObject *__pyx_d; static PyObject *__pyx_b; -static PyObject *__pyx_cython_runtime; +static PyObject *__pyx_cython_runtime = NULL; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static PyObject *__pyx_empty_unicode; @@ -863,7 +864,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -872,7 +873,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -881,7 +882,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -890,7 +891,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -899,7 +900,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -908,7 +909,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -917,7 +918,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -926,7 +927,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -935,7 +936,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -944,7 +945,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -953,7 +954,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -962,7 +963,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -971,7 +972,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -980,7 +981,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -989,7 +990,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -998,7 +999,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1007,7 +1008,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1016,7 +1017,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1025,7 +1026,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1034,7 +1035,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1043,7 +1044,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1078,7 +1079,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do /*--- Type declarations ---*/ -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1087,7 +1088,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1096,7 +1097,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1105,7 +1106,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -3909,7 +3910,7 @@ static PyObject *__pyx_pf_10MDAnalysis_8analysis_6encore_10clustering_12affinity return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -3957,7 +3958,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); __Pyx_GIVEREF(__pyx_v_info->obj); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 * * cdef int i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -3966,7 +3967,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 * cdef int i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -3975,7 +3976,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -3984,7 +3985,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -3998,7 +3999,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -4009,7 +4010,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L4_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -4018,7 +4019,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -4031,7 +4032,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 229, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -4040,7 +4041,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -4054,7 +4055,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L7_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -4065,7 +4066,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -4074,7 +4075,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -4087,7 +4088,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 233, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -4096,7 +4097,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -4105,7 +4106,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -4114,7 +4115,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -4124,7 +4125,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) # <<<<<<<<<<<<<< @@ -4133,7 +4134,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyObject_Malloc((((sizeof(Py_ssize_t)) * 2) * ((size_t)__pyx_v_ndim)))); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -4142,7 +4143,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -4154,7 +4155,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -4163,7 +4164,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -4173,7 +4174,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -4183,7 +4184,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -4193,7 +4194,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -4204,7 +4205,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L9:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -4213,7 +4214,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -4222,7 +4223,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -4231,7 +4232,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -4240,7 +4241,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -4252,7 +4253,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 * cdef int offset * * info.obj = self # <<<<<<<<<<<<<< @@ -4265,7 +4266,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -4275,7 +4276,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(PyDataType_HASFIELDS(__pyx_v_descr) != 0)) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 * * if not PyDataType_HASFIELDS(descr): * t = descr.type_num # <<<<<<<<<<<<<< @@ -4285,7 +4286,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -4305,7 +4306,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L15_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -4322,7 +4323,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L14_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -4331,7 +4332,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -4344,7 +4345,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 263, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -4353,7 +4354,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -4365,7 +4366,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"b"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -4376,7 +4377,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"B"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -4387,7 +4388,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"h"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -4398,7 +4399,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"H"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -4409,7 +4410,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"i"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -4420,7 +4421,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"I"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -4431,7 +4432,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"l"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -4442,7 +4443,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"L"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -4453,7 +4454,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -4464,7 +4465,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -4475,7 +4476,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"f"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -4486,7 +4487,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"d"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -4497,7 +4498,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"g"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -4508,7 +4509,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zf"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -4519,7 +4520,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zd"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -4530,7 +4531,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zg"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -4542,7 +4543,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -4563,7 +4564,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -4572,7 +4573,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -4582,7 +4583,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -4591,7 +4592,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 * return * else: * info.format = PyObject_Malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -4601,7 +4602,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)PyObject_Malloc(0xFF)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 * else: * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -4610,7 +4611,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -4619,7 +4620,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -4629,7 +4630,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_8 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_8 == ((char *)NULL))) __PYX_ERR(1, 289, __pyx_L1_error) __pyx_v_f = __pyx_t_8; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -4639,7 +4640,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -4671,7 +4672,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -4695,7 +4696,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -4705,7 +4706,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) # <<<<<<<<<<<<<< @@ -4714,7 +4715,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->format); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -4723,7 +4724,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -4733,7 +4734,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * PyObject_Free(info.strides) # <<<<<<<<<<<<<< @@ -4742,7 +4743,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->strides); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -4751,7 +4752,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -4763,7 +4764,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -4777,7 +4778,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":776 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":776 * * cdef inline object PyArray_MultiIterNew1(a): * return PyArray_MultiIterNew(1, a) # <<<<<<<<<<<<<< @@ -4791,7 +4792,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -4810,7 +4811,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":778 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":778 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -4824,7 +4825,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":779 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":779 * * cdef inline object PyArray_MultiIterNew2(a, b): * return PyArray_MultiIterNew(2, a, b) # <<<<<<<<<<<<<< @@ -4838,7 +4839,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":778 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":778 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -4857,7 +4858,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":781 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":781 * return PyArray_MultiIterNew(2, a, b) * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< @@ -4871,7 +4872,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 0); - /* 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"../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":784 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< @@ -4918,7 +4919,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("PyArray_MultiIterNew4", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":785 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":785 * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): * return PyArray_MultiIterNew(4, a, b, c, d) # <<<<<<<<<<<<<< @@ -4932,7 +4933,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":784 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":784 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< @@ -4951,7 +4952,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":787 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":787 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -4965,7 +4966,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":788 + /* 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"../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":792 * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): * return d.subarray.shape # <<<<<<<<<<<<<< @@ -5034,7 +5035,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ __pyx_r = ((PyObject*)__pyx_v_d->subarray->shape); goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":791 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":791 * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< @@ -5043,7 +5044,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":794 + /* 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CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -5142,7 +5143,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":806 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":806 * * for childname in descr.names: * fields = descr.fields[childname] # <<<<<<<<<<<<<< @@ -5159,7 +5160,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3)); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":807 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":807 * for childname in descr.names: * fields = descr.fields[childname] * child, new_offset = fields # <<<<<<<<<<<<<< @@ -5194,7 +5195,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -5211,7 +5212,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -5224,7 +5225,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 810, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -5233,7 +5234,7 @@ static CYTHON_INLINE char 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__pyx_t_7; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -5279,7 +5280,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -5292,7 +5293,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 814, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -5301,7 +5302,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -5317,7 +5318,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -5326,7 +5327,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -5335,7 +5336,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -5346,7 +5347,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -5356,7 +5357,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -5366,7 +5367,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -5378,7 +5379,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -5388,7 +5389,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -5401,7 +5402,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __PYX_ERR(1, 834, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -5410,7 +5411,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -5428,7 +5429,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -5446,7 +5447,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -5464,7 +5465,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -5482,7 +5483,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -5500,7 +5501,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -5518,7 +5519,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -5536,7 +5537,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -5554,7 +5555,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -5572,7 +5573,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -5590,7 +5591,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -5608,7 +5609,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -5626,7 +5627,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -5644,7 +5645,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -5664,7 +5665,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -5684,7 +5685,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -5704,7 +5705,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -5722,7 +5723,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -5741,7 +5742,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -5750,7 +5751,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -5760,7 +5761,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -5773,7 +5774,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -5783,7 +5784,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -5793,7 +5794,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -5818,7 +5819,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -5833,7 +5834,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -5844,7 +5845,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -5853,7 +5854,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_baseptr = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -5863,7 +5864,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a goto __pyx_L3; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -5873,7 +5874,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a /*else*/ { Py_INCREF(__pyx_v_base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -5884,7 +5885,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -5893,7 +5894,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -5902,7 +5903,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -5914,7 +5915,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -5928,7 +5929,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -5938,7 +5939,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< @@ -5949,7 +5950,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -5958,7 +5959,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 * return None * else: * return arr.base # <<<<<<<<<<<<<< @@ -5972,7 +5973,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py goto __pyx_L0; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -5987,7 +5988,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -6008,7 +6009,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_array", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -6024,7 +6025,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 * cdef inline int import_array() except -1: * try: * _import_array() # <<<<<<<<<<<<<< @@ -6033,7 +6034,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { */ __pyx_t_4 = _import_array(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 998, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -6047,7 +6048,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 * try: * _import_array() * except Exception: # <<<<<<<<<<<<<< @@ -6062,7 +6063,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -6078,7 +6079,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -6093,7 +6094,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -6116,7 +6117,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -6137,7 +6138,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_umath", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -6153,7 +6154,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1004 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1004 * cdef inline int import_umath() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -6162,7 +6163,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1004, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -6176,7 +6177,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -6191,7 +6192,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -6207,7 +6208,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -6222,7 +6223,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -6245,7 +6246,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* 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"../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1010 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -6291,7 +6292,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1010, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -6305,7 +6306,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1011 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1011 * try: * 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__Pyx_GIVEREF(__pyx_tuple__8); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -6598,7 +6599,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__9); __Pyx_GIVEREF(__pyx_tuple__9); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -6730,8 +6731,8 @@ static int __Pyx_modinit_function_import_code(void) { #ifndef CYTHON_SMALL_CODE #if defined(__clang__) #define CYTHON_SMALL_CODE -#elif defined(__GNUC__) - #define CYTHON_SMALL_CODE __attribute__((optimize("Os"))) +#elif defined(__GNUC__) && (!(defined(__cplusplus)) || (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 4))) + #define CYTHON_SMALL_CODE __attribute__((cold)) #else #define CYTHON_SMALL_CODE #endif @@ -6954,7 +6955,7 @@ if (!__Pyx_RefNanny) { if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_2) < 0) __PYX_ERR(0, 1, __pyx_L1_error) __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -7517,7 +7518,7 @@ static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { /* SaveResetException */ #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 *type = tstate->exc_state.exc_type; *value = tstate->exc_state.exc_value; *tb = tstate->exc_state.exc_traceback; @@ -7532,7 +7533,7 @@ static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject * } static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -8598,7 +8599,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) *value = local_value; *tb = local_tb; #if CYTHON_FAST_THREAD_STATE - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -8652,6 +8653,9 @@ static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_li #if CYTHON_COMPILING_IN_CPYTHON PyObject **cython_runtime_dict; #endif + if (unlikely(!__pyx_cython_runtime)) { + return c_line; + } __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); #if CYTHON_COMPILING_IN_CPYTHON cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); @@ -9727,14 +9731,42 @@ static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, return res; } #endif +static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + assert(PyExceptionClass_Check(exc_type)); + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i #ifndef offsetof @@ -478,6 +478,7 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact + #define PyObject_Unicode PyObject_Str #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) @@ -675,7 +676,7 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); #define __Pyx_PySequence_Tuple(obj)\ @@ -783,7 +784,7 @@ static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } static PyObject *__pyx_m = NULL; static PyObject *__pyx_d; static PyObject *__pyx_b; -static PyObject *__pyx_cython_runtime; +static PyObject *__pyx_cython_runtime = NULL; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static PyObject *__pyx_empty_unicode; @@ -857,7 +858,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -866,7 +867,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -875,7 +876,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -884,7 +885,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -893,7 +894,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -902,7 +903,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -911,7 +912,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -920,7 +921,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -929,7 +930,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -938,7 +939,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -947,7 +948,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -956,7 +957,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -965,7 +966,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -974,7 +975,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -983,7 +984,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -992,7 +993,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1001,7 +1002,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1010,7 +1011,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1019,7 +1020,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1028,7 +1029,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1037,7 +1038,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1072,7 +1073,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do /*--- Type declarations ---*/ -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1081,7 +1082,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1090,7 +1091,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1099,7 +1100,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -1925,7 +1926,7 @@ static PyObject *__pyx_pf_10MDAnalysis_8analysis_6encore_6cutils_PureRMSD(CYTHON return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -1973,7 +1974,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); __Pyx_GIVEREF(__pyx_v_info->obj); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 * * cdef int i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -1982,7 +1983,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 * cdef int i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -1991,7 +1992,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -2000,7 +2001,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2014,7 +2015,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -2025,7 +2026,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L4_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2034,7 +2035,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -2047,7 +2048,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 229, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2056,7 +2057,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2070,7 +2071,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L7_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -2081,7 +2082,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2090,7 +2091,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -2103,7 +2104,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 233, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2112,7 +2113,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -2121,7 +2122,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -2130,7 +2131,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -2140,7 +2141,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) # <<<<<<<<<<<<<< @@ -2149,7 +2150,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyObject_Malloc((((sizeof(Py_ssize_t)) * 2) * ((size_t)__pyx_v_ndim)))); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -2158,7 +2159,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -2170,7 +2171,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -2179,7 +2180,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -2189,7 +2190,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -2199,7 +2200,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -2209,7 +2210,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -2220,7 +2221,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L9:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -2229,7 +2230,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -2238,7 +2239,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -2247,7 +2248,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -2256,7 +2257,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -2268,7 +2269,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 * cdef int offset * * info.obj = self # <<<<<<<<<<<<<< @@ -2281,7 +2282,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -2291,7 +2292,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(PyDataType_HASFIELDS(__pyx_v_descr) != 0)) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 * * if not PyDataType_HASFIELDS(descr): * t = descr.type_num # <<<<<<<<<<<<<< @@ -2301,7 +2302,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -2321,7 +2322,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L15_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -2338,7 +2339,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L14_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -2347,7 +2348,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -2360,7 +2361,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 263, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -2369,7 +2370,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -2381,7 +2382,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"b"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -2392,7 +2393,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"B"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -2403,7 +2404,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"h"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -2414,7 +2415,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"H"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -2425,7 +2426,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"i"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -2436,7 +2437,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"I"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -2447,7 +2448,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"l"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -2458,7 +2459,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"L"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -2469,7 +2470,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -2480,7 +2481,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -2491,7 +2492,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"f"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -2502,7 +2503,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"d"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -2513,7 +2514,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"g"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -2524,7 +2525,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zf"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -2535,7 +2536,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zd"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -2546,7 +2547,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zg"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -2558,7 +2559,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -2579,7 +2580,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -2588,7 +2589,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -2598,7 +2599,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -2607,7 +2608,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 * return * else: * info.format = PyObject_Malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -2617,7 +2618,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)PyObject_Malloc(0xFF)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 * else: * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -2626,7 +2627,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -2635,7 +2636,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -2645,7 +2646,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_8 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_8 == ((char *)NULL))) __PYX_ERR(1, 289, __pyx_L1_error) __pyx_v_f = __pyx_t_8; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -2655,7 +2656,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -2687,7 +2688,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -2711,7 +2712,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -2721,7 +2722,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) # <<<<<<<<<<<<<< @@ -2730,7 +2731,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->format); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -2739,7 +2740,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -2749,7 +2750,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * PyObject_Free(info.strides) # <<<<<<<<<<<<<< @@ -2758,7 +2759,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->strides); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -2767,7 +2768,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -2779,7 +2780,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -2793,7 +2794,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":776 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":776 * * cdef inline object PyArray_MultiIterNew1(a): * return PyArray_MultiIterNew(1, a) # <<<<<<<<<<<<<< @@ -2807,7 +2808,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -2826,7 +2827,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":778 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":778 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -2840,7 +2841,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 0); - /* 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PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -3014,7 +3015,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< @@ -3028,7 +3029,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ int __pyx_t_1; __Pyx_RefNannySetupContext("PyDataType_SHAPE", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":791 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":791 * * cdef inline tuple PyDataType_SHAPE(dtype d): * if 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0; __PYX_ERR(1, 810, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -3249,7 +3250,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -3269,7 +3270,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L8_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":813 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":813 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -3286,7 +3287,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = __pyx_t_7; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -3295,7 +3296,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -3308,7 +3309,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 814, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -3317,7 +3318,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -3333,7 +3334,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -3342,7 +3343,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -3351,7 +3352,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -3362,7 +3363,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -3372,7 +3373,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -3382,7 +3383,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -3394,7 +3395,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -3404,7 +3405,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -3417,7 +3418,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __PYX_ERR(1, 834, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -3426,7 +3427,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -3444,7 +3445,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -3462,7 +3463,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -3480,7 +3481,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -3498,7 +3499,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -3516,7 +3517,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -3534,7 +3535,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -3552,7 +3553,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -3570,7 +3571,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -3588,7 +3589,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -3606,7 +3607,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -3624,7 +3625,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -3642,7 +3643,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -3660,7 +3661,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -3680,7 +3681,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -3700,7 +3701,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -3720,7 +3721,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -3738,7 +3739,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -3757,7 +3758,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -3766,7 +3767,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -3776,7 +3777,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -3789,7 +3790,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -3799,7 +3800,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -3809,7 +3810,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -3834,7 +3835,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -3849,7 +3850,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -3860,7 +3861,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -3869,7 +3870,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_baseptr = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -3879,7 +3880,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a goto __pyx_L3; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -3889,7 +3890,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a /*else*/ { Py_INCREF(__pyx_v_base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -3900,7 +3901,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -3909,7 +3910,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -3918,7 +3919,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -3930,7 +3931,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -3944,7 +3945,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -3954,7 +3955,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< @@ -3965,7 +3966,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -3974,7 +3975,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 * return None * else: * return arr.base # <<<<<<<<<<<<<< @@ -3988,7 +3989,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py goto __pyx_L0; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -4003,7 +4004,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -4024,7 +4025,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_array", 0); - /* 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"../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -4063,7 +4064,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 * try: * _import_array() * except Exception: # <<<<<<<<<<<<<< @@ -4078,7 +4079,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray 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{ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -4153,7 +4154,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_umath", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -4169,7 +4170,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1004 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1004 * cdef inline int import_umath() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -4178,7 +4179,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1004, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -4192,7 +4193,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -4207,7 +4208,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -4223,7 +4224,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -4238,7 +4239,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -4261,7 +4262,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -4282,7 +4283,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { PyObject *__pyx_t_8 = 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"../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -4519,7 +4520,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__4); __Pyx_GIVEREF(__pyx_tuple__4); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -4530,7 +4531,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__5); __Pyx_GIVEREF(__pyx_tuple__5); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -4541,7 +4542,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__6); __Pyx_GIVEREF(__pyx_tuple__6); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -4552,7 +4553,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__7); __Pyx_GIVEREF(__pyx_tuple__7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -4563,7 +4564,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__8); __Pyx_GIVEREF(__pyx_tuple__8); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -4693,8 +4694,8 @@ static int __Pyx_modinit_function_import_code(void) { #ifndef CYTHON_SMALL_CODE #if defined(__clang__) #define CYTHON_SMALL_CODE -#elif defined(__GNUC__) - #define CYTHON_SMALL_CODE __attribute__((optimize("Os"))) +#elif defined(__GNUC__) && (!(defined(__cplusplus)) || (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 4))) + #define CYTHON_SMALL_CODE __attribute__((cold)) #else #define CYTHON_SMALL_CODE #endif @@ -4883,7 +4884,7 @@ if (!__Pyx_RefNanny) { if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) __PYX_ERR(0, 1, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -6143,7 +6144,7 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { /* SaveResetException */ #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 *type = tstate->exc_state.exc_type; *value = tstate->exc_state.exc_value; *tb = tstate->exc_state.exc_traceback; @@ -6158,7 +6159,7 @@ static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject * } static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -6242,7 +6243,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) *value = local_value; *tb = local_tb; #if CYTHON_FAST_THREAD_STATE - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -6347,6 +6348,9 @@ static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_li #if CYTHON_COMPILING_IN_CPYTHON PyObject **cython_runtime_dict; #endif + if (unlikely(!__pyx_cython_runtime)) { + return c_line; + } __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); #if CYTHON_COMPILING_IN_CPYTHON cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); @@ -7422,14 +7426,42 @@ static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, return res; } #endif +static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + assert(PyExceptionClass_Check(exc_type)); + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i #ifndef offsetof @@ -484,6 +484,7 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact + #define PyObject_Unicode PyObject_Str #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) @@ -681,7 +682,7 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); #define __Pyx_PySequence_Tuple(obj)\ @@ -789,7 +790,7 @@ static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } static PyObject *__pyx_m = NULL; static PyObject *__pyx_d; static PyObject *__pyx_b; -static PyObject *__pyx_cython_runtime; +static PyObject *__pyx_cython_runtime = NULL; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static PyObject *__pyx_empty_unicode; @@ -863,7 +864,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -872,7 +873,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -881,7 +882,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -890,7 +891,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -899,7 +900,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -908,7 +909,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -917,7 +918,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -926,7 +927,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -935,7 +936,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -944,7 +945,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -953,7 +954,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -962,7 +963,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -971,7 +972,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -980,7 +981,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -989,7 +990,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -998,7 +999,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1007,7 +1008,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1016,7 +1017,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1025,7 +1026,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1034,7 +1035,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1043,7 +1044,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1078,7 +1079,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do /*--- Type declarations ---*/ -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1087,7 +1088,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1096,7 +1097,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1105,7 +1106,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -2187,7 +2188,7 @@ static PyObject *__pyx_pf_10MDAnalysis_8analysis_6encore_24dimensionality_reduct return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -2235,7 +2236,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); __Pyx_GIVEREF(__pyx_v_info->obj); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 * * cdef int i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -2244,7 +2245,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 * cdef int i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -2253,7 +2254,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -2262,7 +2263,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2276,7 +2277,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -2287,7 +2288,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L4_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2296,7 +2297,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -2309,7 +2310,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 229, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2318,7 +2319,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2332,7 +2333,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L7_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -2343,7 +2344,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2352,7 +2353,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -2365,7 +2366,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 233, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2374,7 +2375,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -2383,7 +2384,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -2392,7 +2393,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -2402,7 +2403,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) # <<<<<<<<<<<<<< @@ -2411,7 +2412,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyObject_Malloc((((sizeof(Py_ssize_t)) * 2) * ((size_t)__pyx_v_ndim)))); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -2420,7 +2421,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -2432,7 +2433,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -2441,7 +2442,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -2451,7 +2452,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -2461,7 +2462,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -2471,7 +2472,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -2482,7 +2483,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L9:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -2491,7 +2492,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -2500,7 +2501,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -2509,7 +2510,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -2518,7 +2519,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -2530,7 +2531,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 * cdef int offset * * info.obj = self # <<<<<<<<<<<<<< @@ -2543,7 +2544,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -2553,7 +2554,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(PyDataType_HASFIELDS(__pyx_v_descr) != 0)) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 * * if not PyDataType_HASFIELDS(descr): * t = descr.type_num # <<<<<<<<<<<<<< @@ -2563,7 +2564,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -2583,7 +2584,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L15_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -2600,7 +2601,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L14_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -2609,7 +2610,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -2622,7 +2623,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 263, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -2631,7 +2632,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -2643,7 +2644,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"b"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -2654,7 +2655,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"B"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -2665,7 +2666,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"h"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -2676,7 +2677,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"H"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -2687,7 +2688,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"i"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -2698,7 +2699,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"I"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -2709,7 +2710,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"l"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -2720,7 +2721,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"L"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -2731,7 +2732,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -2742,7 +2743,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -2753,7 +2754,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"f"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -2764,7 +2765,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"d"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -2775,7 +2776,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"g"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -2786,7 +2787,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zf"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -2797,7 +2798,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zd"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -2808,7 +2809,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zg"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -2820,7 +2821,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -2841,7 +2842,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -2850,7 +2851,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -2860,7 +2861,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -2869,7 +2870,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 * return * else: * info.format = PyObject_Malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -2879,7 +2880,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)PyObject_Malloc(0xFF)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 * else: * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -2888,7 +2889,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -2897,7 +2898,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -2907,7 +2908,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_8 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_8 == ((char *)NULL))) __PYX_ERR(1, 289, __pyx_L1_error) __pyx_v_f = __pyx_t_8; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -2917,7 +2918,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -2949,7 +2950,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -2973,7 +2974,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -2983,7 +2984,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) # <<<<<<<<<<<<<< @@ -2992,7 +2993,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->format); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -3001,7 +3002,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -3011,7 +3012,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * PyObject_Free(info.strides) # <<<<<<<<<<<<<< @@ -3020,7 +3021,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->strides); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -3029,7 +3030,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -3041,7 +3042,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -3055,7 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*__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":778 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":778 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -3102,7 +3103,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":779 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":779 * * cdef inline object PyArray_MultiIterNew2(a, b): * return PyArray_MultiIterNew(2, a, b) # <<<<<<<<<<<<<< @@ -3116,7 +3117,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":778 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":778 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -3135,7 +3136,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":781 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":781 * return PyArray_MultiIterNew(2, a, b) * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< @@ -3149,7 +3150,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 0); - /* 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*__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 814, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -3579,7 +3580,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -3595,7 +3596,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -3604,7 +3605,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -3613,7 +3614,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -3624,7 +3625,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -3634,7 +3635,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -3644,7 +3645,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -3656,7 +3657,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -3666,7 +3667,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -3679,7 +3680,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __PYX_ERR(1, 834, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -3688,7 +3689,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -3706,7 +3707,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -3724,7 +3725,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -3742,7 +3743,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -3760,7 +3761,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -3778,7 +3779,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -3796,7 +3797,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -3814,7 +3815,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -3832,7 +3833,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -3850,7 +3851,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -3868,7 +3869,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -3886,7 +3887,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -3904,7 +3905,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -3922,7 +3923,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -3942,7 +3943,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -3962,7 +3963,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -3982,7 +3983,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -4000,7 +4001,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -4019,7 +4020,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -4028,7 +4029,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -4038,7 +4039,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -4051,7 +4052,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -4061,7 +4062,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -4071,7 +4072,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -4096,7 +4097,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -4111,7 +4112,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -4122,7 +4123,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -4131,7 +4132,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_baseptr = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -4141,7 +4142,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a goto __pyx_L3; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -4151,7 +4152,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a /*else*/ { Py_INCREF(__pyx_v_base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -4162,7 +4163,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -4171,7 +4172,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -4180,7 +4181,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -4192,7 +4193,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -4206,7 +4207,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -4216,7 +4217,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< @@ -4227,7 +4228,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -4236,7 +4237,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 * return None * else: * return arr.base # <<<<<<<<<<<<<< @@ -4250,7 +4251,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py goto __pyx_L0; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -4265,7 +4266,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -4286,7 +4287,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_array", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -4302,7 +4303,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 * cdef inline int import_array() except -1: * try: * _import_array() # <<<<<<<<<<<<<< @@ -4311,7 +4312,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { */ __pyx_t_4 = _import_array(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 998, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -4325,7 +4326,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 * try: * _import_array() * except Exception: # <<<<<<<<<<<<<< @@ -4340,7 +4341,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -4356,7 +4357,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -4371,7 +4372,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -4394,7 +4395,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -4415,7 +4416,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_umath", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -4431,7 +4432,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1004 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1004 * cdef inline int import_umath() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -4440,7 +4441,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1004, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -4454,7 +4455,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -4469,7 +4470,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -4485,7 +4486,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -4500,7 +4501,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -4523,7 +4524,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -4544,7 +4545,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_ufunc", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -4560,7 +4561,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1010 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1010 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -4569,7 +4570,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1010, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -4583,7 +4584,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1011 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1011 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -4597,7 +4598,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -4611,7 +4612,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -4626,7 +4627,7 @@ static CYTHON_INLINE int 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__Pyx_GOTREF(__pyx_tuple__2); __Pyx_GIVEREF(__pyx_tuple__2); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -4779,7 +4780,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__3); __Pyx_GIVEREF(__pyx_tuple__3); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -4790,7 +4791,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__4); __Pyx_GIVEREF(__pyx_tuple__4); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -4801,7 +4802,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__5); __Pyx_GIVEREF(__pyx_tuple__5); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -4812,7 +4813,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__6); __Pyx_GIVEREF(__pyx_tuple__6); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -4823,7 +4824,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__7); __Pyx_GIVEREF(__pyx_tuple__7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -4834,7 +4835,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__8); __Pyx_GIVEREF(__pyx_tuple__8); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -4845,7 +4846,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__9); __Pyx_GIVEREF(__pyx_tuple__9); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -4976,8 +4977,8 @@ static int __Pyx_modinit_function_import_code(void) { #ifndef CYTHON_SMALL_CODE #if defined(__clang__) #define CYTHON_SMALL_CODE -#elif defined(__GNUC__) - #define CYTHON_SMALL_CODE __attribute__((optimize("Os"))) +#elif defined(__GNUC__) && (!(defined(__cplusplus)) || (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 4))) + #define CYTHON_SMALL_CODE __attribute__((cold)) #else #define CYTHON_SMALL_CODE #endif @@ -5178,7 +5179,7 @@ if (!__Pyx_RefNanny) { if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) __PYX_ERR(0, 1, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -6444,7 +6445,7 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { /* SaveResetException */ #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 *type = tstate->exc_state.exc_type; *value = tstate->exc_state.exc_value; *tb = tstate->exc_state.exc_traceback; @@ -6459,7 +6460,7 @@ static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject * } static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -6543,7 +6544,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) *value = local_value; *tb = local_tb; #if CYTHON_FAST_THREAD_STATE - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -6648,6 +6649,9 @@ static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_li #if CYTHON_COMPILING_IN_CPYTHON PyObject **cython_runtime_dict; #endif + if (unlikely(!__pyx_cython_runtime)) { + return c_line; + } __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); #if CYTHON_COMPILING_IN_CPYTHON cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); @@ -7723,14 +7727,42 @@ static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, return res; } #endif +static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + assert(PyExceptionClass_Check(exc_type)); + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i +#ifndef offsetof + #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#endif +#if !defined(WIN32) && !defined(MS_WINDOWS) + #ifndef __stdcall + #define __stdcall + #endif + #ifndef __cdecl + #define __cdecl + #endif + #ifndef __fastcall + #define __fastcall + #endif +#endif +#ifndef DL_IMPORT + #define DL_IMPORT(t) t +#endif +#ifndef DL_EXPORT + #define DL_EXPORT(t) t +#endif +#define __PYX_COMMA , +#ifndef HAVE_LONG_LONG + #if PY_VERSION_HEX >= 0x02070000 + #define HAVE_LONG_LONG + #endif +#endif +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif +#ifdef PYPY_VERSION + #define CYTHON_COMPILING_IN_PYPY 1 + #define CYTHON_COMPILING_IN_PYSTON 0 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #undef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 0 + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #if PY_VERSION_HEX < 0x03050000 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #elif !defined(CYTHON_USE_ASYNC_SLOTS) + #define CYTHON_USE_ASYNC_SLOTS 1 + #endif + #undef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 0 + #undef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 0 + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #undef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 1 + #undef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 0 + #undef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 0 + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 0 + #undef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT 0 + #undef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE 0 +#elif defined(PYSTON_VERSION) + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_PYSTON 1 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #ifndef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 1 + #endif + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #undef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 0 + #ifndef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 1 + #endif + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #ifndef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 0 + #endif + #ifndef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 1 + #endif + #ifndef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 1 + #endif + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 0 + #undef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT 0 + #undef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE 0 +#else + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_PYSTON 0 + #define CYTHON_COMPILING_IN_CPYTHON 1 + #ifndef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 1 + #endif + #if PY_VERSION_HEX < 0x02070000 + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #elif !defined(CYTHON_USE_PYTYPE_LOOKUP) + #define CYTHON_USE_PYTYPE_LOOKUP 1 + #endif + #if PY_MAJOR_VERSION < 3 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #elif !defined(CYTHON_USE_ASYNC_SLOTS) + #define CYTHON_USE_ASYNC_SLOTS 1 + #endif + #if PY_VERSION_HEX < 0x02070000 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #elif !defined(CYTHON_USE_PYLONG_INTERNALS) + #define CYTHON_USE_PYLONG_INTERNALS 1 + #endif + #ifndef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 1 + #endif + #ifndef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 1 + #endif + #if PY_VERSION_HEX < 0x030300F0 + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #elif !defined(CYTHON_USE_UNICODE_WRITER) + #define CYTHON_USE_UNICODE_WRITER 1 + #endif + #ifndef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 0 + #endif + #ifndef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 1 + #endif + #ifndef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 1 + #endif + #ifndef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 1 + #endif + #ifndef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 1 + #endif + #ifndef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT (0 && PY_VERSION_HEX >= 0x03050000) + #endif + #ifndef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1) + #endif +#endif +#if !defined(CYTHON_FAST_PYCCALL) +#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) +#endif +#if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" + #undef SHIFT + #undef BASE + #undef MASK +#endif +#ifndef __has_attribute + #define __has_attribute(x) 0 +#endif +#ifndef __has_cpp_attribute + #define __has_cpp_attribute(x) 0 +#endif +#ifndef CYTHON_RESTRICT + #if defined(__GNUC__) + #define CYTHON_RESTRICT __restrict__ + #elif defined(_MSC_VER) && _MSC_VER >= 1400 + #define CYTHON_RESTRICT __restrict + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_RESTRICT restrict + #else + #define CYTHON_RESTRICT + #endif +#endif +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +#ifndef CYTHON_MAYBE_UNUSED_VAR +# if defined(__cplusplus) + template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } +# else +# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) +# endif +#endif +#ifndef CYTHON_NCP_UNUSED +# if CYTHON_COMPILING_IN_CPYTHON +# define CYTHON_NCP_UNUSED +# else +# define CYTHON_NCP_UNUSED CYTHON_UNUSED +# endif +#endif +#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) +#ifdef _MSC_VER + #ifndef _MSC_STDINT_H_ + #if _MSC_VER < 1300 + typedef unsigned char uint8_t; + typedef unsigned int uint32_t; + #else + typedef unsigned __int8 uint8_t; + typedef unsigned __int32 uint32_t; + #endif + #endif +#else + #include +#endif +#ifndef CYTHON_FALLTHROUGH + #if defined(__cplusplus) && __cplusplus >= 201103L + #if __has_cpp_attribute(fallthrough) + #define CYTHON_FALLTHROUGH [[fallthrough]] + #elif __has_cpp_attribute(clang::fallthrough) + #define CYTHON_FALLTHROUGH [[clang::fallthrough]] + #elif __has_cpp_attribute(gnu::fallthrough) + #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] + #endif + #endif + #ifndef CYTHON_FALLTHROUGH + #if __has_attribute(fallthrough) + #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) + #else + #define CYTHON_FALLTHROUGH + #endif + #endif + #if defined(__clang__ ) && defined(__apple_build_version__) + #if __apple_build_version__ < 7000000 + #undef CYTHON_FALLTHROUGH + #define CYTHON_FALLTHROUGH + #endif + #endif +#endif + +#ifndef __cplusplus + #error "Cython files generated with the C++ option must be compiled with a C++ compiler." +#endif +#ifndef CYTHON_INLINE + #if defined(__clang__) + #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) + #else + #define CYTHON_INLINE inline + #endif +#endif +template +void __Pyx_call_destructor(T& x) { + x.~T(); +} +template +class __Pyx_FakeReference { + public: + __Pyx_FakeReference() : ptr(NULL) { } + __Pyx_FakeReference(const T& ref) : ptr(const_cast(&ref)) { } + T *operator->() { return ptr; } + T *operator&() { return ptr; } + operator T&() { return *ptr; } + template bool operator ==(U other) { return *ptr == other; } + template bool operator !=(U other) { return *ptr != other; } + private: + T *ptr; +}; + +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) + #define Py_OptimizeFlag 0 +#endif +#define __PYX_BUILD_PY_SSIZE_T "n" +#define CYTHON_FORMAT_SSIZE_T "z" +#if PY_MAJOR_VERSION < 3 + #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyClass_Type +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyType_Type +#endif +#ifndef Py_TPFLAGS_CHECKTYPES + #define Py_TPFLAGS_CHECKTYPES 0 +#endif +#ifndef Py_TPFLAGS_HAVE_INDEX + #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#ifndef Py_TPFLAGS_HAVE_NEWBUFFER + #define Py_TPFLAGS_HAVE_NEWBUFFER 0 +#endif +#ifndef Py_TPFLAGS_HAVE_FINALIZE + #define Py_TPFLAGS_HAVE_FINALIZE 0 +#endif +#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) + #ifndef METH_FASTCALL + #define METH_FASTCALL 0x80 + #endif + typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); + typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, + Py_ssize_t nargs, PyObject *kwnames); +#else + #define __Pyx_PyCFunctionFast _PyCFunctionFast + #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords +#endif +#if CYTHON_FAST_PYCCALL +#define __Pyx_PyFastCFunction_Check(func)\ + ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS))))) +#else +#define __Pyx_PyFastCFunction_Check(func) 0 +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) + #define PyObject_Malloc(s) PyMem_Malloc(s) + #define PyObject_Free(p) PyMem_Free(p) + #define PyObject_Realloc(p) PyMem_Realloc(p) +#endif +#if CYTHON_COMPILING_IN_PYSTON + #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) + #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) +#else + #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) + #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) +#endif +#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 + #define __Pyx_PyThreadState_Current PyThreadState_GET() +#elif PY_VERSION_HEX >= 0x03060000 + #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() +#elif PY_VERSION_HEX >= 0x03000000 + #define __Pyx_PyThreadState_Current PyThreadState_GET() +#else + #define __Pyx_PyThreadState_Current _PyThreadState_Current +#endif +#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) +#include "pythread.h" +#define Py_tss_NEEDS_INIT 0 +typedef int Py_tss_t; +static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { + *key = PyThread_create_key(); + return 0; // PyThread_create_key reports success always +} +static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { + Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); + *key = Py_tss_NEEDS_INIT; + return key; +} +static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { + PyObject_Free(key); +} +static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { + return *key != Py_tss_NEEDS_INIT; +} +static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { + PyThread_delete_key(*key); + *key = Py_tss_NEEDS_INIT; +} +static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { + return PyThread_set_key_value(*key, value); +} +static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { + return PyThread_get_key_value(*key); +} +#endif // TSS (Thread Specific Storage) API +#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) +#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) +#else +#define __Pyx_PyDict_NewPresized(n) PyDict_New() +#endif +#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS +#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) +#else +#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) +#endif +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) + #define CYTHON_PEP393_ENABLED 1 + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) + #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) + #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) + #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) +#else + #define CYTHON_PEP393_ENABLED 0 + #define PyUnicode_1BYTE_KIND 1 + #define PyUnicode_2BYTE_KIND 2 + #define PyUnicode_4BYTE_KIND 4 + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) + #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) + #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) + #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) + #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) +#endif +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) +#else + #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ + PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) + #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) + #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) + #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) +#endif +#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) +#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) +#else + #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) +#endif +#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII) + #define PyObject_ASCII(o) PyObject_Repr(o) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBaseString_Type PyUnicode_Type + #define PyStringObject PyUnicodeObject + #define PyString_Type PyUnicode_Type + #define PyString_Check PyUnicode_Check + #define PyString_CheckExact PyUnicode_CheckExact + #define PyObject_Unicode PyObject_Str +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) + #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) +#else + #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) + #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) +#endif +#ifndef PySet_CheckExact + #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) +#endif +#if CYTHON_ASSUME_SAFE_MACROS + #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq) +#else + #define __Pyx_PySequence_SIZE(seq) PySequence_Size(seq) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyIntObject PyLongObject + #define PyInt_Type PyLong_Type + #define PyInt_Check(op) PyLong_Check(op) + #define PyInt_CheckExact(op) PyLong_CheckExact(op) + #define PyInt_FromString PyLong_FromString + #define PyInt_FromUnicode PyLong_FromUnicode + #define PyInt_FromLong PyLong_FromLong + #define PyInt_FromSize_t PyLong_FromSize_t + #define PyInt_FromSsize_t PyLong_FromSsize_t + #define PyInt_AsLong PyLong_AsLong + #define PyInt_AS_LONG PyLong_AS_LONG + #define PyInt_AsSsize_t PyLong_AsSsize_t + #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask + #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask + #define PyNumber_Int PyNumber_Long +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBoolObject PyLongObject +#endif +#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY + #ifndef PyUnicode_InternFromString + #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) + #endif +#endif +#if PY_VERSION_HEX < 0x030200A4 + typedef long Py_hash_t; + #define __Pyx_PyInt_FromHash_t PyInt_FromLong + #define __Pyx_PyInt_AsHash_t PyInt_AsLong +#else + #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t + #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : (Py_INCREF(func), func)) +#else + #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) +#endif +#if CYTHON_USE_ASYNC_SLOTS + #if PY_VERSION_HEX >= 0x030500B1 + #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods + #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) + #else + #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) + #endif +#else + #define __Pyx_PyType_AsAsync(obj) NULL +#endif +#ifndef __Pyx_PyAsyncMethodsStruct + typedef struct { + unaryfunc am_await; + unaryfunc am_aiter; + unaryfunc am_anext; + } __Pyx_PyAsyncMethodsStruct; +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) + #define _USE_MATH_DEFINES +#endif +#include +#ifdef NAN +#define __PYX_NAN() ((float) NAN) +#else +static CYTHON_INLINE float __PYX_NAN() { + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif +#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL) +#define __Pyx_truncl trunc +#else +#define __Pyx_truncl truncl +#endif + + +#define __PYX_ERR(f_index, lineno, Ln_error) \ +{ \ + __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; goto Ln_error; \ +} + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#define __PYX_HAVE__MDAnalysis__lib___augment +#define __PYX_HAVE_API__MDAnalysis__lib___augment +/* Early includes */ +#include +#include +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" +#include "ios" +#include "new" +#include "stdexcept" +#include "typeinfo" +#include +#include "pythread.h" +#include +#include "pystate.h" +#ifdef _OPENMP +#include +#endif /* _OPENMP */ + +#if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS) +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 +#define __PYX_DEFAULT_STRING_ENCODING "" +#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#define __Pyx_uchar_cast(c) ((unsigned char)c) +#define __Pyx_long_cast(x) ((long)x) +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ + (sizeof(type) < sizeof(Py_ssize_t)) ||\ + (sizeof(type) > sizeof(Py_ssize_t) &&\ + likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX) &&\ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ + v == (type)PY_SSIZE_T_MIN))) ||\ + (sizeof(type) == sizeof(Py_ssize_t) &&\ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX))) ) +#if defined (__cplusplus) && __cplusplus >= 201103L + #include + #define __Pyx_sst_abs(value) std::abs(value) +#elif SIZEOF_INT >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) abs(value) +#elif SIZEOF_LONG >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) labs(value) +#elif defined (_MSC_VER) + #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value)) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) +#elif defined (__GNUC__) + #define __Pyx_sst_abs(value) __builtin_llabs(value) +#else + #define __Pyx_sst_abs(value) ((value<0) ? -value : value) +#endif +static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) +#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#else + #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#endif +#define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) +static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { + const Py_UNICODE *u_end = u; + while (*u_end++) ; + return (size_t)(u_end - u - 1); +} +#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) +#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode +#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode +#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) +#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); +#define __Pyx_PySequence_Tuple(obj)\ + (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj)) +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +#if CYTHON_ASSUME_SAFE_MACROS +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) +#else +#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) +#endif +#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x)) +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII +static int __Pyx_sys_getdefaultencoding_not_ascii; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + PyObject* ascii_chars_u = NULL; + PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { + __Pyx_sys_getdefaultencoding_not_ascii = 0; + } else { + char ascii_chars[128]; + int c; + for (c = 0; c < 128; c++) { + ascii_chars[c] = c; + } + __Pyx_sys_getdefaultencoding_not_ascii = 1; + ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); + if (!ascii_chars_u) goto bad; + ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + PyErr_Format( + PyExc_ValueError, + "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", + default_encoding_c); + goto bad; + } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); + } + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + Py_XDECREF(ascii_chars_u); + Py_XDECREF(ascii_chars_b); + return -1; +} +#endif +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) +#else +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +static char* __PYX_DEFAULT_STRING_ENCODING; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; + strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + return -1; +} +#endif +#endif + + +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ + #define likely(x) (x) + #define unlikely(x) (x) +#endif /* __GNUC__ */ +static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } + +static PyObject *__pyx_m = NULL; +static PyObject *__pyx_d; +static PyObject *__pyx_b; +static PyObject *__pyx_cython_runtime = NULL; +static PyObject *__pyx_empty_tuple; +static PyObject *__pyx_empty_bytes; +static PyObject *__pyx_empty_unicode; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; + +/* Header.proto */ +#if !defined(CYTHON_CCOMPLEX) + #if defined(__cplusplus) + #define CYTHON_CCOMPLEX 1 + #elif defined(_Complex_I) + #define CYTHON_CCOMPLEX 1 + #else + #define CYTHON_CCOMPLEX 0 + #endif +#endif +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #include + #else + #include + #endif +#endif +#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) + #undef _Complex_I + #define _Complex_I 1.0fj +#endif + + +static const char *__pyx_f[] = { + "MDAnalysis/lib/_augment.pyx", + "__init__.pxd", + "stringsource", + "type.pxd", +}; +/* MemviewSliceStruct.proto */ +struct __pyx_memoryview_obj; +typedef struct { + struct __pyx_memoryview_obj *memview; + char *data; + Py_ssize_t shape[8]; + Py_ssize_t strides[8]; + Py_ssize_t suboffsets[8]; +} __Pyx_memviewslice; +#define __Pyx_MemoryView_Len(m) (m.shape[0]) + +/* Atomics.proto */ +#include +#ifndef CYTHON_ATOMICS + #define CYTHON_ATOMICS 1 +#endif +#define __pyx_atomic_int_type int +#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 ||\ + (__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) &&\ + !defined(__i386__) + #define __pyx_atomic_incr_aligned(value, lock) __sync_fetch_and_add(value, 1) + #define __pyx_atomic_decr_aligned(value, lock) __sync_fetch_and_sub(value, 1) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using GNU atomics" + #endif +#elif CYTHON_ATOMICS && defined(_MSC_VER) && 0 + #include + #undef __pyx_atomic_int_type + #define __pyx_atomic_int_type LONG + #define __pyx_atomic_incr_aligned(value, lock) InterlockedIncrement(value) + #define __pyx_atomic_decr_aligned(value, lock) InterlockedDecrement(value) + #ifdef __PYX_DEBUG_ATOMICS + #pragma message ("Using MSVC atomics") + #endif +#elif CYTHON_ATOMICS && (defined(__ICC) || defined(__INTEL_COMPILER)) && 0 + #define __pyx_atomic_incr_aligned(value, lock) _InterlockedIncrement(value) + #define __pyx_atomic_decr_aligned(value, lock) _InterlockedDecrement(value) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using Intel atomics" + #endif +#else + #undef CYTHON_ATOMICS + #define CYTHON_ATOMICS 0 + #ifdef __PYX_DEBUG_ATOMICS + #warning "Not using atomics" + #endif +#endif +typedef volatile __pyx_atomic_int_type __pyx_atomic_int; +#if CYTHON_ATOMICS + #define __pyx_add_acquisition_count(memview)\ + __pyx_atomic_incr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) + #define __pyx_sub_acquisition_count(memview)\ + __pyx_atomic_decr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) +#else + #define __pyx_add_acquisition_count(memview)\ + __pyx_add_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) + #define __pyx_sub_acquisition_count(memview)\ + __pyx_sub_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) +#endif + +/* ForceInitThreads.proto */ +#ifndef __PYX_FORCE_INIT_THREADS + #define __PYX_FORCE_INIT_THREADS 0 +#endif + +/* NoFastGil.proto */ +#define __Pyx_PyGILState_Ensure PyGILState_Ensure +#define __Pyx_PyGILState_Release PyGILState_Release +#define __Pyx_FastGIL_Remember() +#define __Pyx_FastGIL_Forget() +#define __Pyx_FastGilFuncInit() + +/* BufferFormatStructs.proto */ +#define IS_UNSIGNED(type) (((type) -1) > 0) +struct __Pyx_StructField_; +#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) +typedef struct { + const char* name; + struct __Pyx_StructField_* fields; + size_t size; + size_t arraysize[8]; + int ndim; + char typegroup; + char is_unsigned; + int flags; +} __Pyx_TypeInfo; +typedef struct __Pyx_StructField_ { + __Pyx_TypeInfo* type; + const char* name; + size_t offset; +} __Pyx_StructField; +typedef struct { + __Pyx_StructField* field; + size_t parent_offset; +} __Pyx_BufFmt_StackElem; +typedef struct { + __Pyx_StructField root; + __Pyx_BufFmt_StackElem* head; + size_t fmt_offset; + size_t new_count, enc_count; + size_t struct_alignment; + int is_complex; + char enc_type; + char new_packmode; + char enc_packmode; + char is_valid_array; +} __Pyx_BufFmt_Context; + + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 + * # in Cython to enable them only on the right systems. + * + * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + */ +typedef npy_int8 __pyx_t_5numpy_int8_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 + * + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t + */ +typedef npy_int16 __pyx_t_5numpy_int16_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< + * #ctypedef npy_int96 int96_t + * #ctypedef npy_int128 int128_t + */ +typedef npy_int64 __pyx_t_5numpy_int64_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 + * #ctypedef npy_int128 int128_t + * + * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + */ +typedef npy_uint8 __pyx_t_5numpy_uint8_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 + * + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t + */ +typedef npy_uint16 __pyx_t_5numpy_uint16_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< + * #ctypedef npy_uint96 uint96_t + * #ctypedef npy_uint128 uint128_t + */ +typedef npy_uint64 __pyx_t_5numpy_uint64_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 + * #ctypedef npy_uint128 uint128_t + * + * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< + * ctypedef npy_float64 float64_t + * #ctypedef npy_float80 float80_t + */ +typedef npy_float32 __pyx_t_5numpy_float32_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 + * + * ctypedef npy_float32 float32_t + * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< + * #ctypedef npy_float80 float80_t + * #ctypedef npy_float128 float128_t + */ +typedef npy_float64 __pyx_t_5numpy_float64_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 + * # The int types are mapped a bit surprising -- + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t + */ +typedef npy_long __pyx_t_5numpy_int_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong longlong_t + * + */ +typedef npy_longlong __pyx_t_5numpy_long_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_ulong uint_t + */ +typedef npy_longlong __pyx_t_5numpy_longlong_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 + * ctypedef npy_longlong longlong_t + * + * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t + */ +typedef npy_ulong __pyx_t_5numpy_uint_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 + * + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulonglong_t + * + */ +typedef npy_ulonglong __pyx_t_5numpy_ulong_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_intp intp_t + */ +typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 + * ctypedef npy_ulonglong ulonglong_t + * + * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< + * ctypedef npy_uintp uintp_t + * + */ +typedef npy_intp __pyx_t_5numpy_intp_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 + * + * ctypedef npy_intp intp_t + * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< + * + * ctypedef npy_double float_t + */ +typedef npy_uintp __pyx_t_5numpy_uintp_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 + * ctypedef npy_uintp uintp_t + * + * ctypedef npy_double float_t # <<<<<<<<<<<<<< + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t + */ +typedef npy_double __pyx_t_5numpy_float_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 + * ctypedef npy_double float_t + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cfloat cfloat_t + */ +typedef npy_longdouble __pyx_t_5numpy_longdouble_t; +/* Declarations.proto */ +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< float > __pyx_t_float_complex; + #else + typedef float _Complex __pyx_t_float_complex; + #endif +#else + typedef struct { float real, imag; } __pyx_t_float_complex; +#endif +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); + +/* Declarations.proto */ +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< double > __pyx_t_double_complex; + #else + typedef double _Complex __pyx_t_double_complex; + #endif +#else + typedef struct { double real, imag; } __pyx_t_double_complex; +#endif +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); 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r = NULL; __Pyx_DECREF(tmp);}} while(0) + +/* PyObjectGetAttrStr.proto */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) +#endif + +/* GetBuiltinName.proto */ +static PyObject *__Pyx_GetBuiltinName(PyObject *name); + +/* RaiseArgTupleInvalid.proto */ +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +/* RaiseDoubleKeywords.proto */ +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +/* ParseKeywords.proto */ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ + const char* function_name); + +/* GetModuleGlobalName.proto */ +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); + +/* PyCFunctionFastCall.proto */ +#if CYTHON_FAST_PYCCALL +static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs); +#else +#define __Pyx_PyCFunction_FastCall(func, args, nargs) (assert(0), NULL) +#endif + +/* PyFunctionFastCall.proto */ +#if CYTHON_FAST_PYCALL +#define __Pyx_PyFunction_FastCall(func, args, nargs)\ + __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) +#if 1 || PY_VERSION_HEX < 0x030600B1 +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs); +#else +#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs) +#endif +#endif + +/* PyObjectCall.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); +#else +#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) +#endif + +/* PyObjectCallMethO.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); +#endif + +/* PyObjectCallOneArg.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + +/* IncludeStringH.proto */ +#include + +/* MemviewSliceInit.proto */ +#define __Pyx_BUF_MAX_NDIMS %(BUF_MAX_NDIMS)d +#define __Pyx_MEMVIEW_DIRECT 1 +#define __Pyx_MEMVIEW_PTR 2 +#define __Pyx_MEMVIEW_FULL 4 +#define __Pyx_MEMVIEW_CONTIG 8 +#define __Pyx_MEMVIEW_STRIDED 16 +#define __Pyx_MEMVIEW_FOLLOW 32 +#define __Pyx_IS_C_CONTIG 1 +#define __Pyx_IS_F_CONTIG 2 +static int __Pyx_init_memviewslice( + struct __pyx_memoryview_obj *memview, + int ndim, + __Pyx_memviewslice *memviewslice, + int memview_is_new_reference); +static CYTHON_INLINE int __pyx_add_acquisition_count_locked( + __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); +static CYTHON_INLINE int __pyx_sub_acquisition_count_locked( + __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); +#define __pyx_get_slice_count_pointer(memview) (memview->acquisition_count_aligned_p) +#define __pyx_get_slice_count(memview) (*__pyx_get_slice_count_pointer(memview)) +#define __PYX_INC_MEMVIEW(slice, have_gil) __Pyx_INC_MEMVIEW(slice, have_gil, __LINE__) +#define __PYX_XDEC_MEMVIEW(slice, have_gil) __Pyx_XDEC_MEMVIEW(slice, have_gil, __LINE__) +static CYTHON_INLINE void __Pyx_INC_MEMVIEW(__Pyx_memviewslice *, int, int); +static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *, int, int); + +/* PyThreadStateGet.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate; +#define __Pyx_PyThreadState_assign __pyx_tstate = __Pyx_PyThreadState_Current; +#define __Pyx_PyErr_Occurred() __pyx_tstate->curexc_type +#else +#define __Pyx_PyThreadState_declare +#define __Pyx_PyThreadState_assign +#define __Pyx_PyErr_Occurred() PyErr_Occurred() +#endif + +/* PyErrFetchRestore.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_PyErr_Clear() __Pyx_ErrRestore(NULL, NULL, NULL) +#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb) +#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb) +#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb) +#define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL)) +#else +#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) +#endif +#else +#define __Pyx_PyErr_Clear() PyErr_Clear() +#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) +#define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb) +#define __Pyx_ErrRestoreInState(tstate, type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetchInState(tstate, type, value, tb) PyErr_Fetch(type, value, tb) +#define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb) +#endif + +/* RaiseException.proto */ +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); + +/* DictGetItem.proto */ +#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key); +#define __Pyx_PyObject_Dict_GetItem(obj, name)\ + (likely(PyDict_CheckExact(obj)) ?\ + __Pyx_PyDict_GetItem(obj, name) : PyObject_GetItem(obj, name)) +#else +#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) +#define __Pyx_PyObject_Dict_GetItem(obj, name) PyObject_GetItem(obj, name) +#endif + +/* RaiseTooManyValuesToUnpack.proto */ +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +/* RaiseNeedMoreValuesToUnpack.proto */ +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +/* RaiseNoneIterError.proto */ +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +/* ExtTypeTest.proto */ +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); + +/* SaveResetException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); +#else +#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) +#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) +#endif + +/* PyErrExceptionMatches.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err) +static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err); +#else +#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err) +#endif + +/* GetException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) +static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); +#endif + +/* ListCompAppend.proto */ +#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS +static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len)) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) +#endif + +/* ArgTypeTest.proto */ +#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\ + ((likely((Py_TYPE(obj) == type) | (none_allowed && (obj == Py_None)))) ? 1 :\ + __Pyx__ArgTypeTest(obj, type, name, exact)) +static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact); + +/* BytesEquals.proto */ +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); + +/* UnicodeEquals.proto */ +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); + +/* StrEquals.proto */ +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals +#else +#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals +#endif + +/* None.proto */ +static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); + +/* UnaryNegOverflows.proto */ +#define UNARY_NEG_WOULD_OVERFLOW(x)\ + (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) + +static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *); /*proto*/ +/* GetAttr.proto */ +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); + +/* GetItemInt.proto */ +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ + __Pyx_GetItemInt_Generic(o, to_py_func(i)))) +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ + (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ + (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck); + +/* ObjectGetItem.proto */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key); +#else +#define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key) +#endif + +/* decode_c_string_utf16.proto */ +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = 0; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16LE(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = -1; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16BE(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = 1; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} + +/* decode_c_string.proto */ +static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); + +/* GetAttr3.proto */ +static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *); + +/* SwapException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); +#endif + +/* Import.proto */ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +/* FastTypeChecks.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type) +static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b); +static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type); +static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2); +#else +#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) +#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type) +#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2)) +#endif +#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) + +static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +/* PyIntBinop.proto */ +#if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace); +#else +#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace)\ + (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) +#endif + +/* ListExtend.proto */ +static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject* none = _PyList_Extend((PyListObject*)L, v); + if (unlikely(!none)) + return -1; + Py_DECREF(none); + return 0; +#else + return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); +#endif +} + +/* ListAppend.proto */ +#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS +static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) +#endif + +/* None.proto */ +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); + +/* None.proto */ +static CYTHON_INLINE long __Pyx_div_long(long, long); + +/* WriteUnraisableException.proto */ +static void __Pyx_WriteUnraisable(const char *name, int clineno, + int lineno, const char *filename, + int full_traceback, int nogil); + +/* ImportFrom.proto */ +static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); + +/* HasAttr.proto */ +static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); + +/* PyObject_GenericGetAttrNoDict.proto */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr +#endif + +/* PyObject_GenericGetAttr.proto */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr +#endif + +/* SetVTable.proto */ +static int __Pyx_SetVtable(PyObject *dict, void *vtable); + +/* SetupReduce.proto */ +static int __Pyx_setup_reduce(PyObject* type_obj); + +/* CLineInTraceback.proto */ +#ifdef CYTHON_CLINE_IN_TRACEBACK +#define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0) +#else +static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line); +#endif + +/* CodeObjectCache.proto */ +typedef struct { + PyCodeObject* code_object; + int code_line; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); + +/* AddTraceback.proto */ +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); + +#if PY_MAJOR_VERSION < 3 + static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); + static void __Pyx_ReleaseBuffer(Py_buffer *view); +#else + #define __Pyx_GetBuffer PyObject_GetBuffer + #define __Pyx_ReleaseBuffer PyBuffer_Release +#endif + + +/* BufferStructDeclare.proto */ +typedef struct { + Py_ssize_t shape, strides, suboffsets; +} __Pyx_Buf_DimInfo; +typedef struct { + size_t refcount; + Py_buffer pybuffer; +} __Pyx_Buffer; +typedef struct { + __Pyx_Buffer *rcbuffer; + char *data; + __Pyx_Buf_DimInfo diminfo[8]; +} __Pyx_LocalBuf_ND; + +/* MemviewSliceIsContig.proto */ +static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim); + +/* OverlappingSlices.proto */ +static int __pyx_slices_overlap(__Pyx_memviewslice *slice1, + __Pyx_memviewslice *slice2, + int ndim, size_t itemsize); + +/* Capsule.proto */ +static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); + +/* IsLittleEndian.proto */ +static CYTHON_INLINE int __Pyx_Is_Little_Endian(void); + +/* BufferFormatCheck.proto */ +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); +static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type); + +/* TypeInfoCompare.proto */ +static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); + +/* MemviewSliceValidateAndInit.proto */ +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj); + +/* ObjectToMemviewSlice.proto */ +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_float(PyObject *, int writable_flag); + +/* ObjectToMemviewSlice.proto */ +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_float(PyObject *, int writable_flag); + +/* ObjectToMemviewSlice.proto */ +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_int64_t(PyObject *, int writable_flag); + +/* MemviewDtypeToObject.proto */ +static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp); +static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +/* CppExceptionConversion.proto */ +#ifndef __Pyx_CppExn2PyErr +#include +#include +#include +#include +static void __Pyx_CppExn2PyErr() { + try { + if (PyErr_Occurred()) + ; // let the latest Python exn pass through and ignore the current one + else + throw; + } catch (const std::bad_alloc& exn) { + PyErr_SetString(PyExc_MemoryError, exn.what()); + } catch (const std::bad_cast& exn) { + PyErr_SetString(PyExc_TypeError, exn.what()); + } catch (const std::bad_typeid& exn) { + PyErr_SetString(PyExc_TypeError, exn.what()); + } catch (const std::domain_error& exn) { + PyErr_SetString(PyExc_ValueError, exn.what()); + } catch (const std::invalid_argument& exn) { + PyErr_SetString(PyExc_ValueError, exn.what()); + } catch (const std::ios_base::failure& exn) { + PyErr_SetString(PyExc_IOError, exn.what()); + } catch (const std::out_of_range& exn) { + PyErr_SetString(PyExc_IndexError, exn.what()); + } catch (const std::overflow_error& exn) { + PyErr_SetString(PyExc_OverflowError, exn.what()); + } catch (const std::range_error& exn) { + PyErr_SetString(PyExc_ArithmeticError, exn.what()); + } catch (const std::underflow_error& exn) { + PyErr_SetString(PyExc_ArithmeticError, exn.what()); + } catch (const std::exception& exn) { + PyErr_SetString(PyExc_RuntimeError, exn.what()); + } + catch (...) + { + PyErr_SetString(PyExc_RuntimeError, "Unknown exception"); + } +} +#endif + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_int64(npy_int64 value); + +/* MemviewDtypeToObject.proto */ +static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_5numpy_int64_t(const char *itemp); +static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_int64_t(const char *itemp, PyObject *obj); + +/* RealImag.proto */ +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #define __Pyx_CREAL(z) ((z).real()) + #define __Pyx_CIMAG(z) ((z).imag()) + #else + #define __Pyx_CREAL(z) (__real__(z)) + #define __Pyx_CIMAG(z) (__imag__(z)) + #endif +#else + #define __Pyx_CREAL(z) ((z).real) + #define __Pyx_CIMAG(z) ((z).imag) +#endif +#if defined(__cplusplus) && CYTHON_CCOMPLEX\ + && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103) + #define __Pyx_SET_CREAL(z,x) ((z).real(x)) + #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) +#else + #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) + #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) +#endif + +/* Arithmetic.proto */ +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq_float(a, b) ((a)==(b)) + #define __Pyx_c_sum_float(a, b) ((a)+(b)) + #define __Pyx_c_diff_float(a, b) ((a)-(b)) + #define __Pyx_c_prod_float(a, b) ((a)*(b)) + #define __Pyx_c_quot_float(a, b) ((a)/(b)) + #define __Pyx_c_neg_float(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero_float(z) ((z)==(float)0) + #define __Pyx_c_conj_float(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs_float(z) (::std::abs(z)) + #define __Pyx_c_pow_float(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero_float(z) ((z)==0) + #define __Pyx_c_conj_float(z) (conjf(z)) + #if 1 + #define __Pyx_c_abs_float(z) (cabsf(z)) + #define __Pyx_c_pow_float(a, b) (cpowf(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex); + #if 1 + static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex, __pyx_t_float_complex); + #endif +#endif + +/* Arithmetic.proto */ +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq_double(a, b) ((a)==(b)) + #define __Pyx_c_sum_double(a, b) ((a)+(b)) + #define __Pyx_c_diff_double(a, b) ((a)-(b)) + #define __Pyx_c_prod_double(a, b) ((a)*(b)) + #define __Pyx_c_quot_double(a, b) ((a)/(b)) + #define __Pyx_c_neg_double(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero_double(z) ((z)==(double)0) + #define __Pyx_c_conj_double(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs_double(z) (::std::abs(z)) + #define __Pyx_c_pow_double(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero_double(z) ((z)==0) + #define __Pyx_c_conj_double(z) (conj(z)) + #if 1 + #define __Pyx_c_abs_double(z) (cabs(z)) + #define __Pyx_c_pow_double(a, b) (cpow(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex); + #if 1 + static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex); + #endif +#endif + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); + +/* MemviewSliceCopyTemplate.proto */ +static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object); + +/* CIntFromPy.proto */ +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE npy_int64 __Pyx_PyInt_As_npy_int64(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +/* CIntFromPy.proto */ +static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); + +/* CheckBinaryVersion.proto */ +static int __Pyx_check_binary_version(void); + +/* PyIdentifierFromString.proto */ +#if !defined(__Pyx_PyIdentifier_FromString) +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) +#else + #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) +#endif +#endif + +/* ModuleImport.proto */ +static PyObject *__Pyx_ImportModule(const char *name); + +/* TypeImport.proto */ +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); + +/* FunctionImport.proto */ +static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig); + +/* InitStrings.proto */ +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); + +static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *__pyx_v_self); /* proto*/ +static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto*/ +static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj); /* proto*/ +static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_dst, PyObject *__pyx_v_src); /* proto*/ +static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memoryview_obj *__pyx_v_self, struct __pyx_memoryview_obj *__pyx_v_dst, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryview_setitem_indexed(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ +static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ +static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ + +/* Module declarations from 'cython.view' */ + +/* Module declarations from 'cython' */ + +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'cpython' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'cpython.mem' */ + +/* Module declarations from 'numpy' */ + +/* Module declarations from 'numpy' */ +static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; +static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; +static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; +static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; +static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; +static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ + +/* Module declarations from 'MDAnalysis.lib._cutil' */ +static float (*__pyx_f_10MDAnalysis_3lib_6_cutil__dot)(float *, float *); /*proto*/ +static void (*__pyx_f_10MDAnalysis_3lib_6_cutil__cross)(float *, float *, float *); /*proto*/ +static float (*__pyx_f_10MDAnalysis_3lib_6_cutil__norm)(float *); /*proto*/ + +/* Module declarations from 'libcpp.vector' */ + +/* Module declarations from 'MDAnalysis.lib._augment' */ +static PyTypeObject *__pyx_array_type = 0; +static PyTypeObject *__pyx_MemviewEnum_type = 0; +static PyTypeObject *__pyx_memoryview_type = 0; +static PyTypeObject *__pyx_memoryviewslice_type = 0; +static PyObject *generic = 0; +static PyObject *strided = 0; +static PyObject *indirect = 0; +static PyObject *contiguous = 0; +static PyObject *indirect_contiguous = 0; +static int __pyx_memoryview_thread_locks_used; +static PyThread_type_lock __pyx_memoryview_thread_locks[8]; +static int __Pyx_carray_from_py_float(PyObject *, float *, Py_ssize_t); /*proto*/ +static int __Pyx_carray_from_py_float___5b_3_5d_(PyObject *, float (*)[3], Py_ssize_t); /*proto*/ +static PyObject *__pyx_convert_vector_to_py_float(const std::vector &); /*proto*/ +static PyObject *__pyx_convert_vector_to_py_int(const std::vector &); /*proto*/ +static struct __pyx_array_obj *__pyx_array_new(PyObject *, Py_ssize_t, char *, char *, char *); /*proto*/ +static void *__pyx_align_pointer(void *, size_t); /*proto*/ +static PyObject *__pyx_memoryview_new(PyObject *, int, int, __Pyx_TypeInfo *); /*proto*/ +static CYTHON_INLINE int __pyx_memoryview_check(PyObject *); /*proto*/ +static PyObject *_unellipsify(PyObject *, int); /*proto*/ +static PyObject *assert_direct_dimensions(Py_ssize_t *, int); /*proto*/ +static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_obj *, PyObject *); /*proto*/ +static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int, int); /*proto*/ +static char *__pyx_pybuffer_index(Py_buffer *, char *, Py_ssize_t, Py_ssize_t); /*proto*/ +static int __pyx_memslice_transpose(__Pyx_memviewslice *); /*proto*/ +static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice, int, PyObject *(*)(char *), int (*)(char *, PyObject *), int); /*proto*/ +static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *); /*proto*/ +static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static Py_ssize_t abs_py_ssize_t(Py_ssize_t); /*proto*/ +static char __pyx_get_best_slice_order(__Pyx_memviewslice *, int); /*proto*/ +static void _copy_strided_to_strided(char *, Py_ssize_t *, char *, Py_ssize_t *, Py_ssize_t *, Py_ssize_t *, int, size_t); /*proto*/ +static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/ +static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/ +static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *, Py_ssize_t *, Py_ssize_t, int, char); /*proto*/ +static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/ +static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/ +static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/ +static int __pyx_memoryview_err(PyObject *, char *); /*proto*/ +static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/ +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/ +static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/ +static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ +static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ +static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/ +static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ +static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *, PyObject *); /*proto*/ +static __Pyx_TypeInfo __Pyx_TypeInfo_float = { "float", NULL, sizeof(float), { 0 }, 0, 'R', 0, 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t = { "int64_t", NULL, sizeof(__pyx_t_5numpy_int64_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int64_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int64_t), 0 }; +#define __Pyx_MODULE_NAME "MDAnalysis.lib._augment" +extern int __pyx_module_is_main_MDAnalysis__lib___augment; +int __pyx_module_is_main_MDAnalysis__lib___augment = 0; + +/* Implementation of 'MDAnalysis.lib._augment' */ +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_RuntimeError; +static PyObject *__pyx_builtin_ImportError; +static PyObject *__pyx_builtin_TypeError; +static PyObject *__pyx_builtin_OverflowError; +static PyObject *__pyx_builtin_enumerate; +static PyObject *__pyx_builtin_IndexError; +static PyObject *__pyx_builtin_MemoryError; +static PyObject *__pyx_builtin_Ellipsis; +static PyObject *__pyx_builtin_id; +static const char __pyx_k_N[] = "N"; +static const char __pyx_k_O[] = "O"; +static const char __pyx_k_c[] = "c"; +static const char __pyx_k_i[] = "i"; +static const char __pyx_k_j[] = "j"; +static const char __pyx_k_n[] = "n"; +static const char __pyx_k_r[] = "r"; +static const char __pyx_k_dm[] = "dm"; +static const char __pyx_k_id[] = "id"; +static const char __pyx_k_np[] = "np"; +static const char __pyx_k_all[] = "__all__"; +static const char __pyx_k_box[] = "box"; +static const char __pyx_k_end[] = "end"; +static const char __pyx_k_new[] = "__new__"; +static const char __pyx_k_obj[] = "obj"; +static const char __pyx_k_base[] = "base"; +static const char __pyx_k_dict[] = "__dict__"; +static const char __pyx_k_hi_x[] = "hi_x"; +static const char __pyx_k_hi_y[] = "hi_y"; +static const char __pyx_k_hi_z[] = "hi_z"; +static const char __pyx_k_lo_x[] = "lo_x"; +static const char __pyx_k_lo_y[] = "lo_y"; +static const char __pyx_k_lo_z[] = "lo_z"; +static const char __pyx_k_main[] = "__main__"; +static const char __pyx_k_mode[] = "mode"; +static const char __pyx_k_name[] = "name"; +static const char __pyx_k_ndim[] = "ndim"; +static const char __pyx_k_norm[] = "norm"; +static const char __pyx_k_pack[] = "pack"; +static const char __pyx_k_size[] = "size"; +static const char __pyx_k_step[] = "step"; +static const char __pyx_k_stop[] = "stop"; +static const char __pyx_k_test[] = "__test__"; +static const char __pyx_k_ASCII[] = "ASCII"; +static const char __pyx_k_class[] = "__class__"; +static const char __pyx_k_coord[] = "coord"; +static const char __pyx_k_dtype[] = "dtype"; +static const char __pyx_k_error[] = "error"; +static const char __pyx_k_flags[] = "flags"; +static const char __pyx_k_int64[] = "int64"; +static const char __pyx_k_nreal[] = "nreal"; +static const char __pyx_k_numpy[] = "numpy"; +static const char __pyx_k_other[] = "other"; +static const char __pyx_k_range[] = "range"; +static const char __pyx_k_shape[] = "shape"; +static const char __pyx_k_start[] = "start"; +static const char __pyx_k_encode[] = "encode"; +static const char __pyx_k_format[] = "format"; +static const char __pyx_k_import[] = "__import__"; +static const char __pyx_k_name_2[] = "__name__"; +static const char __pyx_k_output[] = "output"; +static const char __pyx_k_pickle[] = "pickle"; +static const char __pyx_k_reduce[] = "__reduce__"; +static const char __pyx_k_shiftX[] = "shiftX"; +static const char __pyx_k_shiftY[] = "shiftY"; +static const char __pyx_k_shiftZ[] = "shiftZ"; +static const char __pyx_k_struct[] = "struct"; +static const char __pyx_k_unpack[] = "unpack"; +static const char __pyx_k_update[] = "update"; +static const char __pyx_k_asarray[] = "asarray"; +static const char __pyx_k_float32[] = "float32"; +static const char __pyx_k_fortran[] = "fortran"; +static const char __pyx_k_indices[] = "indices"; +static const char __pyx_k_mdamath[] = "mdamath"; +static const char __pyx_k_memview[] = "memview"; +static const char __pyx_k_reshape[] = "reshape"; +static const char __pyx_k_results[] = "results"; +static const char __pyx_k_Ellipsis[] = "Ellipsis"; +static const char __pyx_k_getstate[] = "__getstate__"; +static const char __pyx_k_itemsize[] = "itemsize"; +static const char __pyx_k_pyx_type[] = "__pyx_type"; +static const char __pyx_k_setstate[] = "__setstate__"; +static const char __pyx_k_TypeError[] = "TypeError"; +static const char __pyx_k_enumerate[] = "enumerate"; +static const char __pyx_k_pyx_state[] = "__pyx_state"; +static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; +static const char __pyx_k_IndexError[] = "IndexError"; +static const char __pyx_k_ValueError[] = "ValueError"; +static const char __pyx_k_pyx_result[] = "__pyx_result"; +static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; +static const char __pyx_k_reciprocal[] = "reciprocal"; +static const char __pyx_k_ImportError[] = "ImportError"; +static const char __pyx_k_MemoryError[] = "MemoryError"; +static const char __pyx_k_PickleError[] = "PickleError"; +static const char __pyx_k_coordinates[] = "coordinates"; +static const char __pyx_k_translation[] = "translation"; +static const char __pyx_k_RuntimeError[] = "RuntimeError"; +static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; +static const char __pyx_k_stringsource[] = "stringsource"; +static const char __pyx_k_undo_augment[] = "undo_augment"; +static const char __pyx_k_OverflowError[] = "OverflowError"; +static const char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; +static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; +static const char __pyx_k_View_MemoryView[] = "View.MemoryView"; +static const char __pyx_k_allocate_buffer[] = "allocate_buffer"; +static const char __pyx_k_dtype_is_object[] = "dtype_is_object"; +static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; +static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; +static const char __pyx_k_pyx_unpickle_Enum[] = "__pyx_unpickle_Enum"; +static const char __pyx_k_triclinic_vectors[] = "triclinic_vectors"; +static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; +static const char __pyx_k_strided_and_direct[] = ""; +static const char __pyx_k_augment_coordinates[] = "augment_coordinates"; +static const char __pyx_k_strided_and_indirect[] = ""; +static const char __pyx_k_contiguous_and_direct[] = ""; +static const char __pyx_k_MemoryView_of_r_object[] = ""; +static const char __pyx_k_MDAnalysis_lib__augment[] = "MDAnalysis.lib._augment"; +static const char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; +static const char __pyx_k_contiguous_and_indirect[] = ""; +static const char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; +static const char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; +static const char __pyx_k_MDAnalysis_lib__augment_pyx[] = "MDAnalysis/lib/_augment.pyx"; +static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; +static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; +static const char __pyx_k_strided_and_direct_or_indirect[] = ""; +static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; +static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; +static const char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; +static const char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; +static const char __pyx_k_Cannot_assign_to_read_only_memor[] = "Cannot assign to read-only memoryview"; +static const char __pyx_k_Cannot_create_writable_memory_vi[] = "Cannot create writable memory view from read-only memoryview"; +static const char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; +static const char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; +static const char __pyx_k_Incompatible_checksums_s_vs_0xb0[] = "Incompatible checksums (%s vs 0xb068931 = (name))"; +static const char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; +static const char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; +static const char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; +static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; +static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; +static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; +static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; +static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; +static const char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_n_s_ASCII; +static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; +static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; +static PyObject *__pyx_kp_s_Cannot_assign_to_read_only_memor; +static PyObject *__pyx_kp_s_Cannot_create_writable_memory_vi; +static PyObject *__pyx_kp_s_Cannot_index_with_type_s; +static PyObject *__pyx_n_s_Ellipsis; +static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; +static PyObject *__pyx_n_s_ImportError; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0xb0; +static PyObject *__pyx_n_s_IndexError; +static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; +static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; +static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; +static PyObject *__pyx_n_s_MDAnalysis_lib__augment; +static PyObject *__pyx_kp_s_MDAnalysis_lib__augment_pyx; +static PyObject *__pyx_n_s_MemoryError; +static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; +static PyObject *__pyx_kp_s_MemoryView_of_r_object; +static PyObject *__pyx_n_s_N; +static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_n_b_O; +static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; +static PyObject *__pyx_n_s_OverflowError; +static PyObject *__pyx_n_s_PickleError; +static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_n_s_TypeError; +static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; +static PyObject *__pyx_n_s_ValueError; +static PyObject *__pyx_n_s_View_MemoryView; +static PyObject *__pyx_n_s_all; +static PyObject *__pyx_n_s_allocate_buffer; +static PyObject *__pyx_n_s_asarray; +static PyObject *__pyx_n_s_augment_coordinates; +static PyObject *__pyx_n_s_base; +static PyObject *__pyx_n_s_box; +static PyObject *__pyx_n_s_c; +static PyObject *__pyx_n_u_c; +static PyObject *__pyx_n_s_class; +static PyObject *__pyx_n_s_cline_in_traceback; +static PyObject *__pyx_kp_s_contiguous_and_direct; +static PyObject *__pyx_kp_s_contiguous_and_indirect; +static PyObject *__pyx_n_s_coord; +static PyObject *__pyx_n_s_coordinates; +static PyObject *__pyx_n_s_dict; +static PyObject *__pyx_n_s_dm; +static PyObject *__pyx_n_s_dtype; +static PyObject *__pyx_n_s_dtype_is_object; +static PyObject *__pyx_n_s_encode; +static PyObject *__pyx_n_s_end; +static PyObject *__pyx_n_s_enumerate; +static PyObject *__pyx_n_s_error; +static PyObject *__pyx_n_s_flags; +static PyObject *__pyx_n_s_float32; +static PyObject *__pyx_n_s_format; +static PyObject *__pyx_n_s_fortran; +static PyObject *__pyx_n_u_fortran; +static PyObject *__pyx_n_s_getstate; +static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; +static PyObject *__pyx_n_s_hi_x; +static PyObject *__pyx_n_s_hi_y; +static PyObject *__pyx_n_s_hi_z; +static PyObject *__pyx_n_s_i; +static PyObject *__pyx_n_s_id; +static PyObject *__pyx_n_s_import; +static PyObject *__pyx_n_s_indices; +static PyObject *__pyx_n_s_int64; +static PyObject *__pyx_n_s_itemsize; +static PyObject *__pyx_kp_s_itemsize_0_for_cython_array; +static PyObject *__pyx_n_s_j; +static PyObject *__pyx_n_s_lo_x; +static PyObject *__pyx_n_s_lo_y; +static PyObject *__pyx_n_s_lo_z; +static PyObject *__pyx_n_s_main; +static PyObject *__pyx_n_s_mdamath; +static PyObject *__pyx_n_s_memview; +static PyObject *__pyx_n_s_mode; +static PyObject *__pyx_n_s_n; +static PyObject *__pyx_n_s_name; +static PyObject *__pyx_n_s_name_2; +static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; +static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_n_s_ndim; +static PyObject *__pyx_n_s_new; +static PyObject *__pyx_kp_s_no_default___reduce___due_to_non; +static PyObject *__pyx_n_s_norm; +static PyObject *__pyx_n_s_np; +static PyObject *__pyx_n_s_nreal; +static PyObject *__pyx_n_s_numpy; +static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to; +static PyObject *__pyx_kp_s_numpy_core_umath_failed_to_impor; +static PyObject *__pyx_n_s_obj; +static PyObject *__pyx_n_s_other; +static PyObject *__pyx_n_s_output; +static PyObject *__pyx_n_s_pack; +static PyObject *__pyx_n_s_pickle; +static PyObject *__pyx_n_s_pyx_PickleError; +static PyObject *__pyx_n_s_pyx_checksum; +static PyObject *__pyx_n_s_pyx_getbuffer; +static PyObject *__pyx_n_s_pyx_result; +static PyObject *__pyx_n_s_pyx_state; +static PyObject *__pyx_n_s_pyx_type; +static PyObject *__pyx_n_s_pyx_unpickle_Enum; +static PyObject *__pyx_n_s_pyx_vtable; +static PyObject *__pyx_n_s_r; +static PyObject *__pyx_n_s_range; +static PyObject *__pyx_n_s_reciprocal; +static PyObject *__pyx_n_s_reduce; +static PyObject *__pyx_n_s_reduce_cython; +static PyObject *__pyx_n_s_reduce_ex; +static PyObject *__pyx_n_s_reshape; +static PyObject *__pyx_n_s_results; +static PyObject *__pyx_n_s_setstate; +static PyObject *__pyx_n_s_setstate_cython; +static PyObject *__pyx_n_s_shape; +static PyObject *__pyx_n_s_shiftX; +static PyObject *__pyx_n_s_shiftY; +static PyObject *__pyx_n_s_shiftZ; +static PyObject *__pyx_n_s_size; +static PyObject *__pyx_n_s_start; +static PyObject *__pyx_n_s_step; +static PyObject *__pyx_n_s_stop; +static PyObject *__pyx_kp_s_strided_and_direct; +static PyObject *__pyx_kp_s_strided_and_direct_or_indirect; +static PyObject *__pyx_kp_s_strided_and_indirect; +static PyObject *__pyx_kp_s_stringsource; +static PyObject *__pyx_n_s_struct; +static PyObject *__pyx_n_s_test; +static PyObject *__pyx_n_s_translation; +static PyObject *__pyx_n_s_triclinic_vectors; +static PyObject *__pyx_kp_s_unable_to_allocate_array_data; +static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; +static PyObject *__pyx_n_s_undo_augment; +static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; +static PyObject *__pyx_n_s_unpack; +static PyObject *__pyx_n_s_update; +static PyObject *__pyx_pf_10MDAnalysis_3lib_8_augment_augment_coordinates(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_coordinates, __Pyx_memviewslice __pyx_v_box, float __pyx_v_r); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_8_augment_2undo_augment(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_results, __Pyx_memviewslice __pyx_v_translation, int __pyx_v_nreal); /* proto */ +static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__len__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ +static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_12__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ +static PyObject *__pyx_pf___pyx_array___reduce_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_array_2__setstate_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ +static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ +static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_MemviewEnum_2__setstate_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ +static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_memoryview___reduce_cython__(CYTHON_UNUSED struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_memoryview_2__setstate_cython__(CYTHON_UNUSED struct __pyx_memoryview_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ +static void __pyx_memoryviewslice___pyx_pf_15View_dot_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_memoryviewslice___reduce_cython__(CYTHON_UNUSED struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_memoryviewslice_2__setstate_cython__(CYTHON_UNUSED struct __pyx_memoryviewslice_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView___pyx_unpickle_Enum(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_int_0; +static PyObject *__pyx_int_1; +static PyObject *__pyx_int_3; +static PyObject *__pyx_int_184977713; +static PyObject *__pyx_int_neg_1; +static PyObject *__pyx_tuple_; +static PyObject *__pyx_tuple__2; +static PyObject *__pyx_tuple__3; +static PyObject *__pyx_tuple__4; +static PyObject *__pyx_tuple__5; +static PyObject *__pyx_tuple__6; +static PyObject *__pyx_tuple__7; +static PyObject *__pyx_tuple__8; +static PyObject *__pyx_tuple__9; +static PyObject *__pyx_slice__25; +static PyObject *__pyx_slice__26; +static PyObject *__pyx_slice__27; +static PyObject *__pyx_tuple__10; +static PyObject *__pyx_tuple__11; +static PyObject *__pyx_tuple__12; +static PyObject *__pyx_tuple__13; +static PyObject *__pyx_tuple__14; +static PyObject *__pyx_tuple__15; +static PyObject *__pyx_tuple__16; +static PyObject *__pyx_tuple__17; +static PyObject *__pyx_tuple__18; +static PyObject *__pyx_tuple__19; +static PyObject *__pyx_tuple__20; +static PyObject *__pyx_tuple__21; +static PyObject *__pyx_tuple__22; +static PyObject *__pyx_tuple__23; +static PyObject *__pyx_tuple__24; +static PyObject *__pyx_tuple__28; +static PyObject *__pyx_tuple__29; +static PyObject *__pyx_tuple__30; +static PyObject *__pyx_tuple__31; +static PyObject *__pyx_tuple__33; +static PyObject *__pyx_tuple__35; +static PyObject *__pyx_tuple__36; +static PyObject *__pyx_tuple__37; +static PyObject *__pyx_tuple__38; +static PyObject *__pyx_tuple__39; +static PyObject *__pyx_tuple__40; +static PyObject *__pyx_codeobj__32; +static PyObject *__pyx_codeobj__34; +static PyObject *__pyx_codeobj__41; +/* Late includes */ + +/* "MDAnalysis/lib/_augment.pyx":39 + * @cython.boundscheck(False) + * @cython.wraparound(False) + * def augment_coordinates(float[:, ::1] coordinates, float[:] box, float r): # <<<<<<<<<<<<<< + * r"""Calculates the periodic images of particles which are within a distance + * `r` from the box walls. + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10MDAnalysis_3lib_8_augment_1augment_coordinates(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_10MDAnalysis_3lib_8_augment_augment_coordinates[] = "Calculates the periodic images of particles which are within a distance\n `r` from the box walls.\n\n The algorithm works by generating explicit periodic images of atoms residing\n close to any of the six box walls. The steps involved in generating images\n involves the evaluation of reciprocal box vectors followed by the\n calculation of distances of atoms from the walls by means of projection onto\n the reciprocal vectors. If the distance is less than a specified cutoff\n distance, relevant periodic images are generated using box translation\n vectors :math:`\\vec{t}` with\n\n .. math:: \\vec{t}=l\\cdot\\vec{a}+m\\cdot\\vec{b}+n\\cdot \\vec{c}\\,,\n\n where :math:`l,\\,m,\\,n \\in \\{-1,\\,0,\\,1\\}` are the neighboring cell indices\n in :math:`x`-, :math:`y`-, and :math:`z`-direction relative to the central\n cell with box vectors :math:`\\vec{a},\\,\\vec{b},\\,\\vec{c}`.\n\n For instance, an atom close to the :math:`xy`-plane containing the origin\n will generate a periodic image outside the central cell and close to the\n opposite :math:`xy`-plane of the box, i.e., shifted by\n :math:`\\vec{t} = 0\\cdot\\vec{a}+0\\cdot\\vec{b}+1\\cdot\\vec{c}=\\vec{c}`.\n\n Likewise, if the particle is close to more than one box walls, images along\n the diagonals are also generated::\n\n x x\n +------------+ +------------+\n | | augment | |\n | | -------> | |\n | o | x | o |\n +------------+ +------------+\n\n Parameters\n ----------\n coordinates : numpy.ndarray\n Input coordinate array of shape ``(n, 3)`` and dtype ``numpy.float32``\n used to generate duplicate images in the vicinity of the central cell. All\n coordinates must be within the primary unit cell.\n box : numpy.ndarray\n Box dimensio""ns of shape ``(6,)`` and dtype ``numpy.float32``. The\n dimensions must be provided in the same format as returned\n by :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`:\n ``[lx, ly, lz, alpha, beta, gamma]``\n r : float\n Thickness of cutoff region for duplicate image generation.\n\n Returns\n -------\n output : numpy.ndarray\n Coordinates of duplicate (augmented) particles (dtype ``numpy.float32``).\n indices : numpy.ndarray\n Original indices of the augmented coordinates (dtype ``numpy.int64``).\n Maps the indices of augmented particles to their original particle index\n such that ``indices[augmented_index] = original_index``.\n\n Note\n ----\n Output does not return coordinates from the initial array.\n To merge the particles with their respective images, the following operation\n is necessary when generating the images:\n\n .. code-block:: python\n\n images, mapping = augment_coordinates(coordinates, box, max_cutoff)\n all_coords = numpy.concatenate([coordinates, images])\n\n\n See Also\n --------\n :meth:`undo_augment`\n\n\n .. versionadded:: 0.19.0\n "; 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+ + /* "MDAnalysis/lib/_augment.pyx":155 + * lo_x = _dot(&coord[0], &reciprocal[0][0]) <= r + * hi_x = _dot(&other[0], &reciprocal[0][0]) <= r + * lo_y = _dot(&coord[0], &reciprocal[1][0]) <= r # <<<<<<<<<<<<<< + * hi_y = _dot(&other[0], &reciprocal[1][0]) <= r + * lo_z = _dot(&coord[0], &reciprocal[2][0]) <= r + */ + __pyx_v_lo_y = (__pyx_f_10MDAnalysis_3lib_6_cutil__dot((&(__pyx_v_coord[0])), (&((__pyx_v_reciprocal[1])[0]))) <= __pyx_v_r); + + /* "MDAnalysis/lib/_augment.pyx":156 + * hi_x = _dot(&other[0], &reciprocal[0][0]) <= r + * lo_y = _dot(&coord[0], &reciprocal[1][0]) <= r + * hi_y = _dot(&other[0], &reciprocal[1][0]) <= r # <<<<<<<<<<<<<< + * lo_z = _dot(&coord[0], &reciprocal[2][0]) <= r + * hi_z = _dot(&other[0], &reciprocal[2][0]) <= r + */ + __pyx_v_hi_y = (__pyx_f_10MDAnalysis_3lib_6_cutil__dot((&(__pyx_v_other[0])), (&((__pyx_v_reciprocal[1])[0]))) <= __pyx_v_r); + + /* "MDAnalysis/lib/_augment.pyx":157 + * lo_y = _dot(&coord[0], &reciprocal[1][0]) <= r + * hi_y = _dot(&other[0], &reciprocal[1][0]) <= r + * lo_z = _dot(&coord[0], &reciprocal[2][0]) <= r # <<<<<<<<<<<<<< + * hi_z = _dot(&other[0], &reciprocal[2][0]) <= r + * + */ + __pyx_v_lo_z = (__pyx_f_10MDAnalysis_3lib_6_cutil__dot((&(__pyx_v_coord[0])), (&((__pyx_v_reciprocal[2])[0]))) <= __pyx_v_r); + + /* "MDAnalysis/lib/_augment.pyx":158 + * hi_y = _dot(&other[0], &reciprocal[1][0]) <= r + * lo_z = _dot(&coord[0], &reciprocal[2][0]) <= r + * hi_z = _dot(&other[0], &reciprocal[2][0]) <= r # <<<<<<<<<<<<<< + * + * if lo_x: + */ + __pyx_v_hi_z = (__pyx_f_10MDAnalysis_3lib_6_cutil__dot((&(__pyx_v_other[0])), (&((__pyx_v_reciprocal[2])[0]))) <= __pyx_v_r); + + /* "MDAnalysis/lib/_augment.pyx":160 + * hi_z = _dot(&other[0], &reciprocal[2][0]) <= r + * + * if lo_x: # <<<<<<<<<<<<<< + * # if X, face piece + * for j in range(3): + */ + __pyx_t_15 = (__pyx_v_lo_x != 0); + if (__pyx_t_15) { + + /* "MDAnalysis/lib/_augment.pyx":162 + * if lo_x: + * # if X, face piece + * for j in range(3): # <<<<<<<<<<<<<< + * # add to output + * output.push_back(coord[j] + shiftX[j]) + */ + for (__pyx_t_10 = 0; __pyx_t_10 < 3; __pyx_t_10+=1) { + __pyx_v_j = __pyx_t_10; + + /* "MDAnalysis/lib/_augment.pyx":164 + * for j in range(3): + * # add to output + * output.push_back(coord[j] + shiftX[j]) # <<<<<<<<<<<<<< + * # keep record of which index this augmented + * # position was created from + */ + try { + __pyx_v_output.push_back(((__pyx_v_coord[__pyx_v_j]) + (__pyx_v_shiftX[__pyx_v_j]))); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 164, __pyx_L1_error) + } + } + + /* "MDAnalysis/lib/_augment.pyx":167 + * # keep record of which index this augmented + * # position was created from + * indices.push_back(i) # <<<<<<<<<<<<<< + * + * if lo_y: + */ + try { + __pyx_v_indices.push_back(__pyx_v_i); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 167, __pyx_L1_error) + } + + /* "MDAnalysis/lib/_augment.pyx":169 + * indices.push_back(i) + * + * if lo_y: # <<<<<<<<<<<<<< + * # if X&Y, edge piece + * for j in range(3): + */ + __pyx_t_15 = (__pyx_v_lo_y != 0); + if (__pyx_t_15) { + + /* "MDAnalysis/lib/_augment.pyx":171 + * if lo_y: + * # if X&Y, edge piece + * for j in range(3): # <<<<<<<<<<<<<< + * output.push_back(coord[j] + shiftX[j] + shiftY[j]) + * indices.push_back(i) + */ + for (__pyx_t_10 = 0; __pyx_t_10 < 3; __pyx_t_10+=1) { + __pyx_v_j = __pyx_t_10; + + /* "MDAnalysis/lib/_augment.pyx":172 + * # if X&Y, edge piece + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] + shiftY[j]) # <<<<<<<<<<<<<< + * indices.push_back(i) + * + */ + try { + __pyx_v_output.push_back((((__pyx_v_coord[__pyx_v_j]) + (__pyx_v_shiftX[__pyx_v_j])) + (__pyx_v_shiftY[__pyx_v_j]))); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 172, __pyx_L1_error) + } + } + + /* "MDAnalysis/lib/_augment.pyx":173 + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] + shiftY[j]) + * indices.push_back(i) # <<<<<<<<<<<<<< + * + * if lo_z: + */ + try { + __pyx_v_indices.push_back(__pyx_v_i); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 173, __pyx_L1_error) + } + + /* "MDAnalysis/lib/_augment.pyx":175 + * indices.push_back(i) + * + * if lo_z: # <<<<<<<<<<<<<< + * # if X&Y&Z, corner piece + * for j in range(3): + */ + __pyx_t_15 = (__pyx_v_lo_z != 0); + if (__pyx_t_15) { + + /* "MDAnalysis/lib/_augment.pyx":177 + * if lo_z: + * # if X&Y&Z, corner piece + * for j in range(3): # <<<<<<<<<<<<<< + * output.push_back(coord[j] + shiftX[j] + shiftY[j] + shiftZ[j]) + * indices.push_back(i) + */ + for (__pyx_t_10 = 0; __pyx_t_10 < 3; __pyx_t_10+=1) { + __pyx_v_j = __pyx_t_10; + + /* "MDAnalysis/lib/_augment.pyx":178 + * # if X&Y&Z, corner piece + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] + shiftY[j] + shiftZ[j]) # <<<<<<<<<<<<<< + * indices.push_back(i) + * + */ + try { + __pyx_v_output.push_back(((((__pyx_v_coord[__pyx_v_j]) + (__pyx_v_shiftX[__pyx_v_j])) + (__pyx_v_shiftY[__pyx_v_j])) + (__pyx_v_shiftZ[__pyx_v_j]))); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 178, __pyx_L1_error) + } + } + + /* "MDAnalysis/lib/_augment.pyx":179 + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] + shiftY[j] + shiftZ[j]) + * indices.push_back(i) # <<<<<<<<<<<<<< + * + * elif hi_z: + */ + try { + __pyx_v_indices.push_back(__pyx_v_i); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 179, __pyx_L1_error) + } + + /* "MDAnalysis/lib/_augment.pyx":175 + * indices.push_back(i) + * + * if lo_z: # <<<<<<<<<<<<<< + * # if X&Y&Z, corner piece + * for j in range(3): + */ + goto __pyx_L19; + } + + /* "MDAnalysis/lib/_augment.pyx":181 + * indices.push_back(i) + * + * elif hi_z: # <<<<<<<<<<<<<< + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] + shiftY[j] - shiftZ[j]) + */ + __pyx_t_15 = (__pyx_v_hi_z != 0); + if (__pyx_t_15) { + + /* "MDAnalysis/lib/_augment.pyx":182 + * + * elif hi_z: + * for j in range(3): # <<<<<<<<<<<<<< + * output.push_back(coord[j] + shiftX[j] + shiftY[j] - shiftZ[j]) + * indices.push_back(i) + */ + for (__pyx_t_10 = 0; __pyx_t_10 < 3; __pyx_t_10+=1) { + __pyx_v_j = __pyx_t_10; + + /* "MDAnalysis/lib/_augment.pyx":183 + * elif hi_z: + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] + shiftY[j] - shiftZ[j]) # <<<<<<<<<<<<<< + * indices.push_back(i) + * + */ + try { + __pyx_v_output.push_back(((((__pyx_v_coord[__pyx_v_j]) + (__pyx_v_shiftX[__pyx_v_j])) + (__pyx_v_shiftY[__pyx_v_j])) - (__pyx_v_shiftZ[__pyx_v_j]))); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 183, __pyx_L1_error) + } + } + + /* "MDAnalysis/lib/_augment.pyx":184 + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] + shiftY[j] - shiftZ[j]) + * indices.push_back(i) # <<<<<<<<<<<<<< + * + * elif hi_y: + */ + try { + __pyx_v_indices.push_back(__pyx_v_i); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 184, __pyx_L1_error) + } + + /* "MDAnalysis/lib/_augment.pyx":181 + * indices.push_back(i) + * + * elif hi_z: # <<<<<<<<<<<<<< + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] + shiftY[j] - shiftZ[j]) + */ + } + __pyx_L19:; + + /* "MDAnalysis/lib/_augment.pyx":169 + * indices.push_back(i) + * + * if lo_y: # <<<<<<<<<<<<<< + * # if X&Y, edge piece + * for j in range(3): + */ + goto __pyx_L16; + } + + /* "MDAnalysis/lib/_augment.pyx":186 + * indices.push_back(i) + * + * elif hi_y: # <<<<<<<<<<<<<< + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] - shiftY[j]) + */ + __pyx_t_15 = (__pyx_v_hi_y != 0); + if (__pyx_t_15) { + + /* "MDAnalysis/lib/_augment.pyx":187 + * + * elif hi_y: + * for j in range(3): # <<<<<<<<<<<<<< + * output.push_back(coord[j] + shiftX[j] - shiftY[j]) + * indices.push_back(i) + */ + for (__pyx_t_10 = 0; __pyx_t_10 < 3; __pyx_t_10+=1) { + __pyx_v_j = __pyx_t_10; + + /* "MDAnalysis/lib/_augment.pyx":188 + * elif hi_y: + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] - shiftY[j]) # <<<<<<<<<<<<<< + * indices.push_back(i) + * + */ + try { + __pyx_v_output.push_back((((__pyx_v_coord[__pyx_v_j]) + (__pyx_v_shiftX[__pyx_v_j])) - (__pyx_v_shiftY[__pyx_v_j]))); + } catch(...) { + __Pyx_CppExn2PyErr(); 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__pyx_t_10 < 3; __pyx_t_10+=1) { + __pyx_v_j = __pyx_t_10; + + /* "MDAnalysis/lib/_augment.pyx":198 + * elif hi_z: + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] - shiftY[j] - shiftZ[j]) # <<<<<<<<<<<<<< + * indices.push_back(i) + * + */ + try { + __pyx_v_output.push_back(((((__pyx_v_coord[__pyx_v_j]) + (__pyx_v_shiftX[__pyx_v_j])) - (__pyx_v_shiftY[__pyx_v_j])) - (__pyx_v_shiftZ[__pyx_v_j]))); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 198, __pyx_L1_error) + } + } + + /* "MDAnalysis/lib/_augment.pyx":199 + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] - shiftY[j] - shiftZ[j]) + * indices.push_back(i) # <<<<<<<<<<<<<< + * + * if lo_z: + */ + try { + __pyx_v_indices.push_back(__pyx_v_i); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 199, __pyx_L1_error) + } + + /* "MDAnalysis/lib/_augment.pyx":196 + * indices.push_back(i) + * + * elif hi_z: # <<<<<<<<<<<<<< + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] - shiftY[j] - shiftZ[j]) + */ + } + __pyx_L26:; + + /* "MDAnalysis/lib/_augment.pyx":186 + * indices.push_back(i) + * + * elif hi_y: # <<<<<<<<<<<<<< + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] - shiftY[j]) + */ + } + __pyx_L16:; + + /* "MDAnalysis/lib/_augment.pyx":201 + * indices.push_back(i) + * + * if lo_z: # <<<<<<<<<<<<<< + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] + shiftZ[j]) + */ + __pyx_t_15 = (__pyx_v_lo_z != 0); + if (__pyx_t_15) { + + /* "MDAnalysis/lib/_augment.pyx":202 + * + * if lo_z: + * for j in range(3): # <<<<<<<<<<<<<< + * output.push_back(coord[j] + shiftX[j] + shiftZ[j]) + * indices.push_back(i) + */ + for (__pyx_t_10 = 0; __pyx_t_10 < 3; __pyx_t_10+=1) { + __pyx_v_j = __pyx_t_10; + + /* "MDAnalysis/lib/_augment.pyx":203 + * if lo_z: + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] + shiftZ[j]) # <<<<<<<<<<<<<< + * indices.push_back(i) + * + */ + try { + __pyx_v_output.push_back((((__pyx_v_coord[__pyx_v_j]) + (__pyx_v_shiftX[__pyx_v_j])) + (__pyx_v_shiftZ[__pyx_v_j]))); 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__pyx_t_10 < 3; __pyx_t_10+=1) { + __pyx_v_j = __pyx_t_10; + + /* "MDAnalysis/lib/_augment.pyx":208 + * elif hi_z: + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] - shiftZ[j]) # <<<<<<<<<<<<<< + * indices.push_back(i) + * + */ + try { + __pyx_v_output.push_back((((__pyx_v_coord[__pyx_v_j]) + (__pyx_v_shiftX[__pyx_v_j])) - (__pyx_v_shiftZ[__pyx_v_j]))); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 208, __pyx_L1_error) + } + } + + /* "MDAnalysis/lib/_augment.pyx":209 + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] - shiftZ[j]) + * indices.push_back(i) # <<<<<<<<<<<<<< + * + * elif hi_x: + */ + try { + __pyx_v_indices.push_back(__pyx_v_i); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 209, __pyx_L1_error) + } + + /* "MDAnalysis/lib/_augment.pyx":206 + * indices.push_back(i) + * + * elif hi_z: # <<<<<<<<<<<<<< + * for j in range(3): + * output.push_back(coord[j] + shiftX[j] - shiftZ[j]) + */ + } + __pyx_L31:; + + /* "MDAnalysis/lib/_augment.pyx":160 + * hi_z = _dot(&other[0], &reciprocal[2][0]) <= r + * + * if lo_x: # <<<<<<<<<<<<<< + * # if X, face piece + * for j in range(3): + */ + goto __pyx_L13; 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if stop < 0: # <<<<<<<<<<<<<< + * stop = 0 + * elif stop > shape: + */ + __pyx_t_2 = ((__pyx_v_stop < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":856 + * stop += shape + * if stop < 0: + * stop = 0 # <<<<<<<<<<<<<< + * elif stop > shape: + * stop = shape + */ + __pyx_v_stop = 0; + + /* "View.MemoryView":855 + * if stop < 0: + * stop += shape + * if stop < 0: # <<<<<<<<<<<<<< + * stop = 0 + * elif stop > shape: + */ + } + + /* "View.MemoryView":853 + * + * if have_stop: + * if stop < 0: # <<<<<<<<<<<<<< + * stop += shape + * if stop < 0: + */ + goto __pyx_L17; + } + + /* "View.MemoryView":857 + * if stop < 0: + * stop = 0 + * elif stop > shape: # <<<<<<<<<<<<<< + * stop = shape + * else: + */ + __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":858 + * stop = 0 + * elif stop > shape: + * stop = shape # <<<<<<<<<<<<<< + * else: + * if negative_step: + */ + __pyx_v_stop = __pyx_v_shape; + + /* "View.MemoryView":857 + * if stop < 0: + * 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(((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1126 + * for i in range(ndim): + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< + * break + * + */ + __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); + + /* "View.MemoryView":1127 + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] + * break # <<<<<<<<<<<<<< + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + */ + goto __pyx_L7_break; + + /* "View.MemoryView":1125 + * + * for i in range(ndim): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * f_stride = mslice.strides[i] + * break + */ + } + } + __pyx_L7_break:; + + /* "View.MemoryView":1129 + * break + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< + * return 'C' + * else: + */ + __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1130 + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + * return 'C' # <<<<<<<<<<<<<< + * else: + * return 'F' + */ + __pyx_r = 'C'; + goto __pyx_L0; + + /* "View.MemoryView":1129 + * break + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< + * return 'C' + * else: + */ + } + + /* "View.MemoryView":1132 + * return 'C' + * else: + * return 'F' # <<<<<<<<<<<<<< + * + * @cython.cdivision(True) + */ + /*else*/ { + __pyx_r = 'F'; + goto __pyx_L0; + } + + /* "View.MemoryView":1111 + * + * @cname('__pyx_get_best_slice_order') + * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< + * """ + * Figure out the best memory access order for a given slice. + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1135 + * + * @cython.cdivision(True) + * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< + * char *dst_data, Py_ssize_t *dst_strides, + * Py_ssize_t *src_shape, 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dst_shape[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t src_stride = src_strides[0] + * cdef Py_ssize_t dst_stride = dst_strides[0] + */ + __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); + + /* "View.MemoryView":1144 + * cdef Py_ssize_t src_extent = src_shape[0] + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + */ + __pyx_v_src_stride = (__pyx_v_src_strides[0]); + + /* "View.MemoryView":1145 + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] + * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< + * + * if ndim == 1: + */ + __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); + + /* "View.MemoryView":1147 + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + */ + __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1148 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ + __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L5_bool_binop_done; + } + __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L5_bool_binop_done; + } + + /* "View.MemoryView":1149 + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< + * memcpy(dst_data, src_data, itemsize * dst_extent) + * else: + */ + __pyx_t_2 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize); + if (__pyx_t_2) { + __pyx_t_2 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride)); + } + __pyx_t_3 = (__pyx_t_2 != 0); + __pyx_t_1 = __pyx_t_3; + __pyx_L5_bool_binop_done:; + + /* "View.MemoryView":1148 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ + if (__pyx_t_1) { + + /* "View.MemoryView":1150 + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< + * else: + * for i in range(dst_extent): + */ + (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent))); + + /* "View.MemoryView":1148 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ + goto __pyx_L4; + } + + /* "View.MemoryView":1152 + * memcpy(dst_data, src_data, itemsize * dst_extent) + * else: + * for i in range(dst_extent): # <<<<<<<<<<<<<< + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride + */ + /*else*/ { + __pyx_t_4 = __pyx_v_dst_extent; + __pyx_t_5 = __pyx_t_4; + for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { + __pyx_v_i = __pyx_t_6; + + /* "View.MemoryView":1153 + * else: + * for i in range(dst_extent): + * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< + * src_data += src_stride + * dst_data += dst_stride + */ + (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); + + /* "View.MemoryView":1154 + * for i in range(dst_extent): + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride # <<<<<<<<<<<<<< + * dst_data += dst_stride + * else: + */ + __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); + + /* "View.MemoryView":1155 + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride + * dst_data += dst_stride # <<<<<<<<<<<<<< + * else: + * for i in range(dst_extent): + */ + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L4:; + + /* "View.MemoryView":1147 + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + */ + goto __pyx_L3; + } + + /* "View.MemoryView":1157 + * dst_data += dst_stride + * else: + * for i in range(dst_extent): # <<<<<<<<<<<<<< + * _copy_strided_to_strided(src_data, src_strides + 1, + * dst_data, dst_strides + 1, + */ + /*else*/ { + __pyx_t_4 = __pyx_v_dst_extent; + __pyx_t_5 = __pyx_t_4; + for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { + __pyx_v_i = __pyx_t_6; + + /* "View.MemoryView":1158 + * else: + * for i in range(dst_extent): + * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< + * dst_data, dst_strides + 1, + * src_shape + 1, dst_shape + 1, + */ + _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); + + /* "View.MemoryView":1162 + * src_shape + 1, dst_shape + 1, + * ndim - 1, itemsize) + * src_data += src_stride # <<<<<<<<<<<<<< + * dst_data += dst_stride + * + */ + __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); + + /* "View.MemoryView":1163 + * ndim - 1, itemsize) + * src_data += src_stride + * dst_data += dst_stride # <<<<<<<<<<<<<< + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, + */ + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L3:; + + /* "View.MemoryView":1135 + * + * @cython.cdivision(True) + * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< + * char *dst_data, Py_ssize_t *dst_strides, + * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, + */ + + /* function exit code */ +} + +/* "View.MemoryView":1165 + * dst_data += dst_stride + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + */ + +static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { + + /* "View.MemoryView":1168 + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< + * src.shape, dst.shape, ndim, itemsize) + * + */ + _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1165 + * dst_data += dst_stride + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + */ + + /* function exit code */ +} + +/* "View.MemoryView":1172 + * + * @cname('__pyx_memoryview_slice_get_size') + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + */ + +static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { + int __pyx_v_i; + Py_ssize_t __pyx_v_size; + Py_ssize_t __pyx_r; + Py_ssize_t __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + + /* "View.MemoryView":1175 + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + __pyx_t_1 = __pyx_v_src->memview->view.itemsize; + __pyx_v_size = __pyx_t_1; + + /* "View.MemoryView":1177 + * cdef Py_ssize_t size = src.memview.view.itemsize + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * size *= src.shape[i] + * + */ + __pyx_t_2 = __pyx_v_ndim; + __pyx_t_3 = __pyx_t_2; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_i = __pyx_t_4; + + /* "View.MemoryView":1178 + * + * for i in range(ndim): + * size *= src.shape[i] # <<<<<<<<<<<<<< + * + * return size + */ + __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i])); + } + + /* "View.MemoryView":1180 + * size *= src.shape[i] + * + * return size # <<<<<<<<<<<<<< + * + * @cname('__pyx_fill_contig_strides_array') + */ + __pyx_r = __pyx_v_size; + goto __pyx_L0; + + /* "View.MemoryView":1172 + * + * @cname('__pyx_memoryview_slice_get_size') + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1183 + * + * @cname('__pyx_fill_contig_strides_array') + * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< + * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, + * int ndim, char order) nogil: + */ + +static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { + int __pyx_v_idx; + Py_ssize_t __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + + /* "View.MemoryView":1192 + * cdef int idx + * + * if order == 'F': # <<<<<<<<<<<<<< + * for idx in range(ndim): + * strides[idx] = stride + */ + __pyx_t_1 = ((__pyx_v_order == 'F') != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1193 + * + * if order == 'F': + * for idx in range(ndim): # <<<<<<<<<<<<<< + * strides[idx] = stride + * stride = stride * shape[idx] + */ + __pyx_t_2 = __pyx_v_ndim; + __pyx_t_3 = __pyx_t_2; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_idx = __pyx_t_4; + + /* "View.MemoryView":1194 + * if order == 'F': + * for idx in range(ndim): + * strides[idx] = stride # <<<<<<<<<<<<<< + * stride = stride * shape[idx] + * else: + */ + (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; + + /* "View.MemoryView":1195 + * for idx in range(ndim): + * strides[idx] = stride + * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * else: + * for idx in range(ndim - 1, -1, -1): + */ + __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); + } + + /* "View.MemoryView":1192 + * cdef int idx + * + * if order == 'F': # <<<<<<<<<<<<<< + * for idx in range(ndim): + * strides[idx] = stride + */ + goto __pyx_L3; + } + + /* "View.MemoryView":1197 + * stride = stride * shape[idx] + * else: + * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< + * strides[idx] = stride + * stride = stride * shape[idx] + */ + /*else*/ { + for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { + __pyx_v_idx = __pyx_t_2; + + /* "View.MemoryView":1198 + * else: + * for idx in range(ndim - 1, -1, -1): + * strides[idx] = stride # <<<<<<<<<<<<<< + * stride = stride * shape[idx] + * + */ + (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; + + /* "View.MemoryView":1199 + * for idx in range(ndim - 1, -1, -1): + * strides[idx] = stride + * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * + * return stride + */ + __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); + } + } + __pyx_L3:; + + /* "View.MemoryView":1201 + * stride = stride * shape[idx] + * + * return stride # <<<<<<<<<<<<<< + * + * @cname('__pyx_memoryview_copy_data_to_temp') + */ + __pyx_r = __pyx_v_stride; + goto __pyx_L0; + + /* "View.MemoryView":1183 + * + * @cname('__pyx_fill_contig_strides_array') + * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< + * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, + * int ndim, char order) nogil: + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1204 + * + * @cname('__pyx_memoryview_copy_data_to_temp') + * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *tmpslice, + * char order, + */ + +static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_tmpslice, char __pyx_v_order, int __pyx_v_ndim) { + int __pyx_v_i; + void *__pyx_v_result; + size_t __pyx_v_itemsize; + size_t __pyx_v_size; + void *__pyx_r; + Py_ssize_t __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + struct __pyx_memoryview_obj *__pyx_t_4; + int __pyx_t_5; + int __pyx_t_6; + + /* "View.MemoryView":1215 + * cdef void *result + * + * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< + * cdef size_t size = slice_get_size(src, ndim) + * + */ + __pyx_t_1 = __pyx_v_src->memview->view.itemsize; + __pyx_v_itemsize = __pyx_t_1; + + /* "View.MemoryView":1216 + * + * cdef size_t itemsize = src.memview.view.itemsize + * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<< + * + * result = malloc(size) + */ + __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim); + + /* "View.MemoryView":1218 + * cdef size_t size = slice_get_size(src, ndim) + * + * result = malloc(size) # <<<<<<<<<<<<<< + * if not result: + * _err(MemoryError, NULL) + */ + __pyx_v_result = malloc(__pyx_v_size); + + /* "View.MemoryView":1219 + * + * result = malloc(size) + * if not result: # <<<<<<<<<<<<<< + * _err(MemoryError, NULL) + * + */ + __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1220 + * result = malloc(size) + * if not result: + * _err(MemoryError, NULL) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 1220, __pyx_L1_error) + + /* "View.MemoryView":1219 + * + * result = malloc(size) + * if not result: # <<<<<<<<<<<<<< + * _err(MemoryError, NULL) + * + */ + } + + /* "View.MemoryView":1223 + * + * + * tmpslice.data = result # <<<<<<<<<<<<<< + * tmpslice.memview = src.memview + * for i in range(ndim): + */ + __pyx_v_tmpslice->data = ((char *)__pyx_v_result); + + /* "View.MemoryView":1224 + * + * tmpslice.data = result + * tmpslice.memview = src.memview # <<<<<<<<<<<<<< + * for i in range(ndim): + * tmpslice.shape[i] = src.shape[i] + */ + __pyx_t_4 = __pyx_v_src->memview; + __pyx_v_tmpslice->memview = __pyx_t_4; + + /* "View.MemoryView":1225 + * tmpslice.data = result + * tmpslice.memview = src.memview + * for i in range(ndim): # <<<<<<<<<<<<<< + * tmpslice.shape[i] = src.shape[i] + * tmpslice.suboffsets[i] = -1 + */ + __pyx_t_3 = __pyx_v_ndim; + __pyx_t_5 = __pyx_t_3; + for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { + __pyx_v_i = __pyx_t_6; + + /* "View.MemoryView":1226 + * tmpslice.memview = src.memview + * for i in range(ndim): + * tmpslice.shape[i] = src.shape[i] # <<<<<<<<<<<<<< + * tmpslice.suboffsets[i] = -1 + * + */ + (__pyx_v_tmpslice->shape[__pyx_v_i]) = (__pyx_v_src->shape[__pyx_v_i]); + + /* "View.MemoryView":1227 + * for i in range(ndim): + * tmpslice.shape[i] = src.shape[i] + * tmpslice.suboffsets[i] = -1 # <<<<<<<<<<<<<< + * + * fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize, + */ + (__pyx_v_tmpslice->suboffsets[__pyx_v_i]) = -1L; + } + + /* "View.MemoryView":1229 + * tmpslice.suboffsets[i] = -1 + * + * fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize, # <<<<<<<<<<<<<< + * ndim, order) + * + */ + (void)(__pyx_fill_contig_strides_array((&(__pyx_v_tmpslice->shape[0])), (&(__pyx_v_tmpslice->strides[0])), __pyx_v_itemsize, __pyx_v_ndim, __pyx_v_order)); + + /* "View.MemoryView":1233 + * + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * if tmpslice.shape[i] == 1: + * tmpslice.strides[i] = 0 + */ + __pyx_t_3 = __pyx_v_ndim; + __pyx_t_5 = __pyx_t_3; + for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { + __pyx_v_i = __pyx_t_6; + + /* "View.MemoryView":1234 + * + * for i in range(ndim): + * if tmpslice.shape[i] == 1: # <<<<<<<<<<<<<< + * tmpslice.strides[i] = 0 + * + */ + __pyx_t_2 = (((__pyx_v_tmpslice->shape[__pyx_v_i]) == 1) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1235 + * for i in range(ndim): + * if tmpslice.shape[i] == 1: + * tmpslice.strides[i] = 0 # <<<<<<<<<<<<<< + * + * if slice_is_contig(src[0], order, ndim): + */ + (__pyx_v_tmpslice->strides[__pyx_v_i]) = 0; + + /* "View.MemoryView":1234 + * + * for i in range(ndim): + * if tmpslice.shape[i] == 1: # <<<<<<<<<<<<<< + * tmpslice.strides[i] = 0 + * + */ + } + } + + /* "View.MemoryView":1237 + * tmpslice.strides[i] = 0 + * + * if slice_is_contig(src[0], order, ndim): # <<<<<<<<<<<<<< + * memcpy(result, src.data, size) + * else: + */ + __pyx_t_2 = (__pyx_memviewslice_is_contig((__pyx_v_src[0]), __pyx_v_order, __pyx_v_ndim) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1238 + * + * if slice_is_contig(src[0], order, ndim): + * memcpy(result, src.data, size) # <<<<<<<<<<<<<< + * else: + * copy_strided_to_strided(src, tmpslice, ndim, itemsize) + */ + (void)(memcpy(__pyx_v_result, __pyx_v_src->data, __pyx_v_size)); + + /* "View.MemoryView":1237 + * tmpslice.strides[i] = 0 + * + * if slice_is_contig(src[0], order, ndim): # <<<<<<<<<<<<<< + * 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broadcast_leading(&src, src_ndim, dst_ndim) + * elif dst_ndim < src_ndim: + */ + goto __pyx_L3; + } + + /* "View.MemoryView":1282 + * if src_ndim < dst_ndim: + * broadcast_leading(&src, src_ndim, dst_ndim) + * elif dst_ndim < src_ndim: # <<<<<<<<<<<<<< + * broadcast_leading(&dst, dst_ndim, src_ndim) + * + */ + __pyx_t_2 = ((__pyx_v_dst_ndim < __pyx_v_src_ndim) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1283 + * broadcast_leading(&src, src_ndim, dst_ndim) + * elif dst_ndim < src_ndim: + * broadcast_leading(&dst, dst_ndim, src_ndim) # <<<<<<<<<<<<<< + * + * cdef int ndim = max(src_ndim, dst_ndim) + */ + __pyx_memoryview_broadcast_leading((&__pyx_v_dst), __pyx_v_dst_ndim, __pyx_v_src_ndim); + + /* "View.MemoryView":1282 + * if src_ndim < dst_ndim: + * broadcast_leading(&src, src_ndim, dst_ndim) + * elif dst_ndim < src_ndim: # <<<<<<<<<<<<<< + * broadcast_leading(&dst, dst_ndim, src_ndim) + * + */ + } + __pyx_L3:; + + /* "View.MemoryView":1285 + * broadcast_leading(&dst, dst_ndim, src_ndim) + * + * cdef int ndim = max(src_ndim, dst_ndim) # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + __pyx_t_3 = __pyx_v_dst_ndim; + __pyx_t_4 = __pyx_v_src_ndim; + if (((__pyx_t_3 > __pyx_t_4) != 0)) { + __pyx_t_5 = __pyx_t_3; + } else { + __pyx_t_5 = __pyx_t_4; + } + __pyx_v_ndim = __pyx_t_5; + + /* "View.MemoryView":1287 + * cdef int ndim = max(src_ndim, dst_ndim) + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * if src.shape[i] != dst.shape[i]: + * if src.shape[i] == 1: + */ + __pyx_t_5 = __pyx_v_ndim; + __pyx_t_3 = __pyx_t_5; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_i = __pyx_t_4; + + /* "View.MemoryView":1288 + * + * for i in range(ndim): + * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< + * if src.shape[i] == 1: + * broadcasting = True + */ + __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) != (__pyx_v_dst.shape[__pyx_v_i])) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1289 + * for i in range(ndim): + * if src.shape[i] != dst.shape[i]: + * if src.shape[i] == 1: # <<<<<<<<<<<<<< + * broadcasting = True + * src.strides[i] = 0 + */ + __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) == 1) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1290 + * if src.shape[i] != dst.shape[i]: + * if src.shape[i] == 1: + * broadcasting = True # <<<<<<<<<<<<<< + * src.strides[i] = 0 + * else: + */ + __pyx_v_broadcasting = 1; + + /* "View.MemoryView":1291 + * if src.shape[i] == 1: + * broadcasting = True + * src.strides[i] = 0 # <<<<<<<<<<<<<< + * else: + * _err_extents(i, dst.shape[i], src.shape[i]) + */ + (__pyx_v_src.strides[__pyx_v_i]) = 0; + + /* "View.MemoryView":1289 + * for i in range(ndim): + * if src.shape[i] != dst.shape[i]: + * if src.shape[i] == 1: # <<<<<<<<<<<<<< + * broadcasting = True + * src.strides[i] = 0 + */ + goto __pyx_L7; + } + + /* "View.MemoryView":1293 + * src.strides[i] = 0 + * else: + * _err_extents(i, dst.shape[i], src.shape[i]) # <<<<<<<<<<<<<< + * + * if src.suboffsets[i] >= 0: + */ + /*else*/ { + __pyx_t_6 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(2, 1293, __pyx_L1_error) + } + __pyx_L7:; + + /* "View.MemoryView":1288 + * + * for i in range(ndim): + * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< + * if src.shape[i] == 1: + * broadcasting = True + */ + } + + /* "View.MemoryView":1295 + * _err_extents(i, dst.shape[i], src.shape[i]) + * + * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + */ + __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1296 + * + * if src.suboffsets[i] >= 0: + * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<< + * + * if slices_overlap(&src, &dst, ndim, itemsize): + */ + __pyx_t_6 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Dimension %d is not direct"), __pyx_v_i); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(2, 1296, __pyx_L1_error) + + /* "View.MemoryView":1295 + * _err_extents(i, dst.shape[i], src.shape[i]) + * + * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + */ + } + } + + /* "View.MemoryView":1298 + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< + * + * if not slice_is_contig(src, order, ndim): + */ + __pyx_t_2 = (__pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1300 + * if slices_overlap(&src, &dst, ndim, itemsize): + * + * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< + * order = get_best_order(&dst, ndim) + * + */ + __pyx_t_2 = ((!(__pyx_memviewslice_is_contig(__pyx_v_src, __pyx_v_order, __pyx_v_ndim) != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1301 + * + * if not slice_is_contig(src, order, ndim): + * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<< + * + * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) + */ + __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim); + + /* "View.MemoryView":1300 + * if slices_overlap(&src, &dst, ndim, itemsize): + * + * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< + * order = get_best_order(&dst, ndim) + * + */ + } + + /* "View.MemoryView":1303 + * order = get_best_order(&dst, ndim) + * + * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<< + * src = tmp + * + */ + __pyx_t_7 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_7 == ((void *)NULL))) __PYX_ERR(2, 1303, __pyx_L1_error) + __pyx_v_tmpdata = __pyx_t_7; + + /* "View.MemoryView":1304 + * + * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) + * src = tmp # <<<<<<<<<<<<<< + * + * if not broadcasting: + */ + __pyx_v_src = __pyx_v_tmp; + + /* "View.MemoryView":1298 + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< + * + * if not slice_is_contig(src, order, ndim): + */ + } + + /* "View.MemoryView":1306 + * src = tmp + * + * if not broadcasting: # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1309 + * + * + * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(dst, 'C', ndim) + * elif slice_is_contig(src, 'F', ndim): + */ + __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'C', __pyx_v_ndim) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1310 + * + * if slice_is_contig(src, 'C', ndim): + * direct_copy = slice_is_contig(dst, 'C', ndim) # <<<<<<<<<<<<<< + * elif slice_is_contig(src, 'F', ndim): + * direct_copy = slice_is_contig(dst, 'F', ndim) + */ + __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'C', __pyx_v_ndim); + + /* "View.MemoryView":1309 + * + * + * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(dst, 'C', ndim) + * elif slice_is_contig(src, 'F', ndim): + */ + goto __pyx_L12; + } + + /* "View.MemoryView":1311 + * if slice_is_contig(src, 'C', ndim): + * direct_copy = slice_is_contig(dst, 'C', ndim) + * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(dst, 'F', ndim) + * + */ + __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'F', __pyx_v_ndim) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1312 + * direct_copy = slice_is_contig(dst, 'C', ndim) + * elif slice_is_contig(src, 'F', ndim): + * direct_copy = slice_is_contig(dst, 'F', ndim) # <<<<<<<<<<<<<< + * + * if direct_copy: + */ + __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'F', __pyx_v_ndim); + + /* "View.MemoryView":1311 + * if slice_is_contig(src, 'C', ndim): + * direct_copy = slice_is_contig(dst, 'C', ndim) + * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(dst, 'F', ndim) + * + */ + } + __pyx_L12:; + + /* "View.MemoryView":1314 + * direct_copy = slice_is_contig(dst, 'F', ndim) + * + * if direct_copy: # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + __pyx_t_2 = (__pyx_v_direct_copy != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1316 + * if direct_copy: + * + * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); + + /* "View.MemoryView":1317 + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) + */ + (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim))); + + /* "View.MemoryView":1318 + * refcount_copying(&dst, dtype_is_object, ndim, False) + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * free(tmpdata) + * return 0 + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1319 + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) # <<<<<<<<<<<<<< + * return 0 + * + */ + free(__pyx_v_tmpdata); + + /* "View.MemoryView":1320 + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) + * return 0 # <<<<<<<<<<<<<< + * + * if order == 'F' == get_best_order(&dst, ndim): + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "View.MemoryView":1314 + * direct_copy = slice_is_contig(dst, 'F', ndim) + * + * if direct_copy: # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + } + + /* "View.MemoryView":1306 + * src = tmp + * + * if not broadcasting: # <<<<<<<<<<<<<< + * + * + */ + } + + /* "View.MemoryView":1322 + * return 0 + * + * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = (__pyx_v_order == 'F'); + if (__pyx_t_2) { + __pyx_t_2 = ('F' == __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim)); + } + __pyx_t_8 = (__pyx_t_2 != 0); + if (__pyx_t_8) { + + /* "View.MemoryView":1325 + * + * + * transpose_memslice(&src) # <<<<<<<<<<<<<< + * transpose_memslice(&dst) + * + */ + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(2, 1325, __pyx_L1_error) + + /* "View.MemoryView":1326 + * + * transpose_memslice(&src) + * transpose_memslice(&dst) # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(2, 1326, __pyx_L1_error) + + /* "View.MemoryView":1322 + * return 0 + * + * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< + * + * + */ + } + + /* "View.MemoryView":1328 + * transpose_memslice(&dst) + * + * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< + * copy_strided_to_strided(&src, &dst, ndim, itemsize) + * refcount_copying(&dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); + + /* "View.MemoryView":1329 + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<< + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + */ + copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1330 + * refcount_copying(&dst, dtype_is_object, ndim, False) + * copy_strided_to_strided(&src, &dst, ndim, itemsize) + * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * + * free(tmpdata) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1332 + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + * free(tmpdata) # <<<<<<<<<<<<<< + * return 0 + * + */ + free(__pyx_v_tmpdata); + + /* "View.MemoryView":1333 + * + * free(tmpdata) + * return 0 # <<<<<<<<<<<<<< + * + * @cname('__pyx_memoryview_broadcast_leading') + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "View.MemoryView":1264 + * + * @cname('__pyx_memoryview_copy_contents') + * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice dst, + * int src_ndim, int dst_ndim, + */ + + /* function exit code */ + __pyx_L1_error:; + { + #ifdef WITH_THREAD + PyGILState_STATE __pyx_gilstate_save = __Pyx_PyGILState_Ensure(); + #endif + __Pyx_AddTraceback("View.MemoryView.memoryview_copy_contents", __pyx_clineno, __pyx_lineno, __pyx_filename); + #ifdef WITH_THREAD + __Pyx_PyGILState_Release(__pyx_gilstate_save); + #endif + } + __pyx_r = -1; + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1336 + * + * @cname('__pyx_memoryview_broadcast_leading') + * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< + * int ndim, + * int ndim_other) nogil: + */ + +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslice, int __pyx_v_ndim, int __pyx_v_ndim_other) { + int __pyx_v_i; + int __pyx_v_offset; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":1340 + * int ndim_other) nogil: + * cdef int i + * cdef int offset = ndim_other - ndim # <<<<<<<<<<<<<< + * + * for i in range(ndim - 1, -1, -1): + */ + __pyx_v_offset = (__pyx_v_ndim_other - __pyx_v_ndim); + + /* "View.MemoryView":1342 + * cdef int offset = ndim_other - ndim + * + * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< + * mslice.shape[i + offset] = mslice.shape[i] + * mslice.strides[i + offset] = mslice.strides[i] + */ + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { + __pyx_v_i = __pyx_t_1; + + /* "View.MemoryView":1343 + * + * for i in range(ndim - 1, -1, -1): + * mslice.shape[i + offset] = mslice.shape[i] # <<<<<<<<<<<<<< + * mslice.strides[i + offset] = mslice.strides[i] + * mslice.suboffsets[i + offset] = mslice.suboffsets[i] + */ + (__pyx_v_mslice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->shape[__pyx_v_i]); + + /* "View.MemoryView":1344 + * for i in range(ndim - 1, -1, -1): + * mslice.shape[i + offset] = mslice.shape[i] + * mslice.strides[i + offset] = mslice.strides[i] # <<<<<<<<<<<<<< + * mslice.suboffsets[i + offset] = mslice.suboffsets[i] + * + */ + (__pyx_v_mslice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->strides[__pyx_v_i]); + + /* "View.MemoryView":1345 + * mslice.shape[i + offset] = mslice.shape[i] + * mslice.strides[i + offset] = mslice.strides[i] + * mslice.suboffsets[i + offset] = mslice.suboffsets[i] # <<<<<<<<<<<<<< + * + * for i in range(offset): + */ + (__pyx_v_mslice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->suboffsets[__pyx_v_i]); + } + + /* "View.MemoryView":1347 + * mslice.suboffsets[i + offset] = mslice.suboffsets[i] + * + * for i in range(offset): # <<<<<<<<<<<<<< + * mslice.shape[i] = 1 + * mslice.strides[i] = mslice.strides[0] + */ + __pyx_t_1 = __pyx_v_offset; + __pyx_t_2 = __pyx_t_1; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_i = __pyx_t_3; + + /* "View.MemoryView":1348 + * + * for i in range(offset): + * mslice.shape[i] = 1 # <<<<<<<<<<<<<< + * mslice.strides[i] = mslice.strides[0] + * mslice.suboffsets[i] = -1 + */ + (__pyx_v_mslice->shape[__pyx_v_i]) = 1; + + /* "View.MemoryView":1349 + * for i in range(offset): + * mslice.shape[i] = 1 + * mslice.strides[i] = mslice.strides[0] # <<<<<<<<<<<<<< + * 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Py_CLEAR(p->name); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_Enum(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o; + if (p->name) { + e = (*v)(p->name, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_Enum(PyObject *o) { + PyObject* tmp; + struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o; + tmp = ((PyObject*)p->name); + p->name = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_Enum[] = { + {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_MemviewEnum_1__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_MemviewEnum_3__setstate_cython__, METH_O, 0}, + {0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type___pyx_MemviewEnum = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib._augment.Enum", /*tp_name*/ + sizeof(struct __pyx_MemviewEnum_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ 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(PyCFunction)__pyx_memoryview_copy, METH_NOARGS, 0}, + {"copy_fortran", (PyCFunction)__pyx_memoryview_copy_fortran, METH_NOARGS, 0}, + {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_memoryview_1__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_memoryview_3__setstate_cython__, METH_O, 0}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_memoryview[] = { + {(char *)"T", __pyx_getprop___pyx_memoryview_T, 0, (char *)0, 0}, + {(char *)"base", __pyx_getprop___pyx_memoryview_base, 0, (char *)0, 0}, + {(char *)"shape", __pyx_getprop___pyx_memoryview_shape, 0, (char *)0, 0}, + {(char *)"strides", __pyx_getprop___pyx_memoryview_strides, 0, (char *)0, 0}, + {(char *)"suboffsets", __pyx_getprop___pyx_memoryview_suboffsets, 0, (char *)0, 0}, + {(char *)"ndim", __pyx_getprop___pyx_memoryview_ndim, 0, (char *)0, 0}, + {(char *)"itemsize", __pyx_getprop___pyx_memoryview_itemsize, 0, (char *)0, 0}, + {(char *)"nbytes", 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__pyx_memoryview_getbuffer, /*bf_getbuffer*/ + 0, /*bf_releasebuffer*/ +}; + +static PyTypeObject __pyx_type___pyx_memoryview = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib._augment.memoryview", /*tp_name*/ + sizeof(struct __pyx_memoryview_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_memoryview, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + __pyx_memoryview___repr__, /*tp_repr*/ + 0, /*tp_as_number*/ + &__pyx_tp_as_sequence_memoryview, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_memoryview, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + __pyx_memoryview___str__, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_memoryview, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + 0, /*tp_doc*/ + __pyx_tp_traverse_memoryview, /*tp_traverse*/ + __pyx_tp_clear_memoryview, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_memoryview, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_memoryview, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_memoryview, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct__memoryviewslice __pyx_vtable__memoryviewslice; + +static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_memoryviewslice_obj *p; + PyObject *o = __pyx_tp_new_memoryview(t, a, k); + if (unlikely(!o)) return 0; + p = ((struct __pyx_memoryviewslice_obj *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_memoryview*)__pyx_vtabptr__memoryviewslice; + p->from_object = Py_None; Py_INCREF(Py_None); + p->from_slice.memview = NULL; + return o; +} + +static void __pyx_tp_dealloc__memoryviewslice(PyObject *o) { + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_memoryviewslice___dealloc__(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->from_object); + PyObject_GC_Track(o); + __pyx_tp_dealloc_memoryview(o); +} + +static int __pyx_tp_traverse__memoryviewslice(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + e = __pyx_tp_traverse_memoryview(o, v, a); if (e) return e; + if (p->from_object) { + e = (*v)(p->from_object, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear__memoryviewslice(PyObject *o) { + PyObject* tmp; + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + __pyx_tp_clear_memoryview(o); + tmp = ((PyObject*)p->from_object); + p->from_object = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + __PYX_XDEC_MEMVIEW(&p->from_slice, 1); + return 0; +} + +static PyObject *__pyx_getprop___pyx_memoryviewslice_base(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_16_memoryviewslice_4base_1__get__(o); +} + +static PyMethodDef __pyx_methods__memoryviewslice[] = { + {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_memoryviewslice_1__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_memoryviewslice_3__setstate_cython__, METH_O, 0}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets__memoryviewslice[] = { + {(char *)"base", __pyx_getprop___pyx_memoryviewslice_base, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type___pyx_memoryviewslice = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib._augment._memoryviewslice", /*tp_name*/ + sizeof(struct __pyx_memoryviewslice_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc__memoryviewslice, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___repr__, /*tp_repr*/ + #else + 0, /*tp_repr*/ + #endif + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___str__, /*tp_str*/ + 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PyType_Modified(__pyx_memoryview_type); + + /* "View.MemoryView":990 + * return self.from_object + * + * __pyx_getbuffer = capsule( &__pyx_memoryview_getbuffer, "getbuffer(obj, view, flags)") # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = __pyx_capsule_create(((void *)(&__pyx_memoryview_getbuffer)), ((char *)"getbuffer(obj, view, flags)")); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 990, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem((PyObject *)__pyx_memoryviewslice_type->tp_dict, __pyx_n_s_pyx_getbuffer, __pyx_t_2) < 0) __PYX_ERR(2, 990, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + PyType_Modified(__pyx_memoryviewslice_type); + + /* "(tree fragment)":1 + * def __pyx_unpickle_Enum(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< + * if __pyx_checksum != 0xb068931: + * from pickle import PickleError as __pyx_PickleError + */ + __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_15View_dot_MemoryView_1__pyx_unpickle_Enum, NULL, __pyx_n_s_View_MemoryView); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_Enum, __pyx_t_2) < 0) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "(tree fragment)":9 + * __pyx_unpickle_Enum__set_state( __pyx_result, __pyx_state) + * return __pyx_result + * cdef __pyx_unpickle_Enum__set_state(Enum __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< + * __pyx_result.name = __pyx_state[0] + * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): + */ + + /*--- Wrapped vars code ---*/ + + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + if (__pyx_m) { + if (__pyx_d) { + __Pyx_AddTraceback("init MDAnalysis.lib._augment", 0, __pyx_lineno, __pyx_filename); + } + Py_DECREF(__pyx_m); __pyx_m = 0; + } else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_ImportError, "init MDAnalysis.lib._augment"); + } + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + #if CYTHON_PEP489_MULTI_PHASE_INIT + return (__pyx_m != NULL) ? 0 : -1; + #elif PY_MAJOR_VERSION >= 3 + return __pyx_m; + #else + return; + #endif +} + +/* --- Runtime support code --- */ +/* Refnanny */ +#if CYTHON_REFNANNY +static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { + PyObject *m = NULL, *p = NULL; + void *r = NULL; + m = PyImport_ImportModule((char *)modname); + if (!m) goto end; + p = PyObject_GetAttrString(m, (char *)"RefNannyAPI"); + if (!p) goto end; + r = PyLong_AsVoidPtr(p); +end: + Py_XDECREF(p); + Py_XDECREF(m); + return (__Pyx_RefNannyAPIStruct *)r; +} +#endif + +/* PyObjectGetAttrStr */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#endif + +/* GetBuiltinName */ +static PyObject *__Pyx_GetBuiltinName(PyObject *name) { + PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name); + if (unlikely(!result)) { + PyErr_Format(PyExc_NameError, +#if PY_MAJOR_VERSION >= 3 + "name '%U' is not defined", name); +#else + "name '%.200s' is not defined", PyString_AS_STRING(name)); +#endif + } + return result; +} + +/* RaiseArgTupleInvalid */ +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +/* RaiseDoubleKeywords */ +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +/* ParseKeywords */ +static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; +} + +/* GetModuleGlobalName */ +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { + PyObject *result; +#if !CYTHON_AVOID_BORROWED_REFS +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 + result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash); + if (likely(result)) { + Py_INCREF(result); + } else if (unlikely(PyErr_Occurred())) { + result = NULL; + } else { +#else + result = PyDict_GetItem(__pyx_d, name); + if (likely(result)) { + Py_INCREF(result); + } else { +#endif +#else + result = PyObject_GetItem(__pyx_d, name); + if (!result) { + PyErr_Clear(); +#endif + result = __Pyx_GetBuiltinName(name); + } + return result; +} + +/* PyCFunctionFastCall */ + #if CYTHON_FAST_PYCCALL +static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) { + PyCFunctionObject *func = (PyCFunctionObject*)func_obj; + PyCFunction meth = PyCFunction_GET_FUNCTION(func); + PyObject *self = PyCFunction_GET_SELF(func); + int flags = PyCFunction_GET_FLAGS(func); + assert(PyCFunction_Check(func)); + assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS))); + assert(nargs >= 0); + assert(nargs == 0 || args != NULL); + /* _PyCFunction_FastCallDict() must not be called with an exception set, + because it may clear it (directly or indirectly) and so the + caller loses its exception */ + assert(!PyErr_Occurred()); + if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) { + return (*((__Pyx_PyCFunctionFastWithKeywords)meth)) (self, args, nargs, NULL); + } else { + return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs); + } +} +#endif + +/* PyFunctionFastCall */ + #if CYTHON_FAST_PYCALL +#include "frameobject.h" +static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na, + PyObject *globals) { + PyFrameObject *f; + PyThreadState *tstate = __Pyx_PyThreadState_Current; + PyObject **fastlocals; + Py_ssize_t i; + PyObject *result; + assert(globals != NULL); + /* XXX Perhaps we should create a specialized + PyFrame_New() that doesn't take locals, but does + take builtins without sanity checking them. + */ + assert(tstate != NULL); + f = PyFrame_New(tstate, co, globals, NULL); + if (f == NULL) { + return NULL; + } + fastlocals = f->f_localsplus; + for (i = 0; i < na; i++) { + Py_INCREF(*args); + fastlocals[i] = *args++; + } + result = PyEval_EvalFrameEx(f,0); + ++tstate->recursion_depth; + Py_DECREF(f); + --tstate->recursion_depth; + return result; +} +#if 1 || PY_VERSION_HEX < 0x030600B1 +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs) { + PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); + PyObject *globals = PyFunction_GET_GLOBALS(func); + PyObject *argdefs = PyFunction_GET_DEFAULTS(func); + PyObject *closure; +#if PY_MAJOR_VERSION >= 3 + PyObject *kwdefs; +#endif + PyObject *kwtuple, **k; + PyObject **d; + Py_ssize_t nd; + Py_ssize_t nk; + PyObject *result; + assert(kwargs == NULL || PyDict_Check(kwargs)); + nk = kwargs ? PyDict_Size(kwargs) : 0; + if (Py_EnterRecursiveCall((char*)" while calling a Python object")) { + return NULL; + } + if ( +#if PY_MAJOR_VERSION >= 3 + co->co_kwonlyargcount == 0 && +#endif + likely(kwargs == NULL || nk == 0) && + co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { + if (argdefs == NULL && co->co_argcount == nargs) { + result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); + goto done; + } + else if (nargs == 0 && argdefs != NULL + && co->co_argcount == Py_SIZE(argdefs)) { + /* function called with no arguments, but all parameters have + a default value: use default values as arguments .*/ + args = &PyTuple_GET_ITEM(argdefs, 0); + result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); + goto done; + } + } + if (kwargs != NULL) { + Py_ssize_t pos, i; + kwtuple = PyTuple_New(2 * nk); + if (kwtuple == NULL) { + result = NULL; + goto done; + } + k = &PyTuple_GET_ITEM(kwtuple, 0); + pos = i = 0; + while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { + Py_INCREF(k[i]); + Py_INCREF(k[i+1]); + i += 2; + } + nk = i / 2; + } + else { + kwtuple = NULL; + k = NULL; + } + closure = PyFunction_GET_CLOSURE(func); +#if PY_MAJOR_VERSION >= 3 + kwdefs = PyFunction_GET_KW_DEFAULTS(func); +#endif + if (argdefs != NULL) { + d = &PyTuple_GET_ITEM(argdefs, 0); + nd = Py_SIZE(argdefs); + } + else { + d = NULL; + nd = 0; + } +#if PY_MAJOR_VERSION >= 3 + result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, + args, nargs, + k, (int)nk, + d, (int)nd, kwdefs, closure); +#else + result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, + args, nargs, + k, (int)nk, + d, (int)nd, closure); +#endif + Py_XDECREF(kwtuple); +done: + Py_LeaveRecursiveCall(); + return result; +} +#endif +#endif + +/* PyObjectCall */ + #if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *result; + ternaryfunc call = func->ob_type->tp_call; + if (unlikely(!call)) + return PyObject_Call(func, arg, kw); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = (*call)(func, arg, kw); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +/* PyObjectCallMethO */ + #if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = PyCFunction_GET_FUNCTION(func); + self = PyCFunction_GET_SELF(func); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +/* PyObjectCallOneArg */ + #if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#if CYTHON_FAST_PYCALL + if (PyFunction_Check(func)) { + return __Pyx_PyFunction_FastCall(func, &arg, 1); + } +#endif + if (likely(PyCFunction_Check(func))) { + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); +#if CYTHON_FAST_PYCCALL + } else if (PyCFunction_GET_FLAGS(func) & METH_FASTCALL) { + return __Pyx_PyCFunction_FastCall(func, &arg, 1); +#endif + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_Pack(1, arg); + if (unlikely(!args)) return NULL; + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +#endif + +/* MemviewSliceInit */ + static int +__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, + int ndim, + __Pyx_memviewslice *memviewslice, + int memview_is_new_reference) +{ + __Pyx_RefNannyDeclarations + int i, retval=-1; + Py_buffer *buf = &memview->view; + __Pyx_RefNannySetupContext("init_memviewslice", 0); + if (!buf) { + PyErr_SetString(PyExc_ValueError, + "buf is NULL."); + goto fail; + } else if (memviewslice->memview || memviewslice->data) { + PyErr_SetString(PyExc_ValueError, + "memviewslice is already initialized!"); + goto fail; + } + if (buf->strides) { + for (i = 0; i < ndim; i++) { + memviewslice->strides[i] = buf->strides[i]; + } + } else { + Py_ssize_t stride = buf->itemsize; + for (i = ndim - 1; i >= 0; i--) { + memviewslice->strides[i] = stride; + stride *= buf->shape[i]; + } + } + for (i = 0; i < ndim; i++) { + memviewslice->shape[i] = buf->shape[i]; + if (buf->suboffsets) { + memviewslice->suboffsets[i] = buf->suboffsets[i]; + } else { + memviewslice->suboffsets[i] = -1; + } + } + memviewslice->memview = memview; + memviewslice->data = (char *)buf->buf; + if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { + Py_INCREF(memview); + } + retval = 0; + goto no_fail; +fail: + memviewslice->memview = 0; + memviewslice->data = 0; + retval = -1; +no_fail: + __Pyx_RefNannyFinishContext(); + return retval; +} +#ifndef Py_NO_RETURN +#define Py_NO_RETURN +#endif +static void __pyx_fatalerror(const char *fmt, ...) Py_NO_RETURN { + va_list vargs; + char msg[200]; +#ifdef HAVE_STDARG_PROTOTYPES + va_start(vargs, fmt); +#else + va_start(vargs); +#endif + vsnprintf(msg, 200, fmt, vargs); + va_end(vargs); + Py_FatalError(msg); +} +static CYTHON_INLINE int +__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock) +{ + int result; + PyThread_acquire_lock(lock, 1); + result = (*acquisition_count)++; + PyThread_release_lock(lock); + return result; +} +static CYTHON_INLINE int +__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock) +{ + int result; + PyThread_acquire_lock(lock, 1); + result = (*acquisition_count)--; + PyThread_release_lock(lock); + return result; +} +static CYTHON_INLINE void +__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) +{ + int first_time; + struct __pyx_memoryview_obj *memview = memslice->memview; + if (!memview || (PyObject *) memview == Py_None) + return; + if (__pyx_get_slice_count(memview) < 0) + __pyx_fatalerror("Acquisition count is %d (line %d)", + __pyx_get_slice_count(memview), lineno); + first_time = __pyx_add_acquisition_count(memview) == 0; + if (first_time) { + if (have_gil) { + Py_INCREF((PyObject *) memview); + } else { + PyGILState_STATE _gilstate = PyGILState_Ensure(); + Py_INCREF((PyObject *) memview); + PyGILState_Release(_gilstate); + } + } +} +static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, + int have_gil, int lineno) { + int last_time; + struct __pyx_memoryview_obj *memview = memslice->memview; + if (!memview ) { + return; + } else if ((PyObject *) memview == Py_None) { + memslice->memview = NULL; + return; + } + if (__pyx_get_slice_count(memview) <= 0) + __pyx_fatalerror("Acquisition count is %d (line %d)", + __pyx_get_slice_count(memview), lineno); + last_time = __pyx_sub_acquisition_count(memview) == 1; + memslice->data = NULL; + if (last_time) { + if (have_gil) { + Py_CLEAR(memslice->memview); + } else { + PyGILState_STATE _gilstate = PyGILState_Ensure(); + Py_CLEAR(memslice->memview); + PyGILState_Release(_gilstate); + } + } else { + memslice->memview = NULL; + } +} + +/* PyErrFetchRestore */ + #if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +} +static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +} +#endif + +/* RaiseException */ + #if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + __Pyx_PyThreadState_declare + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_PyThreadState_assign + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + int is_subclass = PyObject_IsSubclass(instance_class, type); + if (!is_subclass) { + instance_class = NULL; + } else if (unlikely(is_subclass == -1)) { + goto bad; + } else { + type = instance_class; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } + if (cause) { + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { +#if CYTHON_COMPILING_IN_PYPY + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); + Py_INCREF(tb); + PyErr_Restore(tmp_type, tmp_value, tb); + Py_XDECREF(tmp_tb); +#else + PyThreadState *tstate = __Pyx_PyThreadState_Current; + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } +#endif + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +/* DictGetItem */ + #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { + PyObject *value; + value = PyDict_GetItemWithError(d, key); + if (unlikely(!value)) { + if (!PyErr_Occurred()) { + PyObject* args = PyTuple_Pack(1, key); + if (likely(args)) + PyErr_SetObject(PyExc_KeyError, args); + Py_XDECREF(args); + } + return NULL; + } + Py_INCREF(value); + return value; +} +#endif + +/* RaiseTooManyValuesToUnpack */ + static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +/* RaiseNeedMoreValuesToUnpack */ + static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +/* RaiseNoneIterError */ + static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +/* ExtTypeTest */ + static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(__Pyx_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + +/* SaveResetException */ + #if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + #if PY_VERSION_HEX >= 0x030700A3 + *type = tstate->exc_state.exc_type; + *value = tstate->exc_state.exc_value; + *tb = tstate->exc_state.exc_traceback; + #else + *type = tstate->exc_type; + *value = tstate->exc_value; + *tb = tstate->exc_traceback; + #endif + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); +} +static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + #if PY_VERSION_HEX >= 0x030700A3 + tmp_type = tstate->exc_state.exc_type; + tmp_value = tstate->exc_state.exc_value; + tmp_tb = tstate->exc_state.exc_traceback; + tstate->exc_state.exc_type = type; + tstate->exc_state.exc_value = value; + tstate->exc_state.exc_traceback = tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = type; + tstate->exc_value = value; + tstate->exc_traceback = tb; + #endif + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +} +#endif + +/* PyErrExceptionMatches */ + #if CYTHON_FAST_THREAD_STATE +static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; icurexc_type; + if (exc_type == err) return 1; + if (unlikely(!exc_type)) return 0; + if (unlikely(PyTuple_Check(err))) + return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); + return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); +} +#endif + +/* GetException */ + #if CYTHON_FAST_THREAD_STATE +static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { +#else +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { +#endif + PyObject *local_type, *local_value, *local_tb; +#if CYTHON_FAST_THREAD_STATE + PyObject *tmp_type, *tmp_value, *tmp_tb; + local_type = tstate->curexc_type; + local_value = tstate->curexc_value; + local_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif + PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_FAST_THREAD_STATE + if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif + goto bad; + #if PY_MAJOR_VERSION >= 3 + if (local_tb) { + if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) + goto bad; + } + #endif + Py_XINCREF(local_tb); + Py_XINCREF(local_type); + Py_XINCREF(local_value); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_FAST_THREAD_STATE + #if PY_VERSION_HEX >= 0x030700A3 + tmp_type = tstate->exc_state.exc_type; + tmp_value = tstate->exc_state.exc_value; + tmp_tb = tstate->exc_state.exc_traceback; + tstate->exc_state.exc_type = local_type; + tstate->exc_state.exc_value = local_value; + tstate->exc_state.exc_traceback = local_tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = local_type; + tstate->exc_value = local_value; + tstate->exc_traceback = local_tb; + #endif + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif + return 0; +bad: + *type = 0; + *value = 0; + *tb = 0; + Py_XDECREF(local_type); + Py_XDECREF(local_value); + Py_XDECREF(local_tb); + return -1; +} + +/* ArgTypeTest */ + static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) +{ + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + else if (exact) { + #if PY_MAJOR_VERSION == 2 + if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; + #endif + } + else { + if (likely(__Pyx_TypeCheck(obj, type))) return 1; + } + PyErr_Format(PyExc_TypeError, + "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", + name, type->tp_name, Py_TYPE(obj)->tp_name); + return 0; +} + +/* BytesEquals */ + static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else + if (s1 == s2) { + return (equals == Py_EQ); + } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { + const char *ps1, *ps2; + Py_ssize_t length = PyBytes_GET_SIZE(s1); + if (length != PyBytes_GET_SIZE(s2)) + return (equals == Py_NE); + ps1 = PyBytes_AS_STRING(s1); + ps2 = PyBytes_AS_STRING(s2); + if (ps1[0] != ps2[0]) { + return (equals == Py_NE); + } else if (length == 1) { + return (equals == Py_EQ); + } else { + int result; +#if CYTHON_USE_UNICODE_INTERNALS + Py_hash_t hash1, hash2; + hash1 = ((PyBytesObject*)s1)->ob_shash; + hash2 = ((PyBytesObject*)s2)->ob_shash; + if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { + return (equals == Py_NE); + } +#endif + result = memcmp(ps1, ps2, (size_t)length); + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { + return (equals == Py_NE); + } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { + return (equals == Py_NE); + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +#endif +} + +/* UnicodeEquals */ + static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else +#if PY_MAJOR_VERSION < 3 + PyObject* owned_ref = NULL; +#endif + int s1_is_unicode, s2_is_unicode; + if (s1 == s2) { + goto return_eq; + } + s1_is_unicode = PyUnicode_CheckExact(s1); + s2_is_unicode = PyUnicode_CheckExact(s2); +#if PY_MAJOR_VERSION < 3 + if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { + owned_ref = PyUnicode_FromObject(s2); + if (unlikely(!owned_ref)) + return -1; + s2 = owned_ref; + s2_is_unicode = 1; + } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { + owned_ref = PyUnicode_FromObject(s1); + if (unlikely(!owned_ref)) + return -1; + s1 = owned_ref; + s1_is_unicode = 1; + } else if (((!s2_is_unicode) & (!s1_is_unicode))) { + return __Pyx_PyBytes_Equals(s1, s2, equals); + } +#endif + if (s1_is_unicode & s2_is_unicode) { + Py_ssize_t length; + int kind; + void *data1, *data2; + if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) + return -1; + length = __Pyx_PyUnicode_GET_LENGTH(s1); + if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { + goto return_ne; + } +#if CYTHON_USE_UNICODE_INTERNALS + { + Py_hash_t hash1, hash2; + #if CYTHON_PEP393_ENABLED + hash1 = ((PyASCIIObject*)s1)->hash; + hash2 = ((PyASCIIObject*)s2)->hash; + #else + hash1 = ((PyUnicodeObject*)s1)->hash; + hash2 = ((PyUnicodeObject*)s2)->hash; + #endif + if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { + goto return_ne; + } + } +#endif + kind = __Pyx_PyUnicode_KIND(s1); + if (kind != __Pyx_PyUnicode_KIND(s2)) { + goto return_ne; + } + data1 = __Pyx_PyUnicode_DATA(s1); + data2 = __Pyx_PyUnicode_DATA(s2); + if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { + goto return_ne; + } else if (length == 1) { + goto return_eq; + } else { + int result = memcmp(data1, data2, (size_t)(length * kind)); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & s2_is_unicode) { + goto return_ne; + } else if ((s2 == Py_None) & s1_is_unicode) { + goto return_ne; + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +return_eq: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ); +return_ne: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_NE); +#endif +} + +/* None */ + static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { + Py_ssize_t q = a / b; + Py_ssize_t r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} + +/* GetAttr */ + static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { +#if CYTHON_USE_TYPE_SLOTS +#if PY_MAJOR_VERSION >= 3 + if (likely(PyUnicode_Check(n))) +#else + if (likely(PyString_Check(n))) +#endif + return __Pyx_PyObject_GetAttrStr(o, n); +#endif + return PyObject_GetAttr(o, n); +} + +/* GetItemInt */ + static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { + PyObject *r; + if (!j) return NULL; + r = PyObject_GetItem(o, j); + Py_DECREF(j); + return r; +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyList_GET_SIZE(o); + } + if ((!boundscheck) || likely((0 <= wrapped_i) & (wrapped_i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, wrapped_i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyTuple_GET_SIZE(o); + } + if ((!boundscheck) || likely((0 <= wrapped_i) & (wrapped_i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS + if (is_list || PyList_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); + if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) { + PyObject *r = PyList_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } + else if (PyTuple_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } else { + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_item)) { + if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (likely(l >= 0)) { + i += l; + } else { + if (!PyErr_ExceptionMatches(PyExc_OverflowError)) + return NULL; + PyErr_Clear(); + } + } + return m->sq_item(o, i); + } + } +#else + if (is_list || PySequence_Check(o)) { + return PySequence_GetItem(o, i); + } +#endif + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +} + +/* ObjectGetItem */ + #if CYTHON_USE_TYPE_SLOTS +static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { + PyObject *runerr; + Py_ssize_t key_value; + PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; + if (unlikely(!(m && m->sq_item))) { + PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); + return NULL; + } + key_value = __Pyx_PyIndex_AsSsize_t(index); + if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { + return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); + } + if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { + PyErr_Clear(); + PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); + } + return NULL; +} +static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { + PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; + if (likely(m && m->mp_subscript)) { + return m->mp_subscript(obj, key); + } + return __Pyx_PyObject_GetIndex(obj, key); +} +#endif + +/* decode_c_string */ + static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { + Py_ssize_t length; + if (unlikely((start < 0) | (stop < 0))) { + size_t slen = strlen(cstring); + if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { + PyErr_SetString(PyExc_OverflowError, + "c-string too long to convert to Python"); + return NULL; + } + length = (Py_ssize_t) slen; + if (start < 0) { + start += length; + if (start < 0) + start = 0; + } + if (stop < 0) + stop += length; + } + length = stop - start; + if (unlikely(length <= 0)) + return PyUnicode_FromUnicode(NULL, 0); + cstring += start; + if (decode_func) { + return decode_func(cstring, length, errors); + } else { + return PyUnicode_Decode(cstring, length, encoding, errors); + } +} + +/* GetAttr3 */ + static PyObject *__Pyx_GetAttr3Default(PyObject *d) { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) + return NULL; + __Pyx_PyErr_Clear(); + Py_INCREF(d); + return d; +} +static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { + PyObject *r = __Pyx_GetAttr(o, n); + return (likely(r)) ? r : __Pyx_GetAttr3Default(d); +} + +/* SwapException */ + #if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + #if PY_VERSION_HEX >= 0x030700A3 + tmp_type = tstate->exc_state.exc_type; + tmp_value = tstate->exc_state.exc_value; + tmp_tb = tstate->exc_state.exc_traceback; + tstate->exc_state.exc_type = *type; + tstate->exc_state.exc_value = *value; + tstate->exc_state.exc_traceback = *tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = *type; + tstate->exc_value = *value; + tstate->exc_traceback = *tb; + #endif + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} +#else +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); + PyErr_SetExcInfo(*type, *value, *tb); + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} +#endif + +/* Import */ + static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_MAJOR_VERSION < 3 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_MAJOR_VERSION < 3 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + +/* FastTypeChecks */ + #if CYTHON_COMPILING_IN_CPYTHON +static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { + while (a) { + a = a->tp_base; + if (a == b) + return 1; + } + return b == &PyBaseObject_Type; +} +static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { + PyObject *mro; + if (a == b) return 1; + mro = a->tp_mro; + if (likely(mro)) { + Py_ssize_t i, n; + n = PyTuple_GET_SIZE(mro); + for (i = 0; i < n; i++) { + if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) + return 1; + } + return 0; + } + return __Pyx_InBases(a, b); +} +#if PY_MAJOR_VERSION == 2 +static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { + PyObject *exception, *value, *tb; + int res; + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ErrFetch(&exception, &value, &tb); + res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; + if (unlikely(res == -1)) { + PyErr_WriteUnraisable(err); + res = 0; + } + if (!res) { + res = PyObject_IsSubclass(err, exc_type2); + if (unlikely(res == -1)) { + PyErr_WriteUnraisable(err); + res = 0; + } + } + __Pyx_ErrRestore(exception, value, tb); + return res; +} +#else +static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { + int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; + if (!res) { + res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); + } + return res; +} +#endif +static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + assert(PyExceptionClass_Check(exc_type)); + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i= 0 || (x^b) >= 0)) + return PyInt_FromLong(x); + return PyLong_Type.tp_as_number->nb_add(op1, op2); + } + #endif + #if CYTHON_USE_PYLONG_INTERNALS + if (likely(PyLong_CheckExact(op1))) { + const long b = intval; + long a, x; +#ifdef HAVE_LONG_LONG + const PY_LONG_LONG llb = intval; + PY_LONG_LONG lla, llx; +#endif + const digit* digits = ((PyLongObject*)op1)->ob_digit; + const Py_ssize_t size = Py_SIZE(op1); + if (likely(__Pyx_sst_abs(size) <= 1)) { + a = likely(size) ? digits[0] : 0; + if (size == -1) a = -a; + } else { + switch (size) { + case -2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case 2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case -3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case 3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case -4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case 4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + default: return PyLong_Type.tp_as_number->nb_add(op1, op2); + } + } + x = a + b; + return PyLong_FromLong(x); +#ifdef HAVE_LONG_LONG + long_long: + llx = lla + llb; + return PyLong_FromLongLong(llx); +#endif + + + } + #endif + if (PyFloat_CheckExact(op1)) { + const long b = intval; + double a = PyFloat_AS_DOUBLE(op1); + double result; + PyFPE_START_PROTECT("add", return NULL) + result = ((double)a) + (double)b; + PyFPE_END_PROTECT(result) + return PyFloat_FromDouble(result); + } + return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); +} +#endif + +/* None */ + static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); +} + +/* None */ + static CYTHON_INLINE long __Pyx_div_long(long a, long b) { + long q = a / b; + long r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} + +/* WriteUnraisableException */ + static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, + CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, + int full_traceback, CYTHON_UNUSED int nogil) { + PyObject *old_exc, *old_val, *old_tb; + PyObject *ctx; + __Pyx_PyThreadState_declare +#ifdef WITH_THREAD + PyGILState_STATE state; + if (nogil) + state = PyGILState_Ensure(); +#ifdef _MSC_VER + else state = (PyGILState_STATE)-1; +#endif +#endif + __Pyx_PyThreadState_assign + __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); + if (full_traceback) { + Py_XINCREF(old_exc); + Py_XINCREF(old_val); + Py_XINCREF(old_tb); + __Pyx_ErrRestore(old_exc, old_val, old_tb); + PyErr_PrintEx(1); + } + #if PY_MAJOR_VERSION < 3 + ctx = PyString_FromString(name); + #else + ctx = PyUnicode_FromString(name); + #endif + __Pyx_ErrRestore(old_exc, old_val, old_tb); + if (!ctx) { + PyErr_WriteUnraisable(Py_None); + } else { + PyErr_WriteUnraisable(ctx); + Py_DECREF(ctx); + } +#ifdef WITH_THREAD + if (nogil) + PyGILState_Release(state); +#endif +} + +/* ImportFrom */ + static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { + PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); + if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { + PyErr_Format(PyExc_ImportError, + #if PY_MAJOR_VERSION < 3 + "cannot import name %.230s", PyString_AS_STRING(name)); + #else + "cannot import name %S", name); + #endif + } + return value; +} + +/* HasAttr */ + static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { + PyObject *r; + if (unlikely(!__Pyx_PyBaseString_Check(n))) { + PyErr_SetString(PyExc_TypeError, + "hasattr(): attribute name must be string"); + return -1; + } + r = __Pyx_GetAttr(o, n); + if (unlikely(!r)) { + PyErr_Clear(); + return 0; + } else { + Py_DECREF(r); + return 1; + } +} + +/* PyObject_GenericGetAttrNoDict */ + #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { + PyErr_Format(PyExc_AttributeError, +#if PY_MAJOR_VERSION >= 3 + "'%.50s' object has no attribute '%U'", + tp->tp_name, attr_name); +#else + "'%.50s' object has no attribute '%.400s'", + tp->tp_name, PyString_AS_STRING(attr_name)); +#endif + return NULL; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { + PyObject *descr; + PyTypeObject *tp = Py_TYPE(obj); + if (unlikely(!PyString_Check(attr_name))) { + return PyObject_GenericGetAttr(obj, attr_name); + } + assert(!tp->tp_dictoffset); + descr = _PyType_Lookup(tp, attr_name); + if (unlikely(!descr)) { + return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); + } + Py_INCREF(descr); + #if PY_MAJOR_VERSION < 3 + if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) + #endif + { + descrgetfunc f = Py_TYPE(descr)->tp_descr_get; + if (unlikely(f)) { + PyObject *res = f(descr, obj, (PyObject *)tp); + Py_DECREF(descr); + return res; + } + } + return descr; +} +#endif + +/* PyObject_GenericGetAttr */ + #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { + if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { + return PyObject_GenericGetAttr(obj, attr_name); + } + return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); +} +#endif + +/* SetVTable */ + static int __Pyx_SetVtable(PyObject *dict, void *vtable) { +#if PY_VERSION_HEX >= 0x02070000 + PyObject *ob = PyCapsule_New(vtable, 0, 0); +#else + PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); +#endif + if (!ob) + goto bad; + if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) + goto bad; + Py_DECREF(ob); + return 0; +bad: + Py_XDECREF(ob); + return -1; +} + +/* SetupReduce */ + static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { + int ret; + PyObject *name_attr; + name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2); + if (likely(name_attr)) { + ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); + } else { + ret = -1; + } + if (unlikely(ret < 0)) { + PyErr_Clear(); + ret = 0; + } + Py_XDECREF(name_attr); + return ret; +} +static int __Pyx_setup_reduce(PyObject* type_obj) { + int ret = 0; + PyObject *object_reduce = NULL; + PyObject *object_reduce_ex = NULL; + PyObject *reduce = NULL; + PyObject *reduce_ex = NULL; + PyObject *reduce_cython = NULL; + PyObject *setstate = NULL; + PyObject *setstate_cython = NULL; +#if CYTHON_USE_PYTYPE_LOOKUP + if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto GOOD; +#else + if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto GOOD; +#endif +#if CYTHON_USE_PYTYPE_LOOKUP + object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; +#else + object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; +#endif + reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto BAD; + if (reduce_ex == object_reduce_ex) { +#if CYTHON_USE_PYTYPE_LOOKUP + object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; +#else + object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; +#endif + reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto BAD; + if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { + reduce_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_cython); if (unlikely(!reduce_cython)) goto BAD; + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto BAD; + setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); + if (!setstate) PyErr_Clear(); + if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { + setstate_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate_cython); if (unlikely(!setstate_cython)) goto BAD; + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto BAD; + } + PyType_Modified((PyTypeObject*)type_obj); + } + } + goto GOOD; +BAD: + if (!PyErr_Occurred()) + PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); + ret = -1; +GOOD: +#if !CYTHON_USE_PYTYPE_LOOKUP + Py_XDECREF(object_reduce); + Py_XDECREF(object_reduce_ex); +#endif + Py_XDECREF(reduce); + Py_XDECREF(reduce_ex); + Py_XDECREF(reduce_cython); + Py_XDECREF(setstate); + Py_XDECREF(setstate_cython); + return ret; +} + +/* CLineInTraceback */ + #ifndef CYTHON_CLINE_IN_TRACEBACK +static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { + PyObject *use_cline; + PyObject *ptype, *pvalue, *ptraceback; +#if CYTHON_COMPILING_IN_CPYTHON + PyObject **cython_runtime_dict; +#endif + if (unlikely(!__pyx_cython_runtime)) { + return c_line; + } + __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); +#if CYTHON_COMPILING_IN_CPYTHON + cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); + if (likely(cython_runtime_dict)) { + use_cline = __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback); + } else +#endif + { + PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); + if (use_cline_obj) { + use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; + Py_DECREF(use_cline_obj); + } else { + PyErr_Clear(); + use_cline = NULL; + } + } + if (!use_cline) { + c_line = 0; + PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); + } + else if (PyObject_Not(use_cline) != 0) { + c_line = 0; + } + __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); + return c_line; +} +#endif + +/* CodeObjectCache */ + static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = start + (end - start) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} + +/* AddTraceback */ + #include "compile.h" +#include "frameobject.h" +#include "traceback.h" +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + #if PY_MAJOR_VERSION < 3 + py_srcfile = PyString_FromString(filename); + #else + py_srcfile = PyUnicode_FromString(filename); + #endif + if (!py_srcfile) goto bad; + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #endif + } + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + #else + py_funcname = PyUnicode_FromString(funcname); + #endif + } + if (!py_funcname) goto bad; + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + PyThreadState *tstate = __Pyx_PyThreadState_Current; + if (c_line) { + c_line = __Pyx_CLineForTraceback(tstate, c_line); + } + py_code = __pyx_find_code_object(c_line ? -c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); + } + py_frame = PyFrame_New( + tstate, /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + __Pyx_PyFrame_SetLineNumber(py_frame, py_line); + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} + +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (__Pyx_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); + if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if ((0)) {} + else if (__Pyx_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); + view->obj = NULL; + Py_DECREF(obj); +} +#endif + + + /* MemviewSliceIsContig */ + static int +__pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim) +{ + int i, index, step, start; + Py_ssize_t itemsize = mvs.memview->view.itemsize; + if (order == 'F') { + step = 1; + start = 0; + } else { + step = -1; + start = ndim - 1; + } + for (i = 0; i < ndim; i++) { + index = start + step * i; + if (mvs.suboffsets[index] >= 0 || mvs.strides[index] != itemsize) + return 0; + itemsize *= mvs.shape[index]; + } + return 1; +} + +/* OverlappingSlices */ + static void +__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, + void **out_start, void **out_end, + int ndim, size_t itemsize) +{ + char *start, *end; + int i; + start = end = slice->data; + for (i = 0; i < ndim; i++) { + Py_ssize_t stride = slice->strides[i]; + Py_ssize_t extent = slice->shape[i]; + if (extent == 0) { + *out_start = *out_end = start; + return; + } else { + if (stride > 0) + end += stride * (extent - 1); + else + start += stride * (extent - 1); + } + } + *out_start = start; + *out_end = end + itemsize; +} +static int +__pyx_slices_overlap(__Pyx_memviewslice *slice1, + __Pyx_memviewslice *slice2, + int ndim, size_t itemsize) +{ + void *start1, *end1, *start2, *end2; + __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); + __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); + return (start1 < end2) && (start2 < end1); +} + +/* Capsule */ + static CYTHON_INLINE PyObject * +__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) +{ + PyObject *cobj; +#if PY_VERSION_HEX >= 0x02070000 + cobj = PyCapsule_New(p, sig, NULL); +#else + cobj = PyCObject_FromVoidPtr(p, NULL); +#endif + return cobj; +} + +/* IsLittleEndian */ + static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) +{ + union { + uint32_t u32; + uint8_t u8[4]; + } S; + S.u32 = 0x01020304; + return S.u8[0] == 4; +} + +/* BufferFormatCheck */ + static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type) { + stack[0].field = &ctx->root; + stack[0].parent_offset = 0; + ctx->root.type = type; + ctx->root.name = "buffer dtype"; + ctx->root.offset = 0; + ctx->head = stack; + ctx->head->field = &ctx->root; + ctx->fmt_offset = 0; + ctx->head->parent_offset = 0; + ctx->new_packmode = '@'; + ctx->enc_packmode = '@'; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->is_complex = 0; + ctx->is_valid_array = 0; + ctx->struct_alignment = 0; + while (type->typegroup == 'S') { + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = 0; + type = type->fields->type; + } +} +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; + } else { + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; + } + } + *ts = t; + return count; +} +static int __Pyx_BufFmt_ExpectNumber(const char **ts) { + int number = __Pyx_BufFmt_ParseNumber(ts); + if (number == -1) + PyErr_Format(PyExc_ValueError,\ + "Does not understand character buffer dtype format string ('%c')", **ts); + return number; +} +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + PyErr_Format(PyExc_ValueError, + "Unexpected format string character: '%c'", ch); +} +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'c': return "'char'"; + case 'b': return "'signed char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 's': case 'p': return "a string"; + case 0: return "end"; + default: return "unparseable format string"; + } +} +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; + } + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +/* These are for computing the padding at the end of the struct to align + on the first member of the struct. This will probably the same as above, + but we don't have any guarantees. + */ +typedef struct { short x; char c; } __Pyx_pad_short; +typedef struct { int x; char c; } __Pyx_pad_int; +typedef struct { long x; char c; } __Pyx_pad_long; +typedef struct { float x; char c; } __Pyx_pad_float; +typedef struct { double x; char c; } __Pyx_pad_double; +typedef struct { long double x; char c; } __Pyx_pad_longdouble; +typedef struct { void *x; char c; } __Pyx_pad_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); + case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); + case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': + return 'H'; + case 'b': case 'h': case 'i': + case 'l': case 'q': case 's': case 'p': + return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': + return 'U'; + case 'f': case 'd': case 'g': + return (is_complex ? 'C' : 'R'); + case 'O': + return 'O'; + case 'P': + return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; + } + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset, arraysize = 1; + if (ctx->enc_type == 0) return 0; + if (ctx->head->field->type->arraysize[0]) { + int i, ndim = 0; + if (ctx->enc_type == 's' || ctx->enc_type == 'p') { + ctx->is_valid_array = ctx->head->field->type->ndim == 1; + ndim = 1; + if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { + PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %zu", + ctx->head->field->type->arraysize[0], ctx->enc_count); + return -1; + } + } + if (!ctx->is_valid_array) { + PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", + ctx->head->field->type->ndim, ndim); + return -1; + } + for (i = 0; i < ctx->head->field->type->ndim; i++) { + arraysize *= ctx->head->field->type->arraysize[i]; + } + ctx->is_valid_array = 0; + ctx->enc_count = 1; + } + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + } + if (ctx->enc_packmode == '@') { + size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + size_t align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + if (ctx->struct_alignment == 0) + ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, + ctx->is_complex); + } + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + if ((type->typegroup == 'H' || group == 'H') && type->size == size) { + } else { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + } + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", + (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); + return -1; + } + ctx->fmt_offset += size; + if (arraysize) + ctx->fmt_offset += (arraysize - 1) * size; + --ctx->enc_count; + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + break; + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } + } + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} +static PyObject * +__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) +{ + const char *ts = *tsp; + int i = 0, number; + int ndim = ctx->head->field->type->ndim; +; + ++ts; + if (ctx->new_count != 1) { + PyErr_SetString(PyExc_ValueError, + "Cannot handle repeated arrays in format string"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + while (*ts && *ts != ')') { + switch (*ts) { + case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; + default: break; + } + number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) + return PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %d", + ctx->head->field->type->arraysize[i], number); + if (*ts != ',' && *ts != ')') + return PyErr_Format(PyExc_ValueError, + "Expected a comma in format string, got '%c'", *ts); + if (*ts == ',') ts++; + i++; + } + if (i != ndim) + return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", + ctx->head->field->type->ndim, i); + if (!*ts) { + PyErr_SetString(PyExc_ValueError, + "Unexpected end of format string, expected ')'"); + return NULL; + } + ctx->is_valid_array = 1; + ctx->new_count = 1; + *tsp = ++ts; + return Py_None; +} +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case '\r': + case '\n': + ++ts; + break; + case '<': + if (!__Pyx_Is_Little_Endian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_Is_Little_Endian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + ctx->new_packmode = *ts++; + break; + case 'T': + { + const char* ts_after_sub; + size_t i, struct_count = ctx->new_count; + size_t struct_alignment = ctx->struct_alignment; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + ctx->enc_count = 0; + ctx->struct_alignment = 0; + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + if (struct_alignment) ctx->struct_alignment = struct_alignment; + } + break; + case '}': + { + size_t alignment = ctx->struct_alignment; + ++ts; + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + if (alignment && ctx->fmt_offset % alignment) { + ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); + } + } + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->enc_packmode = ctx->new_packmode; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } + CYTHON_FALLTHROUGH; + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': case 'p': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex && + ctx->enc_packmode == ctx->new_packmode) { + ctx->enc_count += ctx->new_count; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; + } + CYTHON_FALLTHROUGH; + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + case ':': + ++ts; + while(*ts != ':') ++ts; + ++ts; + break; + case '(': + if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; + break; + default: + { + int number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + ctx->new_count = (size_t)number; + } + } + } +} + +/* TypeInfoCompare */ + static int +__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) +{ + int i; + if (!a || !b) + return 0; + if (a == b) + return 1; + if (a->size != b->size || a->typegroup != b->typegroup || + a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { + if (a->typegroup == 'H' || b->typegroup == 'H') { + return a->size == b->size; + } else { + return 0; + } + } + if (a->ndim) { + for (i = 0; i < a->ndim; i++) + if (a->arraysize[i] != b->arraysize[i]) + return 0; + } + if (a->typegroup == 'S') { + if (a->flags != b->flags) + return 0; + if (a->fields || b->fields) { + if (!(a->fields && b->fields)) + return 0; + for (i = 0; a->fields[i].type && b->fields[i].type; i++) { + __Pyx_StructField *field_a = a->fields + i; + __Pyx_StructField *field_b = b->fields + i; + if (field_a->offset != field_b->offset || + !__pyx_typeinfo_cmp(field_a->type, field_b->type)) + return 0; + } + return !a->fields[i].type && !b->fields[i].type; + } + } + return 1; +} + +/* MemviewSliceValidateAndInit */ + static int +__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) +{ + if (buf->shape[dim] <= 1) + return 1; + if (buf->strides) { + if (spec & __Pyx_MEMVIEW_CONTIG) { + if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { + if (buf->strides[dim] != sizeof(void *)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly contiguous " + "in dimension %d.", dim); + goto fail; + } + } else if (buf->strides[dim] != buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_FOLLOW) { + Py_ssize_t stride = buf->strides[dim]; + if (stride < 0) + stride = -stride; + if (stride < buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } + } + } else { + if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not contiguous in " + "dimension %d", dim); + goto fail; + } else if (spec & (__Pyx_MEMVIEW_PTR)) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not indirect in " + "dimension %d", dim); + goto fail; + } else if (buf->suboffsets) { + PyErr_SetString(PyExc_ValueError, + "Buffer exposes suboffsets but no strides"); + goto fail; + } + } + return 1; +fail: + return 0; +} +static int +__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) +{ + if (spec & __Pyx_MEMVIEW_DIRECT) { + if (buf->suboffsets && buf->suboffsets[dim] >= 0) { + PyErr_Format(PyExc_ValueError, + "Buffer not compatible with direct access " + "in dimension %d.", dim); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_PTR) { + if (!buf->suboffsets || (buf->suboffsets && buf->suboffsets[dim] < 0)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly accessible " + "in dimension %d.", dim); + goto fail; + } + } + return 1; +fail: + return 0; +} +static int +__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) +{ + int i; + if (c_or_f_flag & __Pyx_IS_F_CONTIG) { + Py_ssize_t stride = 1; + for (i = 0; i < ndim; i++) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) + { + PyErr_SetString(PyExc_ValueError, + "Buffer not fortran contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { + Py_ssize_t stride = 1; + for (i = ndim - 1; i >- 1; i--) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) { + PyErr_SetString(PyExc_ValueError, + "Buffer not C contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } + return 1; +fail: + return 0; +} +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj) +{ + struct __pyx_memoryview_obj *memview, *new_memview; + __Pyx_RefNannyDeclarations + Py_buffer *buf; + int i, spec = 0, retval = -1; + __Pyx_BufFmt_Context ctx; + int from_memoryview = __pyx_memoryview_check(original_obj); + __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); + if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) + original_obj)->typeinfo)) { + memview = (struct __pyx_memoryview_obj *) original_obj; + new_memview = NULL; + } else { + memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + original_obj, buf_flags, 0, dtype); + new_memview = memview; + if (unlikely(!memview)) + goto fail; + } + buf = &memview->view; + if (buf->ndim != ndim) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + ndim, buf->ndim); + goto fail; + } + if (new_memview) { + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned) buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " + "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", + buf->itemsize, + (buf->itemsize > 1) ? "s" : "", + dtype->name, + dtype->size, + (dtype->size > 1) ? "s" : ""); + goto fail; + } + for (i = 0; i < ndim; i++) { + spec = axes_specs[i]; + if (!__pyx_check_strides(buf, i, ndim, spec)) + goto fail; + if (!__pyx_check_suboffsets(buf, i, ndim, spec)) + goto fail; + } + if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, + new_memview != NULL) == -1)) { + goto fail; + } + retval = 0; + goto no_fail; +fail: + Py_XDECREF(new_memview); + retval = -1; +no_fail: + __Pyx_RefNannyFinishContext(); + return retval; +} + +/* ObjectToMemviewSlice */ + static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_float(PyObject *obj, int writable_flag) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_FOLLOW), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, + (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 2, + &__Pyx_TypeInfo_float, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +/* ObjectToMemviewSlice */ + static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_float(PyObject *obj, int writable_flag) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS_RO | writable_flag, 1, + &__Pyx_TypeInfo_float, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +/* ObjectToMemviewSlice */ + static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_int64_t(PyObject *obj, int writable_flag) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS_RO | writable_flag, 1, + &__Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +/* CIntFromPyVerify */ + #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) +#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) +#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ + {\ + func_type value = func_value;\ + if (sizeof(target_type) < sizeof(func_type)) {\ + if (unlikely(value != (func_type) (target_type) value)) {\ + func_type zero = 0;\ + if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ + return (target_type) -1;\ + if (is_unsigned && unlikely(value < zero))\ + goto raise_neg_overflow;\ + else\ + goto raise_overflow;\ + }\ + }\ + return (target_type) value;\ + } + +/* MemviewDtypeToObject */ + static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp) { + return (PyObject *) PyFloat_FromDouble(*(float *) itemp); +} +static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj) { + float value = __pyx_PyFloat_AsFloat(obj); + if ((value == (float)-1) && PyErr_Occurred()) + return 0; + *(float *) itemp = value; + return 1; +} + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_int64(npy_int64 value) { + const npy_int64 neg_one = (npy_int64) -1, const_zero = (npy_int64) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(npy_int64) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(npy_int64) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(npy_int64) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(npy_int64) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(npy_int64) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(npy_int64), + little, !is_unsigned); + } +} + +/* MemviewDtypeToObject */ + static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_5numpy_int64_t(const char *itemp) { + return (PyObject *) __Pyx_PyInt_From_npy_int64(*(__pyx_t_5numpy_int64_t *) itemp); +} +static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_int64_t(const char *itemp, PyObject *obj) { + __pyx_t_5numpy_int64_t value = __Pyx_PyInt_As_npy_int64(obj); + if ((value == ((npy_int64)-1)) && PyErr_Occurred()) + return 0; + *(__pyx_t_5numpy_int64_t *) itemp = value; + return 1; +} + +/* Declarations */ + #if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +/* Arithmetic */ + #if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + #if 1 + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + if (b.imag == 0) { + return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); + } else if (fabsf(b.real) >= fabsf(b.imag)) { + if (b.real == 0 && b.imag == 0) { + return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); + } else { + float r = b.imag / b.real; + float s = 1.0 / (b.real + b.imag * r); + return __pyx_t_float_complex_from_parts( + (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); + } + } else { + float r = b.real / b.imag; + float s = 1.0 / (b.imag + b.real * r); + return __pyx_t_float_complex_from_parts( + (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); + } + } + #else + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + if (b.imag == 0) { + return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); + } else { + float denom = b.real * b.real + b.imag * b.imag; + return __pyx_t_float_complex_from_parts( + (a.real * b.real + a.imag * b.imag) / denom, + (a.imag * b.real - a.real * b.imag) / denom); + } + } + #endif + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod_float(a, a); + return __Pyx_c_prod_float(a, a); + case 3: + z = __Pyx_c_prod_float(a, a); + return __Pyx_c_prod_float(z, a); + case 4: + z = __Pyx_c_prod_float(a, a); + return __Pyx_c_prod_float(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } else if (b.imag == 0) { + z.real = powf(a.real, b.real); + z.imag = 0; + return z; + } else if (a.real > 0) { + r = a.real; + theta = 0; + } else { + r = -a.real; + theta = atan2f(0, -1); + } + } else { + r = __Pyx_c_abs_float(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +/* Declarations */ + #if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +/* Arithmetic */ + #if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + #if 1 + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + if (b.imag == 0) { + return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } else if (fabs(b.real) >= fabs(b.imag)) { + if (b.real == 0 && b.imag == 0) { + return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); + } else { + double r = b.imag / b.real; + double s = 1.0 / (b.real + b.imag * r); + return __pyx_t_double_complex_from_parts( + (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); + } + } else { + double r = b.real / b.imag; + double s = 1.0 / (b.imag + b.real * r); + return __pyx_t_double_complex_from_parts( + (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); + } + } + #else + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + if (b.imag == 0) { + return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } else { + double denom = b.real * b.real + b.imag * b.imag; + return __pyx_t_double_complex_from_parts( + (a.real * b.real + a.imag * b.imag) / denom, + (a.imag * b.real - a.real * b.imag) / denom); + } + } + #endif + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod_double(a, a); + return __Pyx_c_prod_double(a, a); + case 3: + z = __Pyx_c_prod_double(a, a); + return __Pyx_c_prod_double(z, a); + case 4: + z = __Pyx_c_prod_double(a, a); + return __Pyx_c_prod_double(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } else if (b.imag == 0) { + z.real = pow(a.real, b.real); + z.imag = 0; + return z; + } else if (a.real > 0) { + r = a.real; + theta = 0; + } else { + r = -a.real; + theta = atan2(0, -1); + } + } else { + r = __Pyx_c_abs_double(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { + const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum NPY_TYPES) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(enum NPY_TYPES) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), + little, !is_unsigned); + } +} + +/* MemviewSliceCopyTemplate */ + static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object) +{ + __Pyx_RefNannyDeclarations + int i; + __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; + struct __pyx_memoryview_obj *from_memview = from_mvs->memview; + Py_buffer *buf = &from_memview->view; + PyObject *shape_tuple = NULL; + PyObject *temp_int = NULL; + struct __pyx_array_obj *array_obj = NULL; + struct __pyx_memoryview_obj *memview_obj = NULL; + __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); + for (i = 0; i < ndim; i++) { + if (from_mvs->suboffsets[i] >= 0) { + PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " + "indirect dimensions (axis %d)", i); + goto fail; + } + } + shape_tuple = PyTuple_New(ndim); + if (unlikely(!shape_tuple)) { + goto fail; + } + __Pyx_GOTREF(shape_tuple); + for(i = 0; i < ndim; i++) { + temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); + if(unlikely(!temp_int)) { + goto fail; + } else { + PyTuple_SET_ITEM(shape_tuple, i, temp_int); + temp_int = NULL; + } + } + array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); + if (unlikely(!array_obj)) { + goto fail; + } + __Pyx_GOTREF(array_obj); + memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + (PyObject *) array_obj, contig_flag, + dtype_is_object, + from_mvs->memview->typeinfo); + if (unlikely(!memview_obj)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) + goto fail; + if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, + dtype_is_object) < 0)) + goto fail; + goto no_fail; +fail: + __Pyx_XDECREF(new_mvs.memview); + new_mvs.memview = NULL; + new_mvs.data = NULL; +no_fail: + __Pyx_XDECREF(shape_tuple); + __Pyx_XDECREF(temp_int); + __Pyx_XDECREF(array_obj); + __Pyx_RefNannyFinishContext(); + return new_mvs; +} + +/* CIntFromPy */ + static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + case -2: + if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + } +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; + } + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +/* CIntFromPy */ + static CYTHON_INLINE npy_int64 __Pyx_PyInt_As_npy_int64(PyObject *x) { + const npy_int64 neg_one = (npy_int64) -1, const_zero = (npy_int64) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(npy_int64) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(npy_int64, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (npy_int64) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (npy_int64) 0; + case 1: __PYX_VERIFY_RETURN_INT(npy_int64, digit, digits[0]) + case 2: + if (8 * sizeof(npy_int64) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) >= 2 * PyLong_SHIFT) { + return (npy_int64) (((((npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(npy_int64) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) >= 3 * PyLong_SHIFT) { + return (npy_int64) (((((((npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(npy_int64) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) >= 4 * PyLong_SHIFT) { + return (npy_int64) (((((((((npy_int64)digits[3]) << PyLong_SHIFT) | (npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (npy_int64) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(npy_int64) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_int64, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(npy_int64) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_int64, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (npy_int64) 0; + case -1: __PYX_VERIFY_RETURN_INT(npy_int64, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(npy_int64, digit, +digits[0]) + case -2: + if (8 * sizeof(npy_int64) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 2 * PyLong_SHIFT) { + return (npy_int64) (((npy_int64)-1)*(((((npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(npy_int64) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 2 * PyLong_SHIFT) { + return (npy_int64) ((((((npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(npy_int64) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 3 * PyLong_SHIFT) { + return (npy_int64) (((npy_int64)-1)*(((((((npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(npy_int64) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 3 * PyLong_SHIFT) { + return (npy_int64) ((((((((npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(npy_int64) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 4 * PyLong_SHIFT) { + return (npy_int64) (((npy_int64)-1)*(((((((((npy_int64)digits[3]) << PyLong_SHIFT) | (npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(npy_int64) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 4 * PyLong_SHIFT) { + return (npy_int64) ((((((((((npy_int64)digits[3]) << PyLong_SHIFT) | (npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); + } + } + break; + } +#endif + if (sizeof(npy_int64) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_int64, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(npy_int64) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_int64, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + npy_int64 val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (npy_int64) -1; + } + } else { + npy_int64 val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (npy_int64) -1; + val = __Pyx_PyInt_As_npy_int64(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to npy_int64"); + return (npy_int64) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to npy_int64"); + return (npy_int64) -1; +} + +/* CIntFromPy */ + static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *x) { + const size_t neg_one = (size_t) -1, const_zero = (size_t) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(size_t) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(size_t, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (size_t) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (size_t) 0; + case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, digits[0]) + case 2: + if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) >= 2 * PyLong_SHIFT) { + return (size_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) >= 3 * PyLong_SHIFT) { + return (size_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) >= 4 * PyLong_SHIFT) { + return (size_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (size_t) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(size_t) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(size_t) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (size_t) 0; + case -1: __PYX_VERIFY_RETURN_INT(size_t, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, +digits[0]) + case -2: + if (8 * sizeof(size_t) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { + return (size_t) (((size_t)-1)*(((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { + return (size_t) ((((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { + return (size_t) (((size_t)-1)*(((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { + return (size_t) ((((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) { + return (size_t) (((size_t)-1)*(((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) { + return (size_t) ((((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + } +#endif + if (sizeof(size_t) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(size_t) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + size_t val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (size_t) -1; + } + } else { + size_t val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (size_t) -1; + val = __Pyx_PyInt_As_size_t(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to size_t"); + return (size_t) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to size_t"); + return (size_t) -1; +} + +/* CIntFromPy */ + static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = (long) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + case -2: + if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + } +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = (long) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + +/* CIntFromPy */ + static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { + const char neg_one = (char) -1, const_zero = (char) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(char) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (char) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (char) 0; + case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) + case 2: + if (8 * sizeof(char) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { + return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(char) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { + return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(char) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { + return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (char) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(char) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (char) 0; + case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) + case -2: + if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(char) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(char) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(char) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { + return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + } +#endif + if (sizeof(char) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + char val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (char) -1; + } + } else { + char val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (char) -1; + val = __Pyx_PyInt_As_char(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to char"); + return (char) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to char"); + return (char) -1; +} + +/* CheckBinaryVersion */ + static int __Pyx_check_binary_version(void) { + char ctversion[4], rtversion[4]; + PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); + if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + return PyErr_WarnEx(NULL, message, 1); + } + return 0; +} + +/* ModuleImport */ + #ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + +/* TypeImport */ + #ifndef __PYX_HAVE_RT_ImportType +#define __PYX_HAVE_RT_ImportType +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, + size_t size, int strict) +{ + PyObject *py_module = 0; + PyObject *result = 0; + PyObject *py_name = 0; + char warning[200]; + Py_ssize_t basicsize; +#ifdef Py_LIMITED_API + PyObject *py_basicsize; +#endif + py_module = __Pyx_ImportModule(module_name); + if (!py_module) + goto bad; + py_name = __Pyx_PyIdentifier_FromString(class_name); + if (!py_name) + goto bad; + result = PyObject_GetAttr(py_module, py_name); + Py_DECREF(py_name); + py_name = 0; + Py_DECREF(py_module); + py_module = 0; + if (!result) + goto bad; + if (!PyType_Check(result)) { + PyErr_Format(PyExc_TypeError, + "%.200s.%.200s is not a type object", + module_name, class_name); + goto bad; + } +#ifndef Py_LIMITED_API + basicsize = ((PyTypeObject *)result)->tp_basicsize; +#else + py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); + if (!py_basicsize) + goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; +#endif + if (!strict && (size_t)basicsize > size) { + PyOS_snprintf(warning, sizeof(warning), + "%s.%s size changed, may indicate binary incompatibility. Expected %zd, got %zd", + module_name, class_name, basicsize, size); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; + } + else if ((size_t)basicsize != size) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s has the wrong size, try recompiling. Expected %zd, got %zd", + module_name, class_name, basicsize, size); + goto bad; + } + return (PyTypeObject *)result; +bad: + Py_XDECREF(py_module); + Py_XDECREF(result); + return NULL; +} +#endif + +/* FunctionImport */ + #ifndef __PYX_HAVE_RT_ImportFunction +#define __PYX_HAVE_RT_ImportFunction +static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig) { + PyObject *d = 0; + PyObject *cobj = 0; + union { + void (*fp)(void); + void *p; + } tmp; + d = PyObject_GetAttrString(module, (char *)"__pyx_capi__"); + if (!d) + goto bad; + cobj = PyDict_GetItemString(d, funcname); + if (!cobj) { + PyErr_Format(PyExc_ImportError, + "%.200s does not export expected C function %.200s", + PyModule_GetName(module), funcname); + goto bad; + } +#if PY_VERSION_HEX >= 0x02070000 + if (!PyCapsule_IsValid(cobj, sig)) { + PyErr_Format(PyExc_TypeError, + "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)", + PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj)); + goto bad; + } + tmp.p = PyCapsule_GetPointer(cobj, sig); +#else + {const char *desc, *s1, *s2; + desc = (const char *)PyCObject_GetDesc(cobj); + if (!desc) + goto bad; + s1 = desc; s2 = sig; + while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; } + if (*s1 != *s2) { + PyErr_Format(PyExc_TypeError, + "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)", + PyModule_GetName(module), funcname, sig, desc); + goto bad; + } + tmp.p = PyCObject_AsVoidPtr(cobj);} +#endif + *f = tmp.fp; + if (!(*f)) + goto bad; + Py_DECREF(d); + return 0; +bad: + Py_XDECREF(d); + return -1; +} +#endif + +/* InitStrings */ + static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + if (t->is_unicode) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + #else + if (t->is_unicode | t->is_str) { + if (t->intern) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->encoding) { + *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); + } else { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + if (PyObject_Hash(*t->p) == -1) + return -1; + ++t; + } + return 0; +} + +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); +} +static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { + Py_ssize_t ignore; + return __Pyx_PyObject_AsStringAndSize(o, &ignore); +} +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +#if !CYTHON_PEP393_ENABLED +static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { + char* defenc_c; + PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); + if (!defenc) return NULL; + defenc_c = PyBytes_AS_STRING(defenc); +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + { + char* end = defenc_c + PyBytes_GET_SIZE(defenc); + char* c; + for (c = defenc_c; c < end; c++) { + if ((unsigned char) (*c) >= 128) { + PyUnicode_AsASCIIString(o); + return NULL; + } + } + } +#endif + *length = PyBytes_GET_SIZE(defenc); + return defenc_c; +} +#else +static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { + if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL; +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + if (likely(PyUnicode_IS_ASCII(o))) { + *length = PyUnicode_GET_LENGTH(o); + return PyUnicode_AsUTF8(o); + } else { + PyUnicode_AsASCIIString(o); + return NULL; + } +#else + return PyUnicode_AsUTF8AndSize(o, length); +#endif +} +#endif +#endif +static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT + if ( +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + __Pyx_sys_getdefaultencoding_not_ascii && +#endif + PyUnicode_Check(o)) { + return __Pyx_PyUnicode_AsStringAndSize(o, length); + } else +#endif +#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) + if (PyByteArray_Check(o)) { + *length = PyByteArray_GET_SIZE(o); + return PyByteArray_AS_STRING(o); + } else +#endif + { + char* result; + int r = PyBytes_AsStringAndSize(o, &result, length); + if (unlikely(r < 0)) { + return NULL; + } else { + return result; + } + } +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + int is_true = x == Py_True; + if (is_true | (x == Py_False) | (x == Py_None)) return is_true; + else return PyObject_IsTrue(x); +} +static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) { +#if PY_MAJOR_VERSION >= 3 + if (PyLong_Check(result)) { + if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, + "__int__ returned non-int (type %.200s). " + "The ability to return an instance of a strict subclass of int " + "is deprecated, and may be removed in a future version of Python.", + Py_TYPE(result)->tp_name)) { + Py_DECREF(result); + return NULL; + } + return result; + } +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type %.200s)", + type_name, type_name, Py_TYPE(result)->tp_name); + Py_DECREF(result); + return NULL; +} +static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { +#if CYTHON_USE_TYPE_SLOTS + PyNumberMethods *m; +#endif + const char *name = NULL; + PyObject *res = NULL; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x) || PyLong_Check(x))) +#else + if (likely(PyLong_Check(x))) +#endif + return __Pyx_NewRef(x); +#if CYTHON_USE_TYPE_SLOTS + m = Py_TYPE(x)->tp_as_number; + #if PY_MAJOR_VERSION < 3 + if (m && m->nb_int) { + name = "int"; + res = m->nb_int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = m->nb_long(x); + } + #else + if (likely(m && m->nb_int)) { + name = "int"; + res = m->nb_int(x); + } + #endif +#else + if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) { + res = PyNumber_Int(x); + } +#endif + if (likely(res)) { +#if PY_MAJOR_VERSION < 3 + if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) { +#else + if (unlikely(!PyLong_CheckExact(res))) { +#endif + return __Pyx_PyNumber_IntOrLongWrongResultType(res, name); + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject *x; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(b))) { + if (sizeof(Py_ssize_t) >= sizeof(long)) + return PyInt_AS_LONG(b); + else + return PyInt_AsSsize_t(x); + } +#endif + if (likely(PyLong_CheckExact(b))) { + #if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)b)->ob_digit; + const Py_ssize_t size = Py_SIZE(b); + if (likely(__Pyx_sst_abs(size) <= 1)) { + ival = likely(size) ? digits[0] : 0; + if (size == -1) ival = -ival; + return ival; + } else { + switch (size) { + case 2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + } + } + #endif + return PyLong_AsSsize_t(b); + } + x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) { + return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False); +} +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { + return PyInt_FromSize_t(ival); +} + + +#endif /* Py_PYTHON_H */ diff --git a/package/MDAnalysis/lib/_cutil.cpp b/package/MDAnalysis/lib/_cutil.cpp new file mode 100644 index 00000000000..4f5c03ec31e --- /dev/null +++ b/package/MDAnalysis/lib/_cutil.cpp @@ -0,0 +1,28436 @@ +/* Generated by Cython 0.28.5 */ + +/* BEGIN: Cython Metadata +{ + "distutils": { + "depends": [ + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h", + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include/numpy/ufuncobject.h", + "MDAnalysis/lib/include/calc_distances.h" + ], + "extra_compile_args": [ + "-ffast-math", + "-O3", + "-funroll-loops", + "-std=c++11", + "-stdlib=libc++" + ], + "include_dirs": [ + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include", + "MDAnalysis/lib/include" + ], + "language": "c++", + "libraries": [ + "m" + ], + "name": "MDAnalysis.lib._cutil", + "sources": [ + "MDAnalysis/lib/_cutil.pyx" + ] + }, + "module_name": "MDAnalysis.lib._cutil" +} +END: Cython Metadata */ + +#define PY_SSIZE_T_CLEAN +#include "Python.h" +#ifndef Py_PYTHON_H + #error Python headers needed to compile C extensions, please install development version of Python. +#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) + #error Cython requires Python 2.6+ or Python 3.3+. +#else +#define CYTHON_ABI "0_28_5" +#define CYTHON_FUTURE_DIVISION 0 +#include +#ifndef offsetof + #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#endif +#if !defined(WIN32) && !defined(MS_WINDOWS) + #ifndef __stdcall + #define __stdcall + #endif + #ifndef __cdecl + #define __cdecl + #endif + #ifndef __fastcall + #define __fastcall + #endif +#endif +#ifndef DL_IMPORT + #define DL_IMPORT(t) t +#endif +#ifndef DL_EXPORT + #define DL_EXPORT(t) t +#endif +#define __PYX_COMMA , +#ifndef HAVE_LONG_LONG + #if PY_VERSION_HEX >= 0x02070000 + #define HAVE_LONG_LONG + #endif +#endif +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif +#ifdef PYPY_VERSION + #define CYTHON_COMPILING_IN_PYPY 1 + #define CYTHON_COMPILING_IN_PYSTON 0 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #undef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 0 + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #if PY_VERSION_HEX < 0x03050000 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #elif !defined(CYTHON_USE_ASYNC_SLOTS) + #define CYTHON_USE_ASYNC_SLOTS 1 + #endif + #undef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 0 + #undef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 0 + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #undef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 1 + #undef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 0 + #undef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 0 + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 0 + #undef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT 0 + #undef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE 0 +#elif defined(PYSTON_VERSION) + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_PYSTON 1 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #ifndef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 1 + #endif + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #undef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 0 + #ifndef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 1 + #endif + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #ifndef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 0 + #endif + #ifndef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 1 + #endif + #ifndef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 1 + #endif + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 0 + #undef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT 0 + #undef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE 0 +#else + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_PYSTON 0 + #define CYTHON_COMPILING_IN_CPYTHON 1 + #ifndef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 1 + #endif + #if PY_VERSION_HEX < 0x02070000 + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #elif !defined(CYTHON_USE_PYTYPE_LOOKUP) + #define CYTHON_USE_PYTYPE_LOOKUP 1 + #endif + #if PY_MAJOR_VERSION < 3 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #elif !defined(CYTHON_USE_ASYNC_SLOTS) + #define CYTHON_USE_ASYNC_SLOTS 1 + #endif + #if PY_VERSION_HEX < 0x02070000 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #elif !defined(CYTHON_USE_PYLONG_INTERNALS) + #define CYTHON_USE_PYLONG_INTERNALS 1 + #endif + #ifndef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 1 + #endif + #ifndef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 1 + #endif + #if PY_VERSION_HEX < 0x030300F0 + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #elif !defined(CYTHON_USE_UNICODE_WRITER) + #define CYTHON_USE_UNICODE_WRITER 1 + #endif + #ifndef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 0 + #endif + #ifndef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 1 + #endif + #ifndef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 1 + #endif + #ifndef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 1 + #endif + #ifndef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 1 + #endif + #ifndef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT (0 && PY_VERSION_HEX >= 0x03050000) + #endif + #ifndef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1) + #endif +#endif +#if !defined(CYTHON_FAST_PYCCALL) +#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) +#endif +#if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" + #undef SHIFT + #undef BASE + #undef MASK +#endif +#ifndef __has_attribute + #define __has_attribute(x) 0 +#endif +#ifndef __has_cpp_attribute + #define __has_cpp_attribute(x) 0 +#endif +#ifndef CYTHON_RESTRICT + #if defined(__GNUC__) + #define CYTHON_RESTRICT __restrict__ + #elif defined(_MSC_VER) && _MSC_VER >= 1400 + #define CYTHON_RESTRICT __restrict + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_RESTRICT restrict + #else + #define CYTHON_RESTRICT + #endif +#endif +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +#ifndef CYTHON_MAYBE_UNUSED_VAR +# if defined(__cplusplus) + template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } +# else +# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) +# endif +#endif +#ifndef CYTHON_NCP_UNUSED +# if CYTHON_COMPILING_IN_CPYTHON +# define CYTHON_NCP_UNUSED +# else +# define CYTHON_NCP_UNUSED CYTHON_UNUSED +# endif +#endif +#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) +#ifdef _MSC_VER + #ifndef _MSC_STDINT_H_ + #if _MSC_VER < 1300 + typedef unsigned char uint8_t; + typedef unsigned int uint32_t; + #else + typedef unsigned __int8 uint8_t; + typedef unsigned __int32 uint32_t; + #endif + #endif +#else + #include +#endif +#ifndef CYTHON_FALLTHROUGH + #if defined(__cplusplus) && __cplusplus >= 201103L + #if __has_cpp_attribute(fallthrough) + #define CYTHON_FALLTHROUGH [[fallthrough]] + #elif __has_cpp_attribute(clang::fallthrough) + #define CYTHON_FALLTHROUGH [[clang::fallthrough]] + #elif __has_cpp_attribute(gnu::fallthrough) + #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] + #endif + #endif + #ifndef CYTHON_FALLTHROUGH + #if __has_attribute(fallthrough) + #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) + #else + #define CYTHON_FALLTHROUGH + #endif + #endif + #if defined(__clang__ ) && defined(__apple_build_version__) + #if __apple_build_version__ < 7000000 + #undef CYTHON_FALLTHROUGH + #define CYTHON_FALLTHROUGH + #endif + #endif +#endif + +#ifndef __cplusplus + #error "Cython files generated with the C++ option must be compiled with a C++ compiler." +#endif +#ifndef CYTHON_INLINE + #if defined(__clang__) + #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) + #else + #define CYTHON_INLINE inline + #endif +#endif +template +void __Pyx_call_destructor(T& x) { + x.~T(); +} +template +class __Pyx_FakeReference { + public: + __Pyx_FakeReference() : ptr(NULL) { } + __Pyx_FakeReference(const T& ref) : ptr(const_cast(&ref)) { } + T *operator->() { return ptr; } + T *operator&() { return ptr; } + operator T&() { return *ptr; } + template bool operator ==(U other) { return *ptr == other; } + template bool operator !=(U other) { return *ptr != other; } + private: + T *ptr; +}; + +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) + #define Py_OptimizeFlag 0 +#endif +#define __PYX_BUILD_PY_SSIZE_T "n" +#define CYTHON_FORMAT_SSIZE_T "z" +#if PY_MAJOR_VERSION < 3 + #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyClass_Type +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyType_Type +#endif +#ifndef Py_TPFLAGS_CHECKTYPES + #define Py_TPFLAGS_CHECKTYPES 0 +#endif +#ifndef Py_TPFLAGS_HAVE_INDEX + #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#ifndef Py_TPFLAGS_HAVE_NEWBUFFER + #define Py_TPFLAGS_HAVE_NEWBUFFER 0 +#endif +#ifndef Py_TPFLAGS_HAVE_FINALIZE + #define Py_TPFLAGS_HAVE_FINALIZE 0 +#endif +#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) + #ifndef METH_FASTCALL + #define METH_FASTCALL 0x80 + #endif + typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); + typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, + Py_ssize_t nargs, PyObject *kwnames); +#else + #define __Pyx_PyCFunctionFast _PyCFunctionFast + #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords +#endif +#if CYTHON_FAST_PYCCALL +#define __Pyx_PyFastCFunction_Check(func)\ + ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS))))) +#else +#define __Pyx_PyFastCFunction_Check(func) 0 +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) + #define PyObject_Malloc(s) PyMem_Malloc(s) + #define PyObject_Free(p) PyMem_Free(p) + #define PyObject_Realloc(p) PyMem_Realloc(p) +#endif +#if CYTHON_COMPILING_IN_PYSTON + #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) + #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) +#else + #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) + #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) +#endif +#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 + #define __Pyx_PyThreadState_Current PyThreadState_GET() +#elif PY_VERSION_HEX >= 0x03060000 + #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() +#elif PY_VERSION_HEX >= 0x03000000 + #define __Pyx_PyThreadState_Current PyThreadState_GET() +#else + #define __Pyx_PyThreadState_Current _PyThreadState_Current +#endif +#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) +#include "pythread.h" +#define Py_tss_NEEDS_INIT 0 +typedef int Py_tss_t; +static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { + *key = PyThread_create_key(); + return 0; // PyThread_create_key reports success always +} +static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { + Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); + *key = Py_tss_NEEDS_INIT; + return key; +} +static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { + PyObject_Free(key); +} +static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { + return *key != Py_tss_NEEDS_INIT; +} +static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { + PyThread_delete_key(*key); + *key = Py_tss_NEEDS_INIT; +} +static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { + return PyThread_set_key_value(*key, value); +} +static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { + return PyThread_get_key_value(*key); +} +#endif // TSS (Thread Specific Storage) API +#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) +#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) +#else +#define __Pyx_PyDict_NewPresized(n) PyDict_New() +#endif +#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS +#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) +#else +#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) +#endif +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) + #define CYTHON_PEP393_ENABLED 1 + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) + #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) + #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) + #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) +#else + #define CYTHON_PEP393_ENABLED 0 + #define PyUnicode_1BYTE_KIND 1 + #define PyUnicode_2BYTE_KIND 2 + #define PyUnicode_4BYTE_KIND 4 + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) + #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) + #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) + #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) + #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) +#endif +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) +#else + #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ + PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) + #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) + #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) + #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) +#endif +#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) +#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) +#else + #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) +#endif +#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII) + #define PyObject_ASCII(o) PyObject_Repr(o) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBaseString_Type PyUnicode_Type + #define PyStringObject PyUnicodeObject + #define PyString_Type PyUnicode_Type + #define PyString_Check PyUnicode_Check + #define PyString_CheckExact PyUnicode_CheckExact + #define PyObject_Unicode PyObject_Str +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) + #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) +#else + #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) + #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) +#endif +#ifndef PySet_CheckExact + #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) +#endif +#if CYTHON_ASSUME_SAFE_MACROS + #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq) +#else + #define __Pyx_PySequence_SIZE(seq) PySequence_Size(seq) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyIntObject PyLongObject + #define PyInt_Type PyLong_Type + #define PyInt_Check(op) PyLong_Check(op) + #define PyInt_CheckExact(op) PyLong_CheckExact(op) + #define PyInt_FromString PyLong_FromString + #define PyInt_FromUnicode PyLong_FromUnicode + #define PyInt_FromLong PyLong_FromLong + #define PyInt_FromSize_t PyLong_FromSize_t + #define PyInt_FromSsize_t PyLong_FromSsize_t + #define PyInt_AsLong PyLong_AsLong + #define PyInt_AS_LONG PyLong_AS_LONG + #define PyInt_AsSsize_t PyLong_AsSsize_t + #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask + #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask + #define PyNumber_Int PyNumber_Long +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBoolObject PyLongObject +#endif +#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY + #ifndef PyUnicode_InternFromString + #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) + #endif +#endif +#if PY_VERSION_HEX < 0x030200A4 + typedef long Py_hash_t; + #define __Pyx_PyInt_FromHash_t PyInt_FromLong + #define __Pyx_PyInt_AsHash_t PyInt_AsLong +#else + #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t + #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : (Py_INCREF(func), func)) +#else + #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) +#endif +#if CYTHON_USE_ASYNC_SLOTS + #if PY_VERSION_HEX >= 0x030500B1 + #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods + #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) + #else + #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) + #endif +#else + #define __Pyx_PyType_AsAsync(obj) NULL +#endif +#ifndef __Pyx_PyAsyncMethodsStruct + typedef struct { + unaryfunc am_await; + unaryfunc am_aiter; + unaryfunc am_anext; + } __Pyx_PyAsyncMethodsStruct; +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) + #define _USE_MATH_DEFINES +#endif +#include +#ifdef NAN +#define __PYX_NAN() ((float) NAN) +#else +static CYTHON_INLINE float __PYX_NAN() { + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif +#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL) +#define __Pyx_truncl trunc +#else +#define __Pyx_truncl truncl +#endif + + +#define __PYX_ERR(f_index, lineno, Ln_error) \ +{ \ + __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; goto Ln_error; \ +} + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#define __PYX_HAVE__MDAnalysis__lib___cutil +#define __PYX_HAVE_API__MDAnalysis__lib___cutil +/* Early includes */ +#include +#include +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" +#include +#include "ios" +#include "new" +#include "stdexcept" +#include "typeinfo" +#include +#include +#include +#include +#include "calc_distances.h" +#include "pythread.h" +#include +#include "pystate.h" +#ifdef _OPENMP +#include +#endif /* _OPENMP */ + +#if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS) +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 +#define __PYX_DEFAULT_STRING_ENCODING "" +#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#define __Pyx_uchar_cast(c) ((unsigned char)c) +#define __Pyx_long_cast(x) ((long)x) +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ + (sizeof(type) < sizeof(Py_ssize_t)) ||\ + (sizeof(type) > sizeof(Py_ssize_t) &&\ + likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX) &&\ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ + v == (type)PY_SSIZE_T_MIN))) ||\ + (sizeof(type) == sizeof(Py_ssize_t) &&\ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX))) ) +#if defined (__cplusplus) && __cplusplus >= 201103L + #include + #define __Pyx_sst_abs(value) std::abs(value) +#elif SIZEOF_INT >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) abs(value) +#elif SIZEOF_LONG >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) labs(value) +#elif defined (_MSC_VER) + #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value)) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) +#elif defined (__GNUC__) + #define __Pyx_sst_abs(value) __builtin_llabs(value) +#else + #define __Pyx_sst_abs(value) ((value<0) ? -value : value) +#endif +static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) +#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#else + #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#endif +#define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) +static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { + const Py_UNICODE *u_end = u; + while (*u_end++) ; + return (size_t)(u_end - u - 1); +} +#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) +#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode +#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode +#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) +#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); +#define __Pyx_PySequence_Tuple(obj)\ + (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj)) +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +#if CYTHON_ASSUME_SAFE_MACROS +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) +#else +#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) +#endif +#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x)) +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII +static int __Pyx_sys_getdefaultencoding_not_ascii; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + PyObject* ascii_chars_u = NULL; + PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { + __Pyx_sys_getdefaultencoding_not_ascii = 0; + } else { + char ascii_chars[128]; + int c; + for (c = 0; c < 128; c++) { + ascii_chars[c] = c; + } + __Pyx_sys_getdefaultencoding_not_ascii = 1; + ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); + if (!ascii_chars_u) goto bad; + ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + PyErr_Format( + PyExc_ValueError, + "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", + default_encoding_c); + goto bad; + } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); + } + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + Py_XDECREF(ascii_chars_u); + Py_XDECREF(ascii_chars_b); + return -1; +} +#endif +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) +#else +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +static char* __PYX_DEFAULT_STRING_ENCODING; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; + strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + return -1; +} +#endif +#endif + + +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ + #define likely(x) (x) + #define unlikely(x) (x) +#endif /* __GNUC__ */ +static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } + +static PyObject *__pyx_m = NULL; +static PyObject *__pyx_d; +static PyObject *__pyx_b; +static PyObject *__pyx_cython_runtime = NULL; +static PyObject *__pyx_empty_tuple; +static PyObject *__pyx_empty_bytes; +static PyObject *__pyx_empty_unicode; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; + +/* Header.proto */ +#if !defined(CYTHON_CCOMPLEX) + #if defined(__cplusplus) + #define CYTHON_CCOMPLEX 1 + #elif defined(_Complex_I) + #define CYTHON_CCOMPLEX 1 + #else + #define CYTHON_CCOMPLEX 0 + #endif +#endif +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #include + #else + #include + #endif +#endif +#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) + #undef _Complex_I + #define _Complex_I 1.0fj +#endif + + +static const char *__pyx_f[] = { + "MDAnalysis/lib/_cutil.pyx", + "__init__.pxd", + "stringsource", + "type.pxd", +}; +/* MemviewSliceStruct.proto */ +struct __pyx_memoryview_obj; +typedef struct { + struct __pyx_memoryview_obj *memview; + char *data; + Py_ssize_t shape[8]; + Py_ssize_t strides[8]; + Py_ssize_t suboffsets[8]; +} __Pyx_memviewslice; +#define __Pyx_MemoryView_Len(m) (m.shape[0]) + +/* Atomics.proto */ +#include +#ifndef CYTHON_ATOMICS + #define CYTHON_ATOMICS 1 +#endif +#define __pyx_atomic_int_type int +#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 ||\ + (__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) &&\ + !defined(__i386__) + #define __pyx_atomic_incr_aligned(value, lock) __sync_fetch_and_add(value, 1) + #define __pyx_atomic_decr_aligned(value, lock) __sync_fetch_and_sub(value, 1) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using GNU atomics" + #endif +#elif CYTHON_ATOMICS && defined(_MSC_VER) && 0 + #include + #undef __pyx_atomic_int_type + #define __pyx_atomic_int_type LONG + #define __pyx_atomic_incr_aligned(value, lock) InterlockedIncrement(value) + #define __pyx_atomic_decr_aligned(value, lock) InterlockedDecrement(value) + #ifdef __PYX_DEBUG_ATOMICS + #pragma message ("Using MSVC atomics") + #endif +#elif CYTHON_ATOMICS && (defined(__ICC) || defined(__INTEL_COMPILER)) && 0 + #define __pyx_atomic_incr_aligned(value, lock) _InterlockedIncrement(value) + #define __pyx_atomic_decr_aligned(value, lock) _InterlockedDecrement(value) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using Intel atomics" + #endif +#else + #undef CYTHON_ATOMICS + #define CYTHON_ATOMICS 0 + #ifdef __PYX_DEBUG_ATOMICS + #warning "Not using atomics" + #endif +#endif +typedef volatile __pyx_atomic_int_type __pyx_atomic_int; +#if CYTHON_ATOMICS + #define __pyx_add_acquisition_count(memview)\ + __pyx_atomic_incr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) + #define __pyx_sub_acquisition_count(memview)\ + __pyx_atomic_decr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) +#else + #define __pyx_add_acquisition_count(memview)\ + __pyx_add_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) + #define __pyx_sub_acquisition_count(memview)\ + __pyx_sub_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) +#endif + +/* ForceInitThreads.proto */ +#ifndef __PYX_FORCE_INIT_THREADS + #define __PYX_FORCE_INIT_THREADS 0 +#endif + +/* NoFastGil.proto */ +#define __Pyx_PyGILState_Ensure PyGILState_Ensure +#define __Pyx_PyGILState_Release PyGILState_Release +#define __Pyx_FastGIL_Remember() +#define __Pyx_FastGIL_Forget() +#define __Pyx_FastGilFuncInit() + +/* BufferFormatStructs.proto */ +#define IS_UNSIGNED(type) (((type) -1) > 0) +struct __Pyx_StructField_; +#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) +typedef struct { + const char* name; + struct __Pyx_StructField_* fields; + size_t size; + size_t arraysize[8]; + int ndim; + char typegroup; + char is_unsigned; + int flags; +} __Pyx_TypeInfo; +typedef struct __Pyx_StructField_ { + __Pyx_TypeInfo* type; + const char* name; + size_t offset; +} __Pyx_StructField; +typedef struct { + __Pyx_StructField* field; + size_t parent_offset; +} __Pyx_BufFmt_StackElem; +typedef struct { + __Pyx_StructField root; + __Pyx_BufFmt_StackElem* head; + size_t fmt_offset; + size_t new_count, enc_count; + size_t struct_alignment; + int is_complex; + char enc_type; + char new_packmode; + char enc_packmode; + char is_valid_array; +} __Pyx_BufFmt_Context; + + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 + * # in Cython to enable them only on the right systems. + * + * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + */ +typedef npy_int8 __pyx_t_5numpy_int8_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 + * + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t + */ +typedef npy_int16 __pyx_t_5numpy_int16_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< + * #ctypedef npy_int96 int96_t + * #ctypedef npy_int128 int128_t + */ +typedef npy_int64 __pyx_t_5numpy_int64_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 + * #ctypedef npy_int128 int128_t + * + * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + */ +typedef npy_uint8 __pyx_t_5numpy_uint8_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 + * + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t + */ +typedef npy_uint16 __pyx_t_5numpy_uint16_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< + * #ctypedef npy_uint96 uint96_t + * #ctypedef npy_uint128 uint128_t + */ +typedef npy_uint64 __pyx_t_5numpy_uint64_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 + * #ctypedef npy_uint128 uint128_t + * + * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< + * ctypedef npy_float64 float64_t + * #ctypedef npy_float80 float80_t + */ +typedef npy_float32 __pyx_t_5numpy_float32_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 + * + * ctypedef npy_float32 float32_t + * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< + * #ctypedef npy_float80 float80_t + * #ctypedef npy_float128 float128_t + */ +typedef npy_float64 __pyx_t_5numpy_float64_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 + * # The int types are mapped a bit surprising -- + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t + */ +typedef npy_long __pyx_t_5numpy_int_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong longlong_t + * + */ +typedef npy_longlong __pyx_t_5numpy_long_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_ulong uint_t + */ +typedef npy_longlong __pyx_t_5numpy_longlong_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 + * ctypedef npy_longlong longlong_t + * + * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t + */ +typedef npy_ulong __pyx_t_5numpy_uint_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 + * + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulonglong_t + * + */ +typedef npy_ulonglong __pyx_t_5numpy_ulong_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_intp intp_t + */ +typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 + * ctypedef npy_ulonglong ulonglong_t + * + * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< + * ctypedef npy_uintp uintp_t + * + */ +typedef npy_intp __pyx_t_5numpy_intp_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 + * + * ctypedef npy_intp intp_t + * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< + * + * ctypedef npy_double float_t + */ +typedef npy_uintp __pyx_t_5numpy_uintp_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 + * ctypedef npy_uintp uintp_t + * + * ctypedef npy_double float_t # <<<<<<<<<<<<<< + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t + */ +typedef npy_double __pyx_t_5numpy_float_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 + * ctypedef npy_double float_t + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cfloat cfloat_t + */ +typedef npy_longdouble __pyx_t_5numpy_longdouble_t; +/* Declarations.proto */ +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< float > __pyx_t_float_complex; + #else + typedef float _Complex __pyx_t_float_complex; + #endif +#else + typedef struct { float real, imag; } __pyx_t_float_complex; +#endif +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); + +/* Declarations.proto */ +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< double > __pyx_t_double_complex; + #else + typedef double _Complex __pyx_t_double_complex; + #endif +#else + typedef struct { double real, imag; } __pyx_t_double_complex; +#endif +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); 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+ +/* RaiseDoubleKeywords.proto */ +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +/* ParseKeywords.proto */ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ + const char* function_name); + +/* RaiseArgTupleInvalid.proto */ +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +/* SliceObject.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice( + PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, + PyObject** py_start, PyObject** py_stop, PyObject** py_slice, + int has_cstart, int has_cstop, int wraparound); + +/* GetItemInt.proto */ +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ + __Pyx_GetItemInt_Generic(o, to_py_func(i)))) +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ + (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ + (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck); + +/* PySequenceContains.proto */ +static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) { + int result = PySequence_Contains(seq, item); + return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); +} + +/* RaiseException.proto */ +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); + +/* Import.proto */ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +/* ImportFrom.proto */ +static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); + +/* IncludeStringH.proto */ +#include + +/* PyObjectCallNoArg.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); +#else +#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) +#endif + +/* SaveResetException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); +#else +#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) +#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) +#endif + +/* FastTypeChecks.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type) +static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b); +static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type); +static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2); +#else +#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) +#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type) +#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2)) +#endif +#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) + +/* GetException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) +static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); +#endif + +/* PyObjectSetAttrStr.proto */ +#if CYTHON_USE_TYPE_SLOTS +#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o, n, NULL) +static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value); +#else +#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n) +#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v) +#endif + +/* ListAppend.proto */ +#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS +static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) +#endif + +/* DictGetItem.proto */ +#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key); +#define __Pyx_PyObject_Dict_GetItem(obj, name)\ + (likely(PyDict_CheckExact(obj)) ?\ + __Pyx_PyDict_GetItem(obj, name) : PyObject_GetItem(obj, name)) +#else +#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) +#define __Pyx_PyObject_Dict_GetItem(obj, name) PyObject_GetItem(obj, name) +#endif + +/* RaiseTooManyValuesToUnpack.proto */ +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +/* RaiseNeedMoreValuesToUnpack.proto */ +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +/* RaiseNoneIterError.proto */ +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +/* ExtTypeTest.proto */ +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); + +/* PyErrExceptionMatches.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err) +static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err); +#else +#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err) +#endif + +/* ListCompAppend.proto */ +#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS +static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len)) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) +#endif + +/* ArgTypeTest.proto */ +#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\ + ((likely((Py_TYPE(obj) == type) | (none_allowed && (obj == Py_None)))) ? 1 :\ + __Pyx__ArgTypeTest(obj, type, name, exact)) +static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact); + +/* BytesEquals.proto */ +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); + +/* UnicodeEquals.proto */ +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); + +/* StrEquals.proto */ +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals +#else +#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals +#endif + +/* None.proto */ +static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); + +/* UnaryNegOverflows.proto */ +#define UNARY_NEG_WOULD_OVERFLOW(x)\ + (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) + +static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *); /*proto*/ +/* GetAttr.proto */ +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); + +/* ObjectGetItem.proto */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key); +#else +#define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key) +#endif + +/* decode_c_string_utf16.proto */ +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = 0; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16LE(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = -1; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16BE(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = 1; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} + +/* decode_c_string.proto */ +static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); + +/* GetAttr3.proto */ +static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *); + +/* SwapException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); +#endif + +static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +/* PyIntBinop.proto */ +#if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace); +#else +#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace)\ + (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) +#endif + +/* ListExtend.proto */ +static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject* none = _PyList_Extend((PyListObject*)L, v); + if (unlikely(!none)) + return -1; + Py_DECREF(none); + return 0; +#else + return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); +#endif +} + +/* None.proto */ +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); + +/* None.proto */ +static CYTHON_INLINE long __Pyx_div_long(long, long); + +/* HasAttr.proto */ +static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); + +/* PyObject_GenericGetAttrNoDict.proto */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr +#endif + +/* PyObject_GenericGetAttr.proto */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr +#endif + +/* SetVTable.proto */ +static int __Pyx_SetVtable(PyObject *dict, void *vtable); + +/* SetupReduce.proto */ +static int __Pyx_setup_reduce(PyObject* type_obj); + +/* CLineInTraceback.proto */ +#ifdef CYTHON_CLINE_IN_TRACEBACK +#define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0) +#else +static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line); +#endif + +/* CodeObjectCache.proto */ +typedef struct { + PyCodeObject* code_object; + int code_line; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); + +/* AddTraceback.proto */ +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); + +#if PY_MAJOR_VERSION < 3 + static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); + static void __Pyx_ReleaseBuffer(Py_buffer *view); +#else + #define __Pyx_GetBuffer PyObject_GetBuffer + #define __Pyx_ReleaseBuffer PyBuffer_Release +#endif + + +/* BufferStructDeclare.proto */ +typedef struct { + Py_ssize_t shape, strides, suboffsets; +} __Pyx_Buf_DimInfo; +typedef struct { + size_t refcount; + Py_buffer pybuffer; +} __Pyx_Buffer; +typedef struct { + __Pyx_Buffer *rcbuffer; + char *data; + __Pyx_Buf_DimInfo diminfo[8]; +} __Pyx_LocalBuf_ND; + +/* MemviewSliceIsContig.proto */ +static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim); + +/* OverlappingSlices.proto */ +static int __pyx_slices_overlap(__Pyx_memviewslice *slice1, + __Pyx_memviewslice *slice2, + int ndim, size_t itemsize); + +/* Capsule.proto */ +static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); + +/* IsLittleEndian.proto */ +static CYTHON_INLINE int __Pyx_Is_Little_Endian(void); + +/* BufferFormatCheck.proto */ +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); +static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type); + +/* TypeInfoCompare.proto */ +static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); + +/* MemviewSliceValidateAndInit.proto */ +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj); + +/* ObjectToMemviewSlice.proto */ +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_int64_t(PyObject *, int writable_flag); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_int64(npy_int64 value); + +/* MemviewDtypeToObject.proto */ +static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_5numpy_int64_t(const char *itemp); +static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_int64_t(const char *itemp, PyObject *obj); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +/* CppExceptionConversion.proto */ +#ifndef __Pyx_CppExn2PyErr +#include +#include +#include +#include +static void __Pyx_CppExn2PyErr() { + try { + if (PyErr_Occurred()) + ; // let the latest Python exn pass through and ignore the current one + else + throw; + } catch (const std::bad_alloc& exn) { + PyErr_SetString(PyExc_MemoryError, exn.what()); + } catch (const std::bad_cast& exn) { + PyErr_SetString(PyExc_TypeError, exn.what()); + } catch (const std::bad_typeid& exn) { + PyErr_SetString(PyExc_TypeError, exn.what()); + } catch (const std::domain_error& exn) { + PyErr_SetString(PyExc_ValueError, exn.what()); + } catch (const std::invalid_argument& exn) { + PyErr_SetString(PyExc_ValueError, exn.what()); + } catch (const std::ios_base::failure& exn) { + PyErr_SetString(PyExc_IOError, exn.what()); + } catch (const std::out_of_range& exn) { + PyErr_SetString(PyExc_IndexError, exn.what()); + } catch (const std::overflow_error& exn) { + PyErr_SetString(PyExc_OverflowError, exn.what()); + } catch (const std::range_error& exn) { + PyErr_SetString(PyExc_ArithmeticError, exn.what()); + } catch (const std::underflow_error& exn) { + PyErr_SetString(PyExc_ArithmeticError, exn.what()); + } catch (const std::exception& exn) { + PyErr_SetString(PyExc_RuntimeError, exn.what()); + } + catch (...) + { + PyErr_SetString(PyExc_RuntimeError, "Unknown exception"); + } +} +#endif + +/* MemviewDtypeToObject.proto */ +static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp); +static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj); + +/* RealImag.proto */ +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #define __Pyx_CREAL(z) ((z).real()) + #define __Pyx_CIMAG(z) ((z).imag()) + #else + #define __Pyx_CREAL(z) (__real__(z)) + #define __Pyx_CIMAG(z) (__imag__(z)) + #endif +#else + #define __Pyx_CREAL(z) ((z).real) + #define __Pyx_CIMAG(z) ((z).imag) +#endif +#if defined(__cplusplus) && CYTHON_CCOMPLEX\ + && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103) + #define __Pyx_SET_CREAL(z,x) ((z).real(x)) + #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) +#else + #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) + #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) +#endif + +/* Arithmetic.proto */ +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq_float(a, b) ((a)==(b)) + #define __Pyx_c_sum_float(a, b) ((a)+(b)) + #define __Pyx_c_diff_float(a, b) ((a)-(b)) + #define __Pyx_c_prod_float(a, b) ((a)*(b)) + #define __Pyx_c_quot_float(a, b) ((a)/(b)) + #define __Pyx_c_neg_float(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero_float(z) ((z)==(float)0) + #define __Pyx_c_conj_float(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs_float(z) (::std::abs(z)) + #define __Pyx_c_pow_float(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero_float(z) ((z)==0) + #define __Pyx_c_conj_float(z) (conjf(z)) + #if 1 + #define __Pyx_c_abs_float(z) (cabsf(z)) + #define __Pyx_c_pow_float(a, b) (cpowf(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex); + #if 1 + static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex, __pyx_t_float_complex); + #endif +#endif + +/* Arithmetic.proto */ +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq_double(a, b) ((a)==(b)) + #define __Pyx_c_sum_double(a, b) ((a)+(b)) + #define __Pyx_c_diff_double(a, b) ((a)-(b)) + #define __Pyx_c_prod_double(a, b) ((a)*(b)) + #define __Pyx_c_quot_double(a, b) ((a)/(b)) + #define __Pyx_c_neg_double(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero_double(z) ((z)==(double)0) + #define __Pyx_c_conj_double(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs_double(z) (::std::abs(z)) + #define __Pyx_c_pow_double(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero_double(z) ((z)==0) + #define __Pyx_c_conj_double(z) (conj(z)) + #if 1 + #define __Pyx_c_abs_double(z) (cabs(z)) + #define __Pyx_c_pow_double(a, b) (cpow(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex); + #if 1 + static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex); + #endif +#endif + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); + +/* MemviewSliceCopyTemplate.proto */ +static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object); + +/* CIntFromPy.proto */ +static CYTHON_INLINE npy_int64 __Pyx_PyInt_As_npy_int64(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); + +/* ObjectToMemviewSlice.proto */ +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_Py_ssize_t(PyObject *, int writable_flag); + +/* ObjectToMemviewSlice.proto */ +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_float(PyObject *, int writable_flag); + +/* ObjectToMemviewSlice.proto */ +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_int(PyObject *, int writable_flag); + +/* ObjectToMemviewSlice.proto */ +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *, int writable_flag); + +/* ObjectToMemviewSlice.proto */ +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_nn___pyx_t_5numpy_int32_t(PyObject *, int writable_flag); + +/* CheckBinaryVersion.proto */ +static int __Pyx_check_binary_version(void); + +/* FunctionExport.proto */ +static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig); + +/* PyIdentifierFromString.proto */ +#if !defined(__Pyx_PyIdentifier_FromString) +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) +#else + #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) +#endif +#endif + +/* ModuleImport.proto */ +static PyObject *__Pyx_ImportModule(const char *name); + +/* TypeImport.proto */ +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); + +/* InitStrings.proto */ +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); + +static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *__pyx_v_self); /* proto*/ +static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto*/ +static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj); /* proto*/ +static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_dst, PyObject *__pyx_v_src); /* proto*/ +static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memoryview_obj *__pyx_v_self, struct __pyx_memoryview_obj *__pyx_v_dst, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryview_setitem_indexed(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ +static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ +static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ + +/* Module declarations from 'cython.view' */ + +/* Module declarations from 'cython' */ + +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'cpython' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'cpython.mem' */ + +/* Module declarations from 'numpy' */ + +/* Module declarations from 'numpy' */ +static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; +static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; +static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; +static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; +static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; +static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ + +/* Module declarations from 'libc.math' */ + +/* Module declarations from 'libcpp.utility' */ + +/* Module declarations from 'libcpp.set' */ + +/* Module declarations from 'libcpp.map' */ + +/* Module declarations from 'libcpp.vector' */ + +/* Module declarations from 'MDAnalysis.lib._cutil' */ +static PyTypeObject *__pyx_array_type = 0; +static PyTypeObject *__pyx_MemviewEnum_type = 0; +static PyTypeObject *__pyx_memoryview_type = 0; +static PyTypeObject *__pyx_memoryviewslice_type = 0; +static PyObject *generic = 0; +static PyObject *strided = 0; +static PyObject *indirect = 0; +static PyObject *contiguous = 0; +static PyObject *indirect_contiguous = 0; +static int __pyx_memoryview_thread_locks_used; +static PyThread_type_lock __pyx_memoryview_thread_locks[8]; +static __pyx_t_10MDAnalysis_3lib_6_cutil_intset __pyx_f_10MDAnalysis_3lib_6_cutil_difference(__pyx_t_10MDAnalysis_3lib_6_cutil_intset, __pyx_t_10MDAnalysis_3lib_6_cutil_intset); /*proto*/ +static int __Pyx_carray_from_py_float(PyObject *, float *, Py_ssize_t); /*proto*/ +static int __Pyx_carray_from_py_float___5b_3_5d_(PyObject *, float (*)[3], Py_ssize_t); /*proto*/ +static PyObject *__pyx_convert_vector_to_py_int(const std::vector &); /*proto*/ +static struct __pyx_array_obj *__pyx_array_new(PyObject *, Py_ssize_t, char *, char *, char *); /*proto*/ +static void *__pyx_align_pointer(void *, size_t); /*proto*/ +static PyObject *__pyx_memoryview_new(PyObject *, int, int, __Pyx_TypeInfo *); /*proto*/ +static CYTHON_INLINE int __pyx_memoryview_check(PyObject *); /*proto*/ +static PyObject *_unellipsify(PyObject *, int); /*proto*/ +static PyObject *assert_direct_dimensions(Py_ssize_t *, int); /*proto*/ +static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_obj *, PyObject *); /*proto*/ +static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int, int); /*proto*/ +static char *__pyx_pybuffer_index(Py_buffer *, char *, Py_ssize_t, Py_ssize_t); /*proto*/ +static int __pyx_memslice_transpose(__Pyx_memviewslice *); /*proto*/ +static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice, int, PyObject *(*)(char *), int (*)(char *, PyObject *), int); /*proto*/ +static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *); /*proto*/ +static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static Py_ssize_t abs_py_ssize_t(Py_ssize_t); /*proto*/ +static char __pyx_get_best_slice_order(__Pyx_memviewslice *, int); /*proto*/ +static void _copy_strided_to_strided(char *, Py_ssize_t *, char *, Py_ssize_t *, Py_ssize_t *, Py_ssize_t *, int, size_t); /*proto*/ +static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/ +static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/ +static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *, Py_ssize_t *, Py_ssize_t, int, char); /*proto*/ +static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/ +static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/ +static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/ +static int __pyx_memoryview_err(PyObject *, char *); /*proto*/ +static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/ +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/ +static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/ +static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ +static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ +static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/ +static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ +static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *, PyObject *); /*proto*/ +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t = { "int64_t", NULL, sizeof(__pyx_t_5numpy_int64_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int64_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int64_t), 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_Py_ssize_t = { "Py_ssize_t", NULL, sizeof(Py_ssize_t), { 0 }, 0, IS_UNSIGNED(Py_ssize_t) ? 'U' : 'I', IS_UNSIGNED(Py_ssize_t), 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_float = { "float", NULL, sizeof(float), { 0 }, 0, 'R', 0, 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_int = { "int", NULL, sizeof(int), { 0 }, 0, IS_UNSIGNED(int) ? 'U' : 'I', IS_UNSIGNED(int), 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int32_t = { "int32_t", NULL, sizeof(__pyx_t_5numpy_int32_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int32_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int32_t), 0 }; +#define __Pyx_MODULE_NAME "MDAnalysis.lib._cutil" +extern int __pyx_module_is_main_MDAnalysis__lib___cutil; +int __pyx_module_is_main_MDAnalysis__lib___cutil = 0; + +/* Implementation of 'MDAnalysis.lib._cutil' */ +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_AttributeError; +static PyObject *__pyx_builtin_RuntimeError; +static PyObject *__pyx_builtin_ImportError; +static PyObject *__pyx_builtin_TypeError; +static PyObject *__pyx_builtin_OverflowError; +static PyObject *__pyx_builtin_enumerate; +static PyObject *__pyx_builtin_IndexError; +static PyObject *__pyx_builtin_MemoryError; +static PyObject *__pyx_builtin_Ellipsis; +static PyObject *__pyx_builtin_id; +static const char __pyx_k_O[] = "O"; +static const char __pyx_k_a[] = "a"; +static const char __pyx_k_b[] = "b"; +static const char __pyx_k_c[] = "c"; +static const char __pyx_k_i[] = "i"; +static const char __pyx_k_j[] = "j"; +static const char __pyx_k_id[] = "id"; +static const char __pyx_k_ix[] = "ix"; +static const char __pyx_k_np[] = "np"; +static const char __pyx_k_all[] = "__all__"; +static const char __pyx_k_box[] = "box"; +static const char __pyx_k_new[] = "__new__"; +static const char __pyx_k_obj[] = "obj"; +static const char __pyx_k_ref[] = "ref"; +static const char __pyx_k_vec[] = "vec"; +static const char __pyx_k_atom[] = "atom"; +static const char __pyx_k_base[] = "base"; +static const char __pyx_k_dict[] = "__dict__"; +static const char __pyx_k_done[] = "done"; +static const char __pyx_k_main[] = "__main__"; +static const char __pyx_k_mode[] = "mode"; +static const char __pyx_k_name[] = "name"; +static const char __pyx_k_ndim[] = "ndim"; +static const char __pyx_k_pack[] = "pack"; +static const char __pyx_k_size[] = "size"; +static const char __pyx_k_sort[] = "sort"; +static const char __pyx_k_step[] = "step"; +static const char __pyx_k_stop[] = "stop"; +static const char __pyx_k_test[] = "__test__"; +static const char __pyx_k_todo[] = "todo"; +static const char __pyx_k_ASCII[] = "ASCII"; +static const char __pyx_k_array[] = "array"; +static const char __pyx_k_atoms[] = "atoms"; +static const char __pyx_k_bonds[] = "bonds"; +static const char __pyx_k_class[] = "__class__"; +static const char __pyx_k_dtype[] = "dtype"; +static const char __pyx_k_empty[] = "empty"; +static const char __pyx_k_error[] = "error"; +static const char __pyx_k_flags[] = "flags"; +static const char __pyx_k_frags[] = "frags"; +static const char __pyx_k_int32[] = "int32"; +static const char __pyx_k_int64[] = "int64"; +static const char __pyx_k_numpy[] = "numpy"; +static const char __pyx_k_ortho[] = "ortho"; +static const char __pyx_k_other[] = "other"; +static const char __pyx_k_range[] = "range"; +static const char __pyx_k_shape[] = "shape"; +static const char __pyx_k_start[] = "start"; +static const char __pyx_k_zeros[] = "zeros"; +static const char __pyx_k_encode[] = "encode"; +static const char __pyx_k_format[] = "format"; +static const char __pyx_k_import[] = "__import__"; +static const char __pyx_k_name_2[] = "__name__"; +static const char __pyx_k_natoms[] = "natoms"; +static const char __pyx_k_newpos[] = "newpos"; +static const char __pyx_k_nloops[] = "nloops"; +static const char __pyx_k_oldpos[] = "oldpos"; +static const char __pyx_k_pickle[] = "pickle"; +static const char __pyx_k_reduce[] = "__reduce__"; +static const char __pyx_k_result[] = "result"; +static const char __pyx_k_struct[] = "struct"; +static const char __pyx_k_unpack[] = "unpack"; +static const char __pyx_k_update[] = "update"; +static const char __pyx_k_values[] = "values"; +static const char __pyx_k_asarray[] = "asarray"; +static const char __pyx_k_bonding[] = "bonding"; +static const char __pyx_k_bondmap[] = "bondmap"; +static const char __pyx_k_float32[] = "float32"; +static const char __pyx_k_fortran[] = "fortran"; +static const char __pyx_k_ix_view[] = "ix_view"; +static const char __pyx_k_mdamath[] = "mdamath"; +static const char __pyx_k_memview[] = "memview"; +static const char __pyx_k_tri_box[] = "tri_box"; +static const char __pyx_k_Ellipsis[] = "Ellipsis"; +static const char __pyx_k_bondlist[] = "bondlist"; +static const char __pyx_k_getstate[] = "__getstate__"; +static const char __pyx_k_itemsize[] = "itemsize"; +static const char __pyx_k_n_values[] = "n_values"; +static const char __pyx_k_pyx_type[] = "__pyx_type"; +static const char __pyx_k_setstate[] = "__setstate__"; +static const char __pyx_k_TypeError[] = "TypeError"; +static const char __pyx_k_atomgroup[] = "atomgroup"; +static const char __pyx_k_enumerate[] = "enumerate"; +static const char __pyx_k_frag_done[] = "frag_done"; +static const char __pyx_k_frag_todo[] = "frag_todo"; +static const char __pyx_k_ix_to_rel[] = "ix_to_rel"; +static const char __pyx_k_positions[] = "positions"; +static const char __pyx_k_pyx_state[] = "__pyx_state"; +static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; +static const char __pyx_k_refpoints[] = "refpoints"; +static const char __pyx_k_this_frag[] = "this_frag"; +static const char __pyx_k_IndexError[] = "IndexError"; +static const char __pyx_k_MDAnalysis[] = "MDAnalysis"; +static const char __pyx_k_ValueError[] = "ValueError"; +static const char __pyx_k_atoms_view[] = "atoms_view"; +static const char __pyx_k_bonds_view[] = "bonds_view"; +static const char __pyx_k_dimensions[] = "dimensions"; +static const char __pyx_k_make_whole[] = "make_whole"; +static const char __pyx_k_pyx_result[] = "__pyx_result"; +static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; +static const char __pyx_k_to_indices[] = "to_indices"; +static const char __pyx_k_ImportError[] = "ImportError"; +static const char __pyx_k_MemoryError[] = "MemoryError"; +static const char __pyx_k_NoDataError[] = "NoDataError"; +static const char __pyx_k_PickleError[] = "PickleError"; +static const char __pyx_k_inverse_box[] = "inverse_box"; +static const char __pyx_k_RuntimeError[] = "RuntimeError"; +static const char __pyx_k_is_monotonic[] = "is_monotonic"; +static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; +static const char __pyx_k_stringsource[] = "stringsource"; +static const char __pyx_k_OverflowError[] = "OverflowError"; +static const char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; +static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; +static const char __pyx_k_unique_int_1d[] = "unique_int_1d"; +static const char __pyx_k_AttributeError[] = "AttributeError"; +static const char __pyx_k_find_fragments[] = "find_fragments"; +static const char __pyx_k_reference_atom[] = "reference_atom"; +static const char __pyx_k_View_MemoryView[] = "View.MemoryView"; +static const char __pyx_k_allocate_buffer[] = "allocate_buffer"; +static const char __pyx_k_dtype_is_object[] = "dtype_is_object"; +static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; +static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; +static const char __pyx_k_pyx_unpickle_Enum[] = "__pyx_unpickle_Enum"; +static const char __pyx_k_triclinic_vectors[] = "triclinic_vectors"; +static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; +static const char __pyx_k_strided_and_direct[] = ""; +static const char __pyx_k_strided_and_indirect[] = ""; +static const char __pyx_k_MDAnalysis_lib__cutil[] = "MDAnalysis.lib._cutil"; +static const char __pyx_k_contiguous_and_direct[] = ""; +static const char __pyx_k_MemoryView_of_r_object[] = ""; +static const char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; +static const char __pyx_k_contiguous_and_indirect[] = ""; +static const char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; +static const char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; +static const char __pyx_k_MDAnalysis_lib__cutil_pyx[] = "MDAnalysis/lib/_cutil.pyx"; +static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; +static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; +static const char __pyx_k_strided_and_direct_or_indirect[] = ""; +static const char __pyx_k_One_or_more_dimensions_was_zero[] = "One or more dimensions was zero. You can set dimensions using 'atomgroup.dimensions='"; +static const char __pyx_k_Reference_atom_not_in_atomgroup[] = "Reference atom not in atomgroup"; +static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; +static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; +static const char __pyx_k_AtomGroup_was_not_contiguous_fro[] = "AtomGroup was not contiguous from bonds, process failed"; +static const char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; +static const char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; +static const char __pyx_k_Cannot_assign_to_read_only_memor[] = "Cannot assign to read-only memoryview"; +static const char __pyx_k_Cannot_create_writable_memory_vi[] = "Cannot create writable memory view from read-only memoryview"; +static const char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; +static const char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; +static const char __pyx_k_Incompatible_checksums_s_vs_0xb0[] = "Incompatible checksums (%s vs 0xb068931 = (name))"; +static const char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; +static const char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; +static const char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; +static const char __pyx_k_The_atomgroup_is_required_to_hav[] = "The atomgroup is required to have bonds"; +static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; +static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; +static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; +static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; +static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; +static const char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_n_s_ASCII; +static PyObject *__pyx_kp_s_AtomGroup_was_not_contiguous_fro; +static PyObject *__pyx_n_s_AttributeError; +static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; +static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; +static PyObject *__pyx_kp_s_Cannot_assign_to_read_only_memor; +static PyObject *__pyx_kp_s_Cannot_create_writable_memory_vi; +static PyObject *__pyx_kp_s_Cannot_index_with_type_s; +static PyObject *__pyx_n_s_Ellipsis; +static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; +static PyObject *__pyx_n_s_ImportError; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0xb0; +static PyObject *__pyx_n_s_IndexError; +static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; +static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; +static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; +static PyObject *__pyx_n_s_MDAnalysis; +static PyObject *__pyx_n_s_MDAnalysis_lib__cutil; +static PyObject *__pyx_kp_s_MDAnalysis_lib__cutil_pyx; +static PyObject *__pyx_n_s_MemoryError; +static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; +static PyObject *__pyx_kp_s_MemoryView_of_r_object; +static PyObject *__pyx_n_s_NoDataError; +static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_n_b_O; +static PyObject *__pyx_kp_s_One_or_more_dimensions_was_zero; +static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; +static PyObject *__pyx_n_s_OverflowError; +static PyObject *__pyx_n_s_PickleError; +static PyObject *__pyx_kp_s_Reference_atom_not_in_atomgroup; +static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_kp_s_The_atomgroup_is_required_to_hav; +static PyObject *__pyx_n_s_TypeError; +static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; +static PyObject *__pyx_n_s_ValueError; +static PyObject *__pyx_n_s_View_MemoryView; +static PyObject *__pyx_n_s_a; +static PyObject *__pyx_n_s_all; +static PyObject *__pyx_n_s_allocate_buffer; +static PyObject *__pyx_n_s_array; +static PyObject *__pyx_n_s_asarray; +static PyObject *__pyx_n_s_atom; +static PyObject *__pyx_n_s_atomgroup; +static PyObject *__pyx_n_s_atoms; +static PyObject *__pyx_n_s_atoms_view; +static PyObject *__pyx_n_s_b; +static PyObject *__pyx_n_s_base; +static PyObject *__pyx_n_s_bonding; +static PyObject *__pyx_n_s_bondlist; +static PyObject *__pyx_n_s_bondmap; +static PyObject *__pyx_n_s_bonds; +static PyObject *__pyx_n_s_bonds_view; +static PyObject *__pyx_n_s_box; +static PyObject *__pyx_n_s_c; +static PyObject *__pyx_n_u_c; +static PyObject *__pyx_n_s_class; +static PyObject *__pyx_n_s_cline_in_traceback; +static PyObject *__pyx_kp_s_contiguous_and_direct; +static PyObject *__pyx_kp_s_contiguous_and_indirect; +static PyObject *__pyx_n_s_dict; +static PyObject *__pyx_n_s_dimensions; +static PyObject *__pyx_n_s_done; +static PyObject *__pyx_n_s_dtype; +static PyObject *__pyx_n_s_dtype_is_object; +static PyObject *__pyx_n_s_empty; +static PyObject *__pyx_n_s_encode; +static PyObject *__pyx_n_s_enumerate; +static PyObject *__pyx_n_s_error; +static PyObject *__pyx_n_s_find_fragments; +static PyObject *__pyx_n_s_flags; +static PyObject *__pyx_n_s_float32; +static PyObject *__pyx_n_s_format; +static PyObject *__pyx_n_s_fortran; +static PyObject *__pyx_n_u_fortran; +static PyObject *__pyx_n_s_frag_done; +static PyObject *__pyx_n_s_frag_todo; +static PyObject *__pyx_n_s_frags; +static PyObject *__pyx_n_s_getstate; +static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; +static PyObject *__pyx_n_s_i; +static PyObject *__pyx_n_s_id; +static PyObject *__pyx_n_s_import; +static PyObject *__pyx_n_s_int32; +static PyObject *__pyx_n_s_int64; +static PyObject *__pyx_n_s_inverse_box; +static PyObject *__pyx_n_s_is_monotonic; +static PyObject *__pyx_n_s_itemsize; +static PyObject *__pyx_kp_s_itemsize_0_for_cython_array; +static PyObject *__pyx_n_s_ix; +static PyObject *__pyx_n_s_ix_to_rel; +static PyObject *__pyx_n_s_ix_view; +static PyObject *__pyx_n_s_j; +static PyObject *__pyx_n_s_main; +static PyObject *__pyx_n_s_make_whole; +static PyObject *__pyx_n_s_mdamath; +static PyObject *__pyx_n_s_memview; +static PyObject *__pyx_n_s_mode; +static PyObject *__pyx_n_s_n_values; +static PyObject *__pyx_n_s_name; +static PyObject *__pyx_n_s_name_2; +static PyObject *__pyx_n_s_natoms; +static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; +static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_n_s_ndim; +static PyObject *__pyx_n_s_new; +static PyObject *__pyx_n_s_newpos; +static PyObject *__pyx_n_s_nloops; +static PyObject *__pyx_kp_s_no_default___reduce___due_to_non; +static PyObject *__pyx_n_s_np; +static PyObject *__pyx_n_s_numpy; +static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to; +static PyObject *__pyx_kp_s_numpy_core_umath_failed_to_impor; +static PyObject *__pyx_n_s_obj; +static PyObject *__pyx_n_s_oldpos; +static PyObject *__pyx_n_s_ortho; +static PyObject *__pyx_n_s_other; +static PyObject *__pyx_n_s_pack; +static PyObject *__pyx_n_s_pickle; +static PyObject *__pyx_n_s_positions; +static PyObject *__pyx_n_s_pyx_PickleError; +static PyObject *__pyx_n_s_pyx_checksum; +static PyObject *__pyx_n_s_pyx_getbuffer; +static PyObject *__pyx_n_s_pyx_result; +static PyObject *__pyx_n_s_pyx_state; +static PyObject *__pyx_n_s_pyx_type; +static PyObject *__pyx_n_s_pyx_unpickle_Enum; +static PyObject *__pyx_n_s_pyx_vtable; +static PyObject *__pyx_n_s_range; +static PyObject *__pyx_n_s_reduce; +static PyObject *__pyx_n_s_reduce_cython; +static PyObject *__pyx_n_s_reduce_ex; +static PyObject *__pyx_n_s_ref; +static PyObject *__pyx_n_s_reference_atom; +static PyObject *__pyx_n_s_refpoints; +static PyObject *__pyx_n_s_result; +static PyObject *__pyx_n_s_setstate; +static PyObject *__pyx_n_s_setstate_cython; +static PyObject *__pyx_n_s_shape; +static PyObject *__pyx_n_s_size; +static PyObject *__pyx_n_s_sort; +static PyObject *__pyx_n_s_start; +static PyObject *__pyx_n_s_step; +static PyObject *__pyx_n_s_stop; +static PyObject *__pyx_kp_s_strided_and_direct; +static PyObject *__pyx_kp_s_strided_and_direct_or_indirect; +static PyObject *__pyx_kp_s_strided_and_indirect; +static PyObject *__pyx_kp_s_stringsource; +static PyObject *__pyx_n_s_struct; +static PyObject *__pyx_n_s_test; +static PyObject *__pyx_n_s_this_frag; +static PyObject *__pyx_n_s_to_indices; +static PyObject *__pyx_n_s_todo; +static PyObject *__pyx_n_s_tri_box; +static PyObject *__pyx_n_s_triclinic_vectors; +static PyObject *__pyx_kp_s_unable_to_allocate_array_data; +static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; +static PyObject *__pyx_n_s_unique_int_1d; +static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; +static PyObject *__pyx_n_s_unpack; +static PyObject *__pyx_n_s_update; +static PyObject *__pyx_n_s_values; +static PyObject *__pyx_n_s_vec; +static PyObject *__pyx_n_s_zeros; +static PyObject *__pyx_pf_10MDAnalysis_3lib_6_cutil_unique_int_1d(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_values); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6_cutil_2make_whole(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_atomgroup, PyObject *__pyx_v_reference_atom); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6_cutil_4find_fragments(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_atoms, PyObject *__pyx_v_bondlist); /* proto */ +static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__len__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ +static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_12__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ +static PyObject *__pyx_pf___pyx_array___reduce_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_array_2__setstate_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ +static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ +static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_MemviewEnum_2__setstate_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ +static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); 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__pyx_L0:; + __Pyx_XDECREF((PyObject *)__pyx_v_memviewsliceobj); + __Pyx_XDECREF(__pyx_v_index); + __Pyx_XGIVEREF((PyObject *)__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "View.MemoryView":802 + * + * @cname('__pyx_memoryview_slice_memviewslice') + * cdef int slice_memviewslice( # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * Py_ssize_t shape, Py_ssize_t stride, Py_ssize_t suboffset, + */ + +static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, Py_ssize_t __pyx_v_shape, Py_ssize_t __pyx_v_stride, Py_ssize_t __pyx_v_suboffset, int __pyx_v_dim, int __pyx_v_new_ndim, int *__pyx_v_suboffset_dim, Py_ssize_t __pyx_v_start, Py_ssize_t __pyx_v_stop, Py_ssize_t __pyx_v_step, int __pyx_v_have_start, int __pyx_v_have_stop, int __pyx_v_have_step, int __pyx_v_is_slice) { + Py_ssize_t __pyx_v_new_shape; + int __pyx_v_negative_step; + int __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":822 + * cdef bint negative_step + * + * if not is_slice: # <<<<<<<<<<<<<< + * + * if start < 0: + */ + __pyx_t_1 = ((!(__pyx_v_is_slice != 0)) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":824 + * if not is_slice: + * + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if not 0 <= start < shape: + */ + __pyx_t_1 = ((__pyx_v_start < 0) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":825 + * + * if start < 0: + * start += shape # <<<<<<<<<<<<<< + * if not 0 <= start < shape: + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) + */ + __pyx_v_start = (__pyx_v_start + __pyx_v_shape); + + /* "View.MemoryView":824 + * if not is_slice: + * + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if not 0 <= start < shape: + */ + } + + /* "View.MemoryView":826 + * if start < 0: + * start += shape + * if not 0 <= start < shape: # <<<<<<<<<<<<<< + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) + * else: + */ + __pyx_t_1 = (0 <= __pyx_v_start); + if (__pyx_t_1) { + __pyx_t_1 = (__pyx_v_start < __pyx_v_shape); + } + __pyx_t_2 = ((!(__pyx_t_1 != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":827 + * start += shape + * if not 0 <= start < shape: + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) # <<<<<<<<<<<<<< + * else: + * + */ + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"Index out of bounds (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 827, __pyx_L1_error) + + /* "View.MemoryView":826 + * if start < 0: + * start += shape + * if not 0 <= start < shape: # <<<<<<<<<<<<<< + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) + * else: + */ + } + + /* "View.MemoryView":822 + * cdef bint negative_step + * + * if not is_slice: # <<<<<<<<<<<<<< + * + * if start < 0: + */ + goto __pyx_L3; + } + + /* "View.MemoryView":830 + * else: + * + * negative_step = have_step != 0 and step < 0 # <<<<<<<<<<<<<< + * + * if have_step and step == 0: + */ + /*else*/ { + __pyx_t_1 = ((__pyx_v_have_step != 0) != 0); + if (__pyx_t_1) { + } else { + __pyx_t_2 = __pyx_t_1; + goto __pyx_L6_bool_binop_done; + } + __pyx_t_1 = ((__pyx_v_step < 0) != 0); + __pyx_t_2 = __pyx_t_1; + __pyx_L6_bool_binop_done:; + __pyx_v_negative_step = __pyx_t_2; + + /* "View.MemoryView":832 + * negative_step = have_step != 0 and step < 0 + * + * if have_step and step == 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) + * + */ + __pyx_t_1 = (__pyx_v_have_step != 0); + if (__pyx_t_1) { + } else { + __pyx_t_2 = __pyx_t_1; + goto __pyx_L9_bool_binop_done; + } + __pyx_t_1 = ((__pyx_v_step == 0) != 0); + __pyx_t_2 = __pyx_t_1; + __pyx_L9_bool_binop_done:; + if (__pyx_t_2) { + + /* "View.MemoryView":833 + * + * if have_step and step == 0: + * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Step may not be zero (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 833, __pyx_L1_error) + + /* "View.MemoryView":832 + * negative_step = have_step != 0 and step < 0 + * + * if have_step and step == 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) + * + */ + } + + /* "View.MemoryView":836 + * + * + * if have_start: # <<<<<<<<<<<<<< + * if start < 0: + * start += shape + */ + __pyx_t_2 = (__pyx_v_have_start != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":837 + * + * if have_start: + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if start < 0: + */ + __pyx_t_2 = ((__pyx_v_start < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":838 + * if have_start: + * if start < 0: + * start += shape # <<<<<<<<<<<<<< + * if start < 0: + * start = 0 + */ + __pyx_v_start = (__pyx_v_start + __pyx_v_shape); + + /* "View.MemoryView":839 + * if start < 0: + * start += shape + * if start < 0: # <<<<<<<<<<<<<< + * start = 0 + * elif start >= shape: + */ + __pyx_t_2 = ((__pyx_v_start < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":840 + * start += shape + * if start < 0: + * start = 0 # <<<<<<<<<<<<<< + * elif start >= shape: + * if negative_step: + */ + __pyx_v_start = 0; + + /* "View.MemoryView":839 + * if start < 0: + * start += shape + * if start < 0: # <<<<<<<<<<<<<< + * start = 0 + * elif start >= shape: + */ + } + + /* "View.MemoryView":837 + * + * if have_start: + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if start < 0: + */ + goto __pyx_L12; + } + + /* "View.MemoryView":841 + * if start < 0: + * start = 0 + * elif start >= shape: # <<<<<<<<<<<<<< + * if negative_step: + * start = shape - 1 + */ + __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":842 + * start = 0 + * elif start >= shape: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ + __pyx_t_2 = (__pyx_v_negative_step != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":843 + * elif start >= shape: + * if negative_step: + * start = shape - 1 # <<<<<<<<<<<<<< + * else: + * start = shape + */ + __pyx_v_start = (__pyx_v_shape - 1); + + /* "View.MemoryView":842 + * start = 0 + * elif start >= shape: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ + goto __pyx_L14; + } + + /* "View.MemoryView":845 + * start = shape - 1 + * else: + * start = shape # <<<<<<<<<<<<<< + * else: + * if negative_step: + */ + /*else*/ { + __pyx_v_start = __pyx_v_shape; + } + __pyx_L14:; + + /* "View.MemoryView":841 + * if start < 0: + * start = 0 + * elif start >= shape: # <<<<<<<<<<<<<< + * if negative_step: + * start = shape - 1 + */ + } + __pyx_L12:; + + /* "View.MemoryView":836 + * + * + * if have_start: # <<<<<<<<<<<<<< + * if start < 0: + * start += shape + */ + goto __pyx_L11; + } + + /* "View.MemoryView":847 + * start = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ + /*else*/ { + __pyx_t_2 = (__pyx_v_negative_step != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":848 + * else: + * if negative_step: + * start = shape - 1 # <<<<<<<<<<<<<< + * else: + * start = 0 + */ + __pyx_v_start = (__pyx_v_shape - 1); + + /* "View.MemoryView":847 + * start = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ + goto __pyx_L15; + } + + /* "View.MemoryView":850 + * start = shape - 1 + * else: + * start = 0 # <<<<<<<<<<<<<< + * + * if have_stop: + */ + /*else*/ { + __pyx_v_start = 0; + } + __pyx_L15:; + } + __pyx_L11:; + + /* "View.MemoryView":852 + * start = 0 + * + * if have_stop: # <<<<<<<<<<<<<< + * if stop < 0: + * stop += shape + */ + __pyx_t_2 = (__pyx_v_have_stop != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":853 + * + * if have_stop: + * if stop < 0: # <<<<<<<<<<<<<< + * stop += shape + * if stop < 0: + */ + __pyx_t_2 = ((__pyx_v_stop < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":854 + * if have_stop: + * if stop < 0: + * stop += shape # <<<<<<<<<<<<<< + * if stop < 0: + * stop = 0 + */ + __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); + + /* "View.MemoryView":855 + * if stop < 0: + * stop += shape + * if stop < 0: # <<<<<<<<<<<<<< + * stop = 0 + * elif stop > shape: + */ + __pyx_t_2 = ((__pyx_v_stop < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":856 + * stop += shape + * if stop < 0: + * stop = 0 # <<<<<<<<<<<<<< + * elif stop > shape: + * stop = shape + */ + __pyx_v_stop = 0; + + /* "View.MemoryView":855 + * if stop < 0: + * stop += shape + * if stop < 0: # <<<<<<<<<<<<<< + * stop = 0 + * elif stop > shape: + */ + } + + /* "View.MemoryView":853 + * + * if have_stop: + * if stop < 0: # <<<<<<<<<<<<<< + * stop += shape + * if stop < 0: + */ + goto __pyx_L17; + } + + /* "View.MemoryView":857 + * if stop < 0: + * stop = 0 + * elif stop > shape: # <<<<<<<<<<<<<< + * stop = shape + * else: + */ + __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":858 + * stop = 0 + * elif stop > shape: + * stop = shape # <<<<<<<<<<<<<< + * else: + * if negative_step: + */ + __pyx_v_stop = __pyx_v_shape; + + /* "View.MemoryView":857 + * if stop < 0: + * stop = 0 + * elif stop > shape: # <<<<<<<<<<<<<< + * stop = shape + * else: + */ + } + __pyx_L17:; + + /* "View.MemoryView":852 + * start = 0 + * + * if have_stop: # <<<<<<<<<<<<<< + * if stop < 0: + * stop += shape + */ + goto __pyx_L16; + } + + /* "View.MemoryView":860 + * stop = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * stop = -1 + * else: + */ + /*else*/ { + __pyx_t_2 = (__pyx_v_negative_step != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":861 + * else: + * if negative_step: + * stop = -1 # <<<<<<<<<<<<<< + * else: + * stop = shape + */ + __pyx_v_stop = -1L; + + /* "View.MemoryView":860 + * stop = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * stop = -1 + * else: + */ + goto __pyx_L19; + } + + /* "View.MemoryView":863 + * stop = -1 + * else: + * stop = shape # <<<<<<<<<<<<<< + * + * if not have_step: + */ + /*else*/ { + __pyx_v_stop = __pyx_v_shape; + } + __pyx_L19:; + } + __pyx_L16:; + + /* "View.MemoryView":865 + * stop = shape + * + * if not have_step: # <<<<<<<<<<<<<< + * step = 1 + * + */ + __pyx_t_2 = ((!(__pyx_v_have_step != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":866 + * + * if not have_step: + * step = 1 # <<<<<<<<<<<<<< + * + * + */ + __pyx_v_step = 1; + + /* "View.MemoryView":865 + * stop = shape + * + * if not have_step: # <<<<<<<<<<<<<< + * step = 1 + * + */ + } + + /* "View.MemoryView":870 + * + * with cython.cdivision(True): + * new_shape = (stop - start) // step # <<<<<<<<<<<<<< + * + * if (stop - start) - step * new_shape: + */ + __pyx_v_new_shape = ((__pyx_v_stop - __pyx_v_start) / __pyx_v_step); + + /* "View.MemoryView":872 + * new_shape = (stop - start) // step + * + * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< + * new_shape += 1 + * + */ + __pyx_t_2 = (((__pyx_v_stop - __pyx_v_start) - (__pyx_v_step * __pyx_v_new_shape)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":873 + * + * if (stop - start) - step * new_shape: + * new_shape += 1 # <<<<<<<<<<<<<< + * + * if new_shape < 0: + */ + __pyx_v_new_shape = (__pyx_v_new_shape + 1); + + /* "View.MemoryView":872 + * new_shape = (stop - start) // step + * + * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< + * new_shape += 1 + * + */ + } + + /* "View.MemoryView":875 + * new_shape += 1 + * + * if new_shape < 0: # <<<<<<<<<<<<<< + * new_shape = 0 + * + */ + __pyx_t_2 = ((__pyx_v_new_shape < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":876 + * + * if new_shape < 0: + * new_shape = 0 # <<<<<<<<<<<<<< + * + * + */ + __pyx_v_new_shape = 0; + + /* "View.MemoryView":875 + * new_shape += 1 + * + * if new_shape < 0: # <<<<<<<<<<<<<< + * new_shape = 0 + * + */ + } + + /* "View.MemoryView":879 + * + * + * dst.strides[new_ndim] = stride * step # <<<<<<<<<<<<<< + * dst.shape[new_ndim] = new_shape + * dst.suboffsets[new_ndim] = suboffset + */ + (__pyx_v_dst->strides[__pyx_v_new_ndim]) = (__pyx_v_stride * __pyx_v_step); + + /* "View.MemoryView":880 + * + * dst.strides[new_ndim] = stride * step + * dst.shape[new_ndim] = new_shape # <<<<<<<<<<<<<< + * dst.suboffsets[new_ndim] = suboffset + * + */ + (__pyx_v_dst->shape[__pyx_v_new_ndim]) = __pyx_v_new_shape; + + /* "View.MemoryView":881 + * dst.strides[new_ndim] = stride * step + * dst.shape[new_ndim] = new_shape + * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< + * + * + */ + (__pyx_v_dst->suboffsets[__pyx_v_new_ndim]) = __pyx_v_suboffset; + } + __pyx_L3:; + + /* "View.MemoryView":884 + * + * + * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< + * dst.data += start * stride + * else: + */ + __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":885 + * + * if suboffset_dim[0] < 0: + * dst.data += start * stride # <<<<<<<<<<<<<< + * else: + * dst.suboffsets[suboffset_dim[0]] += start * stride + */ + __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); + + /* "View.MemoryView":884 + * + * + * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< + * dst.data += start * stride + * else: + */ + goto __pyx_L23; + } + + /* "View.MemoryView":887 + * dst.data += start * stride + * else: + * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< + * + * if suboffset >= 0: + */ + /*else*/ { + __pyx_t_3 = (__pyx_v_suboffset_dim[0]); + (__pyx_v_dst->suboffsets[__pyx_t_3]) = ((__pyx_v_dst->suboffsets[__pyx_t_3]) + (__pyx_v_start * __pyx_v_stride)); + } + __pyx_L23:; + + /* "View.MemoryView":889 + * dst.suboffsets[suboffset_dim[0]] += start * stride + * + * if suboffset >= 0: # <<<<<<<<<<<<<< + * if not is_slice: + * if new_ndim == 0: + */ + __pyx_t_2 = ((__pyx_v_suboffset >= 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":890 + * + * if suboffset >= 0: + * if not is_slice: # <<<<<<<<<<<<<< + * if new_ndim == 0: + * dst.data = ( dst.data)[0] + suboffset + */ + __pyx_t_2 = ((!(__pyx_v_is_slice != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":891 + * if suboffset >= 0: + * if not is_slice: + * if new_ndim == 0: # <<<<<<<<<<<<<< + * dst.data = ( dst.data)[0] + suboffset + * else: + */ + __pyx_t_2 = ((__pyx_v_new_ndim == 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":892 + * if not is_slice: + * if new_ndim == 0: + * dst.data = ( dst.data)[0] + suboffset # <<<<<<<<<<<<<< + * else: + * _err_dim(IndexError, "All dimensions preceding dimension %d " + */ + __pyx_v_dst->data = ((((char **)__pyx_v_dst->data)[0]) + __pyx_v_suboffset); + + /* "View.MemoryView":891 + * if suboffset >= 0: + * if not is_slice: + * if new_ndim == 0: # <<<<<<<<<<<<<< + * dst.data = ( dst.data)[0] + suboffset + * else: + */ + goto __pyx_L26; + } + + /* "View.MemoryView":894 + * dst.data = ( dst.data)[0] + suboffset + * else: + * _err_dim(IndexError, "All dimensions preceding dimension %d " # <<<<<<<<<<<<<< + * "must be indexed and not sliced", dim) + * else: + */ + 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"View.MemoryView":1082 + * + * @cname('__pyx_memoryview_copy_object_from_slice') + * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< + * """ + * Create a new memoryview object from a given memoryview object and slice. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_5); + __Pyx_AddTraceback("View.MemoryView.memoryview_copy_from_slice", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "View.MemoryView":1104 + * + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< + * if arg < 0: + * return -arg + */ + +static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { + Py_ssize_t __pyx_r; + int __pyx_t_1; + + /* "View.MemoryView":1105 + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: + * if arg < 0: # <<<<<<<<<<<<<< + * return -arg + * else: + */ + __pyx_t_1 = ((__pyx_v_arg < 0) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1106 + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: + * if arg < 0: + * return -arg # <<<<<<<<<<<<<< + * else: + * return arg + */ + __pyx_r = (-__pyx_v_arg); + goto __pyx_L0; + + /* "View.MemoryView":1105 + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: + * if arg < 0: # <<<<<<<<<<<<<< + * return -arg + * else: + */ + } + + /* "View.MemoryView":1108 + * return -arg + * else: + * return arg # <<<<<<<<<<<<<< + * + * @cname('__pyx_get_best_slice_order') + */ + /*else*/ { + __pyx_r = __pyx_v_arg; + goto __pyx_L0; + } + + /* "View.MemoryView":1104 + * + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< + * if arg < 0: + * return -arg + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1111 + * + * @cname('__pyx_get_best_slice_order') + * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< + * """ + * Figure out the best memory access order for a given slice. + */ + +static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int __pyx_v_ndim) { + int __pyx_v_i; + Py_ssize_t __pyx_v_c_stride; + Py_ssize_t __pyx_v_f_stride; + char __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + + /* "View.MemoryView":1116 + * """ + * cdef int i + * cdef Py_ssize_t c_stride = 0 # <<<<<<<<<<<<<< + * cdef Py_ssize_t f_stride = 0 + * + */ + __pyx_v_c_stride = 0; + + /* "View.MemoryView":1117 + * cdef int i + * cdef Py_ssize_t c_stride = 0 + * cdef Py_ssize_t f_stride = 0 # <<<<<<<<<<<<<< + * + * for i in range(ndim - 1, -1, -1): + */ + __pyx_v_f_stride = 0; + + /* "View.MemoryView":1119 + * cdef Py_ssize_t f_stride = 0 + * + * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] + */ + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { + __pyx_v_i = __pyx_t_1; + + /* "View.MemoryView":1120 + * + * for i in range(ndim - 1, -1, -1): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * c_stride = mslice.strides[i] + * break + */ + __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1121 + * for i in range(ndim - 1, -1, -1): + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< + * break + * + */ + __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); + + /* "View.MemoryView":1122 + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] + * break # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + goto __pyx_L4_break; + + /* "View.MemoryView":1120 + * + * for i in range(ndim - 1, -1, -1): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * c_stride = mslice.strides[i] + * break + */ + } + } + __pyx_L4_break:; + + /* "View.MemoryView":1124 + * break + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] + */ + __pyx_t_1 = __pyx_v_ndim; + __pyx_t_3 = __pyx_t_1; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_i = __pyx_t_4; + + /* "View.MemoryView":1125 + * + * for i in range(ndim): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * f_stride = mslice.strides[i] + * break + */ + __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1126 + * for i in range(ndim): + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< + * break + * + */ + __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); + + /* "View.MemoryView":1127 + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] + * break # <<<<<<<<<<<<<< + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + */ + goto __pyx_L7_break; + + /* "View.MemoryView":1125 + * + * for i in range(ndim): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * f_stride = mslice.strides[i] + * break + */ + } + } + __pyx_L7_break:; + + /* "View.MemoryView":1129 + * break + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< + * return 'C' + * else: + */ + __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1130 + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + * return 'C' # <<<<<<<<<<<<<< + * else: + * return 'F' + */ + __pyx_r = 'C'; + goto __pyx_L0; + + /* "View.MemoryView":1129 + * break + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< + * return 'C' + * else: + */ + } + + /* "View.MemoryView":1132 + * return 'C' + * else: + * return 'F' # <<<<<<<<<<<<<< + * + * @cython.cdivision(True) + */ + /*else*/ { + __pyx_r = 'F'; + goto __pyx_L0; + } + + /* "View.MemoryView":1111 + * + * @cname('__pyx_get_best_slice_order') + * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< + * """ + * Figure out the best memory access order for a given slice. + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1135 + * + * @cython.cdivision(True) + * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< + * char *dst_data, Py_ssize_t *dst_strides, + * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, + */ + +static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v_src_strides, char *__pyx_v_dst_data, Py_ssize_t *__pyx_v_dst_strides, Py_ssize_t *__pyx_v_src_shape, Py_ssize_t *__pyx_v_dst_shape, int __pyx_v_ndim, size_t __pyx_v_itemsize) { + CYTHON_UNUSED Py_ssize_t __pyx_v_i; + CYTHON_UNUSED Py_ssize_t __pyx_v_src_extent; + Py_ssize_t __pyx_v_dst_extent; + Py_ssize_t __pyx_v_src_stride; + Py_ssize_t __pyx_v_dst_stride; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + Py_ssize_t __pyx_t_4; + Py_ssize_t __pyx_t_5; + Py_ssize_t __pyx_t_6; + + /* "View.MemoryView":1142 + * + * cdef Py_ssize_t i + * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] + */ + __pyx_v_src_extent = (__pyx_v_src_shape[0]); + + /* "View.MemoryView":1143 + * cdef Py_ssize_t i + * cdef Py_ssize_t src_extent = src_shape[0] + * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t src_stride = src_strides[0] + * cdef Py_ssize_t dst_stride = dst_strides[0] + */ + __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); + + /* "View.MemoryView":1144 + * cdef Py_ssize_t src_extent = src_shape[0] + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + */ + __pyx_v_src_stride = (__pyx_v_src_strides[0]); + + /* "View.MemoryView":1145 + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] + * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< + * + * if ndim == 1: + */ + __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); + + /* "View.MemoryView":1147 + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + */ + __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1148 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ + __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L5_bool_binop_done; + } + __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L5_bool_binop_done; + } + + /* "View.MemoryView":1149 + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< + * memcpy(dst_data, src_data, itemsize * dst_extent) + * else: + */ + __pyx_t_2 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize); + if (__pyx_t_2) { + __pyx_t_2 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride)); + } + __pyx_t_3 = (__pyx_t_2 != 0); + __pyx_t_1 = __pyx_t_3; + __pyx_L5_bool_binop_done:; + + /* "View.MemoryView":1148 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ + if (__pyx_t_1) { + + /* "View.MemoryView":1150 + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< + * else: + * for i in range(dst_extent): + */ + (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent))); + + /* "View.MemoryView":1148 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ + goto __pyx_L4; + } + + /* "View.MemoryView":1152 + * memcpy(dst_data, src_data, itemsize * dst_extent) + * else: + * for i in range(dst_extent): # <<<<<<<<<<<<<< + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride + */ + /*else*/ { + __pyx_t_4 = __pyx_v_dst_extent; + __pyx_t_5 = __pyx_t_4; + for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { + __pyx_v_i = __pyx_t_6; + + /* "View.MemoryView":1153 + * else: + * for i in range(dst_extent): + * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< + * src_data += src_stride + * dst_data += dst_stride + */ + (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); + + /* "View.MemoryView":1154 + * for i in range(dst_extent): + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride # <<<<<<<<<<<<<< + * dst_data += dst_stride + * else: + */ + __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); + + /* "View.MemoryView":1155 + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride + * dst_data += dst_stride # <<<<<<<<<<<<<< + * else: + * for i in range(dst_extent): + */ + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L4:; + + /* "View.MemoryView":1147 + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + */ + goto __pyx_L3; + } + + /* "View.MemoryView":1157 + * dst_data += dst_stride + * else: + * for i in range(dst_extent): # <<<<<<<<<<<<<< + * _copy_strided_to_strided(src_data, src_strides + 1, + * dst_data, dst_strides + 1, + */ + /*else*/ { + __pyx_t_4 = __pyx_v_dst_extent; + __pyx_t_5 = __pyx_t_4; + for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { + __pyx_v_i = __pyx_t_6; + + /* "View.MemoryView":1158 + * else: + * for i in range(dst_extent): + * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< + * dst_data, dst_strides + 1, + * src_shape + 1, dst_shape + 1, + */ + _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); + + /* "View.MemoryView":1162 + * src_shape + 1, dst_shape + 1, + * ndim - 1, itemsize) + * src_data += src_stride # <<<<<<<<<<<<<< + * dst_data += dst_stride + * + */ + __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); + + /* "View.MemoryView":1163 + * ndim - 1, itemsize) + * src_data += src_stride + * dst_data += dst_stride # <<<<<<<<<<<<<< + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, + */ + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L3:; + + /* "View.MemoryView":1135 + * + * @cython.cdivision(True) + * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< + * char *dst_data, Py_ssize_t *dst_strides, + * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, + */ + + /* function exit code */ +} + +/* "View.MemoryView":1165 + * dst_data += dst_stride + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + */ + +static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { + + /* "View.MemoryView":1168 + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< + * src.shape, dst.shape, ndim, itemsize) + * + */ + _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1165 + * dst_data += dst_stride + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + */ + + /* function exit code */ +} + +/* "View.MemoryView":1172 + * + * @cname('__pyx_memoryview_slice_get_size') + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + */ + +static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { + int __pyx_v_i; + Py_ssize_t __pyx_v_size; + Py_ssize_t __pyx_r; + Py_ssize_t __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + + /* "View.MemoryView":1175 + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + __pyx_t_1 = __pyx_v_src->memview->view.itemsize; + __pyx_v_size = __pyx_t_1; + + /* "View.MemoryView":1177 + * cdef Py_ssize_t size = src.memview.view.itemsize + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * size *= src.shape[i] + * + */ + __pyx_t_2 = __pyx_v_ndim; + __pyx_t_3 = __pyx_t_2; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_i = __pyx_t_4; + + /* "View.MemoryView":1178 + * + * for i in range(ndim): + * size *= src.shape[i] # <<<<<<<<<<<<<< + * + * return size + */ + __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i])); + } + + /* "View.MemoryView":1180 + * size *= src.shape[i] + * + * return size # <<<<<<<<<<<<<< + * + * @cname('__pyx_fill_contig_strides_array') + */ + __pyx_r = __pyx_v_size; + goto __pyx_L0; + + /* "View.MemoryView":1172 + * + * @cname('__pyx_memoryview_slice_get_size') + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1183 + * + * @cname('__pyx_fill_contig_strides_array') + * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< + * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, + * int ndim, char order) nogil: + */ + +static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { + int __pyx_v_idx; + Py_ssize_t __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + + /* "View.MemoryView":1192 + * cdef int idx + * + * if order == 'F': # <<<<<<<<<<<<<< + * for idx in range(ndim): + * strides[idx] = stride + */ + __pyx_t_1 = ((__pyx_v_order == 'F') != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1193 + * + * if order == 'F': + * for idx in range(ndim): # <<<<<<<<<<<<<< + * strides[idx] = stride + * stride = stride * shape[idx] + */ + __pyx_t_2 = __pyx_v_ndim; + __pyx_t_3 = __pyx_t_2; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_idx = __pyx_t_4; + + /* "View.MemoryView":1194 + * if order == 'F': + * for idx in range(ndim): + * strides[idx] = stride # <<<<<<<<<<<<<< + * stride = stride * shape[idx] + * else: + */ + (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; + + /* "View.MemoryView":1195 + * for idx in range(ndim): + * strides[idx] = stride + * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * else: + * for idx in range(ndim - 1, -1, -1): + */ + __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); + } + + /* "View.MemoryView":1192 + * cdef int idx + * + * if order == 'F': # <<<<<<<<<<<<<< + * for idx in range(ndim): + * strides[idx] = stride + */ + goto __pyx_L3; + } + + /* "View.MemoryView":1197 + * stride = stride * shape[idx] + * else: + * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< + * strides[idx] = stride + * stride = stride * shape[idx] + */ + /*else*/ { + for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { + __pyx_v_idx = __pyx_t_2; + + /* "View.MemoryView":1198 + 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__pyx_v_dtype_is_object, __pyx_v_ndim, 0); + + /* "View.MemoryView":1317 + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) + */ + (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim))); + + /* "View.MemoryView":1318 + * refcount_copying(&dst, dtype_is_object, ndim, False) + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * free(tmpdata) + * return 0 + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1319 + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) # <<<<<<<<<<<<<< + * return 0 + * + */ + free(__pyx_v_tmpdata); + + /* "View.MemoryView":1320 + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) + * return 0 # <<<<<<<<<<<<<< + * + * if order == 'F' == get_best_order(&dst, ndim): + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "View.MemoryView":1314 + * direct_copy = slice_is_contig(dst, 'F', ndim) + * + * if direct_copy: # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + } + + /* "View.MemoryView":1306 + * src = tmp + * + * if not broadcasting: # <<<<<<<<<<<<<< + * + * + */ + } + + /* "View.MemoryView":1322 + * return 0 + * + * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = (__pyx_v_order == 'F'); + if (__pyx_t_2) { + __pyx_t_2 = ('F' == __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim)); + } + __pyx_t_8 = (__pyx_t_2 != 0); + if (__pyx_t_8) { + + /* "View.MemoryView":1325 + * + * + * transpose_memslice(&src) # <<<<<<<<<<<<<< + * transpose_memslice(&dst) + * + */ + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(2, 1325, __pyx_L1_error) + + /* "View.MemoryView":1326 + * + * transpose_memslice(&src) + * transpose_memslice(&dst) # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(2, 1326, __pyx_L1_error) + + /* "View.MemoryView":1322 + * return 0 + * + * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< + * + * + */ + } + + /* "View.MemoryView":1328 + * transpose_memslice(&dst) + * + * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< + * copy_strided_to_strided(&src, &dst, ndim, itemsize) + * refcount_copying(&dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); + + /* "View.MemoryView":1329 + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<< + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + */ + copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1330 + * refcount_copying(&dst, dtype_is_object, ndim, False) + * copy_strided_to_strided(&src, &dst, ndim, itemsize) + * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * + * free(tmpdata) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1332 + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + * free(tmpdata) # <<<<<<<<<<<<<< + * return 0 + * + */ + free(__pyx_v_tmpdata); + + /* "View.MemoryView":1333 + * + * free(tmpdata) + * return 0 # <<<<<<<<<<<<<< + * + * @cname('__pyx_memoryview_broadcast_leading') + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "View.MemoryView":1264 + * + * @cname('__pyx_memoryview_copy_contents') + * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice dst, + * int src_ndim, int dst_ndim, + */ + + /* function exit code */ + __pyx_L1_error:; + { + #ifdef WITH_THREAD + PyGILState_STATE __pyx_gilstate_save = __Pyx_PyGILState_Ensure(); + #endif + __Pyx_AddTraceback("View.MemoryView.memoryview_copy_contents", __pyx_clineno, __pyx_lineno, __pyx_filename); + #ifdef WITH_THREAD + __Pyx_PyGILState_Release(__pyx_gilstate_save); + #endif + } + __pyx_r = -1; + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1336 + * + * @cname('__pyx_memoryview_broadcast_leading') + * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< + * int ndim, + * int ndim_other) nogil: + */ + +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslice, int __pyx_v_ndim, int __pyx_v_ndim_other) { + int __pyx_v_i; + int __pyx_v_offset; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":1340 + * int ndim_other) 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# <<<<<<<<<<<<<< + * + * @cname('__pyx_memoryview_refcount_objects_in_slice') + */ + __pyx_memoryview_refcount_objects_in_slice(__pyx_v_data, __pyx_v_shape, __pyx_v_strides, __pyx_v_ndim, __pyx_v_inc); + + /* "View.MemoryView":1367 + * + * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil') + * cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< + * Py_ssize_t *strides, int ndim, + * bint inc) with gil: + */ + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + #ifdef WITH_THREAD + __Pyx_PyGILState_Release(__pyx_gilstate_save); + #endif +} + +/* "View.MemoryView":1373 + * + * @cname('__pyx_memoryview_refcount_objects_in_slice') + * cdef void refcount_objects_in_slice(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< + * Py_ssize_t *strides, int ndim, bint inc): + * cdef Py_ssize_t i + */ + +static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, int 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__pyx_vtabptr_memoryview; + p->obj = Py_None; Py_INCREF(Py_None); + p->_size = Py_None; Py_INCREF(Py_None); + p->_array_interface = Py_None; Py_INCREF(Py_None); + p->view.obj = NULL; + if (unlikely(__pyx_memoryview___cinit__(o, a, k) < 0)) goto bad; + return o; + bad: + Py_DECREF(o); o = 0; + return NULL; +} + +static void __pyx_tp_dealloc_memoryview(PyObject *o) { + struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_memoryview___dealloc__(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->obj); + Py_CLEAR(p->_size); + Py_CLEAR(p->_array_interface); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_memoryview(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; + if (p->obj) { + e = (*v)(p->obj, a); if (e) return e; + } + if (p->_size) { + e = (*v)(p->_size, a); if (e) return e; + } + if (p->_array_interface) { + e = (*v)(p->_array_interface, a); if (e) return e; + } + if (p->view.obj) { + e = (*v)(p->view.obj, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_memoryview(PyObject *o) { + PyObject* tmp; + struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; + tmp = ((PyObject*)p->obj); + p->obj = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->_size); + p->_size = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->_array_interface); + p->_array_interface = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + Py_CLEAR(p->view.obj); + return 0; +} +static PyObject *__pyx_sq_item_memoryview(PyObject *o, Py_ssize_t i) { + PyObject *r; + PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; + r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); + Py_DECREF(x); + return r; +} + +static int __pyx_mp_ass_subscript_memoryview(PyObject *o, PyObject *i, PyObject *v) { + if (v) { + return __pyx_memoryview___setitem__(o, i, v); + } + else { + PyErr_Format(PyExc_NotImplementedError, + "Subscript deletion not supported by %.200s", Py_TYPE(o)->tp_name); + return -1; + } +} + +static PyObject *__pyx_getprop___pyx_memoryview_T(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_1T_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_base(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_4base_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_shape(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_5shape_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_strides(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_7strides_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_suboffsets(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_10suboffsets_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_ndim(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_4ndim_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_itemsize(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_8itemsize_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_nbytes(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_6nbytes_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_size(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_4size_1__get__(o); +} + +static PyMethodDef __pyx_methods_memoryview[] = { + {"is_c_contig", (PyCFunction)__pyx_memoryview_is_c_contig, METH_NOARGS, 0}, + {"is_f_contig", (PyCFunction)__pyx_memoryview_is_f_contig, METH_NOARGS, 0}, + {"copy", (PyCFunction)__pyx_memoryview_copy, METH_NOARGS, 0}, + {"copy_fortran", (PyCFunction)__pyx_memoryview_copy_fortran, METH_NOARGS, 0}, + {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_memoryview_1__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_memoryview_3__setstate_cython__, METH_O, 0}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_memoryview[] = { + {(char *)"T", __pyx_getprop___pyx_memoryview_T, 0, (char *)0, 0}, + {(char *)"base", __pyx_getprop___pyx_memoryview_base, 0, (char *)0, 0}, + {(char *)"shape", __pyx_getprop___pyx_memoryview_shape, 0, (char *)0, 0}, + {(char *)"strides", __pyx_getprop___pyx_memoryview_strides, 0, (char *)0, 0}, + {(char *)"suboffsets", __pyx_getprop___pyx_memoryview_suboffsets, 0, (char *)0, 0}, + {(char *)"ndim", __pyx_getprop___pyx_memoryview_ndim, 0, (char *)0, 0}, + {(char *)"itemsize", __pyx_getprop___pyx_memoryview_itemsize, 0, (char *)0, 0}, + {(char *)"nbytes", __pyx_getprop___pyx_memoryview_nbytes, 0, (char *)0, 0}, + {(char *)"size", __pyx_getprop___pyx_memoryview_size, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; + +static PySequenceMethods __pyx_tp_as_sequence_memoryview = { + __pyx_memoryview___len__, /*sq_length*/ + 0, /*sq_concat*/ + 0, /*sq_repeat*/ + __pyx_sq_item_memoryview, /*sq_item*/ + 0, /*sq_slice*/ + 0, /*sq_ass_item*/ + 0, /*sq_ass_slice*/ + 0, /*sq_contains*/ + 0, /*sq_inplace_concat*/ + 0, /*sq_inplace_repeat*/ +}; + +static PyMappingMethods __pyx_tp_as_mapping_memoryview = { + __pyx_memoryview___len__, /*mp_length*/ + __pyx_memoryview___getitem__, /*mp_subscript*/ + __pyx_mp_ass_subscript_memoryview, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_memoryview = { + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getreadbuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getwritebuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getsegcount*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getcharbuffer*/ + #endif + __pyx_memoryview_getbuffer, /*bf_getbuffer*/ + 0, /*bf_releasebuffer*/ +}; + +static PyTypeObject __pyx_type___pyx_memoryview = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib._cutil.memoryview", /*tp_name*/ + sizeof(struct __pyx_memoryview_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_memoryview, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + __pyx_memoryview___repr__, /*tp_repr*/ + 0, /*tp_as_number*/ + &__pyx_tp_as_sequence_memoryview, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_memoryview, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + __pyx_memoryview___str__, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_memoryview, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + 0, /*tp_doc*/ + __pyx_tp_traverse_memoryview, /*tp_traverse*/ + __pyx_tp_clear_memoryview, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_memoryview, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_memoryview, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_memoryview, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct__memoryviewslice __pyx_vtable__memoryviewslice; + +static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_memoryviewslice_obj *p; + PyObject *o = __pyx_tp_new_memoryview(t, a, k); + if (unlikely(!o)) return 0; + p = ((struct __pyx_memoryviewslice_obj *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_memoryview*)__pyx_vtabptr__memoryviewslice; + p->from_object = Py_None; Py_INCREF(Py_None); + p->from_slice.memview = NULL; + return o; +} + +static void __pyx_tp_dealloc__memoryviewslice(PyObject *o) { + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_memoryviewslice___dealloc__(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->from_object); + PyObject_GC_Track(o); + __pyx_tp_dealloc_memoryview(o); +} + +static int __pyx_tp_traverse__memoryviewslice(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + e = __pyx_tp_traverse_memoryview(o, v, a); if (e) return e; + if (p->from_object) { + e = (*v)(p->from_object, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear__memoryviewslice(PyObject *o) { + PyObject* tmp; + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + __pyx_tp_clear_memoryview(o); + tmp = ((PyObject*)p->from_object); + p->from_object = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + __PYX_XDEC_MEMVIEW(&p->from_slice, 1); + return 0; +} + +static PyObject *__pyx_getprop___pyx_memoryviewslice_base(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_16_memoryviewslice_4base_1__get__(o); +} + +static PyMethodDef __pyx_methods__memoryviewslice[] = { + {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_memoryviewslice_1__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_memoryviewslice_3__setstate_cython__, METH_O, 0}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets__memoryviewslice[] = { + {(char *)"base", __pyx_getprop___pyx_memoryviewslice_base, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type___pyx_memoryviewslice = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib._cutil._memoryviewslice", /*tp_name*/ + sizeof(struct __pyx_memoryviewslice_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc__memoryviewslice, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___repr__, /*tp_repr*/ + #else + 0, /*tp_repr*/ + #endif + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___str__, /*tp_str*/ + #else + 0, /*tp_str*/ + #endif + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + "Internal class for passing memoryview slices to Python", /*tp_doc*/ + __pyx_tp_traverse__memoryviewslice, /*tp_traverse*/ + __pyx_tp_clear__memoryviewslice, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods__memoryviewslice, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets__memoryviewslice, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ 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+ __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + if (__pyx_m) { + if (__pyx_d) { + __Pyx_AddTraceback("init MDAnalysis.lib._cutil", 0, __pyx_lineno, __pyx_filename); + } + Py_DECREF(__pyx_m); __pyx_m = 0; + } else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_ImportError, "init MDAnalysis.lib._cutil"); + } + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + #if CYTHON_PEP489_MULTI_PHASE_INIT + return (__pyx_m != NULL) ? 0 : -1; + #elif PY_MAJOR_VERSION >= 3 + return __pyx_m; + #else + return; + #endif +} + +/* --- Runtime support code --- */ +/* Refnanny */ +#if CYTHON_REFNANNY +static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { + PyObject *m = NULL, *p = NULL; + void *r = NULL; + m = PyImport_ImportModule((char *)modname); + if (!m) goto end; + p = PyObject_GetAttrString(m, (char *)"RefNannyAPI"); + if (!p) goto end; + r = PyLong_AsVoidPtr(p); +end: + Py_XDECREF(p); + Py_XDECREF(m); + return (__Pyx_RefNannyAPIStruct *)r; +} +#endif + +/* PyObjectGetAttrStr */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#endif + +/* GetBuiltinName */ +static PyObject *__Pyx_GetBuiltinName(PyObject *name) { + PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name); + if (unlikely(!result)) { + PyErr_Format(PyExc_NameError, +#if PY_MAJOR_VERSION >= 3 + "name '%U' is not defined", name); +#else + "name '%.200s' is not defined", PyString_AS_STRING(name)); +#endif + } + return result; +} + +/* GetModuleGlobalName */ +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { + PyObject *result; +#if !CYTHON_AVOID_BORROWED_REFS +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 + result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash); + if (likely(result)) { + Py_INCREF(result); + } else if (unlikely(PyErr_Occurred())) { + result = NULL; + } else { +#else + result = PyDict_GetItem(__pyx_d, name); + if (likely(result)) { + Py_INCREF(result); + } else { +#endif +#else + result = PyObject_GetItem(__pyx_d, name); + if (!result) { + PyErr_Clear(); +#endif + result = __Pyx_GetBuiltinName(name); + } + return result; +} + +/* PyObjectCall */ + #if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *result; + ternaryfunc call = func->ob_type->tp_call; + if (unlikely(!call)) + return PyObject_Call(func, arg, kw); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = (*call)(func, arg, kw); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +/* MemviewSliceInit */ + static int +__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, + int ndim, + __Pyx_memviewslice *memviewslice, + int memview_is_new_reference) +{ + __Pyx_RefNannyDeclarations + int i, retval=-1; + Py_buffer *buf = &memview->view; + __Pyx_RefNannySetupContext("init_memviewslice", 0); + if (!buf) { + PyErr_SetString(PyExc_ValueError, + "buf is NULL."); + goto fail; + } else if (memviewslice->memview || memviewslice->data) { + PyErr_SetString(PyExc_ValueError, + "memviewslice is already initialized!"); + goto fail; + } + if (buf->strides) { + for (i = 0; i < ndim; i++) { + memviewslice->strides[i] = buf->strides[i]; + } + } else { + Py_ssize_t stride = buf->itemsize; + for (i = ndim - 1; i >= 0; i--) { + memviewslice->strides[i] = stride; + stride *= buf->shape[i]; + } + } + for (i = 0; i < ndim; i++) { + memviewslice->shape[i] = buf->shape[i]; + if (buf->suboffsets) { + memviewslice->suboffsets[i] = buf->suboffsets[i]; + } else { + memviewslice->suboffsets[i] = -1; + } + } + memviewslice->memview = memview; + memviewslice->data = (char *)buf->buf; + if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { + Py_INCREF(memview); + } + retval = 0; + goto no_fail; +fail: + memviewslice->memview = 0; + memviewslice->data = 0; + retval = -1; +no_fail: + __Pyx_RefNannyFinishContext(); + return retval; +} +#ifndef Py_NO_RETURN +#define Py_NO_RETURN +#endif +static void __pyx_fatalerror(const char *fmt, ...) Py_NO_RETURN { + va_list vargs; + char msg[200]; +#ifdef HAVE_STDARG_PROTOTYPES + va_start(vargs, fmt); +#else + va_start(vargs); +#endif + vsnprintf(msg, 200, fmt, vargs); + va_end(vargs); + Py_FatalError(msg); +} +static CYTHON_INLINE int +__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock) +{ + int result; + PyThread_acquire_lock(lock, 1); + result = (*acquisition_count)++; + PyThread_release_lock(lock); + return result; +} +static CYTHON_INLINE int +__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock) +{ + int result; + PyThread_acquire_lock(lock, 1); + result = (*acquisition_count)--; + PyThread_release_lock(lock); + return result; +} +static CYTHON_INLINE void +__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) +{ + int first_time; + struct __pyx_memoryview_obj *memview = memslice->memview; + if (!memview || (PyObject *) memview == Py_None) + return; + if (__pyx_get_slice_count(memview) < 0) + __pyx_fatalerror("Acquisition count is %d (line %d)", + __pyx_get_slice_count(memview), lineno); + first_time = __pyx_add_acquisition_count(memview) == 0; + if (first_time) { + if (have_gil) { + Py_INCREF((PyObject *) memview); + } else { + PyGILState_STATE _gilstate = PyGILState_Ensure(); + Py_INCREF((PyObject *) memview); + PyGILState_Release(_gilstate); + } + } +} +static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, + int have_gil, int lineno) { + int last_time; + struct __pyx_memoryview_obj *memview = memslice->memview; + if (!memview ) { + return; + } else if ((PyObject *) memview == Py_None) { + memslice->memview = NULL; + return; + } + if (__pyx_get_slice_count(memview) <= 0) + __pyx_fatalerror("Acquisition count is %d (line %d)", + __pyx_get_slice_count(memview), lineno); + last_time = __pyx_sub_acquisition_count(memview) == 1; + memslice->data = NULL; + if (last_time) { + if (have_gil) { + Py_CLEAR(memslice->memview); + } else { + PyGILState_STATE _gilstate = PyGILState_Ensure(); + Py_CLEAR(memslice->memview); + PyGILState_Release(_gilstate); + } + } else { + memslice->memview = NULL; + } +} + +/* PyCFunctionFastCall */ + #if CYTHON_FAST_PYCCALL +static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) { + PyCFunctionObject *func = (PyCFunctionObject*)func_obj; + PyCFunction meth = PyCFunction_GET_FUNCTION(func); + PyObject *self = PyCFunction_GET_SELF(func); + int flags = PyCFunction_GET_FLAGS(func); + assert(PyCFunction_Check(func)); + assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS))); + assert(nargs >= 0); + assert(nargs == 0 || args != NULL); + /* _PyCFunction_FastCallDict() must not be called with an exception set, + because it may clear it (directly or indirectly) and so the + caller loses its exception */ + assert(!PyErr_Occurred()); + if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) { + return (*((__Pyx_PyCFunctionFastWithKeywords)meth)) (self, args, nargs, NULL); + } else { + return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs); + } +} +#endif + +/* PyFunctionFastCall */ + #if CYTHON_FAST_PYCALL +#include "frameobject.h" +static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na, + PyObject *globals) { + PyFrameObject *f; + PyThreadState *tstate = __Pyx_PyThreadState_Current; + PyObject **fastlocals; + Py_ssize_t i; + PyObject *result; + assert(globals != NULL); + /* XXX Perhaps we should create a specialized + PyFrame_New() that doesn't take locals, but does + take builtins without sanity checking them. + */ + assert(tstate != NULL); + f = PyFrame_New(tstate, co, globals, NULL); + if (f == NULL) { + return NULL; + } + fastlocals = f->f_localsplus; + for (i = 0; i < na; i++) { + Py_INCREF(*args); + fastlocals[i] = *args++; + } + result = PyEval_EvalFrameEx(f,0); + ++tstate->recursion_depth; + Py_DECREF(f); + --tstate->recursion_depth; + return result; +} +#if 1 || PY_VERSION_HEX < 0x030600B1 +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs) { + PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); + PyObject *globals = PyFunction_GET_GLOBALS(func); + PyObject *argdefs = PyFunction_GET_DEFAULTS(func); + PyObject *closure; +#if PY_MAJOR_VERSION >= 3 + PyObject *kwdefs; +#endif + PyObject *kwtuple, **k; + PyObject **d; + Py_ssize_t nd; + Py_ssize_t nk; + PyObject *result; + assert(kwargs == NULL || PyDict_Check(kwargs)); + nk = kwargs ? PyDict_Size(kwargs) : 0; + if (Py_EnterRecursiveCall((char*)" while calling a Python object")) { + return NULL; + } + if ( +#if PY_MAJOR_VERSION >= 3 + co->co_kwonlyargcount == 0 && +#endif + likely(kwargs == NULL || nk == 0) && + co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { + if (argdefs == NULL && co->co_argcount == nargs) { + result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); + goto done; + } + else if (nargs == 0 && argdefs != NULL + && co->co_argcount == Py_SIZE(argdefs)) { + /* function called with no arguments, but all parameters have + a default value: use default values as arguments .*/ + args = &PyTuple_GET_ITEM(argdefs, 0); + result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); + goto done; + } + } + if (kwargs != NULL) { + Py_ssize_t pos, i; + kwtuple = PyTuple_New(2 * nk); + if (kwtuple == NULL) { + result = NULL; + goto done; + } + k = &PyTuple_GET_ITEM(kwtuple, 0); + pos = i = 0; + while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { + Py_INCREF(k[i]); + Py_INCREF(k[i+1]); + i += 2; + } + nk = i / 2; + } + else { + kwtuple = NULL; + k = NULL; + } + closure = PyFunction_GET_CLOSURE(func); +#if PY_MAJOR_VERSION >= 3 + kwdefs = PyFunction_GET_KW_DEFAULTS(func); +#endif + if (argdefs != NULL) { + d = &PyTuple_GET_ITEM(argdefs, 0); + nd = Py_SIZE(argdefs); + } + else { + d = NULL; + nd = 0; + } +#if PY_MAJOR_VERSION >= 3 + result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, + args, nargs, + k, (int)nk, + d, (int)nd, kwdefs, closure); +#else + result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, + args, nargs, + k, (int)nk, + d, (int)nd, closure); +#endif + Py_XDECREF(kwtuple); +done: + Py_LeaveRecursiveCall(); + return result; +} +#endif +#endif + +/* PyObjectCallMethO */ + #if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = PyCFunction_GET_FUNCTION(func); + self = PyCFunction_GET_SELF(func); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +/* PyObjectCallOneArg */ + #if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#if CYTHON_FAST_PYCALL + if (PyFunction_Check(func)) { + return __Pyx_PyFunction_FastCall(func, &arg, 1); + } +#endif + if (likely(PyCFunction_Check(func))) { + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); +#if CYTHON_FAST_PYCCALL + } else if (PyCFunction_GET_FLAGS(func) & METH_FASTCALL) { + return __Pyx_PyCFunction_FastCall(func, &arg, 1); +#endif + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_Pack(1, arg); + if (unlikely(!args)) return NULL; + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +#endif + +/* PyErrFetchRestore */ + #if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +} +static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +} +#endif + +/* WriteUnraisableException */ + static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, + CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, + int full_traceback, CYTHON_UNUSED int nogil) { + PyObject *old_exc, *old_val, *old_tb; + PyObject *ctx; + __Pyx_PyThreadState_declare +#ifdef WITH_THREAD + PyGILState_STATE state; + if (nogil) + state = PyGILState_Ensure(); +#ifdef _MSC_VER + else state = (PyGILState_STATE)-1; +#endif +#endif + __Pyx_PyThreadState_assign + __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); + if (full_traceback) { + Py_XINCREF(old_exc); + Py_XINCREF(old_val); + Py_XINCREF(old_tb); + __Pyx_ErrRestore(old_exc, old_val, old_tb); + PyErr_PrintEx(1); + } + #if PY_MAJOR_VERSION < 3 + ctx = PyString_FromString(name); + #else + ctx = PyUnicode_FromString(name); + #endif + __Pyx_ErrRestore(old_exc, old_val, old_tb); + if (!ctx) { + PyErr_WriteUnraisable(Py_None); + } else { + PyErr_WriteUnraisable(ctx); + Py_DECREF(ctx); + } +#ifdef WITH_THREAD + if (nogil) + PyGILState_Release(state); +#endif +} + +/* RaiseDoubleKeywords */ + static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +/* ParseKeywords */ + static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; +} + +/* RaiseArgTupleInvalid */ + static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +/* SliceObject */ + static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj, + Py_ssize_t cstart, Py_ssize_t cstop, + PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, + int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { +#if CYTHON_USE_TYPE_SLOTS + PyMappingMethods* mp; +#if PY_MAJOR_VERSION < 3 + PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence; + if (likely(ms && ms->sq_slice)) { + if (!has_cstart) { + if (_py_start && (*_py_start != Py_None)) { + cstart = __Pyx_PyIndex_AsSsize_t(*_py_start); + if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; + } else + cstart = 0; + } + if (!has_cstop) { + if (_py_stop && (*_py_stop != Py_None)) { + cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop); + if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; + } else + cstop = PY_SSIZE_T_MAX; + } + if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) { + Py_ssize_t l = ms->sq_length(obj); + if (likely(l >= 0)) { + if (cstop < 0) { + cstop += l; + if (cstop < 0) cstop = 0; + } + if (cstart < 0) { + cstart += l; + if (cstart < 0) cstart = 0; + } + } else { + if (!PyErr_ExceptionMatches(PyExc_OverflowError)) + goto bad; + PyErr_Clear(); + } + } + return ms->sq_slice(obj, cstart, cstop); + } +#endif + mp = Py_TYPE(obj)->tp_as_mapping; + if (likely(mp && mp->mp_subscript)) +#endif + { + PyObject* result; + PyObject *py_slice, *py_start, *py_stop; + if (_py_slice) { + py_slice = *_py_slice; + } else { + PyObject* owned_start = NULL; + PyObject* owned_stop = NULL; + if (_py_start) { + py_start = *_py_start; + } else { + if (has_cstart) { + owned_start = py_start = PyInt_FromSsize_t(cstart); + if (unlikely(!py_start)) goto bad; + } else + py_start = Py_None; + } + if (_py_stop) { + py_stop = *_py_stop; + } else { + if (has_cstop) { + owned_stop = py_stop = PyInt_FromSsize_t(cstop); + if (unlikely(!py_stop)) { + Py_XDECREF(owned_start); + goto bad; + } + } else + py_stop = Py_None; + } + py_slice = PySlice_New(py_start, py_stop, Py_None); + Py_XDECREF(owned_start); + Py_XDECREF(owned_stop); + if (unlikely(!py_slice)) goto bad; + } +#if CYTHON_USE_TYPE_SLOTS + result = mp->mp_subscript(obj, py_slice); +#else + result = PyObject_GetItem(obj, py_slice); +#endif + if (!_py_slice) { + Py_DECREF(py_slice); + } + return result; + } + PyErr_Format(PyExc_TypeError, + "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name); +bad: + return NULL; +} + +/* GetItemInt */ + static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { + PyObject *r; + if (!j) return NULL; + r = PyObject_GetItem(o, j); + Py_DECREF(j); + return r; +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyList_GET_SIZE(o); + } + if ((!boundscheck) || likely((0 <= wrapped_i) & (wrapped_i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, wrapped_i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyTuple_GET_SIZE(o); + } + if ((!boundscheck) || likely((0 <= wrapped_i) & (wrapped_i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS + if (is_list || PyList_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); + if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) { + PyObject *r = PyList_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } + else if (PyTuple_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } else { + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_item)) { + if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (likely(l >= 0)) { + i += l; + } else { + if (!PyErr_ExceptionMatches(PyExc_OverflowError)) + return NULL; + PyErr_Clear(); + } + } + return m->sq_item(o, i); + } + } +#else + if (is_list || PySequence_Check(o)) { + return PySequence_GetItem(o, i); + } +#endif + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +} + +/* RaiseException */ + #if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + __Pyx_PyThreadState_declare + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_PyThreadState_assign + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + int is_subclass = PyObject_IsSubclass(instance_class, type); + if (!is_subclass) { + instance_class = NULL; + } else if (unlikely(is_subclass == -1)) { + goto bad; + } else { + type = instance_class; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } + if (cause) { + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { +#if CYTHON_COMPILING_IN_PYPY + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); + Py_INCREF(tb); + PyErr_Restore(tmp_type, tmp_value, tb); + Py_XDECREF(tmp_tb); +#else + PyThreadState *tstate = __Pyx_PyThreadState_Current; + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } +#endif + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +/* Import */ + static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_MAJOR_VERSION < 3 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_MAJOR_VERSION < 3 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + +/* ImportFrom */ + static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { + PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); + if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { + PyErr_Format(PyExc_ImportError, + #if PY_MAJOR_VERSION < 3 + "cannot import name %.230s", PyString_AS_STRING(name)); + #else + "cannot import name %S", name); + #endif + } + return value; +} + +/* PyObjectCallNoArg */ + #if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { +#if CYTHON_FAST_PYCALL + if (PyFunction_Check(func)) { + return __Pyx_PyFunction_FastCall(func, NULL, 0); + } +#endif +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || __Pyx_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) { + return __Pyx_PyObject_CallMethO(func, NULL); + } + } + return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL); +} +#endif + +/* SaveResetException */ + #if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + #if PY_VERSION_HEX >= 0x030700A3 + *type = tstate->exc_state.exc_type; + *value = tstate->exc_state.exc_value; + *tb = tstate->exc_state.exc_traceback; + #else + *type = tstate->exc_type; + *value = tstate->exc_value; + *tb = tstate->exc_traceback; + #endif + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); +} +static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + #if PY_VERSION_HEX >= 0x030700A3 + tmp_type = tstate->exc_state.exc_type; + tmp_value = tstate->exc_state.exc_value; + tmp_tb = tstate->exc_state.exc_traceback; + tstate->exc_state.exc_type = type; + tstate->exc_state.exc_value = value; + tstate->exc_state.exc_traceback = tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = type; + tstate->exc_value = value; + tstate->exc_traceback = tb; + #endif + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +} +#endif + +/* FastTypeChecks */ + #if CYTHON_COMPILING_IN_CPYTHON +static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { + while (a) { + a = a->tp_base; + if (a == b) + return 1; + } + return b == &PyBaseObject_Type; +} +static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { + PyObject *mro; + if (a == b) return 1; + mro = a->tp_mro; + if (likely(mro)) { + Py_ssize_t i, n; + n = PyTuple_GET_SIZE(mro); + for (i = 0; i < n; i++) { + if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) + return 1; + } + return 0; + } + return __Pyx_InBases(a, b); +} +#if PY_MAJOR_VERSION == 2 +static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { + PyObject *exception, *value, *tb; + int res; + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ErrFetch(&exception, &value, &tb); + res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; + if (unlikely(res == -1)) { + PyErr_WriteUnraisable(err); + res = 0; + } + if (!res) { + res = PyObject_IsSubclass(err, exc_type2); + if (unlikely(res == -1)) { + PyErr_WriteUnraisable(err); + res = 0; + } + } + __Pyx_ErrRestore(exception, value, tb); + return res; +} +#else +static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { + int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; + if (!res) { + res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); + } + return res; +} +#endif +static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + assert(PyExceptionClass_Check(exc_type)); + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; icurexc_type; + local_value = tstate->curexc_value; + local_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif + PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_FAST_THREAD_STATE + if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif + goto bad; + #if PY_MAJOR_VERSION >= 3 + if (local_tb) { + if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) + goto bad; + } + #endif + Py_XINCREF(local_tb); + Py_XINCREF(local_type); + Py_XINCREF(local_value); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_FAST_THREAD_STATE + #if PY_VERSION_HEX >= 0x030700A3 + tmp_type = tstate->exc_state.exc_type; + tmp_value = tstate->exc_state.exc_value; + tmp_tb = tstate->exc_state.exc_traceback; + tstate->exc_state.exc_type = local_type; + tstate->exc_state.exc_value = local_value; + tstate->exc_state.exc_traceback = local_tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = local_type; + tstate->exc_value = local_value; + tstate->exc_traceback = local_tb; + #endif + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif + return 0; +bad: + *type = 0; + *value = 0; + *tb = 0; + Py_XDECREF(local_type); + Py_XDECREF(local_value); + Py_XDECREF(local_tb); + return -1; +} + +/* PyObjectSetAttrStr */ + #if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_setattro)) + return tp->tp_setattro(obj, attr_name, value); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_setattr)) + return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value); +#endif + return PyObject_SetAttr(obj, attr_name, value); +} +#endif + +/* DictGetItem */ + #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { + PyObject *value; + value = PyDict_GetItemWithError(d, key); + if (unlikely(!value)) { + if (!PyErr_Occurred()) { + PyObject* args = PyTuple_Pack(1, key); + if (likely(args)) + PyErr_SetObject(PyExc_KeyError, args); + Py_XDECREF(args); + } + return NULL; + } + Py_INCREF(value); + return value; +} +#endif + +/* RaiseTooManyValuesToUnpack */ + static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +/* RaiseNeedMoreValuesToUnpack */ + static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +/* RaiseNoneIterError */ + static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +/* ExtTypeTest */ + static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(__Pyx_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + +/* PyErrExceptionMatches */ + #if CYTHON_FAST_THREAD_STATE +static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; icurexc_type; + if (exc_type == err) return 1; + if (unlikely(!exc_type)) return 0; + if (unlikely(PyTuple_Check(err))) + return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); + return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); +} +#endif + +/* ArgTypeTest */ + static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) +{ + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + else if (exact) { + #if PY_MAJOR_VERSION == 2 + if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; + #endif + } + else { + if (likely(__Pyx_TypeCheck(obj, type))) return 1; + } + PyErr_Format(PyExc_TypeError, + "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", + name, type->tp_name, Py_TYPE(obj)->tp_name); + return 0; +} + +/* BytesEquals */ + static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else + if (s1 == s2) { + return (equals == Py_EQ); + } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { + const char *ps1, *ps2; + Py_ssize_t length = PyBytes_GET_SIZE(s1); + if (length != PyBytes_GET_SIZE(s2)) + return (equals == Py_NE); + ps1 = PyBytes_AS_STRING(s1); + ps2 = PyBytes_AS_STRING(s2); + if (ps1[0] != ps2[0]) { + return (equals == Py_NE); + } else if (length == 1) { + return (equals == Py_EQ); + } else { + int result; +#if CYTHON_USE_UNICODE_INTERNALS + Py_hash_t hash1, hash2; + hash1 = ((PyBytesObject*)s1)->ob_shash; + hash2 = ((PyBytesObject*)s2)->ob_shash; + if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { + return (equals == Py_NE); + } +#endif + result = memcmp(ps1, ps2, (size_t)length); + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { + return (equals == Py_NE); + } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { + return (equals == Py_NE); + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +#endif +} + +/* UnicodeEquals */ + static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else +#if PY_MAJOR_VERSION < 3 + PyObject* owned_ref = NULL; +#endif + int s1_is_unicode, s2_is_unicode; + if (s1 == s2) { + goto return_eq; + } + s1_is_unicode = PyUnicode_CheckExact(s1); + s2_is_unicode = PyUnicode_CheckExact(s2); +#if PY_MAJOR_VERSION < 3 + if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { + owned_ref = PyUnicode_FromObject(s2); + if (unlikely(!owned_ref)) + return -1; + s2 = owned_ref; + s2_is_unicode = 1; + } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { + owned_ref = PyUnicode_FromObject(s1); + if (unlikely(!owned_ref)) + return -1; + s1 = owned_ref; + s1_is_unicode = 1; + } else if (((!s2_is_unicode) & (!s1_is_unicode))) { + return __Pyx_PyBytes_Equals(s1, s2, equals); + } +#endif + if (s1_is_unicode & s2_is_unicode) { + Py_ssize_t length; + int kind; + void *data1, *data2; + if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) + return -1; + length = __Pyx_PyUnicode_GET_LENGTH(s1); + if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { + goto return_ne; + } +#if CYTHON_USE_UNICODE_INTERNALS + { + Py_hash_t hash1, hash2; + #if CYTHON_PEP393_ENABLED + hash1 = ((PyASCIIObject*)s1)->hash; + hash2 = ((PyASCIIObject*)s2)->hash; + #else + hash1 = ((PyUnicodeObject*)s1)->hash; + hash2 = ((PyUnicodeObject*)s2)->hash; + #endif + if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { + goto return_ne; + } + } +#endif + kind = __Pyx_PyUnicode_KIND(s1); + if (kind != __Pyx_PyUnicode_KIND(s2)) { + goto return_ne; + } + data1 = __Pyx_PyUnicode_DATA(s1); + data2 = __Pyx_PyUnicode_DATA(s2); + if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { + goto return_ne; + } else if (length == 1) { + goto return_eq; + } else { + int result = memcmp(data1, data2, (size_t)(length * kind)); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & s2_is_unicode) { + goto return_ne; + } else if ((s2 == Py_None) & s1_is_unicode) { + goto return_ne; + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +return_eq: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ); +return_ne: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_NE); +#endif +} + +/* None */ + static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { + Py_ssize_t q = a / b; + Py_ssize_t r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} + +/* GetAttr */ + static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { +#if CYTHON_USE_TYPE_SLOTS +#if PY_MAJOR_VERSION >= 3 + if (likely(PyUnicode_Check(n))) +#else + if (likely(PyString_Check(n))) +#endif + return __Pyx_PyObject_GetAttrStr(o, n); +#endif + return PyObject_GetAttr(o, n); +} + +/* ObjectGetItem */ + #if CYTHON_USE_TYPE_SLOTS +static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { + PyObject *runerr; + Py_ssize_t key_value; + PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; + if (unlikely(!(m && m->sq_item))) { + PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); + return NULL; + } + key_value = __Pyx_PyIndex_AsSsize_t(index); + if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { + return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); + } + if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { + PyErr_Clear(); + PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); + } + return NULL; +} +static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { + PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; + if (likely(m && m->mp_subscript)) { + return m->mp_subscript(obj, key); + } + return __Pyx_PyObject_GetIndex(obj, key); +} +#endif + +/* decode_c_string */ + static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { + Py_ssize_t length; + if (unlikely((start < 0) | (stop < 0))) { + size_t slen = strlen(cstring); + if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { + PyErr_SetString(PyExc_OverflowError, + "c-string too long to convert to Python"); + return NULL; + } + length = (Py_ssize_t) slen; + if (start < 0) { + start += length; + if (start < 0) + start = 0; + } + if (stop < 0) + stop += length; + } + length = stop - start; + if (unlikely(length <= 0)) + return PyUnicode_FromUnicode(NULL, 0); + cstring += start; + if (decode_func) { + return decode_func(cstring, length, errors); + } else { + return PyUnicode_Decode(cstring, length, encoding, errors); + } +} + +/* GetAttr3 */ + static PyObject *__Pyx_GetAttr3Default(PyObject *d) { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) + return NULL; + __Pyx_PyErr_Clear(); + Py_INCREF(d); + return d; +} +static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { + PyObject *r = __Pyx_GetAttr(o, n); + return (likely(r)) ? r : __Pyx_GetAttr3Default(d); +} + +/* SwapException */ + #if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + #if PY_VERSION_HEX >= 0x030700A3 + tmp_type = tstate->exc_state.exc_type; + tmp_value = tstate->exc_state.exc_value; + tmp_tb = tstate->exc_state.exc_traceback; + tstate->exc_state.exc_type = *type; + tstate->exc_state.exc_value = *value; + tstate->exc_state.exc_traceback = *tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = *type; + tstate->exc_value = *value; + tstate->exc_traceback = *tb; + #endif + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} +#else +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); + PyErr_SetExcInfo(*type, *value, *tb); + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} +#endif + +/* PyIntBinop */ + #if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { + #if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(op1))) { + const long b = intval; + long x; + long a = PyInt_AS_LONG(op1); + x = (long)((unsigned long)a + b); + if (likely((x^a) >= 0 || (x^b) >= 0)) + return PyInt_FromLong(x); + return PyLong_Type.tp_as_number->nb_add(op1, op2); + } + #endif + #if CYTHON_USE_PYLONG_INTERNALS + if (likely(PyLong_CheckExact(op1))) { + const long b = intval; + long a, x; +#ifdef HAVE_LONG_LONG + const PY_LONG_LONG llb = intval; + PY_LONG_LONG lla, llx; +#endif + const digit* digits = ((PyLongObject*)op1)->ob_digit; + const Py_ssize_t size = Py_SIZE(op1); + if (likely(__Pyx_sst_abs(size) <= 1)) { + a = likely(size) ? digits[0] : 0; + if (size == -1) a = -a; + } else { + switch (size) { + case -2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case 2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case -3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case 3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case -4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case 4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + default: return PyLong_Type.tp_as_number->nb_add(op1, op2); + } + } + x = a + b; + return PyLong_FromLong(x); +#ifdef HAVE_LONG_LONG + long_long: + llx = lla + llb; + return PyLong_FromLongLong(llx); +#endif + + + } + #endif + if (PyFloat_CheckExact(op1)) { + const long b = intval; + double a = PyFloat_AS_DOUBLE(op1); + double result; + PyFPE_START_PROTECT("add", return NULL) + result = ((double)a) + (double)b; + PyFPE_END_PROTECT(result) + return PyFloat_FromDouble(result); + } + return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); +} +#endif + +/* None */ + static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); +} + +/* None */ + static CYTHON_INLINE long __Pyx_div_long(long a, long b) { + long q = a / b; + long r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} + +/* HasAttr */ + static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { + PyObject *r; + if (unlikely(!__Pyx_PyBaseString_Check(n))) { + PyErr_SetString(PyExc_TypeError, + "hasattr(): attribute name must be string"); + return -1; + } + r = __Pyx_GetAttr(o, n); + if (unlikely(!r)) { + PyErr_Clear(); + return 0; + } else { + Py_DECREF(r); + return 1; + } +} + +/* PyObject_GenericGetAttrNoDict */ + #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { + PyErr_Format(PyExc_AttributeError, +#if PY_MAJOR_VERSION >= 3 + "'%.50s' object has no attribute '%U'", + tp->tp_name, attr_name); +#else + "'%.50s' object has no attribute '%.400s'", + tp->tp_name, PyString_AS_STRING(attr_name)); +#endif + return NULL; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { + PyObject *descr; + PyTypeObject *tp = Py_TYPE(obj); + if (unlikely(!PyString_Check(attr_name))) { + return PyObject_GenericGetAttr(obj, attr_name); + } + assert(!tp->tp_dictoffset); + descr = _PyType_Lookup(tp, attr_name); + if (unlikely(!descr)) { + return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); + } + Py_INCREF(descr); + #if PY_MAJOR_VERSION < 3 + if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) + #endif + { + descrgetfunc f = Py_TYPE(descr)->tp_descr_get; + if (unlikely(f)) { + PyObject *res = f(descr, obj, (PyObject *)tp); + Py_DECREF(descr); + return res; + } + } + return descr; +} +#endif + +/* PyObject_GenericGetAttr */ + #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { + if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { + return PyObject_GenericGetAttr(obj, attr_name); + } + return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); +} +#endif + +/* SetVTable */ + static int __Pyx_SetVtable(PyObject *dict, void *vtable) { +#if PY_VERSION_HEX >= 0x02070000 + PyObject *ob = PyCapsule_New(vtable, 0, 0); +#else + PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); +#endif + if (!ob) + goto bad; + if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) + goto bad; + Py_DECREF(ob); + return 0; +bad: + Py_XDECREF(ob); + return -1; +} + +/* SetupReduce */ + static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { + int ret; + PyObject *name_attr; + name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2); + if (likely(name_attr)) { + ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); + } else { + ret = -1; + } + if (unlikely(ret < 0)) { + PyErr_Clear(); + ret = 0; + } + Py_XDECREF(name_attr); + return ret; +} +static int __Pyx_setup_reduce(PyObject* type_obj) { + int ret = 0; + PyObject *object_reduce = NULL; + PyObject *object_reduce_ex = NULL; + PyObject *reduce = NULL; + PyObject *reduce_ex = NULL; + PyObject *reduce_cython = NULL; + PyObject *setstate = NULL; + PyObject *setstate_cython = NULL; +#if CYTHON_USE_PYTYPE_LOOKUP + if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto GOOD; +#else + if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto GOOD; +#endif +#if CYTHON_USE_PYTYPE_LOOKUP + object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; +#else + object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; +#endif + reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto BAD; + if (reduce_ex == object_reduce_ex) { +#if CYTHON_USE_PYTYPE_LOOKUP + object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; +#else + object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; +#endif + reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto BAD; + if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { + reduce_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_cython); if (unlikely(!reduce_cython)) goto BAD; + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto BAD; + setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); + if (!setstate) PyErr_Clear(); + if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { + setstate_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate_cython); if (unlikely(!setstate_cython)) goto BAD; + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto BAD; + } + PyType_Modified((PyTypeObject*)type_obj); + } + } + goto GOOD; +BAD: + if (!PyErr_Occurred()) + PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); + ret = -1; +GOOD: +#if !CYTHON_USE_PYTYPE_LOOKUP + Py_XDECREF(object_reduce); + Py_XDECREF(object_reduce_ex); +#endif + Py_XDECREF(reduce); + Py_XDECREF(reduce_ex); + Py_XDECREF(reduce_cython); + Py_XDECREF(setstate); + Py_XDECREF(setstate_cython); + return ret; +} + +/* CLineInTraceback */ + #ifndef CYTHON_CLINE_IN_TRACEBACK +static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { + PyObject *use_cline; + PyObject *ptype, *pvalue, *ptraceback; +#if CYTHON_COMPILING_IN_CPYTHON + PyObject **cython_runtime_dict; +#endif + if (unlikely(!__pyx_cython_runtime)) { + return c_line; + } + __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); +#if CYTHON_COMPILING_IN_CPYTHON + cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); + if (likely(cython_runtime_dict)) { + use_cline = __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback); + } else +#endif + { + PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); + if (use_cline_obj) { + use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; + Py_DECREF(use_cline_obj); + } else { + PyErr_Clear(); + use_cline = NULL; + } + } + if (!use_cline) { + c_line = 0; + PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); + } + else if (PyObject_Not(use_cline) != 0) { + c_line = 0; + } + __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); + return c_line; +} +#endif + +/* CodeObjectCache */ + static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = start + (end - start) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} + +/* AddTraceback */ + #include "compile.h" +#include "frameobject.h" +#include "traceback.h" +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + #if PY_MAJOR_VERSION < 3 + py_srcfile = PyString_FromString(filename); + #else + py_srcfile = PyUnicode_FromString(filename); + #endif + if (!py_srcfile) goto bad; + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #endif + } + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + #else + py_funcname = PyUnicode_FromString(funcname); + #endif + } + if (!py_funcname) goto bad; + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + PyThreadState *tstate = __Pyx_PyThreadState_Current; + if (c_line) { + c_line = __Pyx_CLineForTraceback(tstate, c_line); + } + py_code = __pyx_find_code_object(c_line ? -c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); + } + py_frame = PyFrame_New( + tstate, /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + __Pyx_PyFrame_SetLineNumber(py_frame, py_line); + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} + +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (__Pyx_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); + if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if ((0)) {} + else if (__Pyx_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); + view->obj = NULL; + Py_DECREF(obj); +} +#endif + + + /* MemviewSliceIsContig */ + static int +__pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim) +{ + int i, index, step, start; + Py_ssize_t itemsize = mvs.memview->view.itemsize; + if (order == 'F') { + step = 1; + start = 0; + } else { + step = -1; + start = ndim - 1; + } + for (i = 0; i < ndim; i++) { + index = start + step * i; + if (mvs.suboffsets[index] >= 0 || mvs.strides[index] != itemsize) + return 0; + itemsize *= mvs.shape[index]; + } + return 1; +} + +/* OverlappingSlices */ + static void +__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, + void **out_start, void **out_end, + int ndim, size_t itemsize) +{ + char *start, *end; + int i; + start = end = slice->data; + for (i = 0; i < ndim; i++) { + Py_ssize_t stride = slice->strides[i]; + Py_ssize_t extent = slice->shape[i]; + if (extent == 0) { + *out_start = *out_end = start; + return; + } else { + if (stride > 0) + end += stride * (extent - 1); + else + start += stride * (extent - 1); + } + } + *out_start = start; + *out_end = end + itemsize; +} +static int +__pyx_slices_overlap(__Pyx_memviewslice *slice1, + __Pyx_memviewslice *slice2, + int ndim, size_t itemsize) +{ + void *start1, *end1, *start2, *end2; + __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); + __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); + return (start1 < end2) && (start2 < end1); +} + +/* Capsule */ + static CYTHON_INLINE PyObject * +__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) +{ + PyObject *cobj; +#if PY_VERSION_HEX >= 0x02070000 + cobj = PyCapsule_New(p, sig, NULL); +#else + cobj = PyCObject_FromVoidPtr(p, NULL); +#endif + return cobj; +} + +/* IsLittleEndian */ + static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) +{ + union { + uint32_t u32; + uint8_t u8[4]; + } S; + S.u32 = 0x01020304; + return S.u8[0] == 4; +} + +/* BufferFormatCheck */ + static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type) { + stack[0].field = &ctx->root; + stack[0].parent_offset = 0; + ctx->root.type = type; + ctx->root.name = "buffer dtype"; + ctx->root.offset = 0; + ctx->head = stack; + ctx->head->field = &ctx->root; + ctx->fmt_offset = 0; + ctx->head->parent_offset = 0; + ctx->new_packmode = '@'; + ctx->enc_packmode = '@'; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->is_complex = 0; + ctx->is_valid_array = 0; + ctx->struct_alignment = 0; + while (type->typegroup == 'S') { + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = 0; + type = type->fields->type; + } +} +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; + } else { + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; + } + } + *ts = t; + return count; +} +static int __Pyx_BufFmt_ExpectNumber(const char **ts) { + int number = __Pyx_BufFmt_ParseNumber(ts); + if (number == -1) + PyErr_Format(PyExc_ValueError,\ + "Does not understand character buffer dtype format string ('%c')", **ts); + return number; +} +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + PyErr_Format(PyExc_ValueError, + "Unexpected format string character: '%c'", ch); +} +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'c': return "'char'"; + case 'b': return "'signed char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 's': case 'p': return "a string"; + case 0: return "end"; + default: return "unparseable format string"; + } +} +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; + } + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +/* These are for computing the padding at the end of the struct to align + on the first member of the struct. This will probably the same as above, + but we don't have any guarantees. + */ +typedef struct { short x; char c; } __Pyx_pad_short; +typedef struct { int x; char c; } __Pyx_pad_int; +typedef struct { long x; char c; } __Pyx_pad_long; +typedef struct { float x; char c; } __Pyx_pad_float; +typedef struct { double x; char c; } __Pyx_pad_double; +typedef struct { long double x; char c; } __Pyx_pad_longdouble; +typedef struct { void *x; char c; } __Pyx_pad_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); + case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); + case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': + return 'H'; + case 'b': case 'h': case 'i': + case 'l': case 'q': case 's': case 'p': + return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': + return 'U'; + case 'f': case 'd': case 'g': + return (is_complex ? 'C' : 'R'); + case 'O': + return 'O'; + case 'P': + return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; + } + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset, arraysize = 1; + if (ctx->enc_type == 0) return 0; + if (ctx->head->field->type->arraysize[0]) { + int i, ndim = 0; + if (ctx->enc_type == 's' || ctx->enc_type == 'p') { + ctx->is_valid_array = ctx->head->field->type->ndim == 1; + ndim = 1; + if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { + PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %zu", + ctx->head->field->type->arraysize[0], ctx->enc_count); + return -1; + } + } + if (!ctx->is_valid_array) { + PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", + ctx->head->field->type->ndim, ndim); + return -1; + } + for (i = 0; i < ctx->head->field->type->ndim; i++) { + arraysize *= ctx->head->field->type->arraysize[i]; + } + ctx->is_valid_array = 0; + ctx->enc_count = 1; + } + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + } + if (ctx->enc_packmode == '@') { + size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + size_t align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + if (ctx->struct_alignment == 0) + ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, + ctx->is_complex); + } + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + if ((type->typegroup == 'H' || group == 'H') && type->size == size) { + } else { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + } + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", + (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); + return -1; + } + ctx->fmt_offset += size; + if (arraysize) + ctx->fmt_offset += (arraysize - 1) * size; + --ctx->enc_count; + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + break; + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } + } + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} +static PyObject * +__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) +{ + const char *ts = *tsp; + int i = 0, number; + int ndim = ctx->head->field->type->ndim; +; + ++ts; + if (ctx->new_count != 1) { + PyErr_SetString(PyExc_ValueError, + "Cannot handle repeated arrays in format string"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + while (*ts && *ts != ')') { + switch (*ts) { + case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; + default: break; + } + number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) + return PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %d", + ctx->head->field->type->arraysize[i], number); + if (*ts != ',' && *ts != ')') + return PyErr_Format(PyExc_ValueError, + "Expected a comma in format string, got '%c'", *ts); + if (*ts == ',') ts++; + i++; + } + if (i != ndim) + return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", + ctx->head->field->type->ndim, i); + if (!*ts) { + PyErr_SetString(PyExc_ValueError, + "Unexpected end of format string, expected ')'"); + return NULL; + } + ctx->is_valid_array = 1; + ctx->new_count = 1; + *tsp = ++ts; + return Py_None; +} +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case '\r': + case '\n': + ++ts; + break; + case '<': + if (!__Pyx_Is_Little_Endian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_Is_Little_Endian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + ctx->new_packmode = *ts++; + break; + case 'T': + { + const char* ts_after_sub; + size_t i, struct_count = ctx->new_count; + size_t struct_alignment = ctx->struct_alignment; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + ctx->enc_count = 0; + ctx->struct_alignment = 0; + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + if (struct_alignment) ctx->struct_alignment = struct_alignment; + } + break; + case '}': + { + size_t alignment = ctx->struct_alignment; + ++ts; + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + if (alignment && ctx->fmt_offset % alignment) { + ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); + } + } + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->enc_packmode = ctx->new_packmode; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } + CYTHON_FALLTHROUGH; + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': case 'p': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex && + ctx->enc_packmode == ctx->new_packmode) { + ctx->enc_count += ctx->new_count; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; + } + CYTHON_FALLTHROUGH; + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + case ':': + ++ts; + while(*ts != ':') ++ts; + ++ts; + break; + case '(': + if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; + break; + default: + { + int number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + ctx->new_count = (size_t)number; + } + } + } +} + +/* TypeInfoCompare */ + static int +__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) +{ + int i; + if (!a || !b) + return 0; + if (a == b) + return 1; + if (a->size != b->size || a->typegroup != b->typegroup || + a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { + if (a->typegroup == 'H' || b->typegroup == 'H') { + return a->size == b->size; + } else { + return 0; + } + } + if (a->ndim) { + for (i = 0; i < a->ndim; i++) + if (a->arraysize[i] != b->arraysize[i]) + return 0; + } + if (a->typegroup == 'S') { + if (a->flags != b->flags) + return 0; + if (a->fields || b->fields) { + if (!(a->fields && b->fields)) + return 0; + for (i = 0; a->fields[i].type && b->fields[i].type; i++) { + __Pyx_StructField *field_a = a->fields + i; + __Pyx_StructField *field_b = b->fields + i; + if (field_a->offset != field_b->offset || + !__pyx_typeinfo_cmp(field_a->type, field_b->type)) + return 0; + } + return !a->fields[i].type && !b->fields[i].type; + } + } + return 1; +} + +/* MemviewSliceValidateAndInit */ + static int +__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) +{ + if (buf->shape[dim] <= 1) + return 1; + if (buf->strides) { + if (spec & __Pyx_MEMVIEW_CONTIG) { + if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { + if (buf->strides[dim] != sizeof(void *)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly contiguous " + "in dimension %d.", dim); + goto fail; + } + } else if (buf->strides[dim] != buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_FOLLOW) { + Py_ssize_t stride = buf->strides[dim]; + if (stride < 0) + stride = -stride; + if (stride < buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } + } + } else { + if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not contiguous in " + "dimension %d", dim); + goto fail; + } else if (spec & (__Pyx_MEMVIEW_PTR)) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not indirect in " + "dimension %d", dim); + goto fail; + } else if (buf->suboffsets) { + PyErr_SetString(PyExc_ValueError, + "Buffer exposes suboffsets but no strides"); + goto fail; + } + } + return 1; +fail: + return 0; +} +static int +__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) +{ + if (spec & __Pyx_MEMVIEW_DIRECT) { + if (buf->suboffsets && buf->suboffsets[dim] >= 0) { + PyErr_Format(PyExc_ValueError, + "Buffer not compatible with direct access " + "in dimension %d.", dim); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_PTR) { + if (!buf->suboffsets || (buf->suboffsets && buf->suboffsets[dim] < 0)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly accessible " + "in dimension %d.", dim); + goto fail; + } + } + return 1; +fail: + return 0; +} +static int +__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) +{ + int i; + if (c_or_f_flag & __Pyx_IS_F_CONTIG) { + Py_ssize_t stride = 1; + for (i = 0; i < ndim; i++) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) + { + PyErr_SetString(PyExc_ValueError, + "Buffer not fortran contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { + Py_ssize_t stride = 1; + for (i = ndim - 1; i >- 1; i--) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) { + PyErr_SetString(PyExc_ValueError, + "Buffer not C contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } + return 1; +fail: + return 0; +} +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj) +{ + struct __pyx_memoryview_obj *memview, *new_memview; + __Pyx_RefNannyDeclarations + Py_buffer *buf; + int i, spec = 0, retval = -1; + __Pyx_BufFmt_Context ctx; + int from_memoryview = __pyx_memoryview_check(original_obj); + __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); + if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) + original_obj)->typeinfo)) { + memview = (struct __pyx_memoryview_obj *) original_obj; + new_memview = NULL; + } else { + memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + original_obj, buf_flags, 0, dtype); + new_memview = memview; + if (unlikely(!memview)) + goto fail; + } + buf = &memview->view; + if (buf->ndim != ndim) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + ndim, buf->ndim); + goto fail; + } + if (new_memview) { + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned) buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " + "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", + buf->itemsize, + (buf->itemsize > 1) ? "s" : "", + dtype->name, + dtype->size, + (dtype->size > 1) ? "s" : ""); + goto fail; + } + for (i = 0; i < ndim; i++) { + spec = axes_specs[i]; + if (!__pyx_check_strides(buf, i, ndim, spec)) + goto fail; + if (!__pyx_check_suboffsets(buf, i, ndim, spec)) + goto fail; + } + if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, + new_memview != NULL) == -1)) { + goto fail; + } + retval = 0; + goto no_fail; +fail: + Py_XDECREF(new_memview); + retval = -1; +no_fail: + __Pyx_RefNannyFinishContext(); + return retval; +} + +/* ObjectToMemviewSlice */ + static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_int64_t(PyObject *obj, int writable_flag) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS_RO | writable_flag, 1, + &__Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_int64(npy_int64 value) { + const npy_int64 neg_one = (npy_int64) -1, const_zero = (npy_int64) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(npy_int64) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(npy_int64) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(npy_int64) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(npy_int64) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(npy_int64) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(npy_int64), + little, !is_unsigned); + } +} + +/* CIntFromPyVerify */ + #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) +#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) +#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ + {\ + func_type value = func_value;\ + if (sizeof(target_type) < sizeof(func_type)) {\ + if (unlikely(value != (func_type) (target_type) value)) {\ + func_type zero = 0;\ + if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ + return (target_type) -1;\ + if (is_unsigned && unlikely(value < zero))\ + goto raise_neg_overflow;\ + else\ + goto raise_overflow;\ + }\ + }\ + return (target_type) value;\ + } + +/* MemviewDtypeToObject */ + static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_5numpy_int64_t(const char *itemp) { + return (PyObject *) __Pyx_PyInt_From_npy_int64(*(__pyx_t_5numpy_int64_t *) itemp); +} +static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_int64_t(const char *itemp, PyObject *obj) { + __pyx_t_5numpy_int64_t value = __Pyx_PyInt_As_npy_int64(obj); + if ((value == ((npy_int64)-1)) && PyErr_Occurred()) + return 0; + *(__pyx_t_5numpy_int64_t *) itemp = value; + return 1; +} + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = (long) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + +/* MemviewDtypeToObject */ + static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp) { + return (PyObject *) PyFloat_FromDouble(*(float *) itemp); +} +static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj) { + float value = __pyx_PyFloat_AsFloat(obj); + if ((value == (float)-1) && PyErr_Occurred()) + return 0; + *(float *) itemp = value; + return 1; +} + +/* Declarations */ + #if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +/* Arithmetic */ + #if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + #if 1 + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + if (b.imag == 0) { + return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); + } else if (fabsf(b.real) >= fabsf(b.imag)) { + if (b.real == 0 && b.imag == 0) { + return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); + } else { + float r = b.imag / b.real; + float s = 1.0 / (b.real + b.imag * r); + return __pyx_t_float_complex_from_parts( + (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); + } + } else { + float r = b.real / b.imag; + float s = 1.0 / (b.imag + b.real * r); + return __pyx_t_float_complex_from_parts( + (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); + } + } + #else + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + if (b.imag == 0) { + return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); + } else { + float denom = b.real * b.real + b.imag * b.imag; + return __pyx_t_float_complex_from_parts( + (a.real * b.real + a.imag * b.imag) / denom, + (a.imag * b.real - a.real * b.imag) / denom); + } + } + #endif + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod_float(a, a); + return __Pyx_c_prod_float(a, a); + case 3: + z = __Pyx_c_prod_float(a, a); + return __Pyx_c_prod_float(z, a); + case 4: + z = __Pyx_c_prod_float(a, a); + return __Pyx_c_prod_float(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } else if (b.imag == 0) { + z.real = powf(a.real, b.real); + z.imag = 0; + return z; + } else if (a.real > 0) { + r = a.real; + theta = 0; + } else { + r = -a.real; + theta = atan2f(0, -1); + } + } else { + r = __Pyx_c_abs_float(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +/* Declarations */ + #if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +/* Arithmetic */ + #if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + #if 1 + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + if (b.imag == 0) { + return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } else if (fabs(b.real) >= fabs(b.imag)) { + if (b.real == 0 && b.imag == 0) { + return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); + } else { + double r = b.imag / b.real; + double s = 1.0 / (b.real + b.imag * r); + return __pyx_t_double_complex_from_parts( + (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); + } + } else { + double r = b.real / b.imag; + double s = 1.0 / (b.imag + b.real * r); + return __pyx_t_double_complex_from_parts( + (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); + } + } + #else + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + if (b.imag == 0) { + return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } else { + double denom = b.real * b.real + b.imag * b.imag; + return __pyx_t_double_complex_from_parts( + (a.real * b.real + a.imag * b.imag) / denom, + (a.imag * b.real - a.real * b.imag) / denom); + } + } + #endif + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod_double(a, a); + return __Pyx_c_prod_double(a, a); + case 3: + z = __Pyx_c_prod_double(a, a); + return __Pyx_c_prod_double(z, a); + case 4: + z = __Pyx_c_prod_double(a, a); + return __Pyx_c_prod_double(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } else if (b.imag == 0) { + z.real = pow(a.real, b.real); + z.imag = 0; + return z; + } else if (a.real > 0) { + r = a.real; + theta = 0; + } else { + r = -a.real; + theta = atan2(0, -1); + } + } else { + r = __Pyx_c_abs_double(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { + const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum NPY_TYPES) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(enum NPY_TYPES) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), + little, !is_unsigned); + } +} + +/* MemviewSliceCopyTemplate */ + static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object) +{ + __Pyx_RefNannyDeclarations + int i; + __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; + struct __pyx_memoryview_obj *from_memview = from_mvs->memview; + Py_buffer *buf = &from_memview->view; + PyObject *shape_tuple = NULL; + PyObject *temp_int = NULL; + struct __pyx_array_obj *array_obj = NULL; + struct __pyx_memoryview_obj *memview_obj = NULL; + __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); + for (i = 0; i < ndim; i++) { + if (from_mvs->suboffsets[i] >= 0) { + PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " + "indirect dimensions (axis %d)", i); + goto fail; + } + } + shape_tuple = PyTuple_New(ndim); + if (unlikely(!shape_tuple)) { + goto fail; + } + __Pyx_GOTREF(shape_tuple); + for(i = 0; i < ndim; i++) { + temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); + if(unlikely(!temp_int)) { + goto fail; + } else { + PyTuple_SET_ITEM(shape_tuple, i, temp_int); + temp_int = NULL; + } + } + array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); + if (unlikely(!array_obj)) { + goto fail; + } + __Pyx_GOTREF(array_obj); + memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + (PyObject *) array_obj, contig_flag, + dtype_is_object, + from_mvs->memview->typeinfo); + if (unlikely(!memview_obj)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) + goto fail; + if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, + dtype_is_object) < 0)) + goto fail; + goto no_fail; +fail: + __Pyx_XDECREF(new_mvs.memview); + new_mvs.memview = NULL; + new_mvs.data = NULL; +no_fail: + __Pyx_XDECREF(shape_tuple); + __Pyx_XDECREF(temp_int); + __Pyx_XDECREF(array_obj); + __Pyx_RefNannyFinishContext(); + return new_mvs; +} + +/* CIntFromPy */ + static CYTHON_INLINE npy_int64 __Pyx_PyInt_As_npy_int64(PyObject *x) { + const npy_int64 neg_one = (npy_int64) -1, const_zero = (npy_int64) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(npy_int64) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(npy_int64, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (npy_int64) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (npy_int64) 0; + case 1: __PYX_VERIFY_RETURN_INT(npy_int64, digit, digits[0]) + case 2: + if (8 * sizeof(npy_int64) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) >= 2 * PyLong_SHIFT) { + return (npy_int64) (((((npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(npy_int64) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) >= 3 * PyLong_SHIFT) { + return (npy_int64) (((((((npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(npy_int64) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) >= 4 * PyLong_SHIFT) { + return (npy_int64) (((((((((npy_int64)digits[3]) << PyLong_SHIFT) | (npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (npy_int64) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(npy_int64) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_int64, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(npy_int64) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_int64, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (npy_int64) 0; + case -1: __PYX_VERIFY_RETURN_INT(npy_int64, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(npy_int64, digit, +digits[0]) + case -2: + if (8 * sizeof(npy_int64) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 2 * PyLong_SHIFT) { + return (npy_int64) (((npy_int64)-1)*(((((npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(npy_int64) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 2 * PyLong_SHIFT) { + return (npy_int64) ((((((npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(npy_int64) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 3 * PyLong_SHIFT) { + return (npy_int64) (((npy_int64)-1)*(((((((npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(npy_int64) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 3 * PyLong_SHIFT) { + return (npy_int64) ((((((((npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(npy_int64) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 4 * PyLong_SHIFT) { + return (npy_int64) (((npy_int64)-1)*(((((((((npy_int64)digits[3]) << PyLong_SHIFT) | (npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(npy_int64) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 4 * PyLong_SHIFT) { + return (npy_int64) ((((((((((npy_int64)digits[3]) << PyLong_SHIFT) | (npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); + } + } + break; + } +#endif + if (sizeof(npy_int64) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_int64, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(npy_int64) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_int64, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + npy_int64 val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (npy_int64) -1; + } + } else { + npy_int64 val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (npy_int64) -1; + val = __Pyx_PyInt_As_npy_int64(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to npy_int64"); + return (npy_int64) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to npy_int64"); + return (npy_int64) -1; +} + +/* CIntFromPy */ + static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + case -2: + if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + } +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; + } + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +/* CIntFromPy */ + static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *x) { + const size_t neg_one = (size_t) -1, const_zero = (size_t) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(size_t) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(size_t, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (size_t) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (size_t) 0; + case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, digits[0]) + case 2: + if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) >= 2 * PyLong_SHIFT) { + return (size_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) >= 3 * PyLong_SHIFT) { + return (size_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) >= 4 * PyLong_SHIFT) { + return (size_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (size_t) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(size_t) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(size_t) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (size_t) 0; + case -1: __PYX_VERIFY_RETURN_INT(size_t, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, +digits[0]) + case -2: + if (8 * sizeof(size_t) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { + return (size_t) (((size_t)-1)*(((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { + return (size_t) ((((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { + return (size_t) (((size_t)-1)*(((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { + return (size_t) ((((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) { + return (size_t) (((size_t)-1)*(((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) { + return (size_t) ((((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + } +#endif + if (sizeof(size_t) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(size_t) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + size_t val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (size_t) -1; + } + } else { + size_t val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (size_t) -1; + val = __Pyx_PyInt_As_size_t(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to size_t"); + return (size_t) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to size_t"); + return (size_t) -1; +} + +/* CIntFromPy */ + static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = (long) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + case -2: + if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + } +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +/* CIntFromPy */ + static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { + const char neg_one = (char) -1, const_zero = (char) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(char) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (char) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (char) 0; + case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) + case 2: + if (8 * sizeof(char) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { + return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(char) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { + return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(char) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { + return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (char) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(char) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (char) 0; + case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) + case -2: + if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(char) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(char) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(char) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { + return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + } +#endif + if (sizeof(char) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + char val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (char) -1; + } + } else { + char val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (char) -1; + val = __Pyx_PyInt_As_char(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to char"); + return (char) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to char"); + return (char) -1; +} + +/* ObjectToMemviewSlice */ + static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_Py_ssize_t(PyObject *obj, int writable_flag) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS_RO | writable_flag, 1, + &__Pyx_TypeInfo_Py_ssize_t, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +/* ObjectToMemviewSlice */ + static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_float(PyObject *obj, int writable_flag) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS_RO | writable_flag, 1, + &__Pyx_TypeInfo_float, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +/* ObjectToMemviewSlice */ + static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_int(PyObject *obj, int writable_flag) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS_RO | writable_flag, 2, + &__Pyx_TypeInfo_int, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +/* ObjectToMemviewSlice */ + static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *obj, int writable_flag) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS_RO | writable_flag, 2, + &__Pyx_TypeInfo_float, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +/* ObjectToMemviewSlice */ + static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_nn___pyx_t_5numpy_int32_t(PyObject *obj, int writable_flag) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS_RO | writable_flag, 2, + &__Pyx_TypeInfo_nn___pyx_t_5numpy_int32_t, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +/* CheckBinaryVersion */ + static int __Pyx_check_binary_version(void) { + char ctversion[4], rtversion[4]; + PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); + if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + return PyErr_WarnEx(NULL, message, 1); + } + return 0; +} + +/* FunctionExport */ + static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig) { + PyObject *d = 0; + PyObject *cobj = 0; + union { + void (*fp)(void); + void *p; + } tmp; + d = PyObject_GetAttrString(__pyx_m, (char *)"__pyx_capi__"); + if (!d) { + PyErr_Clear(); + d = PyDict_New(); + if (!d) + goto bad; + Py_INCREF(d); + if (PyModule_AddObject(__pyx_m, (char *)"__pyx_capi__", d) < 0) + goto bad; + } + tmp.fp = f; +#if PY_VERSION_HEX >= 0x02070000 + cobj = PyCapsule_New(tmp.p, sig, 0); +#else + cobj = PyCObject_FromVoidPtrAndDesc(tmp.p, (void *)sig, 0); +#endif + if (!cobj) + goto bad; + if (PyDict_SetItemString(d, name, cobj) < 0) + goto bad; + Py_DECREF(cobj); + Py_DECREF(d); + return 0; +bad: + Py_XDECREF(cobj); + Py_XDECREF(d); + return -1; +} + +/* ModuleImport */ + #ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + +/* TypeImport */ + #ifndef __PYX_HAVE_RT_ImportType +#define __PYX_HAVE_RT_ImportType +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, + size_t size, int strict) +{ + PyObject *py_module = 0; + PyObject *result = 0; + PyObject *py_name = 0; + char warning[200]; + Py_ssize_t basicsize; +#ifdef Py_LIMITED_API + PyObject *py_basicsize; +#endif + py_module = __Pyx_ImportModule(module_name); + if (!py_module) + goto bad; + py_name = __Pyx_PyIdentifier_FromString(class_name); + if (!py_name) + goto bad; + result = PyObject_GetAttr(py_module, py_name); + Py_DECREF(py_name); + py_name = 0; + Py_DECREF(py_module); + py_module = 0; + if (!result) + goto bad; + if (!PyType_Check(result)) { + PyErr_Format(PyExc_TypeError, + "%.200s.%.200s is not a type object", + module_name, class_name); + goto bad; + } +#ifndef Py_LIMITED_API + basicsize = ((PyTypeObject *)result)->tp_basicsize; +#else + py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); + if (!py_basicsize) + goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; +#endif + if (!strict && (size_t)basicsize > size) { + PyOS_snprintf(warning, sizeof(warning), + "%s.%s size changed, may indicate binary incompatibility. Expected %zd, got %zd", + module_name, class_name, basicsize, size); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; + } + else if ((size_t)basicsize != size) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s has the wrong size, try recompiling. Expected %zd, got %zd", + module_name, class_name, basicsize, size); + goto bad; + } + return (PyTypeObject *)result; +bad: + Py_XDECREF(py_module); + Py_XDECREF(result); + return NULL; +} +#endif + +/* InitStrings */ + static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + if (t->is_unicode) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + #else + if (t->is_unicode | t->is_str) { + if (t->intern) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->encoding) { + *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); + } else { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + if (PyObject_Hash(*t->p) == -1) + return -1; + ++t; + } + return 0; +} + +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); +} +static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { + Py_ssize_t ignore; + return __Pyx_PyObject_AsStringAndSize(o, &ignore); +} +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +#if !CYTHON_PEP393_ENABLED +static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { + char* defenc_c; + PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); + if (!defenc) return NULL; + defenc_c = PyBytes_AS_STRING(defenc); +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + { + char* end = defenc_c + PyBytes_GET_SIZE(defenc); + char* c; + for (c = defenc_c; c < end; c++) { + if ((unsigned char) (*c) >= 128) { + PyUnicode_AsASCIIString(o); + return NULL; + } + } + } +#endif + *length = PyBytes_GET_SIZE(defenc); + return defenc_c; +} +#else +static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { + if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL; +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + if (likely(PyUnicode_IS_ASCII(o))) { + *length = PyUnicode_GET_LENGTH(o); + return PyUnicode_AsUTF8(o); + } else { + PyUnicode_AsASCIIString(o); + return NULL; + } +#else + return PyUnicode_AsUTF8AndSize(o, length); +#endif +} +#endif +#endif +static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT + if ( +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + __Pyx_sys_getdefaultencoding_not_ascii && +#endif + PyUnicode_Check(o)) { + return __Pyx_PyUnicode_AsStringAndSize(o, length); + } else +#endif +#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) + if (PyByteArray_Check(o)) { + *length = PyByteArray_GET_SIZE(o); + return PyByteArray_AS_STRING(o); + } else +#endif + { + char* result; + int r = PyBytes_AsStringAndSize(o, &result, length); + if (unlikely(r < 0)) { + return NULL; + } else { + return result; + } + } +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + int is_true = x == Py_True; + if (is_true | (x == Py_False) | (x == Py_None)) return is_true; + else return PyObject_IsTrue(x); +} +static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) { +#if PY_MAJOR_VERSION >= 3 + if (PyLong_Check(result)) { + if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, + "__int__ returned non-int (type %.200s). " + "The ability to return an instance of a strict subclass of int " + "is deprecated, and may be removed in a future version of Python.", + Py_TYPE(result)->tp_name)) { + Py_DECREF(result); + return NULL; + } + return result; + } +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type %.200s)", + type_name, type_name, Py_TYPE(result)->tp_name); + Py_DECREF(result); + return NULL; +} +static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { +#if CYTHON_USE_TYPE_SLOTS + PyNumberMethods *m; +#endif + const char *name = NULL; + PyObject *res = NULL; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x) || PyLong_Check(x))) +#else + if (likely(PyLong_Check(x))) +#endif + return __Pyx_NewRef(x); +#if CYTHON_USE_TYPE_SLOTS + m = Py_TYPE(x)->tp_as_number; + #if PY_MAJOR_VERSION < 3 + if (m && m->nb_int) { + name = "int"; + res = m->nb_int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = m->nb_long(x); + } + #else + if (likely(m && m->nb_int)) { + name = "int"; + res = m->nb_int(x); + } + #endif +#else + if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) { + res = PyNumber_Int(x); + } +#endif + if (likely(res)) { +#if PY_MAJOR_VERSION < 3 + if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) { +#else + if (unlikely(!PyLong_CheckExact(res))) { +#endif + return __Pyx_PyNumber_IntOrLongWrongResultType(res, name); + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject *x; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(b))) { + if (sizeof(Py_ssize_t) >= sizeof(long)) + return PyInt_AS_LONG(b); + else + return PyInt_AsSsize_t(x); + } +#endif + if (likely(PyLong_CheckExact(b))) { + #if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)b)->ob_digit; + const Py_ssize_t size = Py_SIZE(b); + if (likely(__Pyx_sst_abs(size) <= 1)) { + ival = likely(size) ? digits[0] : 0; + if (size == -1) ival = -ival; + return ival; + } else { + switch (size) { + case 2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + } + } + #endif + return PyLong_AsSsize_t(b); + } + x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) { + return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False); +} +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { + return PyInt_FromSize_t(ival); +} + + +#endif /* Py_PYTHON_H */ diff --git a/package/MDAnalysis/lib/c_distances.c b/package/MDAnalysis/lib/c_distances.c index bd1ee7124b7..2a2063cc501 100644 --- a/package/MDAnalysis/lib/c_distances.c +++ b/package/MDAnalysis/lib/c_distances.c @@ -1,11 +1,11 @@ -/* Generated by Cython 0.28.2 */ +/* Generated by Cython 0.28.5 */ /* BEGIN: Cython Metadata { "distutils": { "depends": [ - "/home/richard/miniconda2/envs/mda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h", - "/home/richard/miniconda2/envs/mda3/lib/python3.6/site-packages/numpy/core/include/numpy/ufuncobject.h", + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h", + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include/numpy/ufuncobject.h", "MDAnalysis/lib/include/calc_distances.h" ], "extra_compile_args": [ @@ -15,7 +15,7 @@ "-funroll-loops" ], "include_dirs": [ - "/home/richard/miniconda2/envs/mda3/lib/python3.6/site-packages/numpy/core/include", + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include", "MDAnalysis/lib/include" ], "libraries": [ @@ -37,7 +37,7 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) #error Cython requires Python 2.6+ or Python 3.3+. #else -#define CYTHON_ABI "0_28_2" +#define CYTHON_ABI "0_28_5" #define CYTHON_FUTURE_DIVISION 0 #include #ifndef offsetof @@ -483,6 +483,7 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact + #define PyObject_Unicode PyObject_Str #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) @@ -684,7 +685,7 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); #define __Pyx_PySequence_Tuple(obj)\ @@ -792,7 +793,7 @@ static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } static PyObject *__pyx_m = NULL; static PyObject *__pyx_d; static PyObject *__pyx_b; -static PyObject *__pyx_cython_runtime; +static PyObject *__pyx_cython_runtime = NULL; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static PyObject *__pyx_empty_unicode; @@ -939,7 +940,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -948,7 +949,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -957,7 +958,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -966,7 +967,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -975,7 +976,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -984,7 +985,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -993,7 +994,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -1002,7 +1003,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1011,7 +1012,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -1020,7 +1021,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1029,7 +1030,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -1038,7 +1039,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -1047,7 +1048,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -1056,7 +1057,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -1065,7 +1066,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -1074,7 +1075,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1083,7 +1084,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1092,7 +1093,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1101,7 +1102,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1110,7 +1111,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1119,7 +1120,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1158,7 +1159,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1167,7 +1168,7 @@ struct __pyx_memoryviewslice_obj; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1176,7 +1177,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1185,7 +1186,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -1414,6 +1415,9 @@ static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *nam /* None.proto */ static CYTHON_INLINE long __Pyx_div_long(long, long); +/* BufferIndexError.proto */ +static void __Pyx_RaiseBufferIndexError(int axis); + /* MemviewSliceInit.proto */ #define __Pyx_BUF_MAX_NDIMS %(BUF_MAX_NDIMS)d #define __Pyx_MEMVIEW_DIRECT 1 @@ -1827,6 +1831,36 @@ static int __pyx_slices_overlap(__Pyx_memviewslice *slice1, /* Capsule.proto */ static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); +/* IsLittleEndian.proto */ +static CYTHON_INLINE int __Pyx_Is_Little_Endian(void); + +/* BufferFormatCheck.proto */ +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); +static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type); + +/* TypeInfoCompare.proto */ +static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); + +/* MemviewSliceValidateAndInit.proto */ +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj); + +/* ObjectToMemviewSlice.proto */ +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *, int writable_flag); + +/* MemviewDtypeToObject.proto */ +static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp); +static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj); + /* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); @@ -1950,29 +1984,6 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); /* CIntFromPy.proto */ static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); -/* IsLittleEndian.proto */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void); - -/* BufferFormatCheck.proto */ -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type); - -/* TypeInfoCompare.proto */ -static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); - -/* MemviewSliceValidateAndInit.proto */ -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj); - /* ObjectToMemviewSlice.proto */ static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_float(PyObject *, int writable_flag); @@ -2404,7 +2415,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_4calc_distance_array_t static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_6calc_self_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_result); /* proto */ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_8calc_self_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_10calc_self_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_12coord_transform(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_12coord_transform(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_coords, __Pyx_memviewslice __pyx_v_box); /* proto */ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_14calc_bond_distance(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_results); /* proto */ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_16calc_bond_distance_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_18calc_bond_distance_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ @@ -3388,17 +3399,17 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_10calc_self_distance_a /* "MDAnalysis/lib/c_distances.pyx":128 * result.data, distnum) * - * def coord_transform(numpy.ndarray coords, # <<<<<<<<<<<<<< - * numpy.ndarray box): - * cdef int numcoords + * def coord_transform(float[:,:] coords, # <<<<<<<<<<<<<< + * float[:,:] box): + * cdef int numcoords, size */ /* Python wrapper */ static PyObject *__pyx_pw_10MDAnalysis_3lib_11c_distances_13coord_transform(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static PyMethodDef __pyx_mdef_10MDAnalysis_3lib_11c_distances_13coord_transform = {"coord_transform", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_11c_distances_13coord_transform, METH_VARARGS|METH_KEYWORDS, 0}; static PyObject *__pyx_pw_10MDAnalysis_3lib_11c_distances_13coord_transform(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { - PyArrayObject *__pyx_v_coords = 0; - PyArrayObject *__pyx_v_box = 0; + __Pyx_memviewslice __pyx_v_coords = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_memviewslice __pyx_v_box = { 0, 0, { 0 }, { 0 }, { 0 } }; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("coord_transform (wrapper)", 0); @@ -3437,8 +3448,8 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_11c_distances_13coord_transform(PyOb values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } - __pyx_v_coords = ((PyArrayObject *)values[0]); - __pyx_v_box = ((PyArrayObject *)values[1]); + __pyx_v_coords = __Pyx_PyObject_to_MemoryviewSlice_dsds_float(values[0], PyBUF_WRITABLE); 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/* function exit code */ @@ -3594,7 +3698,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_14calc_bond_distance(C __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("calc_bond_distance", 0); - /* "MDAnalysis/lib/c_distances.pyx":140 + /* "MDAnalysis/lib/c_distances.pyx":142 * numpy.ndarray results): * cdef int numcoords * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< @@ -3603,7 +3707,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_14calc_bond_distance(C */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); - /* "MDAnalysis/lib/c_distances.pyx":142 + /* "MDAnalysis/lib/c_distances.pyx":144 * numcoords = coords1.shape[0] * * _calc_bond_distance( coords1.data, coords2.data, # <<<<<<<<<<<<<< @@ -3612,8 +3716,8 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_14calc_bond_distance(C */ _calc_bond_distance(((coordinate *)__pyx_v_coords1->data), ((coordinate *)__pyx_v_coords2->data), __pyx_v_numcoords, ((double *)__pyx_v_results->data)); - /* "MDAnalysis/lib/c_distances.pyx":136 - * box.data) + /* "MDAnalysis/lib/c_distances.pyx":138 + * &box[0,0]) * * def calc_bond_distance(numpy.ndarray coords1, # <<<<<<<<<<<<<< * numpy.ndarray coords2, @@ -3627,7 +3731,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_14calc_bond_distance(C return __pyx_r; } -/* "MDAnalysis/lib/c_distances.pyx":146 +/* "MDAnalysis/lib/c_distances.pyx":148 * results.data) * * def calc_bond_distance_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< @@ -3673,23 +3777,23 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_11c_distances_17calc_bond_distance_o case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coords2)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("calc_bond_distance_ortho", 1, 4, 4, 1); __PYX_ERR(0, 146, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("calc_bond_distance_ortho", 1, 4, 4, 1); __PYX_ERR(0, 148, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_box)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("calc_bond_distance_ortho", 1, 4, 4, 2); __PYX_ERR(0, 146, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("calc_bond_distance_ortho", 1, 4, 4, 2); __PYX_ERR(0, 148, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 3: if (likely((values[3] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_results)) != 0)) kw_args--; 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- /* "MDAnalysis/lib/c_distances.pyx":146 + /* "MDAnalysis/lib/c_distances.pyx":148 * results.data) * * def calc_bond_distance_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< @@ -3766,7 +3870,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_16calc_bond_distance_o return __pyx_r; } -/* "MDAnalysis/lib/c_distances.pyx":158 +/* "MDAnalysis/lib/c_distances.pyx":160 * results.data) * * def calc_bond_distance_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< @@ -3812,23 +3916,23 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_11c_distances_19calc_bond_distance_t case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coords2)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("calc_bond_distance_triclinic", 1, 4, 4, 1); __PYX_ERR(0, 158, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("calc_bond_distance_triclinic", 1, 4, 4, 1); __PYX_ERR(0, 160, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_box)) != 0)) kw_args--; 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- /* "MDAnalysis/lib/c_distances.pyx":158 + /* "MDAnalysis/lib/c_distances.pyx":160 * results.data) * * def calc_bond_distance_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< @@ -3905,7 +4009,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_18calc_bond_distance_t return __pyx_r; } -/* "MDAnalysis/lib/c_distances.pyx":170 +/* "MDAnalysis/lib/c_distances.pyx":172 * results.data) * * def calc_angle(numpy.ndarray coords1, # <<<<<<<<<<<<<< @@ -3951,23 +4055,23 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_11c_distances_21calc_angle(PyObject case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coords2)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("calc_angle", 1, 4, 4, 1); __PYX_ERR(0, 170, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("calc_angle", 1, 4, 4, 1); __PYX_ERR(0, 172, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coords3)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("calc_angle", 1, 4, 4, 2); 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- /* "MDAnalysis/lib/c_distances.pyx":182 + /* "MDAnalysis/lib/c_distances.pyx":184 * results.data) * * def calc_angle_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< @@ -4195,7 +4299,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_22calc_angle_ortho(CYT return __pyx_r; } -/* "MDAnalysis/lib/c_distances.pyx":196 +/* "MDAnalysis/lib/c_distances.pyx":198 * results.data) * * def calc_angle_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< @@ -4244,29 +4348,29 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_11c_distances_25calc_angle_triclinic case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coords2)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("calc_angle_triclinic", 1, 5, 5, 1); __PYX_ERR(0, 196, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("calc_angle_triclinic", 1, 5, 5, 1); __PYX_ERR(0, 198, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coords3)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("calc_angle_triclinic", 1, 5, 5, 2); 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/* function exit code */ @@ -4313,7 +4417,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_24calc_angle_triclinic __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("calc_angle_triclinic", 0); - /* "MDAnalysis/lib/c_distances.pyx":202 + /* "MDAnalysis/lib/c_distances.pyx":204 * numpy.ndarray results): * cdef int numcoords * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< @@ -4322,7 +4426,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_24calc_angle_triclinic */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); - /* "MDAnalysis/lib/c_distances.pyx":204 + /* "MDAnalysis/lib/c_distances.pyx":206 * numcoords = coords1.shape[0] * * _calc_angle_triclinic( coords1.data, coords2.data, # <<<<<<<<<<<<<< @@ -4331,7 +4435,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_24calc_angle_triclinic */ _calc_angle_triclinic(((coordinate *)__pyx_v_coords1->data), ((coordinate *)__pyx_v_coords2->data), ((coordinate *)__pyx_v_coords3->data), __pyx_v_numcoords, ((coordinate *)__pyx_v_box->data), ((double *)__pyx_v_results->data)); - /* "MDAnalysis/lib/c_distances.pyx":196 + /* "MDAnalysis/lib/c_distances.pyx":198 * results.data) * * def calc_angle_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< @@ -4346,7 +4450,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_24calc_angle_triclinic return __pyx_r; } -/* "MDAnalysis/lib/c_distances.pyx":210 +/* "MDAnalysis/lib/c_distances.pyx":212 * results.data) * * def calc_dihedral(numpy.ndarray coords1, # <<<<<<<<<<<<<< @@ -4395,29 +4499,29 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_11c_distances_27calc_dihedral(PyObje case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coords2)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("calc_dihedral", 1, 5, 5, 1); __PYX_ERR(0, 210, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("calc_dihedral", 1, 5, 5, 1); __PYX_ERR(0, 212, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coords3)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("calc_dihedral", 1, 5, 5, 2); 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/* function exit code */ @@ -4464,7 +4568,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_26calc_dihedral(CYTHON __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("calc_dihedral", 0); - /* "MDAnalysis/lib/c_distances.pyx":216 + /* "MDAnalysis/lib/c_distances.pyx":218 * numpy.ndarray results): * cdef int numcoords * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< @@ -4473,7 +4577,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_26calc_dihedral(CYTHON */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); - /* "MDAnalysis/lib/c_distances.pyx":218 + /* "MDAnalysis/lib/c_distances.pyx":220 * numcoords = coords1.shape[0] * * _calc_dihedral( coords1.data, coords2.data, # <<<<<<<<<<<<<< @@ -4482,7 +4586,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_26calc_dihedral(CYTHON */ _calc_dihedral(((coordinate *)__pyx_v_coords1->data), ((coordinate *)__pyx_v_coords2->data), ((coordinate *)__pyx_v_coords3->data), ((coordinate *)__pyx_v_coords4->data), __pyx_v_numcoords, ((double *)__pyx_v_results->data)); 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} -/* "MDAnalysis/lib/c_distances.pyx":261 +/* "MDAnalysis/lib/c_distances.pyx":263 * box.data, box_inverse.data) * * def triclinic_pbc(numpy.ndarray coords, # <<<<<<<<<<<<<< @@ -4993,17 +5097,17 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_11c_distances_35triclinic_pbc(PyObje case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_box)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("triclinic_pbc", 1, 3, 3, 1); __PYX_ERR(0, 261, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("triclinic_pbc", 1, 3, 3, 1); __PYX_ERR(0, 263, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_box_inverse)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("triclinic_pbc", 1, 3, 3, 2); __PYX_ERR(0, 261, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("triclinic_pbc", 1, 3, 3, 2); __PYX_ERR(0, 263, __pyx_L3_error) } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "triclinic_pbc") < 0)) __PYX_ERR(0, 261, __pyx_L3_error) + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "triclinic_pbc") < 0)) __PYX_ERR(0, 263, __pyx_L3_error) } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -5018,15 +5122,15 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_11c_distances_35triclinic_pbc(PyObje } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("triclinic_pbc", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 261, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("triclinic_pbc", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 263, __pyx_L3_error) __pyx_L3_error:; __Pyx_AddTraceback("MDAnalysis.lib.c_distances.triclinic_pbc", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords), __pyx_ptype_5numpy_ndarray, 1, "coords", 0))) __PYX_ERR(0, 261, __pyx_L1_error) - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) __PYX_ERR(0, 262, __pyx_L1_error) - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box_inverse), __pyx_ptype_5numpy_ndarray, 1, "box_inverse", 0))) __PYX_ERR(0, 262, __pyx_L1_error) + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords), __pyx_ptype_5numpy_ndarray, 1, "coords", 0))) __PYX_ERR(0, 263, __pyx_L1_error) + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) __PYX_ERR(0, 264, __pyx_L1_error) + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box_inverse), __pyx_ptype_5numpy_ndarray, 1, "box_inverse", 0))) __PYX_ERR(0, 264, __pyx_L1_error) __pyx_r = __pyx_pf_10MDAnalysis_3lib_11c_distances_34triclinic_pbc(__pyx_self, __pyx_v_coords, __pyx_v_box, __pyx_v_box_inverse); 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} -/* "MDAnalysis/lib/c_distances.pyx":271 +/* "MDAnalysis/lib/c_distances.pyx":273 * * @cython.boundscheck(False) * def contact_matrix_no_pbc(coord, sparse_contacts, cutoff): # <<<<<<<<<<<<<< @@ -5120,17 +5224,17 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_11c_distances_37contact_matrix_no_pb case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_sparse_contacts)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("contact_matrix_no_pbc", 1, 3, 3, 1); __PYX_ERR(0, 271, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("contact_matrix_no_pbc", 1, 3, 3, 1); __PYX_ERR(0, 273, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_cutoff)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("contact_matrix_no_pbc", 1, 3, 3, 2); __PYX_ERR(0, 271, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("contact_matrix_no_pbc", 1, 3, 3, 2); __PYX_ERR(0, 273, __pyx_L3_error) } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "contact_matrix_no_pbc") < 0)) __PYX_ERR(0, 271, __pyx_L3_error) + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "contact_matrix_no_pbc") < 0)) __PYX_ERR(0, 273, __pyx_L3_error) } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; 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__pyx_t_2 = 0; __pyx_v_cutoff2 = __pyx_t_3; - /* "MDAnalysis/lib/c_distances.pyx":274 + /* "MDAnalysis/lib/c_distances.pyx":276 * cdef int rows = len(coord) * cdef double cutoff2 = cutoff ** 2 * cdef float[:, ::1] coord_view = coord # <<<<<<<<<<<<<< * * cdef int i, j */ - __pyx_t_4 = __Pyx_PyObject_to_MemoryviewSlice_d_dc_float(__pyx_v_coord, PyBUF_WRITABLE); if (unlikely(!__pyx_t_4.memview)) __PYX_ERR(0, 274, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyObject_to_MemoryviewSlice_d_dc_float(__pyx_v_coord, PyBUF_WRITABLE); if (unlikely(!__pyx_t_4.memview)) __PYX_ERR(0, 276, __pyx_L1_error) __pyx_v_coord_view = __pyx_t_4; __pyx_t_4.memview = NULL; __pyx_t_4.data = NULL; - /* "MDAnalysis/lib/c_distances.pyx":279 + /* "MDAnalysis/lib/c_distances.pyx":281 * cdef double[3] rr * cdef double dist * for i in range(rows): # <<<<<<<<<<<<<< @@ -5242,18 +5346,18 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_36contact_matrix_no_pb for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { __pyx_v_i = __pyx_t_7; - /* "MDAnalysis/lib/c_distances.pyx":280 + /* "MDAnalysis/lib/c_distances.pyx":282 * cdef double dist * for i in range(rows): * sparse_contacts[i, i] = True # <<<<<<<<<<<<<< * for j in range(i+1, rows): * rr[0] = coord_view[i, 0] - coord_view[j, 0] */ - __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 280, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 282, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 280, __pyx_L1_error) + __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 282, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); - __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 280, __pyx_L1_error) + __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 282, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2); 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(__pyx_v_rr[0]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_13 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_14)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_15 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_16)) )))); - /* "MDAnalysis/lib/c_distances.pyx":283 + /* "MDAnalysis/lib/c_distances.pyx":285 * for j in range(i+1, rows): * rr[0] = coord_view[i, 0] - coord_view[j, 0] * rr[1] = coord_view[i, 1] - coord_view[j, 1] # <<<<<<<<<<<<<< @@ -5310,7 +5414,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_36contact_matrix_no_pb if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_v_coord_view.shape[1]; (__pyx_v_rr[1]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_17 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_18)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_19 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_20)) )))); - /* "MDAnalysis/lib/c_distances.pyx":284 + /* "MDAnalysis/lib/c_distances.pyx":286 * rr[0] = coord_view[i, 0] - coord_view[j, 0] * rr[1] = coord_view[i, 1] - coord_view[j, 1] * rr[2] = coord_view[i, 2] - coord_view[j, 2] # <<<<<<<<<<<<<< @@ -5327,7 +5431,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_36contact_matrix_no_pb if (__pyx_t_24 < 0) __pyx_t_24 += __pyx_v_coord_view.shape[1]; (__pyx_v_rr[2]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_21 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_22)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_23 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_24)) )))); - /* "MDAnalysis/lib/c_distances.pyx":285 + /* "MDAnalysis/lib/c_distances.pyx":287 * rr[1] = coord_view[i, 1] - coord_view[j, 1] * rr[2] = coord_view[i, 2] - coord_view[j, 2] * dist = rr[0]*rr[0] + rr[1]*rr[1] + rr[2]*rr[2] # <<<<<<<<<<<<<< @@ -5336,7 +5440,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_36contact_matrix_no_pb */ __pyx_v_dist = ((((__pyx_v_rr[0]) * (__pyx_v_rr[0])) + ((__pyx_v_rr[1]) * (__pyx_v_rr[1]))) + ((__pyx_v_rr[2]) * (__pyx_v_rr[2]))); 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__pyx_t_9 = 0; - /* "MDAnalysis/lib/c_distances.pyx":286 + /* "MDAnalysis/lib/c_distances.pyx":288 * rr[2] = coord_view[i, 2] - coord_view[j, 2] * dist = rr[0]*rr[0] + rr[1]*rr[1] + rr[2]*rr[2] * if dist < cutoff2: # <<<<<<<<<<<<<< @@ -5401,7 +5505,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_36contact_matrix_no_pb } } - /* "MDAnalysis/lib/c_distances.pyx":271 + /* "MDAnalysis/lib/c_distances.pyx":273 * * @cython.boundscheck(False) * def contact_matrix_no_pbc(coord, sparse_contacts, cutoff): # <<<<<<<<<<<<<< @@ -5426,7 +5530,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_36contact_matrix_no_pb return __pyx_r; } -/* "MDAnalysis/lib/c_distances.pyx":292 +/* "MDAnalysis/lib/c_distances.pyx":294 * * @cython.boundscheck(False) * def contact_matrix_pbc(coord, sparse_contacts, box, cutoff): # <<<<<<<<<<<<<< @@ -5472,23 +5576,23 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_11c_distances_39contact_matrix_pbc(P case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_sparse_contacts)) != 0)) kw_args--; 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__pyx_t_13 < __pyx_t_12; __pyx_t_13+=1) { __pyx_v_j = __pyx_t_13; - /* "MDAnalysis/lib/c_distances.pyx":305 + /* "MDAnalysis/lib/c_distances.pyx":307 * sparse_contacts[i, i] = True * for j in range(i+1, rows): * rr[0] = coord_view[i, 0] - coord_view[j, 0] # <<<<<<<<<<<<<< @@ -5685,7 +5789,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_38contact_matrix_pbc(C if (__pyx_t_17 < 0) __pyx_t_17 += __pyx_v_coord_view.shape[1]; (__pyx_v_rr[0]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_14 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_15)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_16 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_17)) )))); - /* "MDAnalysis/lib/c_distances.pyx":306 + /* "MDAnalysis/lib/c_distances.pyx":308 * for j in range(i+1, rows): * rr[0] = coord_view[i, 0] - coord_view[j, 0] * rr[1] = coord_view[i, 1] - coord_view[j, 1] # <<<<<<<<<<<<<< @@ -5702,7 +5806,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_38contact_matrix_pbc(C if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_v_coord_view.shape[1]; (__pyx_v_rr[1]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_18 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_19)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_20 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_21)) )))); - /* "MDAnalysis/lib/c_distances.pyx":307 + /* "MDAnalysis/lib/c_distances.pyx":309 * rr[0] = coord_view[i, 0] - coord_view[j, 0] * rr[1] = coord_view[i, 1] - coord_view[j, 1] * rr[2] = coord_view[i, 2] - coord_view[j, 2] # <<<<<<<<<<<<<< @@ -5719,7 +5823,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_38contact_matrix_pbc(C if (__pyx_t_25 < 0) __pyx_t_25 += __pyx_v_coord_view.shape[1]; (__pyx_v_rr[2]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_22 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_23)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_24 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_25)) )))); - /* "MDAnalysis/lib/c_distances.pyx":309 + /* "MDAnalysis/lib/c_distances.pyx":311 * rr[2] = coord_view[i, 2] - coord_view[j, 2] * * minimum_image(rr, &box_view[0], &box_inv[0]) # <<<<<<<<<<<<<< @@ -5732,7 +5836,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_38contact_matrix_pbc(C if (__pyx_t_27 < 0) __pyx_t_27 += __pyx_v_box_inv.shape[0]; minimum_image(__pyx_v_rr, (&(*((float *) ( /* dim=0 */ ((char *) (((float *) __pyx_v_box_view.data) + __pyx_t_26)) )))), (&(*((float *) ( /* dim=0 */ ((char *) (((float *) __pyx_v_box_inv.data) + __pyx_t_27)) ))))); - /* "MDAnalysis/lib/c_distances.pyx":311 + /* "MDAnalysis/lib/c_distances.pyx":313 * minimum_image(rr, &box_view[0], &box_inv[0]) * * dist = rr[0]*rr[0] + rr[1]*rr[1] + rr[2]*rr[2] # <<<<<<<<<<<<<< @@ -5741,7 +5845,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_38contact_matrix_pbc(C */ __pyx_v_dist = ((((__pyx_v_rr[0]) * (__pyx_v_rr[0])) + ((__pyx_v_rr[1]) * (__pyx_v_rr[1]))) + ((__pyx_v_rr[2]) * (__pyx_v_rr[2]))); - /* "MDAnalysis/lib/c_distances.pyx":313 + /* "MDAnalysis/lib/c_distances.pyx":315 * dist = rr[0]*rr[0] + rr[1]*rr[1] + rr[2]*rr[2] * * if dist < cutoff2: # <<<<<<<<<<<<<< @@ -5751,17 +5855,17 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_38contact_matrix_pbc(C __pyx_t_28 = ((__pyx_v_dist < __pyx_v_cutoff2) != 0); if (__pyx_t_28) { - /* "MDAnalysis/lib/c_distances.pyx":314 + /* "MDAnalysis/lib/c_distances.pyx":316 * * if dist < cutoff2: * sparse_contacts[i, j] = True # <<<<<<<<<<<<<< * sparse_contacts[j, i] = True */ - __pyx_t_10 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 314, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 316, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_10); - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_j); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 314, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_j); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 316, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 314, __pyx_L1_error) + __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 316, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_10); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_10); @@ -5769,19 +5873,19 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_38contact_matrix_pbc(C PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_9); __pyx_t_10 = 0; __pyx_t_9 = 0; - if (unlikely(PyObject_SetItem(__pyx_v_sparse_contacts, __pyx_t_2, Py_True) < 0)) __PYX_ERR(0, 314, __pyx_L1_error) + if (unlikely(PyObject_SetItem(__pyx_v_sparse_contacts, __pyx_t_2, Py_True) < 0)) __PYX_ERR(0, 316, __pyx_L1_error) __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/c_distances.pyx":315 + /* "MDAnalysis/lib/c_distances.pyx":317 * if dist < cutoff2: * sparse_contacts[i, j] = True * sparse_contacts[j, i] = True # <<<<<<<<<<<<<< */ - __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_j); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 315, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_j); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 317, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 315, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 317, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 315, __pyx_L1_error) + __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 317, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_10); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_2); @@ -5789,10 +5893,10 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_38contact_matrix_pbc(C PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_9); __pyx_t_2 = 0; __pyx_t_9 = 0; - if (unlikely(PyObject_SetItem(__pyx_v_sparse_contacts, __pyx_t_10, Py_True) < 0)) __PYX_ERR(0, 315, __pyx_L1_error) + if (unlikely(PyObject_SetItem(__pyx_v_sparse_contacts, __pyx_t_10, Py_True) < 0)) __PYX_ERR(0, 317, __pyx_L1_error) __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - /* "MDAnalysis/lib/c_distances.pyx":313 + /* "MDAnalysis/lib/c_distances.pyx":315 * dist = rr[0]*rr[0] + rr[1]*rr[1] + rr[2]*rr[2] * * if dist < cutoff2: # <<<<<<<<<<<<<< @@ -5803,7 +5907,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_38contact_matrix_pbc(C } } - /* "MDAnalysis/lib/c_distances.pyx":292 + /* "MDAnalysis/lib/c_distances.pyx":294 * * @cython.boundscheck(False) * def contact_matrix_pbc(coord, sparse_contacts, box, cutoff): # <<<<<<<<<<<<<< @@ -5831,7 +5935,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_38contact_matrix_pbc(C return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -5879,7 +5983,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); __Pyx_GIVEREF(__pyx_v_info->obj); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 * * cdef int i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -5888,7 +5992,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 * cdef int i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -5897,7 +6001,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -5906,7 +6010,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -5920,7 +6024,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -5931,7 +6035,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L4_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -5940,7 +6044,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -5953,7 +6057,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 229, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -5962,7 +6066,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -5976,7 +6080,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L7_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -5987,7 +6091,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -5996,7 +6100,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -6009,7 +6113,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 233, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -6018,7 +6122,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -6027,7 +6131,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -6036,7 +6140,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -6046,7 +6150,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) # <<<<<<<<<<<<<< @@ -6055,7 +6159,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyObject_Malloc((((sizeof(Py_ssize_t)) * 2) * ((size_t)__pyx_v_ndim)))); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -6064,7 +6168,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -6076,7 +6180,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -6085,7 +6189,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -6095,7 +6199,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -6105,7 +6209,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -6115,7 +6219,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -6126,7 +6230,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L9:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -6135,7 +6239,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -6144,7 +6248,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -6153,7 +6257,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -6162,7 +6266,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -6174,7 +6278,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 * cdef int offset * * info.obj = self # <<<<<<<<<<<<<< @@ -6187,7 +6291,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -6197,7 +6301,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(PyDataType_HASFIELDS(__pyx_v_descr) != 0)) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 * * if not PyDataType_HASFIELDS(descr): * t = descr.type_num # <<<<<<<<<<<<<< @@ -6207,7 +6311,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -6227,7 +6331,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L15_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -6244,7 +6348,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L14_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -6253,7 +6357,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -6266,7 +6370,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 263, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -6275,7 +6379,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -6287,7 +6391,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"b"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -6298,7 +6402,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"B"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -6309,7 +6413,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"h"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -6320,7 +6424,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"H"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -6331,7 +6435,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"i"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -6342,7 +6446,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"I"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -6353,7 +6457,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"l"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -6364,7 +6468,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"L"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -6375,7 +6479,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -6386,7 +6490,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -6397,7 +6501,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"f"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -6408,7 +6512,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"d"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -6419,7 +6523,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"g"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -6430,7 +6534,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zf"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -6441,7 +6545,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zd"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -6452,7 +6556,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zg"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -6464,7 +6568,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -6485,7 +6589,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -6494,7 +6598,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -6504,7 +6608,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -6513,7 +6617,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 * return * else: * info.format = PyObject_Malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -6523,7 +6627,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)PyObject_Malloc(0xFF)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 * else: * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -6532,7 +6636,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -6541,7 +6645,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -6551,7 +6655,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_8 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_8 == ((char *)NULL))) __PYX_ERR(1, 289, __pyx_L1_error) __pyx_v_f = __pyx_t_8; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -6561,7 +6665,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -6593,7 +6697,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -6617,7 +6721,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -6627,7 +6731,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) # <<<<<<<<<<<<<< @@ -6636,7 +6740,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->format); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -6645,7 +6749,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -6655,7 +6759,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * PyObject_Free(info.strides) # <<<<<<<<<<<<<< @@ -6664,7 +6768,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->strides); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -6673,7 +6777,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -6685,7 +6789,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -6699,7 +6803,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ PyObject *__pyx_t_1 = NULL; 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goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":791 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":791 * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< @@ -6965,7 +7069,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":794 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":794 * return d.subarray.shape * else: * return () # <<<<<<<<<<<<<< @@ -6979,7 +7083,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ goto __pyx_L0; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< @@ -6994,7 +7098,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -7023,7 +7127,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx char *__pyx_t_9; __Pyx_RefNannySetupContext("_util_dtypestring", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":801 * * cdef dtype child * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -7032,7 +7136,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_endian_detector = 1; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":802 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":802 * cdef dtype child * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -7041,7 +7145,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -7064,7 +7168,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":806 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":806 * * for childname in descr.names: * fields = descr.fields[childname] # <<<<<<<<<<<<<< @@ -7081,7 +7185,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3)); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":807 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":807 * for childname in descr.names: * fields = descr.fields[childname] * child, new_offset = fields # <<<<<<<<<<<<<< @@ -7116,7 +7220,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -7133,7 +7237,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -7146,7 +7250,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 810, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -7155,7 +7259,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -7175,7 +7279,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L8_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":813 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":813 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -7192,7 +7296,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = __pyx_t_7; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -7201,7 +7305,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -7214,7 +7318,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 814, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -7223,7 +7327,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -7239,7 +7343,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -7248,7 +7352,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -7257,7 +7361,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -7268,7 +7372,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -7278,7 +7382,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -7288,7 +7392,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -7300,7 +7404,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -7310,7 +7414,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -7323,7 +7427,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __PYX_ERR(1, 834, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -7332,7 +7436,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -7350,7 +7454,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -7368,7 +7472,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -7386,7 +7490,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -7404,7 +7508,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -7422,7 +7526,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -7440,7 +7544,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -7458,7 +7562,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -7476,7 +7580,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -7494,7 +7598,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -7512,7 +7616,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -7530,7 +7634,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -7548,7 +7652,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -7566,7 +7670,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -7586,7 +7690,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -7606,7 +7710,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -7626,7 +7730,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -7644,7 +7748,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -7663,7 +7767,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -7672,7 +7776,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -7682,7 +7786,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -7695,7 +7799,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -7705,7 +7809,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -7715,7 +7819,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -7740,7 +7844,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -7755,7 +7859,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -7766,7 +7870,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -7775,7 +7879,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_baseptr = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -7785,7 +7889,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a goto __pyx_L3; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -7795,7 +7899,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a /*else*/ { Py_INCREF(__pyx_v_base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -7806,7 +7910,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -7815,7 +7919,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -7824,7 +7928,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -7836,7 +7940,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -7850,7 +7954,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -7860,7 +7964,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< @@ -7871,7 +7975,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -7880,7 +7984,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 * return None * else: * return arr.base # <<<<<<<<<<<<<< @@ -7894,7 +7998,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py goto __pyx_L0; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -7909,7 +8013,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -7930,7 +8034,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_array", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -7946,7 +8050,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 * cdef inline int import_array() except -1: * try: * _import_array() # <<<<<<<<<<<<<< @@ -7955,7 +8059,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { */ __pyx_t_4 = _import_array(); 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if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 271, __pyx_L1_error) + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_10MDAnalysis_3lib_11c_distances_37contact_matrix_no_pbc, NULL, __pyx_n_s_MDAnalysis_lib_c_distances); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 273, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_contact_matrix_no_pbc, __pyx_t_1) < 0) __PYX_ERR(0, 271, __pyx_L1_error) + if (PyDict_SetItem(__pyx_d, __pyx_n_s_contact_matrix_no_pbc, __pyx_t_1) < 0) __PYX_ERR(0, 273, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "MDAnalysis/lib/c_distances.pyx":292 + /* "MDAnalysis/lib/c_distances.pyx":294 * * @cython.boundscheck(False) * def contact_matrix_pbc(coord, sparse_contacts, box, cutoff): # <<<<<<<<<<<<<< * cdef int rows = len(coord) * cdef double cutoff2 = cutoff ** 2 */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_10MDAnalysis_3lib_11c_distances_39contact_matrix_pbc, NULL, __pyx_n_s_MDAnalysis_lib_c_distances); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 292, __pyx_L1_error) + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_10MDAnalysis_3lib_11c_distances_39contact_matrix_pbc, NULL, __pyx_n_s_MDAnalysis_lib_c_distances); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 294, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_contact_matrix_pbc, __pyx_t_1) < 0) __PYX_ERR(0, 292, __pyx_L1_error) + if (PyDict_SetItem(__pyx_d, __pyx_n_s_contact_matrix_pbc, __pyx_t_1) < 0) __PYX_ERR(0, 294, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; /* "MDAnalysis/lib/c_distances.pyx":1 @@ -23709,6 +23813,12 @@ static CYTHON_INLINE long __Pyx_div_long(long a, long b) { return q; } +/* BufferIndexError */ +static void __Pyx_RaiseBufferIndexError(int axis) { + PyErr_Format(PyExc_IndexError, + "Out of bounds on buffer access (axis %d)", axis); +} + /* MemviewSliceInit */ static int __Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, @@ -24377,7 +24487,7 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { /* SaveResetException */ #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 *type = tstate->exc_state.exc_type; *value = tstate->exc_state.exc_value; *tb = tstate->exc_state.exc_traceback; @@ -24392,7 +24502,7 @@ static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject * } static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -24476,7 +24586,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) *value = local_value; *tb = local_tb; #if CYTHON_FAST_THREAD_STATE - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -24635,6 +24745,9 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } else { int result; PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif if (!py_result) return -1; result = __Pyx_PyObject_IsTrue(py_result); @@ -24870,7 +24983,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -25021,14 +25134,42 @@ static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, return res; } #endif +static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + assert(PyExceptionClass_Check(exc_type)); + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } +/* IsLittleEndian */ + static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) +{ + union { + uint32_t u32; + uint8_t u8[4]; + } S; + S.u32 = 0x01020304; + return S.u8[0] == 4; +} + +/* BufferFormatCheck */ + static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type) { + stack[0].field = &ctx->root; + stack[0].parent_offset = 0; + ctx->root.type = type; + ctx->root.name = "buffer dtype"; + ctx->root.offset = 0; + ctx->head = stack; + ctx->head->field = &ctx->root; + ctx->fmt_offset = 0; + ctx->head->parent_offset = 0; + ctx->new_packmode = '@'; + ctx->enc_packmode = '@'; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->is_complex = 0; + ctx->is_valid_array = 0; + ctx->struct_alignment = 0; + while (type->typegroup == 'S') { + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = 0; + type = type->fields->type; + } +} +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; } } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } + *ts = t; + return count; } - -/* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ +static int __Pyx_BufFmt_ExpectNumber(const char **ts) { + int number = __Pyx_BufFmt_ParseNumber(ts); + if (number == -1) + PyErr_Format(PyExc_ValueError,\ + "Does not understand character buffer dtype format string ('%c')", **ts); + return number; +} +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + PyErr_Format(PyExc_ValueError, + "Unexpected format string character: '%c'", ch); +} +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'c': return "'char'"; + case 'b': return "'signed char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 's': case 'p': return "a string"; + case 0: return "end"; + default: return "unparseable format string"; + } +} +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; } - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = (long) 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; #ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; #endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); #ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); + case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); #endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; } } - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); +/* These are for computing the padding at the end of the struct to align + on the first member of the struct. This will probably the same as above, + but we don't have any guarantees. + */ +typedef struct { short x; char c; } __Pyx_pad_short; +typedef struct { int x; char c; } __Pyx_pad_int; +typedef struct { long x; char c; } __Pyx_pad_long; +typedef struct { float x; char c; } __Pyx_pad_float; +typedef struct { double x; char c; } __Pyx_pad_double; +typedef struct { long double x; char c; } __Pyx_pad_longdouble; +typedef struct { void *x; char c; } __Pyx_pad_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); + case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); + case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; +} +static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': + return 'H'; + case 'b': case 'h': case 'i': + case 'l': case 'q': case 's': case 'p': + return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': + return 'U'; + case 'f': case 'd': case 'g': + return (is_complex ? 'C' : 'R'); + case 'O': + return 'O'; + case 'P': + return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; + } +} +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset, arraysize = 1; + if (ctx->enc_type == 0) return 0; + if (ctx->head->field->type->arraysize[0]) { + int i, ndim = 0; + if (ctx->enc_type == 's' || ctx->enc_type == 'p') { + ctx->is_valid_array = ctx->head->field->type->ndim == 1; + ndim = 1; + if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { + PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %zu", + ctx->head->field->type->arraysize[0], ctx->enc_count); + return -1; + } } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; + if (!ctx->is_valid_array) { + PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", + ctx->head->field->type->ndim, ndim); + return -1; } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = 1.0 / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = 1.0 / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } + for (i = 0; i < ctx->head->field->type->ndim; i++) { + arraysize *= ctx->head->field->type->arraysize[i]; } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } + ctx->is_valid_array = 0; + ctx->enc_count = 1; + } + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; + if (ctx->enc_packmode == '@') { + size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + size_t align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + if (ctx->struct_alignment == 0) + ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, + ctx->is_complex); } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + if ((type->typegroup == 'H' || group == 'H') && type->size == size) { + } else { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", + (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); + return -1; } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if (b.imag == 0) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0, -1); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; + ctx->fmt_offset += size; + if (arraysize) + ctx->fmt_offset += (arraysize - 1) * size; + --ctx->enc_count; + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; } - #endif -#endif - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; + break; + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} +static PyObject * +__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) +{ + const char *ts = *tsp; + int i = 0, number; + int ndim = ctx->head->field->type->ndim; +; + ++ts; + if (ctx->new_count != 1) { + PyErr_SetString(PyExc_ValueError, + "Cannot handle repeated arrays in format string"); + return NULL; } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + while (*ts && *ts != ')') { + switch (*ts) { + case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; + default: break; + } + number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) + return PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %d", + ctx->head->field->type->arraysize[i], number); + if (*ts != ',' && *ts != ')') + return PyErr_Format(PyExc_ValueError, + "Expected a comma in format string, got '%c'", *ts); + if (*ts == ',') ts++; + i++; } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; + if (i != ndim) + return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", + ctx->head->field->type->ndim, i); + if (!*ts) { + PyErr_SetString(PyExc_ValueError, + "Unexpected end of format string, expected ')'"); + return NULL; } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = 1.0 / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = 1.0 / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); + ctx->is_valid_array = 1; + ctx->new_count = 1; + *tsp = ++ts; + return Py_None; +} +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case '\r': + case '\n': + ++ts; + break; + case '<': + if (!__Pyx_Is_Little_Endian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_Is_Little_Endian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + ctx->new_packmode = *ts++; + break; + case 'T': + { + const char* ts_after_sub; + size_t i, struct_count = ctx->new_count; + size_t struct_alignment = ctx->struct_alignment; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + ctx->enc_count = 0; + ctx->struct_alignment = 0; + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + if (struct_alignment) ctx->struct_alignment = struct_alignment; + } + break; + case '}': + { + size_t alignment = ctx->struct_alignment; + ++ts; + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + if (alignment && ctx->fmt_offset % alignment) { + ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); + } + } + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->enc_packmode = ctx->new_packmode; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } + CYTHON_FALLTHROUGH; + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': case 'p': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex && + ctx->enc_packmode == ctx->new_packmode) { + ctx->enc_count += ctx->new_count; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; + } + CYTHON_FALLTHROUGH; + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + case ':': + ++ts; + while(*ts != ':') ++ts; + ++ts; + break; + case '(': + if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; + break; + default: + { + int number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + ctx->new_count = (size_t)number; } } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } +} + +/* TypeInfoCompare */ + static int +__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) +{ + int i; + if (!a || !b) + return 0; + if (a == b) + return 1; + if (a->size != b->size || a->typegroup != b->typegroup || + a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { + if (a->typegroup == 'H' || b->typegroup == 'H') { + return a->size == b->size; } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); + return 0; } } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; + if (a->ndim) { + for (i = 0; i < a->ndim; i++) + if (a->arraysize[i] != b->arraysize[i]) + return 0; } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif + if (a->typegroup == 'S') { + if (a->flags != b->flags) + return 0; + if (a->fields || b->fields) { + if (!(a->fields && b->fields)) + return 0; + for (i = 0; a->fields[i].type && b->fields[i].type; i++) { + __Pyx_StructField *field_a = a->fields + i; + __Pyx_StructField *field_b = b->fields + i; + if (field_a->offset != field_b->offset || + !__pyx_typeinfo_cmp(field_a->type, field_b->type)) + return 0; + } + return !a->fields[i].type && !b->fields[i].type; } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; + } + return 1; +} + +/* MemviewSliceValidateAndInit */ + static int +__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) +{ + if (buf->shape[dim] <= 1) + return 1; + if (buf->strides) { + if (spec & __Pyx_MEMVIEW_CONTIG) { + if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { + if (buf->strides[dim] != sizeof(void *)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly contiguous " + "in dimension %d.", dim); + goto fail; } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if (b.imag == 0) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0, -1); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); + } else if (buf->strides[dim] != buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; } - #endif -#endif - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { - const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(enum NPY_TYPES) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif + if (spec & __Pyx_MEMVIEW_FOLLOW) { + Py_ssize_t stride = buf->strides[dim]; + if (stride < 0) + stride = -stride; + if (stride < buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } } } else { - if (sizeof(enum NPY_TYPES) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif + if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not contiguous in " + "dimension %d", dim); + goto fail; + } else if (spec & (__Pyx_MEMVIEW_PTR)) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not indirect in " + "dimension %d", dim); + goto fail; + } else if (buf->suboffsets) { + PyErr_SetString(PyExc_ValueError, + "Buffer exposes suboffsets but no strides"); + goto fail; } } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), - little, !is_unsigned); - } + return 1; +fail: + return 0; } - -/* MemviewSliceCopyTemplate */ - static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object) +static int +__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) { - __Pyx_RefNannyDeclarations - int i; - __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; - struct __pyx_memoryview_obj *from_memview = from_mvs->memview; - Py_buffer *buf = &from_memview->view; - PyObject *shape_tuple = NULL; - PyObject *temp_int = NULL; - struct __pyx_array_obj *array_obj = NULL; - struct __pyx_memoryview_obj *memview_obj = NULL; - __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); - for (i = 0; i < ndim; i++) { - if (from_mvs->suboffsets[i] >= 0) { - PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " - "indirect dimensions (axis %d)", i); + if (spec & __Pyx_MEMVIEW_DIRECT) { + if (buf->suboffsets && buf->suboffsets[dim] >= 0) { + PyErr_Format(PyExc_ValueError, + "Buffer not compatible with direct access " + "in dimension %d.", dim); goto fail; } } - shape_tuple = PyTuple_New(ndim); - if (unlikely(!shape_tuple)) { - goto fail; - } - __Pyx_GOTREF(shape_tuple); - for(i = 0; i < ndim; i++) { - temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); - if(unlikely(!temp_int)) { + if (spec & __Pyx_MEMVIEW_PTR) { + if (!buf->suboffsets || (buf->suboffsets && buf->suboffsets[dim] < 0)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly accessible " + "in dimension %d.", dim); goto fail; - } else { - PyTuple_SET_ITEM(shape_tuple, i, temp_int); - temp_int = NULL; } } - array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); - if (unlikely(!array_obj)) { + return 1; +fail: + return 0; +} +static int +__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) +{ + int i; + if (c_or_f_flag & __Pyx_IS_F_CONTIG) { + Py_ssize_t stride = 1; + for (i = 0; i < ndim; i++) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) + { + PyErr_SetString(PyExc_ValueError, + "Buffer not fortran contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { + Py_ssize_t stride = 1; + for (i = ndim - 1; i >- 1; i--) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) { + PyErr_SetString(PyExc_ValueError, + "Buffer not C contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } + return 1; +fail: + return 0; +} +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj) +{ + struct __pyx_memoryview_obj *memview, *new_memview; + __Pyx_RefNannyDeclarations + Py_buffer *buf; + int i, spec = 0, retval = -1; + __Pyx_BufFmt_Context ctx; + int from_memoryview = __pyx_memoryview_check(original_obj); + __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); + if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) + original_obj)->typeinfo)) { + memview = (struct __pyx_memoryview_obj *) original_obj; + new_memview = NULL; + } else { + memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + original_obj, buf_flags, 0, dtype); + new_memview = memview; + if (unlikely(!memview)) + goto fail; + } + buf = &memview->view; + if (buf->ndim != ndim) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + ndim, buf->ndim); goto fail; } - __Pyx_GOTREF(array_obj); - memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - (PyObject *) array_obj, contig_flag, - dtype_is_object, - from_mvs->memview->typeinfo); - if (unlikely(!memview_obj)) + if (new_memview) { + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned) buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " + "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", + buf->itemsize, + (buf->itemsize > 1) ? "s" : "", + dtype->name, + dtype->size, + (dtype->size > 1) ? "s" : ""); goto fail; - if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) + } + for (i = 0; i < ndim; i++) { + spec = axes_specs[i]; + if (!__pyx_check_strides(buf, i, ndim, spec)) + goto fail; + if (!__pyx_check_suboffsets(buf, i, ndim, spec)) + goto fail; + } + if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag)) goto fail; - if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, - dtype_is_object) < 0)) + if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, + new_memview != NULL) == -1)) { goto fail; + } + retval = 0; goto no_fail; fail: - __Pyx_XDECREF(new_mvs.memview); - new_mvs.memview = NULL; - new_mvs.data = NULL; + Py_XDECREF(new_memview); + retval = -1; no_fail: - __Pyx_XDECREF(shape_tuple); - __Pyx_XDECREF(temp_int); - __Pyx_XDECREF(array_obj); __Pyx_RefNannyFinishContext(); - return new_mvs; + return retval; } -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { +/* ObjectToMemviewSlice */ + static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *obj, int writable_flag) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS_RO | writable_flag, 2, + &__Pyx_TypeInfo_float, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +/* MemviewDtypeToObject */ + static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp) { + return (PyObject *) PyFloat_FromDouble(*(float *) itemp); +} +static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj) { + float value = __pyx_PyFloat_AsFloat(obj); + if ((value == (float)-1) && PyErr_Occurred()) + return 0; + *(float *) itemp = value; + return 1; +} + +/* CIntFromPyVerify */ + #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) +#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) +#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ + {\ + func_type value = func_value;\ + if (sizeof(target_type) < sizeof(func_type)) {\ + if (unlikely(value != (func_type) (target_type) value)) {\ + func_type zero = 0;\ + if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ + return (target_type) -1;\ + if (is_unsigned && unlikely(value < zero))\ + goto raise_neg_overflow;\ + else\ + goto raise_overflow;\ + }\ + }\ + return (target_type) value;\ + } + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { const int neg_one = (int) -1, const_zero = (int) 0; const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { + if (is_unsigned) { if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); #ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); #endif - } } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); #endif - return (int) -1; } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } } -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { + if (is_unsigned) { if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); #ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); #endif - } } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); #endif - return (long) -1; } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } } -/* CIntFromPy */ - static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { - const char neg_one = (char) -1, const_zero = (char) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(char) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; +/* Declarations */ + #if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +/* Arithmetic */ + #if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + #if 1 + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + if (b.imag == 0) { + return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); + } else if (fabsf(b.real) >= fabsf(b.imag)) { + if (b.real == 0 && b.imag == 0) { + return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); + } else { + float r = b.imag / b.real; + float s = 1.0 / (b.real + b.imag * r); + return __pyx_t_float_complex_from_parts( + (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); } - return (char) val; + } else { + float r = b.real / b.imag; + float s = 1.0 / (b.imag + b.real * r); + return __pyx_t_float_complex_from_parts( + (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (char) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(char) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } + } + #else + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + if (b.imag == 0) { + return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) - case -2: - if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - } -#endif - if (sizeof(char) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } + float denom = b.real * b.real + b.imag * b.imag; + return __pyx_t_float_complex_from_parts( + (a.real * b.real + a.imag * b.imag) / denom, + (a.imag * b.real - a.real * b.imag) / denom); } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - char val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); + } + #endif + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod_float(a, a); + return __Pyx_c_prod_float(a, a); + case 3: + z = __Pyx_c_prod_float(a, a); + return __Pyx_c_prod_float(z, a); + case 4: + z = __Pyx_c_prod_float(a, a); + return __Pyx_c_prod_float(z, z); + } } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; + if (a.imag == 0) { + if (a.real == 0) { + return a; + } else if (b.imag == 0) { + z.real = powf(a.real, b.real); + z.imag = 0; + return z; + } else if (a.real > 0) { + r = a.real; + theta = 0; + } else { + r = -a.real; + theta = atan2f(0, -1); + } + } else { + r = __Pyx_c_abs_float(a); + theta = atan2f(a.imag, a.real); } -#endif - return (char) -1; + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; } - } else { - char val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (char) -1; - val = __Pyx_PyInt_As_char(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to char"); - return (char) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to char"); - return (char) -1; -} + #endif +#endif -/* IsLittleEndian */ - static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) -{ - union { - uint32_t u32; - uint8_t u8[4]; - } S; - S.u32 = 0x01020304; - return S.u8[0] == 4; -} - -/* BufferFormatCheck */ - static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type) { - stack[0].field = &ctx->root; - stack[0].parent_offset = 0; - ctx->root.type = type; - ctx->root.name = "buffer dtype"; - ctx->root.offset = 0; - ctx->head = stack; - ctx->head->field = &ctx->root; - ctx->fmt_offset = 0; - ctx->head->parent_offset = 0; - ctx->new_packmode = '@'; - ctx->enc_packmode = '@'; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->is_complex = 0; - ctx->is_valid_array = 0; - ctx->struct_alignment = 0; - while (type->typegroup == 'S') { - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = 0; - type = type->fields->type; - } -} -static int __Pyx_BufFmt_ParseNumber(const char** ts) { - int count; - const char* t = *ts; - if (*t < '0' || *t > '9') { - return -1; - } else { - count = *t++ - '0'; - while (*t >= '0' && *t < '9') { - count *= 10; - count += *t++ - '0'; - } - } - *ts = t; - return count; -} -static int __Pyx_BufFmt_ExpectNumber(const char **ts) { - int number = __Pyx_BufFmt_ParseNumber(ts); - if (number == -1) - PyErr_Format(PyExc_ValueError,\ - "Does not understand character buffer dtype format string ('%c')", **ts); - return number; -} -static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { - PyErr_Format(PyExc_ValueError, - "Unexpected format string character: '%c'", ch); -} -static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { - switch (ch) { - case 'c': return "'char'"; - case 'b': return "'signed char'"; - case 'B': return "'unsigned char'"; - case 'h': return "'short'"; - case 'H': return "'unsigned short'"; - case 'i': return "'int'"; - case 'I': return "'unsigned int'"; - case 'l': return "'long'"; - case 'L': return "'unsigned long'"; - case 'q': return "'long long'"; - case 'Q': return "'unsigned long long'"; - case 'f': return (is_complex ? "'complex float'" : "'float'"); - case 'd': return (is_complex ? "'complex double'" : "'double'"); - case 'g': return (is_complex ? "'complex long double'" : "'long double'"); - case 'T': return "a struct"; - case 'O': return "Python object"; - case 'P': return "a pointer"; - case 's': case 'p': return "a string"; - case 0: return "end"; - default: return "unparseable format string"; - } -} -static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return 2; - case 'i': case 'I': case 'l': case 'L': return 4; - case 'q': case 'Q': return 8; - case 'f': return (is_complex ? 8 : 4); - case 'd': return (is_complex ? 16 : 8); - case 'g': { - PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); - return 0; +/* Declarations */ + #if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); } - case 'O': case 'P': return sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; } -} -static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { - switch (ch) { - case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(short); - case 'i': case 'I': return sizeof(int); - case 'l': case 'L': return sizeof(long); - #ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(PY_LONG_LONG); - #endif - case 'f': return sizeof(float) * (is_complex ? 2 : 1); - case 'd': return sizeof(double) * (is_complex ? 2 : 1); - case 'g': return sizeof(long double) * (is_complex ? 2 : 1); - case 'O': case 'P': return sizeof(void*); - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; } - } -} -typedef struct { char c; short x; } __Pyx_st_short; -typedef struct { char c; int x; } __Pyx_st_int; -typedef struct { char c; long x; } __Pyx_st_long; -typedef struct { char c; float x; } __Pyx_st_float; -typedef struct { char c; double x; } __Pyx_st_double; -typedef struct { char c; long double x; } __Pyx_st_longdouble; -typedef struct { char c; void *x; } __Pyx_st_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); #endif - case 'f': return sizeof(__Pyx_st_float) - sizeof(float); - case 'd': return sizeof(__Pyx_st_double) - sizeof(double); - case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; + +/* Arithmetic */ + #if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); } -} -/* These are for computing the padding at the end of the struct to align - on the first member of the struct. This will probably the same as above, - but we don't have any guarantees. - */ -typedef struct { short x; char c; } __Pyx_pad_short; -typedef struct { int x; char c; } __Pyx_pad_int; -typedef struct { long x; char c; } __Pyx_pad_long; -typedef struct { float x; char c; } __Pyx_pad_float; -typedef struct { double x; char c; } __Pyx_pad_double; -typedef struct { long double x; char c; } __Pyx_pad_longdouble; -typedef struct { void *x; char c; } __Pyx_pad_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); - case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); - case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; } -} -static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { - switch (ch) { - case 'c': - return 'H'; - case 'b': case 'h': case 'i': - case 'l': case 'q': case 's': case 'p': - return 'I'; - case 'B': case 'H': case 'I': case 'L': case 'Q': - return 'U'; - case 'f': case 'd': case 'g': - return (is_complex ? 'C' : 'R'); - case 'O': - return 'O'; - case 'P': - return 'P'; - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; } - } -} -static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { - if (ctx->head == NULL || ctx->head->field == &ctx->root) { - const char* expected; - const char* quote; - if (ctx->head == NULL) { - expected = "end"; - quote = ""; - } else { - expected = ctx->head->field->type->name; - quote = "'"; + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; } - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected %s%s%s but got %s", - quote, expected, quote, - __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); - } else { - __Pyx_StructField* field = ctx->head->field; - __Pyx_StructField* parent = (ctx->head - 1)->field; - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", - field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), - parent->type->name, field->name); - } -} -static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { - char group; - size_t size, offset, arraysize = 1; - if (ctx->enc_type == 0) return 0; - if (ctx->head->field->type->arraysize[0]) { - int i, ndim = 0; - if (ctx->enc_type == 's' || ctx->enc_type == 'p') { - ctx->is_valid_array = ctx->head->field->type->ndim == 1; - ndim = 1; - if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { - PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %zu", - ctx->head->field->type->arraysize[0], ctx->enc_count); - return -1; + #if 1 + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + if (b.imag == 0) { + return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } else if (fabs(b.real) >= fabs(b.imag)) { + if (b.real == 0 && b.imag == 0) { + return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); + } else { + double r = b.imag / b.real; + double s = 1.0 / (b.real + b.imag * r); + return __pyx_t_double_complex_from_parts( + (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); + } + } else { + double r = b.real / b.imag; + double s = 1.0 / (b.imag + b.real * r); + return __pyx_t_double_complex_from_parts( + (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); } } - if (!ctx->is_valid_array) { - PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", - ctx->head->field->type->ndim, ndim); - return -1; - } - for (i = 0; i < ctx->head->field->type->ndim; i++) { - arraysize *= ctx->head->field->type->arraysize[i]; - } - ctx->is_valid_array = 0; - ctx->enc_count = 1; - } - group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); - do { - __Pyx_StructField* field = ctx->head->field; - __Pyx_TypeInfo* type = field->type; - if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { - size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); - } else { - size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + #else + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + if (b.imag == 0) { + return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } else { + double denom = b.real * b.real + b.imag * b.imag; + return __pyx_t_double_complex_from_parts( + (a.real * b.real + a.imag * b.imag) / denom, + (a.imag * b.real - a.real * b.imag) / denom); + } } - if (ctx->enc_packmode == '@') { - size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); - size_t align_mod_offset; - if (align_at == 0) return -1; - align_mod_offset = ctx->fmt_offset % align_at; - if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; - if (ctx->struct_alignment == 0) - ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, - ctx->is_complex); + #endif + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; } - if (type->size != size || type->typegroup != group) { - if (type->typegroup == 'C' && type->fields != NULL) { - size_t parent_offset = ctx->head->parent_offset + field->offset; - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = parent_offset; - continue; - } - if ((type->typegroup == 'H' || group == 'H') && type->size == size) { - } else { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } + static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); } - offset = ctx->head->parent_offset + field->offset; - if (ctx->fmt_offset != offset) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", - (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); - return -1; + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; } - ctx->fmt_offset += size; - if (arraysize) - ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; - while (1) { - if (field == &ctx->root) { - ctx->head = NULL; - if (ctx->enc_count != 0) { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; + #if 1 + static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod_double(a, a); + return __Pyx_c_prod_double(a, a); + case 3: + z = __Pyx_c_prod_double(a, a); + return __Pyx_c_prod_double(z, a); + case 4: + z = __Pyx_c_prod_double(a, a); + return __Pyx_c_prod_double(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } else if (b.imag == 0) { + z.real = pow(a.real, b.real); + z.imag = 0; + return z; + } else if (a.real > 0) { + r = a.real; + theta = 0; + } else { + r = -a.real; + theta = atan2(0, -1); + } + } else { + r = __Pyx_c_abs_double(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { + const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum NPY_TYPES) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(enum NPY_TYPES) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif } - break; - } - ctx->head->field = ++field; - if (field->type == NULL) { - --ctx->head; - field = ctx->head->field; - continue; - } else if (field->type->typegroup == 'S') { - size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; - field = field->type->fields; - ++ctx->head; - ctx->head->field = field; - ctx->head->parent_offset = parent_offset; - break; - } else { - break; - } } - } while (ctx->enc_count); - ctx->enc_type = 0; - ctx->is_complex = 0; - return 0; + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), + little, !is_unsigned); + } } -static PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) + +/* MemviewSliceCopyTemplate */ + static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object) { - const char *ts = *tsp; - int i = 0, number; - int ndim = ctx->head->field->type->ndim; -; - ++ts; - if (ctx->new_count != 1) { - PyErr_SetString(PyExc_ValueError, - "Cannot handle repeated arrays in format string"); - return NULL; + __Pyx_RefNannyDeclarations + int i; + __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; + struct __pyx_memoryview_obj *from_memview = from_mvs->memview; + Py_buffer *buf = &from_memview->view; + PyObject *shape_tuple = NULL; + PyObject *temp_int = NULL; + struct __pyx_array_obj *array_obj = NULL; + struct __pyx_memoryview_obj *memview_obj = NULL; + __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); + for (i = 0; i < ndim; i++) { + if (from_mvs->suboffsets[i] >= 0) { + PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " + "indirect dimensions (axis %d)", i); + goto fail; + } } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - while (*ts && *ts != ')') { - switch (*ts) { - case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; + shape_tuple = PyTuple_New(ndim); + if (unlikely(!shape_tuple)) { + goto fail; + } + __Pyx_GOTREF(shape_tuple); + for(i = 0; i < ndim; i++) { + temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); + if(unlikely(!temp_int)) { + goto fail; + } else { + PyTuple_SET_ITEM(shape_tuple, i, temp_int); + temp_int = NULL; } - number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) - return PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %d", - ctx->head->field->type->arraysize[i], number); - if (*ts != ',' && *ts != ')') - return PyErr_Format(PyExc_ValueError, - "Expected a comma in format string, got '%c'", *ts); - if (*ts == ',') ts++; - i++; } - if (i != ndim) - return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", - ctx->head->field->type->ndim, i); - if (!*ts) { - PyErr_SetString(PyExc_ValueError, - "Unexpected end of format string, expected ')'"); - return NULL; + array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); + if (unlikely(!array_obj)) { + goto fail; } - ctx->is_valid_array = 1; - ctx->new_count = 1; - *tsp = ++ts; - return Py_None; + __Pyx_GOTREF(array_obj); + memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + (PyObject *) array_obj, contig_flag, + dtype_is_object, + from_mvs->memview->typeinfo); + if (unlikely(!memview_obj)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) + goto fail; + if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, + dtype_is_object) < 0)) + goto fail; + goto no_fail; +fail: + __Pyx_XDECREF(new_mvs.memview); + new_mvs.memview = NULL; + new_mvs.data = NULL; +no_fail: + __Pyx_XDECREF(shape_tuple); + __Pyx_XDECREF(temp_int); + __Pyx_XDECREF(array_obj); + __Pyx_RefNannyFinishContext(); + return new_mvs; } -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { - int got_Z = 0; - while (1) { - switch(*ts) { - case 0: - if (ctx->enc_type != 0 && ctx->head == NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - if (ctx->head != NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - return ts; - case ' ': - case '\r': - case '\n': - ++ts; - break; - case '<': - if (!__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); - return NULL; + +/* CIntFromPy */ + static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; } - ctx->new_packmode = '='; - ++ts; - break; - case '=': - case '@': - case '^': - ctx->new_packmode = *ts++; - break; - case 'T': - { - const char* ts_after_sub; - size_t i, struct_count = ctx->new_count; - size_t struct_alignment = ctx->struct_alignment; - ctx->new_count = 1; - ++ts; - if (*ts != '{') { - PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - ctx->enc_count = 0; - ctx->struct_alignment = 0; - ++ts; - ts_after_sub = ts; - for (i = 0; i != struct_count; ++i) { - ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); - if (!ts_after_sub) return NULL; - } - ts = ts_after_sub; - if (struct_alignment) ctx->struct_alignment = struct_alignment; + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + case -2: + if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + } +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } } - break; - case '}': { - size_t alignment = ctx->struct_alignment; - ++ts; - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - if (alignment && ctx->fmt_offset % alignment) { - ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); - } +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; } - return ts; - case 'x': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->fmt_offset += ctx->new_count; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->enc_packmode = ctx->new_packmode; - ++ts; - break; - case 'Z': - got_Z = 1; - ++ts; - if (*ts != 'f' && *ts != 'd' && *ts != 'g') { - __Pyx_BufFmt_RaiseUnexpectedChar('Z'); - return NULL; + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +/* CIntFromPy */ + static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = (long) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; } - CYTHON_FALLTHROUGH; - case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': - case 'l': case 'L': case 'q': case 'Q': - case 'f': case 'd': case 'g': - case 'O': case 'p': - if (ctx->enc_type == *ts && got_Z == ctx->is_complex && - ctx->enc_packmode == ctx->new_packmode) { - ctx->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + case -2: + if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + } +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } } - CYTHON_FALLTHROUGH; - case 's': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; - ++ts; - ctx->new_count = 1; - got_Z = 0; - break; - case ':': - ++ts; - while(*ts != ':') ++ts; - ++ts; - break; - case '(': - if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; - break; - default: { - int number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - ctx->new_count = (size_t)number; +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; } - } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; } -/* TypeInfoCompare */ - static int -__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) -{ - int i; - if (!a || !b) - return 0; - if (a == b) - return 1; - if (a->size != b->size || a->typegroup != b->typegroup || - a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { - if (a->typegroup == 'H' || b->typegroup == 'H') { - return a->size == b->size; +/* CIntFromPy */ + static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { + const char neg_one = (char) -1, const_zero = (char) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(char) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) } else { - return 0; - } - } - if (a->ndim) { - for (i = 0; i < a->ndim; i++) - if (a->arraysize[i] != b->arraysize[i]) - return 0; - } - if (a->typegroup == 'S') { - if (a->flags != b->flags) - return 0; - if (a->fields || b->fields) { - if (!(a->fields && b->fields)) - return 0; - for (i = 0; a->fields[i].type && b->fields[i].type; i++) { - __Pyx_StructField *field_a = a->fields + i; - __Pyx_StructField *field_b = b->fields + i; - if (field_a->offset != field_b->offset || - !__pyx_typeinfo_cmp(field_a->type, field_b->type)) - return 0; + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; } - return !a->fields[i].type && !b->fields[i].type; + return (char) val; } - } - return 1; -} - -/* MemviewSliceValidateAndInit */ - static int -__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) -{ - if (buf->shape[dim] <= 1) - return 1; - if (buf->strides) { - if (spec & __Pyx_MEMVIEW_CONTIG) { - if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { - if (buf->strides[dim] != sizeof(void *)) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly contiguous " - "in dimension %d.", dim); - goto fail; - } - } else if (buf->strides[dim] != buf->itemsize) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (char) 0; + case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) + case 2: + if (8 * sizeof(char) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { + return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(char) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { + return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(char) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { + return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (char) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(char) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (char) 0; + case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) + case -2: + if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(char) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(char) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(char) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { + return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; } - } - if (spec & __Pyx_MEMVIEW_FOLLOW) { - Py_ssize_t stride = buf->strides[dim]; - if (stride < 0) - stride = -stride; - if (stride < buf->itemsize) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; +#endif + if (sizeof(char) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif } } - } else { - if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not contiguous in " - "dimension %d", dim); - goto fail; - } else if (spec & (__Pyx_MEMVIEW_PTR)) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not indirect in " - "dimension %d", dim); - goto fail; - } else if (buf->suboffsets) { - PyErr_SetString(PyExc_ValueError, - "Buffer exposes suboffsets but no strides"); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) -{ - if (spec & __Pyx_MEMVIEW_DIRECT) { - if (buf->suboffsets && buf->suboffsets[dim] >= 0) { - PyErr_Format(PyExc_ValueError, - "Buffer not compatible with direct access " - "in dimension %d.", dim); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_PTR) { - if (!buf->suboffsets || (buf->suboffsets && buf->suboffsets[dim] < 0)) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly accessible " - "in dimension %d.", dim); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) -{ - int i; - if (c_or_f_flag & __Pyx_IS_F_CONTIG) { - Py_ssize_t stride = 1; - for (i = 0; i < ndim; i++) { - if (stride * buf->itemsize != buf->strides[i] && - buf->shape[i] > 1) - { - PyErr_SetString(PyExc_ValueError, - "Buffer not fortran contiguous."); - goto fail; + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + char val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); } - stride = stride * buf->shape[i]; - } - } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { - Py_ssize_t stride = 1; - for (i = ndim - 1; i >- 1; i--) { - if (stride * buf->itemsize != buf->strides[i] && - buf->shape[i] > 1) { - PyErr_SetString(PyExc_ValueError, - "Buffer not C contiguous."); - goto fail; + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; } - stride = stride * buf->shape[i]; +#endif + return (char) -1; } - } - return 1; -fail: - return 0; -} -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj) -{ - struct __pyx_memoryview_obj *memview, *new_memview; - __Pyx_RefNannyDeclarations - Py_buffer *buf; - int i, spec = 0, retval = -1; - __Pyx_BufFmt_Context ctx; - int from_memoryview = __pyx_memoryview_check(original_obj); - __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); - if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) - original_obj)->typeinfo)) { - memview = (struct __pyx_memoryview_obj *) original_obj; - new_memview = NULL; } else { - memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - original_obj, buf_flags, 0, dtype); - new_memview = memview; - if (unlikely(!memview)) - goto fail; - } - buf = &memview->view; - if (buf->ndim != ndim) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - ndim, buf->ndim); - goto fail; - } - if (new_memview) { - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; - } - if ((unsigned) buf->itemsize != dtype->size) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " - "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", - buf->itemsize, - (buf->itemsize > 1) ? "s" : "", - dtype->name, - dtype->size, - (dtype->size > 1) ? "s" : ""); - goto fail; - } - for (i = 0; i < ndim; i++) { - spec = axes_specs[i]; - if (!__pyx_check_strides(buf, i, ndim, spec)) - goto fail; - if (!__pyx_check_suboffsets(buf, i, ndim, spec)) - goto fail; - } - if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag)) - goto fail; - if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, - new_memview != NULL) == -1)) { - goto fail; + char val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (char) -1; + val = __Pyx_PyInt_As_char(tmp); + Py_DECREF(tmp); + return val; } - retval = 0; - goto no_fail; -fail: - Py_XDECREF(new_memview); - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to char"); + return (char) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to char"); + return (char) -1; } /* ObjectToMemviewSlice */ @@ -27860,6 +28039,9 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_DECREF(x); return ival; } +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) { + return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False); +} static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { return PyInt_FromSize_t(ival); } diff --git a/package/MDAnalysis/lib/c_distances_openmp.c b/package/MDAnalysis/lib/c_distances_openmp.c index b1f7ae73411..beaf56097dc 100644 --- a/package/MDAnalysis/lib/c_distances_openmp.c +++ b/package/MDAnalysis/lib/c_distances_openmp.c @@ -1,36 +1,25 @@ -/* Generated by Cython 0.28.2 */ +/* Generated by Cython 0.28.5 */ /* BEGIN: Cython Metadata { "distutils": { - "define_macros": [ - [ - "PARALLEL", - null - ] - ], "depends": [ - "/home/richard/miniconda2/envs/mda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h", - "/home/richard/miniconda2/envs/mda3/lib/python3.6/site-packages/numpy/core/include/numpy/ufuncobject.h", + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h", + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include/numpy/ufuncobject.h", "MDAnalysis/lib/include/calc_distances.h" ], "extra_compile_args": [ - "-fopenmp", "-std=c99", "-ffast-math", "-O3", "-funroll-loops" ], - "extra_link_args": [ - "-fopenmp" - ], "include_dirs": [ - "/home/richard/miniconda2/envs/mda3/lib/python3.6/site-packages/numpy/core/include", + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include", "MDAnalysis/lib/include" ], "libraries": [ - "m", - "gomp" + "m" ], "name": "MDAnalysis.lib.c_distances_openmp", "sources": [ @@ -48,7 +37,7 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) #error Cython requires Python 2.6+ or Python 3.3+. #else -#define CYTHON_ABI "0_28_2" +#define CYTHON_ABI "0_28_5" #define CYTHON_FUTURE_DIVISION 0 #include #ifndef offsetof @@ -494,6 +483,7 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact + #define PyObject_Unicode PyObject_Str #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) @@ -692,7 +682,7 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); #define __Pyx_PySequence_Tuple(obj)\ @@ -800,7 +790,7 @@ static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } static PyObject *__pyx_m = NULL; static PyObject *__pyx_d; static PyObject *__pyx_b; -static PyObject *__pyx_cython_runtime; +static PyObject *__pyx_cython_runtime = NULL; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static PyObject *__pyx_empty_unicode; @@ -838,7 +828,7 @@ static const char *__pyx_f[] = { "type.pxd", }; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -847,7 +837,7 @@ static const char *__pyx_f[] = { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -856,7 +846,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -865,7 +855,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -874,7 +864,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -883,7 +873,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -892,7 +882,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -901,7 +891,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -910,7 +900,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -919,7 +909,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -928,7 +918,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -937,7 +927,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -946,7 +936,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -955,7 +945,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -964,7 +954,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -973,7 +963,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -982,7 +972,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -991,7 +981,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1000,7 +990,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1009,7 +999,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1018,7 +1008,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1053,7 +1043,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do /*--- Type declarations ---*/ -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1062,7 +1052,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1071,7 +1061,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1080,7 +1070,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -4221,7 +4211,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_18c_distances_openmp_34triclinic_pbc return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -4269,7 +4259,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); __Pyx_GIVEREF(__pyx_v_info->obj); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 * * cdef int i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -4278,7 +4268,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 * cdef int i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -4287,7 +4277,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -4296,7 +4286,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -4310,7 +4300,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -4321,7 +4311,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L4_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -4330,7 +4320,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -4343,7 +4333,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 229, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -4352,7 +4342,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -4366,7 +4356,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L7_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -4377,7 +4367,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -4386,7 +4376,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -4399,7 +4389,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 233, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -4408,7 +4398,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -4417,7 +4407,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -4426,7 +4416,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -4436,7 +4426,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) # <<<<<<<<<<<<<< @@ -4445,7 +4435,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyObject_Malloc((((sizeof(Py_ssize_t)) * 2) * ((size_t)__pyx_v_ndim)))); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -4454,7 +4444,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -4466,7 +4456,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -4475,7 +4465,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -4485,7 +4475,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -4495,7 +4485,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -4505,7 +4495,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -4516,7 +4506,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L9:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -4525,7 +4515,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -4534,7 +4524,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -4543,7 +4533,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -4552,7 +4542,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -4564,7 +4554,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 * cdef int offset * * info.obj = self # <<<<<<<<<<<<<< @@ -4577,7 +4567,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -4587,7 +4577,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(PyDataType_HASFIELDS(__pyx_v_descr) != 0)) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 * * if not PyDataType_HASFIELDS(descr): * t = descr.type_num # <<<<<<<<<<<<<< @@ -4597,7 +4587,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -4617,7 +4607,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L15_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -4634,7 +4624,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L14_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -4643,7 +4633,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -4656,7 +4646,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 263, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -4665,7 +4655,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -4677,7 +4667,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"b"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -4688,7 +4678,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"B"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -4699,7 +4689,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"h"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -4710,7 +4700,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"H"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -4721,7 +4711,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"i"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -4732,7 +4722,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"I"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -4743,7 +4733,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"l"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -4754,7 +4744,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"L"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -4765,7 +4755,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -4776,7 +4766,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -4787,7 +4777,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"f"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -4798,7 +4788,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"d"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -4809,7 +4799,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"g"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -4820,7 +4810,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zf"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -4831,7 +4821,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zd"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -4842,7 +4832,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zg"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -4854,7 +4844,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -4875,7 +4865,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -4884,7 +4874,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -4894,7 +4884,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -4903,7 +4893,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 * return * else: * info.format = PyObject_Malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -4913,7 +4903,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)PyObject_Malloc(0xFF)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 * else: * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -4922,7 +4912,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -4931,7 +4921,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -4941,7 +4931,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_8 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_8 == ((char *)NULL))) __PYX_ERR(1, 289, __pyx_L1_error) __pyx_v_f = __pyx_t_8; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -4951,7 +4941,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -4983,7 +4973,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -5007,7 +4997,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -5017,7 +5007,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) # <<<<<<<<<<<<<< @@ -5026,7 +5016,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->format); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -5035,7 +5025,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -5045,7 +5035,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * PyObject_Free(info.strides) # <<<<<<<<<<<<<< @@ -5054,7 +5044,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->strides); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -5063,7 +5053,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -5075,7 +5065,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -5089,7 +5079,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ PyObject *__pyx_t_1 = NULL; 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goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":791 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":791 * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< @@ -5355,7 +5345,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":794 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":794 * return d.subarray.shape * else: * return () # <<<<<<<<<<<<<< @@ -5369,7 +5359,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ goto __pyx_L0; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< @@ -5384,7 +5374,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -5413,7 +5403,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx char *__pyx_t_9; __Pyx_RefNannySetupContext("_util_dtypestring", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":801 * * cdef dtype child * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -5422,7 +5412,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_endian_detector = 1; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":802 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":802 * cdef dtype child * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -5431,7 +5421,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -5454,7 +5444,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":806 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":806 * * for childname in descr.names: * fields = descr.fields[childname] # <<<<<<<<<<<<<< @@ -5471,7 +5461,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3)); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":807 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":807 * for childname in descr.names: * fields = descr.fields[childname] * child, new_offset = fields # <<<<<<<<<<<<<< @@ -5506,7 +5496,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -5523,7 +5513,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -5536,7 +5526,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 810, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -5545,7 +5535,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -5565,7 +5555,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L8_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":813 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":813 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -5582,7 +5572,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = __pyx_t_7; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -5591,7 +5581,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -5604,7 +5594,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 814, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -5613,7 +5603,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -5629,7 +5619,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -5638,7 +5628,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -5647,7 +5637,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -5658,7 +5648,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -5668,7 +5658,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -5678,7 +5668,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -5690,7 +5680,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -5700,7 +5690,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -5713,7 +5703,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __PYX_ERR(1, 834, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -5722,7 +5712,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -5740,7 +5730,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -5758,7 +5748,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -5776,7 +5766,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -5794,7 +5784,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -5812,7 +5802,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -5830,7 +5820,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -5848,7 +5838,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -5866,7 +5856,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -5884,7 +5874,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -5902,7 +5892,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -5920,7 +5910,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -5938,7 +5928,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -5956,7 +5946,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -5976,7 +5966,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -5996,7 +5986,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -6016,7 +6006,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -6034,7 +6024,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -6053,7 +6043,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -6062,7 +6052,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -6072,7 +6062,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -6085,7 +6075,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -6095,7 +6085,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -6105,7 +6095,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -6130,7 +6120,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -6145,7 +6135,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -6156,7 +6146,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -6165,7 +6155,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_baseptr = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -6175,7 +6165,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a goto __pyx_L3; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -6185,7 +6175,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a /*else*/ { Py_INCREF(__pyx_v_base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -6196,7 +6186,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -6205,7 +6195,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -6214,7 +6204,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -6226,7 +6216,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -6240,7 +6230,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -6250,7 +6240,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< @@ -6261,7 +6251,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -6270,7 +6260,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 * return None * else: * return arr.base # <<<<<<<<<<<<<< @@ -6284,7 +6274,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py goto __pyx_L0; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -6299,7 +6289,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -6320,7 +6310,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_array", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -6336,7 +6326,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 * cdef inline int import_array() except -1: * try: * _import_array() # <<<<<<<<<<<<<< @@ -6345,7 +6335,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { */ __pyx_t_4 = _import_array(); 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__pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -6503,7 +6493,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -6519,7 +6509,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -6534,7 +6524,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -6557,7 +6547,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -6578,7 +6568,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_ufunc", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -6594,7 +6584,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1010 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1010 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -6603,7 +6593,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1010, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -6617,7 +6607,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1011 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1011 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -6631,7 +6621,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_GOTREF(__pyx_t_6); 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__Pyx_GIVEREF(__pyx_tuple__2); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -6822,7 +6812,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__3); __Pyx_GIVEREF(__pyx_tuple__3); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -6833,7 +6823,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__4); __Pyx_GIVEREF(__pyx_tuple__4); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -6844,7 +6834,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__5); __Pyx_GIVEREF(__pyx_tuple__5); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -6855,7 +6845,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__6); __Pyx_GIVEREF(__pyx_tuple__6); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -6866,7 +6856,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__7); __Pyx_GIVEREF(__pyx_tuple__7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -6877,7 +6867,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__8); __Pyx_GIVEREF(__pyx_tuple__8); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -7211,8 +7201,8 @@ static int __Pyx_modinit_function_import_code(void) { #ifndef CYTHON_SMALL_CODE #if defined(__clang__) #define CYTHON_SMALL_CODE -#elif defined(__GNUC__) - #define CYTHON_SMALL_CODE __attribute__((optimize("Os"))) +#elif defined(__GNUC__) && (!(defined(__cplusplus)) || (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 4))) + #define CYTHON_SMALL_CODE __attribute__((cold)) #else #define CYTHON_SMALL_CODE #endif @@ -7622,7 +7612,7 @@ if (!__Pyx_RefNanny) { if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) __PYX_ERR(0, 1, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -8330,7 +8320,7 @@ static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { /* SaveResetException */ #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 *type = tstate->exc_state.exc_type; *value = tstate->exc_state.exc_value; *tb = tstate->exc_state.exc_traceback; @@ -8345,7 +8335,7 @@ static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject * } static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -8429,7 +8419,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) *value = local_value; *tb = local_tb; #if CYTHON_FAST_THREAD_STATE - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -8534,6 +8524,9 @@ static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_li #if CYTHON_COMPILING_IN_CPYTHON PyObject **cython_runtime_dict; #endif + if (unlikely(!__pyx_cython_runtime)) { + return c_line; + } __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); #if CYTHON_COMPILING_IN_CPYTHON cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); @@ -9587,14 +9580,42 @@ static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, return res; } #endif +static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + assert(PyExceptionClass_Check(exc_type)); + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i #ifndef offsetof @@ -478,6 +478,7 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact + #define PyObject_Unicode PyObject_Str #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) @@ -677,7 +678,7 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); #define __Pyx_PySequence_Tuple(obj)\ @@ -785,7 +786,7 @@ static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } static PyObject *__pyx_m = NULL; static PyObject *__pyx_d; static PyObject *__pyx_b; -static PyObject *__pyx_cython_runtime; +static PyObject *__pyx_cython_runtime = NULL; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static PyObject *__pyx_empty_unicode; @@ -934,7 +935,7 @@ typedef struct { #define __Pyx_MemoryView_Len(m) (m.shape[0]) -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -943,7 +944,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -952,7 +953,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -961,7 +962,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -970,7 +971,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -979,7 +980,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -988,7 +989,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -997,7 +998,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1006,7 +1007,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -1015,7 +1016,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1024,7 +1025,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -1033,7 +1034,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -1042,7 +1043,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -1051,7 +1052,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -1060,7 +1061,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -1069,7 +1070,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1078,7 +1079,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1087,7 +1088,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1096,7 +1097,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1105,7 +1106,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1114,7 +1115,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1154,7 +1155,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1163,7 +1164,7 @@ struct __pyx_memoryviewslice_obj; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1172,7 +1173,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1181,7 +1182,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -2910,7 +2911,7 @@ static PyArrayObject *__pyx_f_10MDAnalysis_3lib_7formats_11cython_util_ptr_to_nd return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -2958,7 +2959,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); __Pyx_GIVEREF(__pyx_v_info->obj); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 * * cdef int i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -2967,7 +2968,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 * cdef int i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -2976,7 +2977,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -2985,7 +2986,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2999,7 +3000,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -3010,7 +3011,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L4_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -3019,7 +3020,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -3032,7 +3033,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(2, 229, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -3041,7 +3042,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -3055,7 +3056,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L7_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -3066,7 +3067,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -3075,7 +3076,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -3088,7 +3089,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(2, 233, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -3097,7 +3098,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -3106,7 +3107,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -3115,7 +3116,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -3125,7 +3126,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) # <<<<<<<<<<<<<< @@ -3134,7 +3135,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyObject_Malloc((((sizeof(Py_ssize_t)) * 2) * ((size_t)__pyx_v_ndim)))); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -3143,7 +3144,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -3155,7 +3156,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -3164,7 +3165,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -3174,7 +3175,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -3184,7 +3185,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -3194,7 +3195,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -3205,7 +3206,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L9:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -3214,7 +3215,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -3223,7 +3224,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -3232,7 +3233,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -3241,7 +3242,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -3253,7 +3254,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 * cdef int offset * * info.obj = self # <<<<<<<<<<<<<< @@ -3266,7 +3267,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -3276,7 +3277,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(PyDataType_HASFIELDS(__pyx_v_descr) != 0)) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 * * if not PyDataType_HASFIELDS(descr): * t = descr.type_num # <<<<<<<<<<<<<< @@ -3286,7 +3287,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -3306,7 +3307,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L15_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -3323,7 +3324,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L14_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -3332,7 +3333,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -3345,7 +3346,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(2, 263, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -3354,7 +3355,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -3366,7 +3367,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"b"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -3377,7 +3378,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"B"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -3388,7 +3389,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"h"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -3399,7 +3400,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"H"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -3410,7 +3411,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"i"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -3421,7 +3422,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"I"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -3432,7 +3433,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"l"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -3443,7 +3444,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"L"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -3454,7 +3455,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -3465,7 +3466,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -3476,7 +3477,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"f"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -3487,7 +3488,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"d"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -3498,7 +3499,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"g"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -3509,7 +3510,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zf"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -3520,7 +3521,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zd"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -3531,7 +3532,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zg"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -3543,7 +3544,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -3564,7 +3565,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -3573,7 +3574,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -3583,7 +3584,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -3592,7 +3593,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 * return * else: * info.format = PyObject_Malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -3602,7 +3603,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)PyObject_Malloc(0xFF)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 * else: * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -3611,7 +3612,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -3620,7 +3621,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -3630,7 +3631,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_8 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_8 == ((char *)NULL))) __PYX_ERR(2, 289, __pyx_L1_error) __pyx_v_f = __pyx_t_8; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -3640,7 +3641,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -3672,7 +3673,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -3696,7 +3697,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -3706,7 +3707,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) # <<<<<<<<<<<<<< @@ -3715,7 +3716,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->format); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -3724,7 +3725,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -3734,7 +3735,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * PyObject_Free(info.strides) # <<<<<<<<<<<<<< @@ -3743,7 +3744,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->strides); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -3752,7 +3753,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -3764,7 +3765,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -3778,7 +3779,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ PyObject *__pyx_t_1 = NULL; 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goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":791 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":791 * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< @@ -4044,7 +4045,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":794 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":794 * return d.subarray.shape * else: * return () # <<<<<<<<<<<<<< @@ -4058,7 +4059,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ goto __pyx_L0; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< @@ -4073,7 +4074,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -4102,7 +4103,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx char *__pyx_t_9; __Pyx_RefNannySetupContext("_util_dtypestring", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":801 * * cdef dtype child * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -4111,7 +4112,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_endian_detector = 1; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":802 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":802 * cdef dtype child * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -4120,7 +4121,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -4143,7 +4144,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":806 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":806 * * for childname in descr.names: * fields = descr.fields[childname] # <<<<<<<<<<<<<< @@ -4160,7 +4161,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3)); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":807 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":807 * for childname in descr.names: * fields = descr.fields[childname] * child, new_offset = fields # <<<<<<<<<<<<<< @@ -4195,7 +4196,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -4212,7 +4213,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -4225,7 +4226,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); 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__pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -4280,7 +4281,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -4293,7 +4294,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(2, 814, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -4302,7 +4303,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -4318,7 +4319,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -4327,7 +4328,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -4336,7 +4337,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -4347,7 +4348,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -4357,7 +4358,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -4367,7 +4368,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -4379,7 +4380,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -4389,7 +4390,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -4402,7 +4403,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __PYX_ERR(2, 834, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -4411,7 +4412,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -4429,7 +4430,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -4447,7 +4448,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -4465,7 +4466,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -4483,7 +4484,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -4501,7 +4502,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -4519,7 +4520,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -4537,7 +4538,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -4555,7 +4556,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -4573,7 +4574,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -4591,7 +4592,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -4609,7 +4610,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -4627,7 +4628,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -4645,7 +4646,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -4665,7 +4666,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -4685,7 +4686,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -4705,7 +4706,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -4723,7 +4724,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -4742,7 +4743,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -4751,7 +4752,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -4761,7 +4762,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -4774,7 +4775,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -4784,7 +4785,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -4794,7 +4795,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -4819,7 +4820,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -4834,7 +4835,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -4845,7 +4846,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -4854,7 +4855,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_baseptr = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -4864,7 +4865,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a goto __pyx_L3; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -4874,7 +4875,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a /*else*/ { Py_INCREF(__pyx_v_base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -4885,7 +4886,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -4894,7 +4895,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -4903,7 +4904,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -4915,7 +4916,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -4929,7 +4930,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -4939,7 +4940,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< @@ -4950,7 +4951,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -4959,7 +4960,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 * return None * else: * return arr.base # <<<<<<<<<<<<<< @@ -4973,7 +4974,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py goto __pyx_L0; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -4988,7 +4989,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -5009,7 +5010,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_array", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -5025,7 +5026,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 * cdef inline int import_array() except -1: * try: * _import_array() # <<<<<<<<<<<<<< @@ -5034,7 +5035,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { */ __pyx_t_4 = _import_array(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 998, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -5048,7 +5049,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 * try: * _import_array() * except Exception: # <<<<<<<<<<<<<< @@ -5063,7 +5064,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -5079,7 +5080,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -5094,7 +5095,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -5117,7 +5118,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -5138,7 +5139,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { PyObject *__pyx_t_8 = NULL; 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__pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -5192,7 +5193,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -5208,7 +5209,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -5223,7 +5224,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -5246,7 +5247,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -5267,7 +5268,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_ufunc", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -5283,7 +5284,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1010 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1010 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -5292,7 +5293,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 1010, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -5306,7 +5307,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1011 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1011 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -5320,7 +5321,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -5334,7 +5335,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -5349,7 +5350,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -19235,7 +19236,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__2); __Pyx_GIVEREF(__pyx_tuple__2); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -19246,7 +19247,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__3); __Pyx_GIVEREF(__pyx_tuple__3); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -19257,7 +19258,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__4); __Pyx_GIVEREF(__pyx_tuple__4); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -19268,7 +19269,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__5); __Pyx_GIVEREF(__pyx_tuple__5); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -19279,7 +19280,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__6); __Pyx_GIVEREF(__pyx_tuple__6); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -19290,7 +19291,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__7); __Pyx_GIVEREF(__pyx_tuple__7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -19301,7 +19302,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__8); __Pyx_GIVEREF(__pyx_tuple__8); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -19312,7 +19313,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__9); __Pyx_GIVEREF(__pyx_tuple__9); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -19323,7 +19324,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__10); __Pyx_GIVEREF(__pyx_tuple__10); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -19803,8 +19804,8 @@ static int __Pyx_modinit_function_import_code(void) { #ifndef CYTHON_SMALL_CODE #if defined(__clang__) #define CYTHON_SMALL_CODE -#elif defined(__GNUC__) - #define CYTHON_SMALL_CODE __attribute__((optimize("Os"))) +#elif defined(__GNUC__) && (!(defined(__cplusplus)) || (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 4))) + #define CYTHON_SMALL_CODE __attribute__((cold)) #else #define CYTHON_SMALL_CODE #endif @@ -20728,7 +20729,7 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { /* SaveResetException */ #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 *type = tstate->exc_state.exc_type; *value = tstate->exc_state.exc_value; *tb = tstate->exc_state.exc_traceback; @@ -20743,7 +20744,7 @@ static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject * } static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -20827,7 +20828,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) *value = local_value; *tb = local_tb; #if CYTHON_FAST_THREAD_STATE - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -21149,6 +21150,9 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } else { int result; PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif if (!py_result) return -1; result = __Pyx_PyObject_IsTrue(py_result); @@ -21357,7 +21361,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -21508,14 +21512,42 @@ static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, return res; } #endif +static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + assert(PyExceptionClass_Check(exc_type)); + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i #ifndef offsetof @@ -482,6 +482,7 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact + #define PyObject_Unicode PyObject_Str #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) @@ -685,7 +686,7 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); #define __Pyx_PySequence_Tuple(obj)\ @@ -793,7 +794,7 @@ static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } static PyObject *__pyx_m = NULL; static PyObject *__pyx_d; static PyObject *__pyx_b; -static PyObject *__pyx_cython_runtime; +static PyObject *__pyx_cython_runtime = NULL; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static PyObject *__pyx_empty_unicode; @@ -940,7 +941,7 @@ typedef struct { #define __Pyx_FastGilFuncInit() -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -949,7 +950,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -958,7 +959,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -967,7 +968,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -976,7 +977,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -985,7 +986,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -994,7 +995,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -1003,7 +1004,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1012,7 +1013,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -1021,7 +1022,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1030,7 +1031,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -1039,7 +1040,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -1048,7 +1049,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -1057,7 +1058,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -1066,7 +1067,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -1075,7 +1076,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1084,7 +1085,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1093,7 +1094,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1102,7 +1103,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1111,7 +1112,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1120,7 +1121,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1198,7 +1199,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1207,7 +1208,7 @@ struct __pyx_memoryviewslice_obj; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1216,7 +1217,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; 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if (unlikely(__pyx_t_1)) { - /* "MDAnalysis/lib/formats/libdcd.pyx":335 + /* "MDAnalysis/lib/formats/libdcd.pyx":337 * """read header and populate internal fields""" * if not self.is_open: * raise IOError("No file open") # <<<<<<<<<<<<<< * * cdef char* c_remarks */ - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 335, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 337, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __PYX_ERR(0, 335, __pyx_L1_error) + __PYX_ERR(0, 337, __pyx_L1_error) - /* "MDAnalysis/lib/formats/libdcd.pyx":334 + /* "MDAnalysis/lib/formats/libdcd.pyx":336 * cdef void _read_header(self): * """read header and populate internal fields""" * if not self.is_open: # <<<<<<<<<<<<<< @@ -5298,7 +5384,7 @@ static void __pyx_f_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile__read_header(str */ } - /* "MDAnalysis/lib/formats/libdcd.pyx":338 + /* "MDAnalysis/lib/formats/libdcd.pyx":340 * * cdef char* c_remarks * cdef int len_remarks = 0 # <<<<<<<<<<<<<< @@ -5307,7 +5393,7 @@ static void __pyx_f_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile__read_header(str */ __pyx_v_len_remarks = 0; 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__pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/libdcd.pyx":372 + /* "MDAnalysis/lib/formats/libdcd.pyx":374 * if sys.version_info[0] < 3: * py_remarks = unicode(py_remarks, 'ascii', "ignore") * py_remarks = str(py_remarks.encode('ascii', 'ignore')) # <<<<<<<<<<<<<< * else: * if isinstance(py_remarks, bytes): */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_cur_scope->__pyx_v_py_remarks, __pyx_n_s_encode); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 372, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_cur_scope->__pyx_v_py_remarks, __pyx_n_s_encode); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 374, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__7, NULL); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 372, __pyx_L1_error) + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__8, NULL); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 374, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_t_6); 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- /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -11543,7 +11602,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -11555,7 +11614,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -11564,7 +11623,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -11574,7 +11633,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -11584,7 +11643,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -11594,7 +11653,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -11605,7 +11664,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L9:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -11614,7 +11673,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -11623,7 +11682,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -11632,7 +11691,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -11641,7 +11700,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -11653,7 +11712,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 * cdef int offset * * info.obj = self # <<<<<<<<<<<<<< @@ -11666,7 +11725,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -11676,7 +11735,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(PyDataType_HASFIELDS(__pyx_v_descr) != 0)) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 * * if not PyDataType_HASFIELDS(descr): * t = descr.type_num # <<<<<<<<<<<<<< @@ -11686,7 +11745,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -11706,7 +11765,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L15_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -11723,7 +11782,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L14_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -11732,20 +11791,20 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__53, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 263, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__54, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 263, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 263, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -11754,7 +11813,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -11766,7 +11825,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"b"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -11777,7 +11836,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"B"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -11788,7 +11847,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"h"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -11799,7 +11858,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"H"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -11810,7 +11869,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"i"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -11821,7 +11880,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"I"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -11832,7 +11891,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"l"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -11843,7 +11902,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"L"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -11854,7 +11913,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -11865,7 +11924,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -11876,7 +11935,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"f"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -11887,7 +11946,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"d"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -11898,7 +11957,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"g"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -11909,7 +11968,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zf"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -11920,7 +11979,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zd"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -11931,7 +11990,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zg"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -11943,7 +12002,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -11964,7 +12023,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -11973,7 +12032,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -11983,7 +12042,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -11992,7 +12051,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 * return * else: * info.format = PyObject_Malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -12002,7 +12061,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)PyObject_Malloc(0xFF)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 * else: * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -12011,7 +12070,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -12020,7 +12079,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -12030,7 +12089,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_8 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); 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} -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -12096,7 +12155,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -12106,7 +12165,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) # <<<<<<<<<<<<<< @@ -12115,7 +12174,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->format); 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if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 810, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__55, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 810, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 810, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -12634,7 +12693,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -12654,7 +12713,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L8_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":813 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":813 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -12671,7 +12730,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = __pyx_t_7; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -12680,20 +12739,20 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * # One could encode it in the format string and have Cython * # complain instead, BUT: < and > in format strings also imply */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__55, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 814, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__56, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 814, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 814, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -12702,7 +12761,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -12718,7 +12777,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -12727,7 +12786,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -12736,7 +12795,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -12747,7 +12806,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -12757,7 +12816,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -12767,7 +12826,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -12779,7 +12838,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -12789,20 +12848,20 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< * * # Until ticket #99 is fixed, use integers to avoid warnings */ - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__56, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 834, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__57, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 834, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __PYX_ERR(1, 834, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -12811,7 +12870,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -12829,7 +12888,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -12847,7 +12906,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -12865,7 +12924,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -12883,7 +12942,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -12901,7 +12960,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -12919,7 +12978,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -12937,7 +12996,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -12955,7 +13014,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -12973,7 +13032,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -12991,7 +13050,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -13009,7 +13068,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -13027,7 +13086,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -13045,7 +13104,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -13065,7 +13124,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -13085,7 +13144,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -13105,7 +13164,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -13123,7 +13182,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -13142,7 +13201,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -13151,7 +13210,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -13161,7 +13220,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -13174,7 +13233,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -13184,7 +13243,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -13194,7 +13253,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -13219,7 +13278,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -13234,7 +13293,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -13245,7 +13304,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -13254,7 +13313,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_baseptr = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -13264,7 +13323,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a goto __pyx_L3; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -13274,7 +13333,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a /*else*/ { Py_INCREF(__pyx_v_base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -13285,7 +13344,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -13294,7 +13353,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -13303,7 +13362,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -13315,7 +13374,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -13329,7 +13388,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -13339,7 +13398,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< @@ -13350,7 +13409,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -13359,7 +13418,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 * return None * else: * return arr.base # <<<<<<<<<<<<<< @@ -13373,7 +13432,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py goto __pyx_L0; 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/*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 * cdef inline int import_array() except -1: * try: * _import_array() # <<<<<<<<<<<<<< @@ -13434,7 +13493,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { */ __pyx_t_4 = _import_array(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 998, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -13448,7 +13507,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 * try: * _import_array() * except Exception: # <<<<<<<<<<<<<< @@ -13463,14 +13522,14 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_GOTREF(__pyx_t_6); 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PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact + #define PyObject_Unicode PyObject_Str #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) @@ -709,7 +710,7 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); #define __Pyx_PySequence_Tuple(obj)\ @@ -817,7 +818,7 @@ static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } static PyObject *__pyx_m = NULL; static PyObject *__pyx_d; static PyObject *__pyx_b; -static PyObject *__pyx_cython_runtime; +static PyObject *__pyx_cython_runtime = NULL; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static PyObject *__pyx_empty_unicode; @@ -964,7 +965,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -973,7 +974,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -982,7 +983,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -991,7 +992,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -1000,7 +1001,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -1009,7 +1010,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -1018,7 +1019,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -1027,7 +1028,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1036,7 +1037,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -1045,7 +1046,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1054,7 +1055,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -1063,7 +1064,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -1072,7 +1073,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -1081,7 +1082,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -1090,7 +1091,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -1099,7 +1100,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1108,7 +1109,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1117,7 +1118,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1126,7 +1127,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1135,7 +1136,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1144,7 +1145,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1195,7 +1196,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1204,7 +1205,7 @@ struct __pyx_memoryviewslice_obj; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1213,7 +1214,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1222,7 +1223,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -10793,7 +10794,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7XTCFile_6write( return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -10841,7 +10842,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); __Pyx_GIVEREF(__pyx_v_info->obj); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 * * cdef int i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -10850,7 +10851,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 * cdef int i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -10859,7 +10860,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -10868,7 +10869,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -10882,7 +10883,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -10893,7 +10894,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L4_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -10902,7 +10903,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -10915,7 +10916,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 229, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -10924,7 +10925,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -10938,7 +10939,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L7_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -10949,7 +10950,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -10958,7 +10959,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -10971,7 +10972,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 233, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -10980,7 +10981,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -10989,7 +10990,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -10998,7 +10999,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -11008,7 +11009,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) # <<<<<<<<<<<<<< @@ -11017,7 +11018,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyObject_Malloc((((sizeof(Py_ssize_t)) * 2) * ((size_t)__pyx_v_ndim)))); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -11026,7 +11027,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -11038,7 +11039,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -11047,7 +11048,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -11057,7 +11058,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -11067,7 +11068,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -11077,7 +11078,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -11088,7 +11089,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L9:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -11097,7 +11098,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -11106,7 +11107,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -11115,7 +11116,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -11124,7 +11125,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -11136,7 +11137,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 * cdef int offset * * info.obj = self # <<<<<<<<<<<<<< @@ -11149,7 +11150,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -11159,7 +11160,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(PyDataType_HASFIELDS(__pyx_v_descr) != 0)) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 * * if not PyDataType_HASFIELDS(descr): * t = descr.type_num # <<<<<<<<<<<<<< @@ -11169,7 +11170,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -11189,7 +11190,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L15_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -11206,7 +11207,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L14_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -11215,7 +11216,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -11228,7 +11229,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 263, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -11237,7 +11238,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -11249,7 +11250,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"b"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -11260,7 +11261,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"B"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -11271,7 +11272,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"h"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -11282,7 +11283,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"H"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -11293,7 +11294,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"i"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -11304,7 +11305,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"I"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -11315,7 +11316,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"l"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -11326,7 +11327,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"L"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -11337,7 +11338,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -11348,7 +11349,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -11359,7 +11360,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"f"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -11370,7 +11371,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"d"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -11381,7 +11382,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"g"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -11392,7 +11393,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zf"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -11403,7 +11404,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zd"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -11414,7 +11415,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zg"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -11426,7 +11427,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -11447,7 +11448,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -11456,7 +11457,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -11466,7 +11467,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -11475,7 +11476,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 * return * else: * info.format = PyObject_Malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -11485,7 +11486,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)PyObject_Malloc(0xFF)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 * else: * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -11494,7 +11495,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -11503,7 +11504,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -11513,7 +11514,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_8 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_8 == ((char *)NULL))) __PYX_ERR(1, 289, __pyx_L1_error) __pyx_v_f = __pyx_t_8; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -11523,7 +11524,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -11555,7 +11556,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -11579,7 +11580,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -11589,7 +11590,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) # <<<<<<<<<<<<<< @@ -11598,7 +11599,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->format); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -11607,7 +11608,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -11617,7 +11618,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* 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"../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -12137,7 +12138,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L8_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":813 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":813 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -12154,7 +12155,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = __pyx_t_7; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -12163,7 +12164,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -12176,7 +12177,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 814, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -12185,7 +12186,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -12201,7 +12202,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -12210,7 +12211,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -12219,7 +12220,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -12230,7 +12231,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -12240,7 +12241,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -12250,7 +12251,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -12262,7 +12263,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -12272,7 +12273,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -12285,7 +12286,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __PYX_ERR(1, 834, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -12294,7 +12295,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -12312,7 +12313,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -12330,7 +12331,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -12348,7 +12349,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -12366,7 +12367,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -12384,7 +12385,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -12402,7 +12403,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -12420,7 +12421,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -12438,7 +12439,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -12456,7 +12457,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -12474,7 +12475,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -12492,7 +12493,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -12510,7 +12511,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -12528,7 +12529,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -12548,7 +12549,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -12568,7 +12569,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -12588,7 +12589,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -12606,7 +12607,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -12625,7 +12626,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -12634,7 +12635,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -12644,7 +12645,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -12657,7 +12658,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -12667,7 +12668,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -12677,7 +12678,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -12702,7 +12703,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -12717,7 +12718,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -12728,7 +12729,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -12737,7 +12738,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_baseptr = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -12747,7 +12748,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a goto __pyx_L3; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -12757,7 +12758,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a /*else*/ { Py_INCREF(__pyx_v_base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -12768,7 +12769,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -12777,7 +12778,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -12786,7 +12787,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -12798,7 +12799,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 +/* 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"../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< @@ -12833,7 +12834,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -12842,7 +12843,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 * return None * else: * return arr.base # <<<<<<<<<<<<<< @@ -12856,7 +12857,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py goto __pyx_L0; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -12871,7 +12872,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -12892,7 +12893,7 @@ static CYTHON_INLINE int 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__pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -12931,7 +12932,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 * try: * _import_array() * except Exception: # <<<<<<<<<<<<<< @@ -12946,7 +12947,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -12962,7 +12963,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -12977,7 +12978,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -13000,7 +13001,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -13021,7 +13022,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_umath", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -13037,7 +13038,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1004 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1004 * cdef inline int import_umath() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -13046,7 +13047,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1004, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -13060,7 +13061,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -13075,7 +13076,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -13091,7 +13092,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* 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"../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -13217,7 +13218,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -13232,7 +13233,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -27580,7 +27581,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__12); __Pyx_GIVEREF(__pyx_tuple__12); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -27591,7 +27592,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__13); __Pyx_GIVEREF(__pyx_tuple__13); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -27602,7 +27603,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__14); __Pyx_GIVEREF(__pyx_tuple__14); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -27613,7 +27614,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__15); __Pyx_GIVEREF(__pyx_tuple__15); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -27624,7 +27625,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__16); __Pyx_GIVEREF(__pyx_tuple__16); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -27635,7 +27636,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__17); __Pyx_GIVEREF(__pyx_tuple__17); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -27646,7 +27647,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__18); __Pyx_GIVEREF(__pyx_tuple__18); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -27657,7 +27658,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__19); __Pyx_GIVEREF(__pyx_tuple__19); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -27668,7 +27669,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__20); __Pyx_GIVEREF(__pyx_tuple__20); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -28194,8 +28195,8 @@ static int __Pyx_modinit_function_import_code(void) { #ifndef CYTHON_SMALL_CODE #if defined(__clang__) #define CYTHON_SMALL_CODE -#elif defined(__GNUC__) - #define CYTHON_SMALL_CODE __attribute__((optimize("Os"))) +#elif defined(__GNUC__) && (!(defined(__cplusplus)) || (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 4))) + #define CYTHON_SMALL_CODE __attribute__((cold)) #else #define CYTHON_SMALL_CODE #endif @@ -29658,6 +29659,9 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject } else { int result; PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif if (!py_result) return -1; result = __Pyx_PyObject_IsTrue(py_result); @@ -29873,7 +29877,7 @@ static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED /* SaveResetException */ #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 *type = tstate->exc_state.exc_type; *value = tstate->exc_state.exc_value; *tb = tstate->exc_state.exc_traceback; @@ -29888,7 +29892,7 @@ static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject * } static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -29972,7 +29976,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) *value = local_value; *tb = local_tb; #if CYTHON_FAST_THREAD_STATE - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -30363,7 +30367,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; - #if PY_VERSION_HEX >= 0x030700A2 + #if PY_VERSION_HEX >= 0x030700A3 tmp_type = tstate->exc_state.exc_type; tmp_value = tstate->exc_state.exc_value; tmp_tb = tstate->exc_state.exc_traceback; @@ -30514,14 +30518,42 @@ static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, return res; } #endif +static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + assert(PyExceptionClass_Check(exc_type)); + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i +#ifndef offsetof + #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#endif +#if !defined(WIN32) && !defined(MS_WINDOWS) + #ifndef __stdcall + #define __stdcall + #endif + #ifndef __cdecl + #define __cdecl + #endif + #ifndef __fastcall + #define __fastcall + #endif +#endif +#ifndef DL_IMPORT + #define DL_IMPORT(t) t +#endif +#ifndef DL_EXPORT + #define DL_EXPORT(t) t +#endif +#define __PYX_COMMA , +#ifndef HAVE_LONG_LONG + #if PY_VERSION_HEX >= 0x02070000 + #define HAVE_LONG_LONG + #endif +#endif +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif +#ifdef PYPY_VERSION + #define CYTHON_COMPILING_IN_PYPY 1 + #define CYTHON_COMPILING_IN_PYSTON 0 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #undef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 0 + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #if PY_VERSION_HEX < 0x03050000 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #elif !defined(CYTHON_USE_ASYNC_SLOTS) + #define CYTHON_USE_ASYNC_SLOTS 1 + #endif + #undef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 0 + #undef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 0 + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #undef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 1 + #undef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 0 + #undef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 0 + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 0 + #undef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT 0 + #undef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE 0 +#elif defined(PYSTON_VERSION) + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_PYSTON 1 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #ifndef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 1 + #endif + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #undef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 0 + #ifndef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 1 + #endif + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #ifndef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 0 + #endif + #ifndef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 1 + #endif + #ifndef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 1 + #endif + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 0 + #undef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT 0 + #undef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE 0 +#else + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_PYSTON 0 + #define CYTHON_COMPILING_IN_CPYTHON 1 + #ifndef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 1 + #endif + #if PY_VERSION_HEX < 0x02070000 + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #elif !defined(CYTHON_USE_PYTYPE_LOOKUP) + #define CYTHON_USE_PYTYPE_LOOKUP 1 + #endif + #if PY_MAJOR_VERSION < 3 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #elif !defined(CYTHON_USE_ASYNC_SLOTS) + #define CYTHON_USE_ASYNC_SLOTS 1 + #endif + #if PY_VERSION_HEX < 0x02070000 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #elif !defined(CYTHON_USE_PYLONG_INTERNALS) + #define CYTHON_USE_PYLONG_INTERNALS 1 + #endif + #ifndef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 1 + #endif + #ifndef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 1 + #endif + #if PY_VERSION_HEX < 0x030300F0 + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #elif !defined(CYTHON_USE_UNICODE_WRITER) + #define CYTHON_USE_UNICODE_WRITER 1 + #endif + #ifndef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 0 + #endif + #ifndef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 1 + #endif + #ifndef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 1 + #endif + #ifndef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 1 + #endif + #ifndef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 1 + #endif + #ifndef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT (0 && PY_VERSION_HEX >= 0x03050000) + #endif + #ifndef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1) + #endif +#endif +#if !defined(CYTHON_FAST_PYCCALL) +#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) +#endif +#if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" + #undef SHIFT + #undef BASE + #undef MASK +#endif +#ifndef __has_attribute + #define __has_attribute(x) 0 +#endif +#ifndef __has_cpp_attribute + #define __has_cpp_attribute(x) 0 +#endif +#ifndef CYTHON_RESTRICT + #if defined(__GNUC__) + #define CYTHON_RESTRICT __restrict__ + #elif defined(_MSC_VER) && _MSC_VER >= 1400 + #define CYTHON_RESTRICT __restrict + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_RESTRICT restrict + #else + #define CYTHON_RESTRICT + #endif +#endif +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +#ifndef CYTHON_MAYBE_UNUSED_VAR +# if defined(__cplusplus) + template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } +# else +# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) +# endif +#endif +#ifndef CYTHON_NCP_UNUSED +# if CYTHON_COMPILING_IN_CPYTHON +# define CYTHON_NCP_UNUSED +# else +# define CYTHON_NCP_UNUSED CYTHON_UNUSED +# endif +#endif +#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) +#ifdef _MSC_VER + #ifndef _MSC_STDINT_H_ + #if _MSC_VER < 1300 + typedef unsigned char uint8_t; + typedef unsigned int uint32_t; + #else + typedef unsigned __int8 uint8_t; + typedef unsigned __int32 uint32_t; + #endif + #endif +#else + #include +#endif +#ifndef CYTHON_FALLTHROUGH + #if defined(__cplusplus) && __cplusplus >= 201103L + #if __has_cpp_attribute(fallthrough) + #define CYTHON_FALLTHROUGH [[fallthrough]] + #elif __has_cpp_attribute(clang::fallthrough) + #define CYTHON_FALLTHROUGH [[clang::fallthrough]] + #elif __has_cpp_attribute(gnu::fallthrough) + #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] + #endif + #endif + #ifndef CYTHON_FALLTHROUGH + #if __has_attribute(fallthrough) + #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) + #else + #define CYTHON_FALLTHROUGH + #endif + #endif + #if defined(__clang__ ) && defined(__apple_build_version__) + #if __apple_build_version__ < 7000000 + #undef CYTHON_FALLTHROUGH + #define CYTHON_FALLTHROUGH + #endif + #endif +#endif + +#ifndef __cplusplus + #error "Cython files generated with the C++ option must be compiled with a C++ compiler." +#endif +#ifndef CYTHON_INLINE + #if defined(__clang__) + #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) + #else + #define CYTHON_INLINE inline + #endif +#endif +template +void __Pyx_call_destructor(T& x) { + x.~T(); +} +template +class __Pyx_FakeReference { + public: + __Pyx_FakeReference() : ptr(NULL) { } + __Pyx_FakeReference(const T& ref) : ptr(const_cast(&ref)) { } + T *operator->() { return ptr; } + T *operator&() { return ptr; } + operator T&() { return *ptr; } + template bool operator ==(U other) { return *ptr == other; } + template bool operator !=(U other) { return *ptr != other; } + private: + T *ptr; +}; + +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) + #define Py_OptimizeFlag 0 +#endif +#define __PYX_BUILD_PY_SSIZE_T "n" +#define CYTHON_FORMAT_SSIZE_T "z" +#if PY_MAJOR_VERSION < 3 + #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyClass_Type +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyType_Type +#endif +#ifndef Py_TPFLAGS_CHECKTYPES + #define Py_TPFLAGS_CHECKTYPES 0 +#endif +#ifndef Py_TPFLAGS_HAVE_INDEX + #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#ifndef Py_TPFLAGS_HAVE_NEWBUFFER + #define Py_TPFLAGS_HAVE_NEWBUFFER 0 +#endif +#ifndef Py_TPFLAGS_HAVE_FINALIZE + #define Py_TPFLAGS_HAVE_FINALIZE 0 +#endif +#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) + #ifndef METH_FASTCALL + #define METH_FASTCALL 0x80 + #endif + typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); + typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, + Py_ssize_t nargs, PyObject *kwnames); +#else + #define __Pyx_PyCFunctionFast _PyCFunctionFast + #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords +#endif +#if CYTHON_FAST_PYCCALL +#define __Pyx_PyFastCFunction_Check(func)\ + ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS))))) +#else +#define __Pyx_PyFastCFunction_Check(func) 0 +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) + #define PyObject_Malloc(s) PyMem_Malloc(s) + #define PyObject_Free(p) PyMem_Free(p) + #define PyObject_Realloc(p) PyMem_Realloc(p) +#endif +#if CYTHON_COMPILING_IN_PYSTON + #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) + #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) +#else + #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) + #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) +#endif +#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 + #define __Pyx_PyThreadState_Current PyThreadState_GET() +#elif PY_VERSION_HEX >= 0x03060000 + #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() +#elif PY_VERSION_HEX >= 0x03000000 + #define __Pyx_PyThreadState_Current PyThreadState_GET() +#else + #define __Pyx_PyThreadState_Current _PyThreadState_Current +#endif +#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) +#include "pythread.h" +#define Py_tss_NEEDS_INIT 0 +typedef int Py_tss_t; +static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { + *key = PyThread_create_key(); + return 0; // PyThread_create_key reports success always +} +static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { + Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); + *key = Py_tss_NEEDS_INIT; + return key; +} +static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { + PyObject_Free(key); +} +static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { + return *key != Py_tss_NEEDS_INIT; +} +static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { + PyThread_delete_key(*key); + *key = Py_tss_NEEDS_INIT; +} +static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { + return PyThread_set_key_value(*key, value); +} +static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { + return PyThread_get_key_value(*key); +} +#endif // TSS (Thread Specific Storage) API +#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) +#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) +#else +#define __Pyx_PyDict_NewPresized(n) PyDict_New() +#endif +#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS +#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) +#else +#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) +#endif +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) + #define CYTHON_PEP393_ENABLED 1 + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) + #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) + #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) + #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) +#else + #define CYTHON_PEP393_ENABLED 0 + #define PyUnicode_1BYTE_KIND 1 + #define PyUnicode_2BYTE_KIND 2 + #define PyUnicode_4BYTE_KIND 4 + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) + #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) + #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) + #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) + #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) +#endif +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) +#else + #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ + PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) + #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) + #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) + #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) +#endif +#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) +#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) +#else + #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) +#endif +#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII) + #define PyObject_ASCII(o) PyObject_Repr(o) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBaseString_Type PyUnicode_Type + #define PyStringObject PyUnicodeObject + #define PyString_Type PyUnicode_Type + #define PyString_Check PyUnicode_Check + #define PyString_CheckExact PyUnicode_CheckExact + #define PyObject_Unicode PyObject_Str +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) + #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) +#else + #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) + #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) +#endif +#ifndef PySet_CheckExact + #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) +#endif +#if CYTHON_ASSUME_SAFE_MACROS + #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq) +#else + #define __Pyx_PySequence_SIZE(seq) PySequence_Size(seq) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyIntObject PyLongObject + #define PyInt_Type PyLong_Type + #define PyInt_Check(op) PyLong_Check(op) + #define PyInt_CheckExact(op) PyLong_CheckExact(op) + #define PyInt_FromString PyLong_FromString + #define PyInt_FromUnicode PyLong_FromUnicode + #define PyInt_FromLong PyLong_FromLong + #define PyInt_FromSize_t PyLong_FromSize_t + #define PyInt_FromSsize_t PyLong_FromSsize_t + #define PyInt_AsLong PyLong_AsLong + #define PyInt_AS_LONG PyLong_AS_LONG + #define PyInt_AsSsize_t PyLong_AsSsize_t + #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask + #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask + #define PyNumber_Int PyNumber_Long +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBoolObject PyLongObject +#endif +#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY + #ifndef PyUnicode_InternFromString + #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) + #endif +#endif +#if PY_VERSION_HEX < 0x030200A4 + typedef long Py_hash_t; + #define __Pyx_PyInt_FromHash_t PyInt_FromLong + #define __Pyx_PyInt_AsHash_t PyInt_AsLong +#else + #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t + #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : (Py_INCREF(func), func)) +#else + #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) +#endif +#if CYTHON_USE_ASYNC_SLOTS + #if PY_VERSION_HEX >= 0x030500B1 + #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods + #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) + #else + #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) + #endif +#else + #define __Pyx_PyType_AsAsync(obj) NULL +#endif +#ifndef __Pyx_PyAsyncMethodsStruct + typedef struct { + unaryfunc am_await; + unaryfunc am_aiter; + unaryfunc am_anext; + } __Pyx_PyAsyncMethodsStruct; +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) + #define _USE_MATH_DEFINES +#endif +#include +#ifdef NAN +#define __PYX_NAN() ((float) NAN) +#else +static CYTHON_INLINE float __PYX_NAN() { + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif +#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL) +#define __Pyx_truncl trunc +#else +#define __Pyx_truncl truncl +#endif + + +#define __PYX_ERR(f_index, lineno, Ln_error) \ +{ \ + __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; goto Ln_error; \ +} + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#define __PYX_HAVE__MDAnalysis__lib__nsgrid +#define __PYX_HAVE_API__MDAnalysis__lib__nsgrid +/* Early includes */ +#include +#include "ios" +#include "new" +#include "stdexcept" +#include "typeinfo" +#include +#include +#include +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" +#include "pythread.h" +#include +#include "pystate.h" +#ifdef _OPENMP +#include +#endif /* _OPENMP */ + +#if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS) +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 +#define __PYX_DEFAULT_STRING_ENCODING "" +#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#define __Pyx_uchar_cast(c) ((unsigned char)c) +#define __Pyx_long_cast(x) ((long)x) +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ + (sizeof(type) < sizeof(Py_ssize_t)) ||\ + (sizeof(type) > sizeof(Py_ssize_t) &&\ + likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX) &&\ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ + v == (type)PY_SSIZE_T_MIN))) ||\ + (sizeof(type) == sizeof(Py_ssize_t) &&\ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX))) ) +#if defined (__cplusplus) && __cplusplus >= 201103L + #include + #define __Pyx_sst_abs(value) std::abs(value) +#elif SIZEOF_INT >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) abs(value) +#elif SIZEOF_LONG >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) labs(value) +#elif defined (_MSC_VER) + #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value)) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) +#elif defined (__GNUC__) + #define __Pyx_sst_abs(value) __builtin_llabs(value) +#else + #define __Pyx_sst_abs(value) ((value<0) ? -value : value) +#endif +static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) +#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#else + #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#endif +#define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) +static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { + const Py_UNICODE *u_end = u; + while (*u_end++) ; + return (size_t)(u_end - u - 1); +} +#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) +#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode +#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode +#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) +#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); +#define __Pyx_PySequence_Tuple(obj)\ + (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj)) +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +#if CYTHON_ASSUME_SAFE_MACROS +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) +#else +#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) +#endif +#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x)) +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII +static int __Pyx_sys_getdefaultencoding_not_ascii; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + PyObject* ascii_chars_u = NULL; + PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { + __Pyx_sys_getdefaultencoding_not_ascii = 0; + } else { + char ascii_chars[128]; + int c; + for (c = 0; c < 128; c++) { + ascii_chars[c] = c; + } + __Pyx_sys_getdefaultencoding_not_ascii = 1; + ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); + if (!ascii_chars_u) goto bad; + ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + PyErr_Format( + PyExc_ValueError, + "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", + default_encoding_c); + goto bad; + } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); + } + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + Py_XDECREF(ascii_chars_u); + Py_XDECREF(ascii_chars_b); + return -1; +} +#endif +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) +#else +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +static char* __PYX_DEFAULT_STRING_ENCODING; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; + strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + return -1; +} +#endif +#endif + + +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ + #define likely(x) (x) + #define unlikely(x) (x) +#endif /* __GNUC__ */ +static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } + +static PyObject *__pyx_m = NULL; +static PyObject *__pyx_d; +static PyObject *__pyx_b; +static PyObject *__pyx_cython_runtime = NULL; +static PyObject *__pyx_empty_tuple; +static PyObject *__pyx_empty_bytes; +static PyObject *__pyx_empty_unicode; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; + +/* Header.proto */ +#if !defined(CYTHON_CCOMPLEX) + #if defined(__cplusplus) + #define CYTHON_CCOMPLEX 1 + #elif defined(_Complex_I) + #define CYTHON_CCOMPLEX 1 + #else + #define CYTHON_CCOMPLEX 0 + #endif +#endif +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #include + #else + #include + #endif +#endif +#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) + #undef _Complex_I + #define _Complex_I 1.0fj +#endif + + +static const char *__pyx_f[] = { + "MDAnalysis/lib/nsgrid.pyx", + "stringsource", + "__init__.pxd", + "type.pxd", +}; +/* MemviewSliceStruct.proto */ +struct __pyx_memoryview_obj; +typedef struct { + struct __pyx_memoryview_obj *memview; + char *data; + Py_ssize_t shape[8]; + Py_ssize_t strides[8]; + Py_ssize_t suboffsets[8]; +} __Pyx_memviewslice; +#define __Pyx_MemoryView_Len(m) (m.shape[0]) + +/* Atomics.proto */ +#include +#ifndef CYTHON_ATOMICS + #define CYTHON_ATOMICS 1 +#endif +#define __pyx_atomic_int_type int +#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 ||\ + (__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) &&\ + !defined(__i386__) + #define __pyx_atomic_incr_aligned(value, lock) __sync_fetch_and_add(value, 1) + #define __pyx_atomic_decr_aligned(value, lock) __sync_fetch_and_sub(value, 1) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using GNU atomics" + #endif +#elif CYTHON_ATOMICS && defined(_MSC_VER) && 0 + #include + #undef __pyx_atomic_int_type + #define __pyx_atomic_int_type LONG + #define __pyx_atomic_incr_aligned(value, lock) InterlockedIncrement(value) + #define __pyx_atomic_decr_aligned(value, lock) InterlockedDecrement(value) + #ifdef __PYX_DEBUG_ATOMICS + #pragma message ("Using MSVC atomics") + #endif +#elif CYTHON_ATOMICS && (defined(__ICC) || defined(__INTEL_COMPILER)) && 0 + #define __pyx_atomic_incr_aligned(value, lock) _InterlockedIncrement(value) + #define __pyx_atomic_decr_aligned(value, lock) _InterlockedDecrement(value) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using Intel atomics" + #endif +#else + #undef CYTHON_ATOMICS + #define CYTHON_ATOMICS 0 + #ifdef __PYX_DEBUG_ATOMICS + #warning "Not using atomics" + #endif +#endif +typedef volatile __pyx_atomic_int_type __pyx_atomic_int; +#if CYTHON_ATOMICS + #define __pyx_add_acquisition_count(memview)\ + __pyx_atomic_incr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) + #define __pyx_sub_acquisition_count(memview)\ + __pyx_atomic_decr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) +#else + #define __pyx_add_acquisition_count(memview)\ + __pyx_add_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) + #define __pyx_sub_acquisition_count(memview)\ + __pyx_sub_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) +#endif + +/* ForceInitThreads.proto */ +#ifndef __PYX_FORCE_INIT_THREADS + #define __PYX_FORCE_INIT_THREADS 0 +#endif + +/* NoFastGil.proto */ +#define __Pyx_PyGILState_Ensure PyGILState_Ensure +#define __Pyx_PyGILState_Release PyGILState_Release +#define __Pyx_FastGIL_Remember() +#define __Pyx_FastGIL_Forget() +#define __Pyx_FastGilFuncInit() + +/* BufferFormatStructs.proto */ +#define IS_UNSIGNED(type) (((type) -1) > 0) +struct __Pyx_StructField_; +#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) +typedef struct { + const char* name; + struct __Pyx_StructField_* fields; + size_t size; + size_t arraysize[8]; + int ndim; + char typegroup; + char is_unsigned; + int flags; +} __Pyx_TypeInfo; +typedef struct __Pyx_StructField_ { + __Pyx_TypeInfo* type; + const char* name; + size_t offset; +} __Pyx_StructField; +typedef struct { + __Pyx_StructField* field; + size_t parent_offset; +} __Pyx_BufFmt_StackElem; +typedef struct { + __Pyx_StructField root; + __Pyx_BufFmt_StackElem* head; + size_t fmt_offset; + size_t new_count, enc_count; + size_t struct_alignment; + int is_complex; + char enc_type; + char new_packmode; + char enc_packmode; + char is_valid_array; +} __Pyx_BufFmt_Context; + + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 + * # in Cython to enable them only on the right systems. + * + * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + */ +typedef npy_int8 __pyx_t_5numpy_int8_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 + * + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t + */ +typedef npy_int16 __pyx_t_5numpy_int16_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< + * #ctypedef npy_int96 int96_t + * #ctypedef npy_int128 int128_t + */ +typedef npy_int64 __pyx_t_5numpy_int64_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 + * #ctypedef npy_int128 int128_t + * + * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + */ +typedef npy_uint8 __pyx_t_5numpy_uint8_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 + * + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t + */ +typedef npy_uint16 __pyx_t_5numpy_uint16_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< + * #ctypedef npy_uint96 uint96_t + * #ctypedef npy_uint128 uint128_t + */ +typedef npy_uint64 __pyx_t_5numpy_uint64_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 + * #ctypedef npy_uint128 uint128_t + * + * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< + * ctypedef npy_float64 float64_t + * #ctypedef npy_float80 float80_t + */ +typedef npy_float32 __pyx_t_5numpy_float32_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 + * + * ctypedef npy_float32 float32_t + * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< + * #ctypedef npy_float80 float80_t + * #ctypedef npy_float128 float128_t + */ +typedef npy_float64 __pyx_t_5numpy_float64_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 + * # The int types are mapped a bit surprising -- + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t + */ +typedef npy_long __pyx_t_5numpy_int_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong longlong_t + * + */ +typedef npy_longlong __pyx_t_5numpy_long_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_ulong uint_t + */ +typedef npy_longlong __pyx_t_5numpy_longlong_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 + * ctypedef npy_longlong longlong_t + * + * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t + */ +typedef npy_ulong __pyx_t_5numpy_uint_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 + * + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulonglong_t + * + */ +typedef npy_ulonglong __pyx_t_5numpy_ulong_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_intp intp_t + */ +typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 + * ctypedef npy_ulonglong ulonglong_t + * + * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< + * ctypedef npy_uintp uintp_t + * + */ +typedef npy_intp __pyx_t_5numpy_intp_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 + * + * ctypedef npy_intp intp_t + * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< + * + * ctypedef npy_double float_t + */ +typedef npy_uintp __pyx_t_5numpy_uintp_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 + * ctypedef npy_uintp uintp_t + * + * ctypedef npy_double float_t # <<<<<<<<<<<<<< + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t + */ +typedef npy_double __pyx_t_5numpy_float_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 + * ctypedef npy_double float_t + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cfloat cfloat_t + */ +typedef npy_longdouble __pyx_t_5numpy_longdouble_t; + +/* "MDAnalysis/lib/nsgrid.pyx":89 + * DEF EPSILON = 1e-5 + * + * ctypedef np.int_t ns_int # <<<<<<<<<<<<<< + * ctypedef np.float32_t real + * ctypedef real rvec[DIM] + */ +typedef __pyx_t_5numpy_int_t __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int; + +/* "MDAnalysis/lib/nsgrid.pyx":90 + * + * ctypedef np.int_t ns_int + * ctypedef np.float32_t real # <<<<<<<<<<<<<< + * ctypedef real rvec[DIM] + * ctypedef ns_int ivec[DIM] + */ +typedef __pyx_t_5numpy_float32_t __pyx_t_10MDAnalysis_3lib_6nsgrid_real; +/* Declarations.proto */ +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< float > __pyx_t_float_complex; + #else + typedef float _Complex __pyx_t_float_complex; + #endif +#else + typedef struct { float real, imag; } __pyx_t_float_complex; +#endif +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); + +/* Declarations.proto */ +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< double > __pyx_t_double_complex; + #else + typedef double _Complex __pyx_t_double_complex; + #endif +#else + typedef struct { double real, imag; } __pyx_t_double_complex; +#endif +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); + + +/*--- Type declarations ---*/ +struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox; +struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults; +struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid; +struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS; +struct __pyx_array_obj; +struct __pyx_MemviewEnum_obj; +struct __pyx_memoryview_obj; +struct __pyx_memoryviewslice_obj; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 + * ctypedef npy_longdouble longdouble_t + * + * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t + */ +typedef npy_cfloat __pyx_t_5numpy_cfloat_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 + * + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< + * ctypedef npy_clongdouble clongdouble_t + * + */ +typedef npy_cdouble __pyx_t_5numpy_cdouble_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cdouble complex_t + */ +typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; + +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 + * ctypedef npy_clongdouble clongdouble_t + * + * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew1(a): + */ +typedef npy_cdouble __pyx_t_5numpy_complex_t; +struct __pyx_t_10MDAnalysis_3lib_6nsgrid_cPBCBox_t; + +/* "MDAnalysis/lib/nsgrid.pyx":91 + * ctypedef np.int_t ns_int + * ctypedef np.float32_t real + * ctypedef real rvec[DIM] # <<<<<<<<<<<<<< + * ctypedef ns_int ivec[DIM] + * ctypedef real matrix[DIM][DIM] + */ +typedef __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_t_10MDAnalysis_3lib_6nsgrid_rvec[3]; + +/* "MDAnalysis/lib/nsgrid.pyx":92 + * ctypedef np.float32_t real + * ctypedef real rvec[DIM] + * ctypedef ns_int ivec[DIM] # <<<<<<<<<<<<<< + * ctypedef real matrix[DIM][DIM] + * + */ +typedef __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int __pyx_t_10MDAnalysis_3lib_6nsgrid_ivec[3]; + +/* "MDAnalysis/lib/nsgrid.pyx":93 + * ctypedef real rvec[DIM] + * ctypedef ns_int ivec[DIM] + * ctypedef real matrix[DIM][DIM] # <<<<<<<<<<<<<< + * + * ctypedef vector[ns_int] intvec + */ +typedef __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_t_10MDAnalysis_3lib_6nsgrid_matrix[3][3]; + +/* "MDAnalysis/lib/nsgrid.pyx":95 + * ctypedef real matrix[DIM][DIM] + * + * ctypedef vector[ns_int] intvec # <<<<<<<<<<<<<< + * ctypedef vector[real] realvec + * + */ +typedef std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int> __pyx_t_10MDAnalysis_3lib_6nsgrid_intvec; + +/* "MDAnalysis/lib/nsgrid.pyx":96 + * + * ctypedef vector[ns_int] intvec + * ctypedef vector[real] realvec # <<<<<<<<<<<<<< + * + * # Useful Functions + */ +typedef std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_real> __pyx_t_10MDAnalysis_3lib_6nsgrid_realvec; + +/* "MDAnalysis/lib/nsgrid.pyx":110 + * # Utility class to handle PBC # + * ############################### + * cdef struct cPBCBox_t: # <<<<<<<<<<<<<< + * matrix box + * rvec fbox_diag + */ +struct __pyx_t_10MDAnalysis_3lib_6nsgrid_cPBCBox_t { + __pyx_t_10MDAnalysis_3lib_6nsgrid_matrix box; + __pyx_t_10MDAnalysis_3lib_6nsgrid_rvec fbox_diag; + __pyx_t_10MDAnalysis_3lib_6nsgrid_rvec hbox_diag; + __pyx_t_10MDAnalysis_3lib_6nsgrid_rvec mhbox_diag; + __pyx_t_10MDAnalysis_3lib_6nsgrid_real max_cutoff2; +}; + +/* "MDAnalysis/lib/nsgrid.pyx":119 + * + * # Class to handle PBC calculations + * cdef class PBCBox(object): # <<<<<<<<<<<<<< + * """ + * Cython implementation of + */ +struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox { + PyObject_HEAD + struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_PBCBox *__pyx_vtab; + struct __pyx_t_10MDAnalysis_3lib_6nsgrid_cPBCBox_t c_pbcbox; + int is_triclinic; + int periodic; +}; + + +/* "MDAnalysis/lib/nsgrid.pyx":310 + * ######################### + * + * cdef class NSResults(object): # <<<<<<<<<<<<<< + * """Class to store the results + * + */ +struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults { + PyObject_HEAD + struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_vtab; + __pyx_t_10MDAnalysis_3lib_6nsgrid_real cutoff; + __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int npairs; + __Pyx_memviewslice coords; + __Pyx_memviewslice searchcoords; + std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_intvec> indices_buffer; + std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_realvec> distances_buffer; + std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int> pairs_buffer; + std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_real> pair_distances_buffer; + std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_real> pair_distances2_buffer; +}; + + +/* "MDAnalysis/lib/nsgrid.pyx":510 + * return list(self.distances_buffer) + * + * cdef class NSGrid(object): # <<<<<<<<<<<<<< + * """Constructs a uniform cuboidal grid for a brick-shaped box + * + */ +struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid { + PyObject_HEAD + struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSGrid *__pyx_vtab; + __pyx_t_10MDAnalysis_3lib_6nsgrid_real cutoff; + __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int size; + __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int ncoords; + __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int ncells[3]; + __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int cell_offsets[3]; + __pyx_t_10MDAnalysis_3lib_6nsgrid_real cellsize[3]; + __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int nbeads_per_cell; + __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int *nbeads; + __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int *beadids; + __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int *cellids; + int force; +}; + + +/* "MDAnalysis/lib/nsgrid.pyx":686 + * + * + * cdef class FastNS(object): # <<<<<<<<<<<<<< + * """Grid based search between two group of atoms + * + */ +struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS { + PyObject_HEAD + struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *box; + __Pyx_memviewslice coords; + __Pyx_memviewslice coords_bbox; + __pyx_t_10MDAnalysis_3lib_6nsgrid_real cutoff; + struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *grid; + __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int max_gridsize; + int periodic; +}; + + +/* "View.MemoryView":104 + * + * @cname("__pyx_array") + * cdef class array: # <<<<<<<<<<<<<< + * + * cdef: + */ +struct __pyx_array_obj { + PyObject_HEAD + struct __pyx_vtabstruct_array *__pyx_vtab; 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+ __Pyx_memviewslice (*fast_put_atoms_in_bbox)(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *, __Pyx_memviewslice); +}; +static struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_PBCBox *__pyx_vtabptr_10MDAnalysis_3lib_6nsgrid_PBCBox; + + +/* "MDAnalysis/lib/nsgrid.pyx":310 + * ######################### + * + * cdef class NSResults(object): # <<<<<<<<<<<<<< + * """Class to store the results + * + */ + +struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSResults { + void (*add_neighbors)(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *, __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int, __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int, __pyx_t_10MDAnalysis_3lib_6nsgrid_real); + void (*create_buffers)(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *); +}; +static struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_vtabptr_10MDAnalysis_3lib_6nsgrid_NSResults; + + +/* "MDAnalysis/lib/nsgrid.pyx":510 + * return list(self.distances_buffer) + * + * cdef class NSGrid(object): # <<<<<<<<<<<<<< + * """Constructs a uniform cuboidal grid for a brick-shaped box + * + */ + +struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSGrid { + __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int (*coord2cellid)(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *, __pyx_t_10MDAnalysis_3lib_6nsgrid_real *); 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+static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL)) +#else +#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) +#endif +#else +#define __Pyx_PyErr_Clear() PyErr_Clear() +#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) +#define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb) +#define __Pyx_ErrRestoreInState(tstate, type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetchInState(tstate, type, value, tb) PyErr_Fetch(type, value, tb) +#define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb) +#endif + +/* RaiseException.proto */ +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); 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+ +/* Import.proto */ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +/* ImportFrom.proto */ +static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); + +/* GetItemInt.proto */ +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ + __Pyx_GetItemInt_Generic(o, to_py_func(i)))) +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ + (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ + (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck); + +/* SliceObject.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice( + PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, + PyObject** py_start, PyObject** py_stop, PyObject** py_slice, + int has_cstart, int has_cstop, int wraparound); + +/* HasAttr.proto */ +static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); + +/* ExtTypeTest.proto */ +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); + +/* DictGetItem.proto */ +#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key); +#define __Pyx_PyObject_Dict_GetItem(obj, name)\ + (likely(PyDict_CheckExact(obj)) ?\ + __Pyx_PyDict_GetItem(obj, name) : PyObject_GetItem(obj, name)) +#else +#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) +#define __Pyx_PyObject_Dict_GetItem(obj, name) PyObject_GetItem(obj, name) +#endif + +/* RaiseTooManyValuesToUnpack.proto */ +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +/* RaiseNeedMoreValuesToUnpack.proto */ +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +/* RaiseNoneIterError.proto */ +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +/* SaveResetException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); +#else +#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) +#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) +#endif + +/* GetException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) +static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); +#endif + +/* ListCompAppend.proto */ +#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS +static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len)) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) +#endif + +/* IncludeStringH.proto */ +#include + +/* BytesEquals.proto */ +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); + +/* UnicodeEquals.proto */ +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); + +/* StrEquals.proto */ +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals +#else +#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals +#endif + +/* UnaryNegOverflows.proto */ +#define UNARY_NEG_WOULD_OVERFLOW(x)\ + (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) + +static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *); /*proto*/ +/* ObjectGetItem.proto */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key); +#else +#define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key) +#endif + +/* decode_c_string_utf16.proto */ +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = 0; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16LE(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = -1; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16BE(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = 1; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} + +/* decode_c_string.proto */ +static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); + +/* SwapException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); +#endif + +/* FastTypeChecks.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type) +static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b); +static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type); +static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2); +#else +#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) +#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type) +#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2)) +#endif +#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) + +static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +/* PyIntBinop.proto */ +#if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace); +#else +#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace)\ + (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) +#endif + +/* ListExtend.proto */ +static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject* none = _PyList_Extend((PyListObject*)L, v); + if (unlikely(!none)) + return -1; + Py_DECREF(none); + return 0; +#else + return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); +#endif +} + +/* ListAppend.proto */ +#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS +static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) +#endif + +/* None.proto */ +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); + +/* PyObject_GenericGetAttrNoDict.proto */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr +#endif + +/* PyObject_GenericGetAttr.proto */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr +#endif + +/* SetVTable.proto */ +static int __Pyx_SetVtable(PyObject *dict, void *vtable); + +/* SetupReduce.proto */ +static int __Pyx_setup_reduce(PyObject* type_obj); + +/* CLineInTraceback.proto */ +#ifdef CYTHON_CLINE_IN_TRACEBACK +#define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0) +#else +static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line); +#endif + +/* CodeObjectCache.proto */ +typedef struct { + PyCodeObject* code_object; + int code_line; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); + +/* AddTraceback.proto */ +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); + +#if PY_MAJOR_VERSION < 3 + static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); + static void __Pyx_ReleaseBuffer(Py_buffer *view); +#else + #define __Pyx_GetBuffer PyObject_GetBuffer + #define __Pyx_ReleaseBuffer PyBuffer_Release +#endif + + +/* BufferStructDeclare.proto */ +typedef struct { + Py_ssize_t shape, strides, suboffsets; +} __Pyx_Buf_DimInfo; +typedef struct { + size_t refcount; + Py_buffer pybuffer; +} __Pyx_Buffer; +typedef struct { + __Pyx_Buffer *rcbuffer; + char *data; + __Pyx_Buf_DimInfo diminfo[8]; +} __Pyx_LocalBuf_ND; + +/* MemviewSliceIsContig.proto */ +static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim); + +/* OverlappingSlices.proto */ +static int __pyx_slices_overlap(__Pyx_memviewslice *slice1, + __Pyx_memviewslice *slice2, + int ndim, size_t itemsize); + +/* Capsule.proto */ +static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); + +/* None.proto */ +#include + +/* MemviewDtypeToObject.proto */ +static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real(const char *itemp); +static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real(const char *itemp, PyObject *obj); + +/* IsLittleEndian.proto */ +static CYTHON_INLINE int __Pyx_Is_Little_Endian(void); + +/* BufferFormatCheck.proto */ +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); +static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type); + +/* TypeInfoCompare.proto */ +static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); + +/* MemviewSliceValidateAndInit.proto */ +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj); + +/* ObjectToMemviewSlice.proto */ +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real(PyObject *, int writable_flag); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_long(npy_long value); + +/* CppExceptionConversion.proto */ +#ifndef __Pyx_CppExn2PyErr +#include +#include +#include +#include +static void __Pyx_CppExn2PyErr() { + try { + if (PyErr_Occurred()) + ; // let the latest Python exn pass through and ignore the current one + else + throw; + } catch (const std::bad_alloc& exn) { + PyErr_SetString(PyExc_MemoryError, exn.what()); + } catch (const std::bad_cast& exn) { + PyErr_SetString(PyExc_TypeError, exn.what()); + } catch (const std::bad_typeid& exn) { + PyErr_SetString(PyExc_TypeError, exn.what()); + } catch (const std::domain_error& exn) { + PyErr_SetString(PyExc_ValueError, exn.what()); + } catch (const std::invalid_argument& exn) { + PyErr_SetString(PyExc_ValueError, exn.what()); + } catch (const std::ios_base::failure& exn) { + PyErr_SetString(PyExc_IOError, exn.what()); + } catch (const std::out_of_range& exn) { + PyErr_SetString(PyExc_IndexError, exn.what()); + } catch (const std::overflow_error& exn) { + PyErr_SetString(PyExc_OverflowError, exn.what()); + } catch (const std::range_error& exn) { + PyErr_SetString(PyExc_ArithmeticError, exn.what()); + } catch (const std::underflow_error& exn) { + PyErr_SetString(PyExc_ArithmeticError, exn.what()); + } catch (const std::exception& exn) { + PyErr_SetString(PyExc_RuntimeError, exn.what()); + } + catch (...) + { + PyErr_SetString(PyExc_RuntimeError, "Unknown exception"); + } +} +#endif + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +/* RealImag.proto */ +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #define __Pyx_CREAL(z) ((z).real()) + #define __Pyx_CIMAG(z) ((z).imag()) + #else + #define __Pyx_CREAL(z) (__real__(z)) + #define __Pyx_CIMAG(z) (__imag__(z)) + #endif +#else + #define __Pyx_CREAL(z) ((z).real) + #define __Pyx_CIMAG(z) ((z).imag) +#endif +#if defined(__cplusplus) && CYTHON_CCOMPLEX\ + && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103) + #define __Pyx_SET_CREAL(z,x) ((z).real(x)) + #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) +#else + #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) + #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) +#endif + +/* Arithmetic.proto */ +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq_float(a, b) ((a)==(b)) + #define __Pyx_c_sum_float(a, b) ((a)+(b)) + #define __Pyx_c_diff_float(a, b) ((a)-(b)) + #define __Pyx_c_prod_float(a, b) ((a)*(b)) + #define __Pyx_c_quot_float(a, b) ((a)/(b)) + #define __Pyx_c_neg_float(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero_float(z) ((z)==(float)0) + #define __Pyx_c_conj_float(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs_float(z) (::std::abs(z)) + #define __Pyx_c_pow_float(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero_float(z) ((z)==0) + #define __Pyx_c_conj_float(z) (conjf(z)) + #if 1 + #define __Pyx_c_abs_float(z) (cabsf(z)) + #define __Pyx_c_pow_float(a, b) (cpowf(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex); + #if 1 + static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex, __pyx_t_float_complex); + #endif +#endif + +/* Arithmetic.proto */ +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq_double(a, b) ((a)==(b)) + #define __Pyx_c_sum_double(a, b) ((a)+(b)) + #define __Pyx_c_diff_double(a, b) ((a)-(b)) + #define __Pyx_c_prod_double(a, b) ((a)*(b)) + #define __Pyx_c_quot_double(a, b) ((a)/(b)) + #define __Pyx_c_neg_double(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero_double(z) ((z)==(double)0) + #define __Pyx_c_conj_double(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs_double(z) (::std::abs(z)) + #define __Pyx_c_pow_double(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero_double(z) ((z)==0) + #define __Pyx_c_conj_double(z) (conj(z)) + #if 1 + #define __Pyx_c_abs_double(z) (cabs(z)) + #define __Pyx_c_pow_double(a, b) (cpow(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex); + #if 1 + static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex); + #endif +#endif + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); + +/* MemviewSliceCopyTemplate.proto */ +static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object); + +/* CIntFromPy.proto */ +static CYTHON_INLINE npy_long __Pyx_PyInt_As_npy_long(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +/* CopyContentsUtility.proto */ +#define __pyx_memoryview_copy_slice_d_dc_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real_c(slice)\ + __pyx_memoryview_copy_new_contig(&slice, "c", 2,\ + sizeof(__pyx_t_10MDAnalysis_3lib_6nsgrid_real), (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT),\ + 0) + +/* CopyContentsUtility.proto */ +#define __pyx_memoryview_copy_slice_dcd__nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real_f(slice)\ + __pyx_memoryview_copy_new_contig(&slice, "fortran", 2,\ + sizeof(__pyx_t_10MDAnalysis_3lib_6nsgrid_real), (PyBUF_F_CONTIGUOUS | PyBUF_FORMAT),\ + 0) + +/* CIntFromPy.proto */ +static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); + +/* ObjectToMemviewSlice.proto */ +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int(PyObject *, int writable_flag); + +/* CheckBinaryVersion.proto */ +static int __Pyx_check_binary_version(void); + +/* PyIdentifierFromString.proto */ +#if !defined(__Pyx_PyIdentifier_FromString) +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) +#else + #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) +#endif +#endif + +/* ModuleImport.proto */ +static PyObject *__Pyx_ImportModule(const char *name); + +/* TypeImport.proto */ +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); + +/* InitStrings.proto */ +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); + +static void __pyx_f_10MDAnalysis_3lib_6nsgrid_6PBCBox_fast_update(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *__pyx_v_self, __Pyx_memviewslice __pyx_v_box); /* proto*/ +static void __pyx_f_10MDAnalysis_3lib_6nsgrid_6PBCBox_fast_pbc_dx(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *__pyx_v_self, __pyx_t_10MDAnalysis_3lib_6nsgrid_real *__pyx_v_ref, __pyx_t_10MDAnalysis_3lib_6nsgrid_real *__pyx_v_other, __pyx_t_10MDAnalysis_3lib_6nsgrid_real *__pyx_v_dx); /* proto*/ +static __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_f_10MDAnalysis_3lib_6nsgrid_6PBCBox_fast_distance2(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *__pyx_v_self, __pyx_t_10MDAnalysis_3lib_6nsgrid_real *__pyx_v_a, __pyx_t_10MDAnalysis_3lib_6nsgrid_real *__pyx_v_b); /* proto*/ +static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_6PBCBox_fast_put_atoms_in_bbox(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *__pyx_v_self, __Pyx_memviewslice __pyx_v_coords); /* proto*/ +static void __pyx_f_10MDAnalysis_3lib_6nsgrid_9NSResults_add_neighbors(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_v_self, __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int __pyx_v_beadid_i, __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int __pyx_v_beadid_j, __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_v_distance2); /* proto*/ +static void __pyx_f_10MDAnalysis_3lib_6nsgrid_9NSResults_create_buffers(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_v_self); /* proto*/ +static __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int __pyx_f_10MDAnalysis_3lib_6nsgrid_6NSGrid_coord2cellid(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *__pyx_v_self, __pyx_t_10MDAnalysis_3lib_6nsgrid_real *__pyx_v_coord); /* proto*/ +static int __pyx_f_10MDAnalysis_3lib_6nsgrid_6NSGrid_cellid2cellxyz(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *__pyx_v_self, __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int __pyx_v_cellid, __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int *__pyx_v_cellxyz); /* proto*/ +static PyObject *__pyx_f_10MDAnalysis_3lib_6nsgrid_6NSGrid_fill_grid(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *__pyx_v_self, __Pyx_memviewslice __pyx_v_coords); /* proto*/ +static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *__pyx_v_self); /* proto*/ +static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto*/ +static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj); /* proto*/ +static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_dst, PyObject *__pyx_v_src); /* proto*/ +static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memoryview_obj *__pyx_v_self, struct __pyx_memoryview_obj *__pyx_v_dst, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryview_setitem_indexed(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ +static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ +static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ + +/* Module declarations from 'cpython.mem' */ + +/* Module declarations from 'libc.math' */ + +/* Module declarations from 'libcpp.vector' */ + +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'cpython' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'numpy' */ + +/* Module declarations from 'numpy' */ +static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; +static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; +static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; +static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; +static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; +static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ + +/* Module declarations from 'MDAnalysis.lib.nsgrid' */ +static PyTypeObject *__pyx_ptype_10MDAnalysis_3lib_6nsgrid_PBCBox = 0; +static PyTypeObject *__pyx_ptype_10MDAnalysis_3lib_6nsgrid_NSResults = 0; +static PyTypeObject *__pyx_ptype_10MDAnalysis_3lib_6nsgrid_NSGrid = 0; +static PyTypeObject *__pyx_ptype_10MDAnalysis_3lib_6nsgrid_FastNS = 0; +static PyTypeObject *__pyx_array_type = 0; +static PyTypeObject *__pyx_MemviewEnum_type = 0; +static PyTypeObject *__pyx_memoryview_type = 0; +static PyTypeObject *__pyx_memoryviewslice_type = 0; +static PyObject *generic = 0; +static PyObject *strided = 0; +static PyObject *indirect = 0; +static PyObject *contiguous = 0; +static PyObject *indirect_contiguous = 0; +static int __pyx_memoryview_thread_locks_used; +static PyThread_type_lock __pyx_memoryview_thread_locks[8]; +static __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_f_10MDAnalysis_3lib_6nsgrid_rvec_norm2(__pyx_t_10MDAnalysis_3lib_6nsgrid_real *); /*proto*/ +static PyObject *__pyx_f_10MDAnalysis_3lib_6nsgrid___pyx_unpickle_NSResults__set_state(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *, PyObject *); /*proto*/ +static PyObject *__pyx_f_10MDAnalysis_3lib_6nsgrid___pyx_unpickle_FastNS__set_state(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *, PyObject *); /*proto*/ +static PyObject *__pyx_convert_vector_to_py___pyx_t_10MDAnalysis_3lib_6nsgrid_real(const std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_real> &); /*proto*/ +static PyObject *__pyx_convert_vector_to_py___pyx_t_10MDAnalysis_3lib_6nsgrid_realvec(const std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_realvec> &); /*proto*/ +static std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_real> __pyx_convert_vector_from_py___pyx_t_10MDAnalysis_3lib_6nsgrid_real(PyObject *); /*proto*/ +static std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_realvec> __pyx_convert_vector_from_py___pyx_t_10MDAnalysis_3lib_6nsgrid_realvec(PyObject *); /*proto*/ +static PyObject *__pyx_convert_vector_to_py___pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int(const std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int> &); /*proto*/ +static PyObject *__pyx_convert_vector_to_py___pyx_t_10MDAnalysis_3lib_6nsgrid_intvec(const std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_intvec> &); /*proto*/ +static std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int> __pyx_convert_vector_from_py___pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int(PyObject *); /*proto*/ +static std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_intvec> __pyx_convert_vector_from_py___pyx_t_10MDAnalysis_3lib_6nsgrid_intvec(PyObject *); /*proto*/ +static struct __pyx_array_obj *__pyx_array_new(PyObject *, Py_ssize_t, char *, char *, char *); /*proto*/ +static void *__pyx_align_pointer(void *, size_t); /*proto*/ +static PyObject *__pyx_memoryview_new(PyObject *, int, int, __Pyx_TypeInfo *); /*proto*/ +static CYTHON_INLINE int __pyx_memoryview_check(PyObject *); /*proto*/ +static PyObject *_unellipsify(PyObject *, int); /*proto*/ +static PyObject *assert_direct_dimensions(Py_ssize_t *, int); /*proto*/ +static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_obj *, PyObject *); /*proto*/ +static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int, int); /*proto*/ +static char *__pyx_pybuffer_index(Py_buffer *, char *, Py_ssize_t, Py_ssize_t); /*proto*/ +static int __pyx_memslice_transpose(__Pyx_memviewslice *); /*proto*/ +static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice, int, PyObject *(*)(char *), int (*)(char *, PyObject *), int); /*proto*/ +static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *); /*proto*/ +static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static Py_ssize_t abs_py_ssize_t(Py_ssize_t); /*proto*/ +static char __pyx_get_best_slice_order(__Pyx_memviewslice *, int); /*proto*/ +static void _copy_strided_to_strided(char *, Py_ssize_t *, char *, Py_ssize_t *, Py_ssize_t *, Py_ssize_t *, int, size_t); /*proto*/ +static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/ +static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/ +static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *, Py_ssize_t *, Py_ssize_t, int, char); /*proto*/ +static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/ +static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/ +static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/ +static int __pyx_memoryview_err(PyObject *, char *); /*proto*/ +static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/ +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/ +static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/ +static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ +static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ +static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/ +static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ +static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *, PyObject *); /*proto*/ +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real = { "real", NULL, sizeof(__pyx_t_10MDAnalysis_3lib_6nsgrid_real), { 0 }, 0, 'R', 0, 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int = { "ns_int", NULL, sizeof(__pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int), { 0 }, 0, IS_UNSIGNED(__pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int), 0 }; +#define __Pyx_MODULE_NAME "MDAnalysis.lib.nsgrid" +extern int __pyx_module_is_main_MDAnalysis__lib__nsgrid; +int __pyx_module_is_main_MDAnalysis__lib__nsgrid = 0; + +/* Implementation of 'MDAnalysis.lib.nsgrid' */ +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_TypeError; +static PyObject *__pyx_builtin_MemoryError; +static PyObject *__pyx_builtin_RuntimeError; +static PyObject *__pyx_builtin_ImportError; +static PyObject *__pyx_builtin_enumerate; +static PyObject *__pyx_builtin_Ellipsis; +static PyObject *__pyx_builtin_id; +static PyObject *__pyx_builtin_IndexError; +static const char __pyx_k_C[] = "C"; +static const char __pyx_k_O[] = "O"; +static const char __pyx_k_c[] = "c"; +static const char __pyx_k_id[] = "id"; +static const char __pyx_k_np[] = "np"; +static const char __pyx_k_box[] = "box"; +static const char __pyx_k_int[] = "int"; +static const char __pyx_k_new[] = "__new__"; +static const char __pyx_k_obj[] = "obj"; +static const char __pyx_k_pbc[] = "pbc"; +static const char __pyx_k_base[] = "base"; +static const char __pyx_k_copy[] = "copy"; +static const char __pyx_k_dict[] = "__dict__"; +static const char __pyx_k_main[] = "__main__"; +static const char __pyx_k_mode[] = "mode"; +static const char __pyx_k_name[] = "name"; +static const char __pyx_k_ndim[] = "ndim"; +static const char __pyx_k_pack[] = "pack"; +static const char __pyx_k_size[] = "size"; +static const char __pyx_k_sqrt[] = "sqrt"; +static const char __pyx_k_step[] = "step"; +static const char __pyx_k_stop[] = "stop"; +static const char __pyx_k_test[] = "__test__"; +static const char __pyx_k_ASCII[] = "ASCII"; +static const char __pyx_k_class[] = "__class__"; +static const char __pyx_k_dtype[] = "dtype"; +static const char __pyx_k_empty[] = "empty"; +static const char __pyx_k_error[] = "error"; +static const char __pyx_k_flags[] = "flags"; +static const char __pyx_k_force[] = "force"; +static const char __pyx_k_int64[] = "int64"; +static const char __pyx_k_numpy[] = "numpy"; +static const char __pyx_k_order[] = "order"; +static const char __pyx_k_range[] = "range"; +static const char __pyx_k_shape[] = "shape"; +static const char __pyx_k_start[] = "start"; +static const char __pyx_k_astype[] = "astype"; +static const char __pyx_k_coords[] = "coords"; +static const char __pyx_k_cutoff[] = "cutoff"; +static const char __pyx_k_encode[] = "encode"; +static const char __pyx_k_format[] = "format"; +static const char __pyx_k_import[] = "__import__"; +static const char __pyx_k_name_2[] = "__name__"; +static const char __pyx_k_pickle[] = "pickle"; +static const char __pyx_k_reduce[] = "__reduce__"; +static const char __pyx_k_struct[] = "struct"; +static const char __pyx_k_unpack[] = "unpack"; +static const char __pyx_k_update[] = "update"; +static const char __pyx_k_asarray[] = "asarray"; +static const char __pyx_k_float32[] = "float32"; +static const char __pyx_k_fortran[] = "fortran"; +static const char __pyx_k_memview[] = "memview"; +static const char __pyx_k_ncoords[] = "ncoords"; +static const char __pyx_k_reshape[] = "reshape"; +static const char __pyx_k_Ellipsis[] = "Ellipsis"; +static const char __pyx_k_allclose[] = "allclose"; +static const char __pyx_k_getstate[] = "__getstate__"; +static const char __pyx_k_itemsize[] = "itemsize"; +static const char __pyx_k_max_size[] = "max_size"; +static const char __pyx_k_periodic[] = "periodic"; +static const char __pyx_k_pyx_type[] = "__pyx_type"; +static const char __pyx_k_setstate[] = "__setstate__"; +static const char __pyx_k_TypeError[] = "TypeError"; +static const char __pyx_k_enumerate[] = "enumerate"; +static const char __pyx_k_pyx_state[] = "__pyx_state"; +static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; +static const char __pyx_k_IndexError[] = "IndexError"; +static const char __pyx_k_ValueError[] = "ValueError"; +static const char __pyx_k_pyx_result[] = "__pyx_result"; +static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; +static const char __pyx_k_ImportError[] = "ImportError"; +static const char __pyx_k_MemoryError[] = "MemoryError"; +static const char __pyx_k_PickleError[] = "PickleError"; +static const char __pyx_k_RuntimeError[] = "RuntimeError"; +static const char __pyx_k_max_gridsize[] = "max_gridsize"; +static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; +static const char __pyx_k_searchcoords[] = "searchcoords"; +static const char __pyx_k_stringsource[] = "stringsource"; +static const char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; +static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; +static const char __pyx_k_View_MemoryView[] = "View.MemoryView"; +static const char __pyx_k_allocate_buffer[] = "allocate_buffer"; +static const char __pyx_k_dtype_is_object[] = "dtype_is_object"; +static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; +static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; +static const char __pyx_k_pyx_unpickle_Enum[] = "__pyx_unpickle_Enum"; +static const char __pyx_k_triclinic_vectors[] = "triclinic_vectors"; +static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; +static const char __pyx_k_strided_and_direct[] = ""; +static const char __pyx_k_pyx_unpickle_FastNS[] = "__pyx_unpickle_FastNS"; +static const char __pyx_k_strided_and_indirect[] = ""; +static const char __pyx_k_MDAnalysis_lib_nsgrid[] = "MDAnalysis.lib.nsgrid"; +static const char __pyx_k_contiguous_and_direct[] = ""; +static const char __pyx_k_MDAnalysis_lib_mdamath[] = "MDAnalysis.lib.mdamath"; +static const char __pyx_k_MemoryView_of_r_object[] = ""; +static const char __pyx_k_pyx_unpickle_NSResults[] = "__pyx_unpickle_NSResults"; +static const char __pyx_k_Cutoff_must_be_positive[] = "Cutoff must be positive!"; +static const char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; +static const char __pyx_k_contiguous_and_indirect[] = ""; +static const char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; +static const char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; +static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; +static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static const char __pyx_k_Box_must_be_a_x_matrix_Got_x[] = "Box must be a {} x {} matrix. Got: {} x {})"; +static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; +static const char __pyx_k_strided_and_direct_or_indirect[] = ""; +static const char __pyx_k_Neighbor_search_library_mod_MDA[] = "\nNeighbor search library --- :mod:`MDAnalysis.lib.nsgrid`\n========================================================\n\n\nAbout the code\n--------------\n\nThis Neighbor search library is a serialized Cython version greatly\ninspired by the NS grid search implemented in\n`GROMACS `_ .\n\nGROMACS 4.x code (more precisely\n`nsgrid.c `_\nand `ns.c `_ )\nwas used as reference to write this file.\n\nGROMACS 4.x code is released under the GNU Public Licence v2.\n\nAbout the algorithm\n-------------------\n\nThe neighbor search implemented here is based on\n`cell lists `_ which allow\ncomputation of pairs [#]_ with a cost of :math:`O(N)`, instead\nof :math:`O(N^2)`. The basic algorithm is described in\nAppendix F, Page 552 of\n``Understanding Molecular Dynamics: From Algorithm to Applications`` by Frenkel and Smit.\n\nIn brief, the algorithm divides the domain into smaller subdomains called `cells`\nand distributes every particle to these cells based on their positions. Subsequently,\nany distance based query first identifies the corresponding cell position in the\ndomain followed by distance evaluations within the identified cell and\nneighboring cells only. Care must be taken to ensure that `cellsize` is\ngreater than the desired search distance, otherwise all of the neighbours might\nnot reflect in the results.\n\n\n.. [#] a pair correspond to two particles that are considered as neighbors .\n\n\n.. versionadded:: 0.19.0\n"; +static const char __pyx_k_Pickling_of_struct_members_such[] = "Pickling of struct members such as self.c_pbcbox must be explicitly requested with @auto_pickle(True)"; +static const char __pyx_k_coords_must_have_a_shape_of_n_3[] = "coords must have a shape of (n, 3), got {}."; +static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; +static const char __pyx_k_search_coords_must_have_a_shape[] = "search_coords must have a shape of (n, 3), got {}."; +static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; +static const char __pyx_k_Any_of_the_box_dimensions_cannot[] = "Any of the box dimensions cannot be 0"; +static const char __pyx_k_Box_does_not_correspond_to_PBC_x[] = "Box does not correspond to PBC=xyz"; +static const char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; +static const char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; +static const char __pyx_k_Cannot_assign_to_read_only_memor[] = "Cannot assign to read-only memoryview"; +static const char __pyx_k_Cannot_create_writable_memory_vi[] = "Cannot create writable memory view from read-only memoryview"; +static const char __pyx_k_Could_not_allocate_memory_for_NS[] = "Could not allocate memory for NSGrid.beadids ({} bits requested)"; +static const char __pyx_k_Could_not_allocate_memory_from_N[] = "Could not allocate memory from NSGrid.nbeads ({} bits requested)"; +static const char __pyx_k_Cutoff_greater_than_maximum_cuto[] = "Cutoff greater than maximum cutoff ({:.3f}) given the PBC"; +static const char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; +static const char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; +static const char __pyx_k_Incompatible_checksums_s_vs_0x29[] = "Incompatible checksums (%s vs 0x294c292 = (coords, cutoff, distances_buffer, indices_buffer, npairs, pair_distances2_buffer, pair_distances_buffer, pairs_buffer, searchcoords))"; +static const char __pyx_k_Incompatible_checksums_s_vs_0xb0[] = "Incompatible checksums (%s vs 0xb068931 = (name))"; +static const char __pyx_k_Incompatible_checksums_s_vs_0xd3[] = "Incompatible checksums (%s vs 0xd38cfe0 = (box, coords, coords_bbox, cutoff, grid, max_gridsize, periodic))"; +static const char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; +static const char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; +static const char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; +static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; +static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; +static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; +static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; +static const char __pyx_k_self_beadids_self_cellids_self_n[] = "self.beadids,self.cellids,self.nbeads cannot be converted to a Python object for pickling"; +static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; +static const char __pyx_k_Could_not_allocate_memory_from_N_2[] = "Could not allocate memory from NSGrid.cellids ({} bits requested)"; +static const char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_n_s_ASCII; +static PyObject *__pyx_kp_s_Any_of_the_box_dimensions_cannot; +static PyObject *__pyx_kp_s_Box_does_not_correspond_to_PBC_x; +static PyObject *__pyx_kp_s_Box_must_be_a_x_matrix_Got_x; +static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; +static PyObject *__pyx_n_s_C; +static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; +static PyObject *__pyx_kp_s_Cannot_assign_to_read_only_memor; +static PyObject *__pyx_kp_s_Cannot_create_writable_memory_vi; +static PyObject *__pyx_kp_s_Cannot_index_with_type_s; +static PyObject *__pyx_kp_s_Could_not_allocate_memory_for_NS; +static PyObject *__pyx_kp_s_Could_not_allocate_memory_from_N; +static PyObject *__pyx_kp_s_Could_not_allocate_memory_from_N_2; +static PyObject *__pyx_kp_s_Cutoff_greater_than_maximum_cuto; +static PyObject *__pyx_kp_s_Cutoff_must_be_positive; +static PyObject *__pyx_n_s_Ellipsis; +static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; +static PyObject *__pyx_n_s_ImportError; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0x29; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0xb0; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0xd3; +static PyObject *__pyx_n_s_IndexError; +static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; +static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; +static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; +static PyObject *__pyx_n_s_MDAnalysis_lib_mdamath; +static PyObject *__pyx_n_s_MDAnalysis_lib_nsgrid; +static PyObject *__pyx_n_s_MemoryError; +static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; +static PyObject *__pyx_kp_s_MemoryView_of_r_object; +static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_n_b_O; +static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; +static PyObject *__pyx_n_s_PickleError; +static PyObject *__pyx_kp_s_Pickling_of_struct_members_such; +static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_n_s_TypeError; +static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; +static PyObject *__pyx_n_s_ValueError; +static PyObject *__pyx_n_s_View_MemoryView; +static PyObject *__pyx_n_s_allclose; +static PyObject *__pyx_n_s_allocate_buffer; +static PyObject *__pyx_n_s_asarray; +static PyObject *__pyx_n_s_astype; +static PyObject *__pyx_n_s_base; +static PyObject *__pyx_n_s_box; +static PyObject *__pyx_n_s_c; +static PyObject *__pyx_n_u_c; +static PyObject *__pyx_n_s_class; +static PyObject *__pyx_n_s_cline_in_traceback; +static PyObject *__pyx_kp_s_contiguous_and_direct; +static PyObject *__pyx_kp_s_contiguous_and_indirect; +static PyObject *__pyx_n_s_coords; +static PyObject *__pyx_kp_s_coords_must_have_a_shape_of_n_3; +static PyObject *__pyx_n_s_copy; +static PyObject *__pyx_n_s_cutoff; +static PyObject *__pyx_n_s_dict; +static PyObject *__pyx_n_s_dtype; +static PyObject *__pyx_n_s_dtype_is_object; +static PyObject *__pyx_n_s_empty; +static PyObject *__pyx_n_s_encode; +static PyObject *__pyx_n_s_enumerate; +static PyObject *__pyx_n_s_error; +static PyObject *__pyx_n_s_flags; +static PyObject *__pyx_n_s_float32; +static PyObject *__pyx_n_s_force; +static PyObject *__pyx_n_s_format; +static PyObject *__pyx_n_s_fortran; +static PyObject *__pyx_n_u_fortran; +static PyObject *__pyx_n_s_getstate; +static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; +static PyObject *__pyx_n_s_id; +static PyObject *__pyx_n_s_import; +static PyObject *__pyx_n_s_int; +static PyObject *__pyx_n_s_int64; +static PyObject *__pyx_n_s_itemsize; +static PyObject *__pyx_kp_s_itemsize_0_for_cython_array; +static PyObject *__pyx_n_s_main; +static PyObject *__pyx_n_s_max_gridsize; +static PyObject *__pyx_n_s_max_size; +static PyObject *__pyx_n_s_memview; +static PyObject *__pyx_n_s_mode; +static PyObject *__pyx_n_s_name; +static PyObject *__pyx_n_s_name_2; +static PyObject *__pyx_n_s_ncoords; +static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; +static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_n_s_ndim; +static PyObject *__pyx_n_s_new; +static PyObject *__pyx_kp_s_no_default___reduce___due_to_non; +static PyObject *__pyx_n_s_np; +static PyObject *__pyx_n_s_numpy; +static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to; +static PyObject *__pyx_kp_s_numpy_core_umath_failed_to_impor; +static PyObject *__pyx_n_s_obj; +static PyObject *__pyx_n_s_order; +static PyObject *__pyx_n_s_pack; +static PyObject *__pyx_n_s_pbc; +static PyObject *__pyx_n_s_periodic; +static PyObject *__pyx_n_s_pickle; +static PyObject *__pyx_n_s_pyx_PickleError; +static PyObject *__pyx_n_s_pyx_checksum; +static PyObject *__pyx_n_s_pyx_getbuffer; +static PyObject *__pyx_n_s_pyx_result; +static PyObject *__pyx_n_s_pyx_state; +static PyObject *__pyx_n_s_pyx_type; +static PyObject *__pyx_n_s_pyx_unpickle_Enum; +static PyObject *__pyx_n_s_pyx_unpickle_FastNS; +static PyObject *__pyx_n_s_pyx_unpickle_NSResults; +static PyObject *__pyx_n_s_pyx_vtable; +static PyObject *__pyx_n_s_range; +static PyObject *__pyx_n_s_reduce; +static PyObject *__pyx_n_s_reduce_cython; +static PyObject *__pyx_n_s_reduce_ex; +static PyObject *__pyx_n_s_reshape; +static PyObject *__pyx_kp_s_search_coords_must_have_a_shape; +static PyObject *__pyx_n_s_searchcoords; +static PyObject *__pyx_kp_s_self_beadids_self_cellids_self_n; +static PyObject *__pyx_n_s_setstate; +static PyObject *__pyx_n_s_setstate_cython; +static PyObject *__pyx_n_s_shape; +static PyObject *__pyx_n_s_size; +static PyObject *__pyx_n_s_sqrt; +static PyObject *__pyx_n_s_start; +static PyObject *__pyx_n_s_step; +static PyObject *__pyx_n_s_stop; +static PyObject *__pyx_kp_s_strided_and_direct; +static PyObject *__pyx_kp_s_strided_and_direct_or_indirect; +static PyObject *__pyx_kp_s_strided_and_indirect; +static PyObject *__pyx_kp_s_stringsource; +static PyObject *__pyx_n_s_struct; +static PyObject *__pyx_n_s_test; +static PyObject *__pyx_n_s_triclinic_vectors; +static PyObject *__pyx_kp_s_unable_to_allocate_array_data; +static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; +static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; +static PyObject *__pyx_n_s_unpack; +static PyObject *__pyx_n_s_update; +static int __pyx_pf_10MDAnalysis_3lib_6nsgrid_6PBCBox___init__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *__pyx_v_self, __Pyx_memviewslice __pyx_v_box, int __pyx_v_periodic); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6PBCBox_2update(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *__pyx_v_self, __Pyx_memviewslice __pyx_v_box); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6PBCBox_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6PBCBox_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ +static int __pyx_pf_10MDAnalysis_3lib_6nsgrid_9NSResults___init__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_v_self, __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_v_cutoff, __Pyx_memviewslice __pyx_v_coords, __Pyx_memviewslice __pyx_v_searchcoords); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_9NSResults_2get_pairs(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_9NSResults_4get_pair_distances(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_9NSResults_6get_indices(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_9NSResults_8get_distances(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_9NSResults_6cutoff___get__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_9NSResults_10__reduce_cython__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_9NSResults_12__setstate_cython__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ +static int __pyx_pf_10MDAnalysis_3lib_6nsgrid_6NSGrid___init__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *__pyx_v_self, PyObject *__pyx_v_ncoords, PyObject *__pyx_v_cutoff, struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *__pyx_v_box, PyObject *__pyx_v_max_size, PyObject *__pyx_v_force); /* proto */ +static void __pyx_pf_10MDAnalysis_3lib_6nsgrid_6NSGrid_2__dealloc__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6NSGrid_6cutoff___get__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6NSGrid_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6NSGrid_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ +static int __pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS___init__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, PyObject *__pyx_v_cutoff, PyObject *__pyx_v_coords, PyObject *__pyx_v_box, PyObject *__pyx_v_max_gridsize, PyObject *__pyx_v_pbc); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, PyObject *__pyx_v_search_coords); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_6cutoff___get__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_6__reduce_cython__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_8__setstate_cython__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid___pyx_unpickle_NSResults(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_2__pyx_unpickle_FastNS(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ +static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__len__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ +static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_12__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ +static PyObject *__pyx_pf___pyx_array___reduce_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_array_2__setstate_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ +static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ +static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_MemviewEnum_2__setstate_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ +static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); 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/* proto */ +static PyObject *__pyx_pf___pyx_memoryviewslice___reduce_cython__(CYTHON_UNUSED struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf___pyx_memoryviewslice_2__setstate_cython__(CYTHON_UNUSED struct __pyx_memoryviewslice_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView___pyx_unpickle_Enum(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_tp_new_10MDAnalysis_3lib_6nsgrid_PBCBox(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_10MDAnalysis_3lib_6nsgrid_NSResults(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_10MDAnalysis_3lib_6nsgrid_NSGrid(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_10MDAnalysis_3lib_6nsgrid_FastNS(PyTypeObject *t, PyObject *a, PyObject *k); 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+ + /* "MDAnalysis/lib/nsgrid.pyx":172 + * # Update matrix + * self.is_triclinic = False + * for i in range(DIM): # <<<<<<<<<<<<<< + * for j in range(DIM): + * self.c_pbcbox.box[i][j] = box[i, j] + */ + for (__pyx_t_1 = 0; __pyx_t_1 < 3; __pyx_t_1+=1) { + __pyx_v_i = __pyx_t_1; + + /* "MDAnalysis/lib/nsgrid.pyx":173 + * self.is_triclinic = False + * for i in range(DIM): + * for j in range(DIM): # <<<<<<<<<<<<<< + * self.c_pbcbox.box[i][j] = box[i, j] + * + */ + for (__pyx_t_2 = 0; __pyx_t_2 < 3; __pyx_t_2+=1) { + __pyx_v_j = __pyx_t_2; + + /* "MDAnalysis/lib/nsgrid.pyx":174 + * for i in range(DIM): + * for j in range(DIM): + * self.c_pbcbox.box[i][j] = box[i, j] # <<<<<<<<<<<<<< + * + * if i != j: + */ + __pyx_t_3 = __pyx_v_i; + __pyx_t_4 = __pyx_v_j; + if (__pyx_t_3 < 0) __pyx_t_3 += __pyx_v_box.shape[0]; + if (__pyx_t_4 < 0) __pyx_t_4 += __pyx_v_box.shape[1]; + ((__pyx_v_self->c_pbcbox.box[__pyx_v_i])[__pyx_v_j]) = (*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_3 * __pyx_v_box.strides[0]) )) + __pyx_t_4)) ))); + + /* "MDAnalysis/lib/nsgrid.pyx":176 + * self.c_pbcbox.box[i][j] = box[i, j] + * + * if i != j: # <<<<<<<<<<<<<< + * if box[i, j] > EPSILON: + * self.is_triclinic = True + */ + __pyx_t_5 = ((__pyx_v_i != __pyx_v_j) != 0); + if (__pyx_t_5) { + + /* "MDAnalysis/lib/nsgrid.pyx":177 + * + * if i != j: + * if box[i, j] > EPSILON: # <<<<<<<<<<<<<< + * self.is_triclinic = True + * + */ + __pyx_t_6 = __pyx_v_i; + __pyx_t_7 = __pyx_v_j; + if (__pyx_t_6 < 0) __pyx_t_6 += __pyx_v_box.shape[0]; + if (__pyx_t_7 < 0) __pyx_t_7 += __pyx_v_box.shape[1]; + __pyx_t_5 = (((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_6 * __pyx_v_box.strides[0]) )) + __pyx_t_7)) ))) > 1e-05) != 0); + if (__pyx_t_5) { + + /* "MDAnalysis/lib/nsgrid.pyx":178 + * if i != j: + * if box[i, j] > EPSILON: + * self.is_triclinic = True # <<<<<<<<<<<<<< + * + * # Update diagonals + */ + __pyx_v_self->is_triclinic = 1; + + /* "MDAnalysis/lib/nsgrid.pyx":177 + * + * if i != j: + * if box[i, j] > EPSILON: # <<<<<<<<<<<<<< + * self.is_triclinic = True + * + */ + } + + /* "MDAnalysis/lib/nsgrid.pyx":176 + * self.c_pbcbox.box[i][j] = box[i, j] + * + * if i != j: # <<<<<<<<<<<<<< + * if box[i, j] > EPSILON: + * self.is_triclinic = True + */ + } + } + } + + /* "MDAnalysis/lib/nsgrid.pyx":181 + * + * # Update diagonals + * for i in range(DIM): # <<<<<<<<<<<<<< + * self.c_pbcbox.fbox_diag[i] = box[i, i] + * self.c_pbcbox.hbox_diag[i] = self.c_pbcbox.fbox_diag[i] * 0.5 + */ + for (__pyx_t_1 = 0; __pyx_t_1 < 3; __pyx_t_1+=1) { + __pyx_v_i = __pyx_t_1; + + /* "MDAnalysis/lib/nsgrid.pyx":182 + * # Update diagonals + * for i in range(DIM): + * self.c_pbcbox.fbox_diag[i] = box[i, i] # <<<<<<<<<<<<<< + * self.c_pbcbox.hbox_diag[i] = self.c_pbcbox.fbox_diag[i] * 0.5 + * self.c_pbcbox.mhbox_diag[i] = - self.c_pbcbox.hbox_diag[i] + */ + __pyx_t_8 = __pyx_v_i; + __pyx_t_9 = __pyx_v_i; + if (__pyx_t_8 < 0) __pyx_t_8 += __pyx_v_box.shape[0]; + if (__pyx_t_9 < 0) __pyx_t_9 += __pyx_v_box.shape[1]; + (__pyx_v_self->c_pbcbox.fbox_diag[__pyx_v_i]) = (*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_8 * __pyx_v_box.strides[0]) )) + __pyx_t_9)) ))); + + /* "MDAnalysis/lib/nsgrid.pyx":183 + * for i in range(DIM): + * self.c_pbcbox.fbox_diag[i] = box[i, i] + * self.c_pbcbox.hbox_diag[i] = self.c_pbcbox.fbox_diag[i] * 0.5 # <<<<<<<<<<<<<< + * self.c_pbcbox.mhbox_diag[i] = - self.c_pbcbox.hbox_diag[i] + * + */ + (__pyx_v_self->c_pbcbox.hbox_diag[__pyx_v_i]) = ((__pyx_v_self->c_pbcbox.fbox_diag[__pyx_v_i]) * 0.5); + + /* "MDAnalysis/lib/nsgrid.pyx":184 + * self.c_pbcbox.fbox_diag[i] = box[i, i] + * self.c_pbcbox.hbox_diag[i] = self.c_pbcbox.fbox_diag[i] * 0.5 + * self.c_pbcbox.mhbox_diag[i] = - self.c_pbcbox.hbox_diag[i] # <<<<<<<<<<<<<< + * + * # Update maximum cutoff + */ + (__pyx_v_self->c_pbcbox.mhbox_diag[__pyx_v_i]) = (-(__pyx_v_self->c_pbcbox.hbox_diag[__pyx_v_i])); + } + + /* "MDAnalysis/lib/nsgrid.pyx":190 + * # Physical limitation of the cut-off + * # by half the length of the shortest box vector. + * min_hv2 = min(0.25 * rvec_norm2(&box[XX, XX]), 0.25 * rvec_norm2(&box[YY, XX])) # <<<<<<<<<<<<<< + * min_hv2 = min(min_hv2, 0.25 * rvec_norm2(&box[ZZ, XX])) + * + */ + __pyx_t_10 = 1; + __pyx_t_11 = 0; + if (__pyx_t_10 < 0) __pyx_t_10 += __pyx_v_box.shape[0]; + if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_v_box.shape[1]; + __pyx_t_12 = (0.25 * __pyx_f_10MDAnalysis_3lib_6nsgrid_rvec_norm2((&(*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_10 * __pyx_v_box.strides[0]) )) + __pyx_t_11)) )))))); + __pyx_t_13 = 0; + __pyx_t_14 = 0; + if (__pyx_t_13 < 0) __pyx_t_13 += __pyx_v_box.shape[0]; + if (__pyx_t_14 < 0) __pyx_t_14 += __pyx_v_box.shape[1]; + __pyx_t_15 = (0.25 * __pyx_f_10MDAnalysis_3lib_6nsgrid_rvec_norm2((&(*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_13 * __pyx_v_box.strides[0]) )) + __pyx_t_14)) )))))); + if (((__pyx_t_12 < __pyx_t_15) != 0)) { + __pyx_t_16 = __pyx_t_12; + } else { + __pyx_t_16 = __pyx_t_15; + } + __pyx_v_min_hv2 = __pyx_t_16; + + /* "MDAnalysis/lib/nsgrid.pyx":191 + * # by half the length of the shortest box vector. + * min_hv2 = min(0.25 * rvec_norm2(&box[XX, XX]), 0.25 * rvec_norm2(&box[YY, XX])) + * min_hv2 = min(min_hv2, 0.25 * rvec_norm2(&box[ZZ, XX])) # <<<<<<<<<<<<<< + * + * # Limitation to the smallest diagonal element due to optimizations: + */ + __pyx_t_17 = 2; + __pyx_t_18 = 0; + if (__pyx_t_17 < 0) __pyx_t_17 += __pyx_v_box.shape[0]; + if (__pyx_t_18 < 0) __pyx_t_18 += __pyx_v_box.shape[1]; + __pyx_t_16 = (0.25 * __pyx_f_10MDAnalysis_3lib_6nsgrid_rvec_norm2((&(*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_17 * __pyx_v_box.strides[0]) )) + __pyx_t_18)) )))))); + __pyx_t_19 = __pyx_v_min_hv2; + if (((__pyx_t_16 < __pyx_t_19) != 0)) { + __pyx_t_12 = __pyx_t_16; + } else { + __pyx_t_12 = __pyx_t_19; + } + __pyx_v_min_hv2 = __pyx_t_12; + + /* "MDAnalysis/lib/nsgrid.pyx":197 + * # in the grid search and pbc_dx is a lot faster + * # than checking all possible combinations. + * tmp = box[YY, YY] # <<<<<<<<<<<<<< + * if box[ZZ, YY] < 0: + * tmp -= box[ZZ, YY] + */ + __pyx_t_20 = 1; + __pyx_t_21 = 1; + if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_v_box.shape[0]; + if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_v_box.shape[1]; + __pyx_v_tmp = (*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_20 * __pyx_v_box.strides[0]) )) + __pyx_t_21)) ))); + + /* "MDAnalysis/lib/nsgrid.pyx":198 + * # than checking all possible combinations. + * tmp = box[YY, YY] + * if box[ZZ, YY] < 0: # <<<<<<<<<<<<<< + * tmp -= box[ZZ, YY] + * else: + */ + __pyx_t_22 = 2; + __pyx_t_23 = 1; + if (__pyx_t_22 < 0) __pyx_t_22 += __pyx_v_box.shape[0]; + if (__pyx_t_23 < 0) __pyx_t_23 += __pyx_v_box.shape[1]; + __pyx_t_5 = (((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_22 * __pyx_v_box.strides[0]) )) + __pyx_t_23)) ))) < 0.0) != 0); + if (__pyx_t_5) { + + /* "MDAnalysis/lib/nsgrid.pyx":199 + * tmp = box[YY, YY] + * if box[ZZ, YY] < 0: + * tmp -= box[ZZ, YY] # <<<<<<<<<<<<<< + * else: + * tmp += box[ZZ, YY] + */ + __pyx_t_24 = 2; + __pyx_t_25 = 1; + if (__pyx_t_24 < 0) __pyx_t_24 += __pyx_v_box.shape[0]; + if (__pyx_t_25 < 0) __pyx_t_25 += __pyx_v_box.shape[1]; + __pyx_v_tmp = (__pyx_v_tmp - (*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_24 * __pyx_v_box.strides[0]) )) + __pyx_t_25)) )))); 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__pyx_t_12 < 3; __pyx_t_12+=1) { + __pyx_v_xi = __pyx_t_12; + + /* "MDAnalysis/lib/nsgrid.pyx":875 + * cellindex = searchgrid.cellids[current_beadid] + * for xi in range(DIM): + * for yi in range(DIM): # <<<<<<<<<<<<<< + * for zi in range(DIM): + * check = True + */ + for (__pyx_t_13 = 0; __pyx_t_13 < 3; __pyx_t_13+=1) { + __pyx_v_yi = __pyx_t_13; + + /* "MDAnalysis/lib/nsgrid.pyx":876 + * for xi in range(DIM): + * for yi in range(DIM): + * for zi in range(DIM): # <<<<<<<<<<<<<< + * check = True + * #Probe the search coordinates in a brick shaped box + */ + for (__pyx_t_14 = 0; __pyx_t_14 < 3; __pyx_t_14+=1) { + __pyx_v_zi = __pyx_t_14; + + /* "MDAnalysis/lib/nsgrid.pyx":877 + * for yi in range(DIM): + * for zi in range(DIM): + * check = True # <<<<<<<<<<<<<< + * #Probe the search coordinates in a brick shaped box + * probe[XX] = searchcoords_bbox[current_beadid, XX] + (xi - 1) * searchgrid.cellsize[XX] + */ + __pyx_v_check = 1; + + /* "MDAnalysis/lib/nsgrid.pyx":879 + * check = True + * #Probe the search coordinates in a brick shaped box + * probe[XX] = searchcoords_bbox[current_beadid, XX] + (xi - 1) * searchgrid.cellsize[XX] # <<<<<<<<<<<<<< + * probe[YY] = searchcoords_bbox[current_beadid, YY] + (yi - 1) * searchgrid.cellsize[YY] + * probe[ZZ] = searchcoords_bbox[current_beadid, ZZ] + (zi - 1) * searchgrid.cellsize[ZZ] + */ + __pyx_t_15 = __pyx_v_current_beadid; 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+ if (__pyx_t_18 < 0) __pyx_t_18 += __pyx_v_searchcoords_bbox.shape[1]; + (__pyx_v_probe[1]) = ((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_searchcoords_bbox.data + __pyx_t_17 * __pyx_v_searchcoords_bbox.strides[0]) )) + __pyx_t_18)) ))) + ((__pyx_v_yi - 1) * (__pyx_v_searchgrid->cellsize[1]))); + + /* "MDAnalysis/lib/nsgrid.pyx":881 + * probe[XX] = searchcoords_bbox[current_beadid, XX] + (xi - 1) * searchgrid.cellsize[XX] + * probe[YY] = searchcoords_bbox[current_beadid, YY] + (yi - 1) * searchgrid.cellsize[YY] + * probe[ZZ] = searchcoords_bbox[current_beadid, ZZ] + (zi - 1) * searchgrid.cellsize[ZZ] # <<<<<<<<<<<<<< + * # Make sure the probe coordinates is inside the brick-shaped box + * if self.periodic: + */ + __pyx_t_19 = __pyx_v_current_beadid; + __pyx_t_20 = 2; + if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_v_searchcoords_bbox.shape[0]; + if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_v_searchcoords_bbox.shape[1]; + (__pyx_v_probe[2]) = ((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_searchcoords_bbox.data + __pyx_t_19 * __pyx_v_searchcoords_bbox.strides[0]) )) + __pyx_t_20)) ))) + ((__pyx_v_zi - 1) * (__pyx_v_searchgrid->cellsize[2]))); + + /* "MDAnalysis/lib/nsgrid.pyx":883 + * probe[ZZ] = searchcoords_bbox[current_beadid, ZZ] + (zi - 1) * searchgrid.cellsize[ZZ] + * # Make sure the probe coordinates is inside the brick-shaped box + * if self.periodic: # <<<<<<<<<<<<<< + * for m in range(DIM - 1, -1, -1): + * while probe[m] < 0: + */ + __pyx_t_1 = (__pyx_v_self->periodic != 0); + if (__pyx_t_1) { + + /* "MDAnalysis/lib/nsgrid.pyx":884 + * # Make sure the probe coordinates is inside the brick-shaped box + * if self.periodic: + * for m in range(DIM - 1, -1, -1): # <<<<<<<<<<<<<< + * while probe[m] < 0: + * for d in range(m+1): + */ + for (__pyx_t_21 = 2; __pyx_t_21 > -1L; __pyx_t_21-=1) { + __pyx_v_m = __pyx_t_21; + + /* "MDAnalysis/lib/nsgrid.pyx":885 + * if self.periodic: + * for m in range(DIM - 1, -1, -1): + * while probe[m] < 0: # <<<<<<<<<<<<<< + * for d in range(m+1): + * probe[d] += self.box.c_pbcbox.box[m][d] + */ + while (1) { + __pyx_t_1 = (((__pyx_v_probe[__pyx_v_m]) < 0.0) != 0); + if (!__pyx_t_1) break; + + /* "MDAnalysis/lib/nsgrid.pyx":886 + * for m in range(DIM - 1, -1, -1): + * while probe[m] < 0: + * for d in range(m+1): # <<<<<<<<<<<<<< + * probe[d] += self.box.c_pbcbox.box[m][d] + * while probe[m] >= self.box.c_pbcbox.box[m][m]: + */ + __pyx_t_22 = (__pyx_v_m + 1); + __pyx_t_23 = __pyx_t_22; + for (__pyx_t_24 = 0; __pyx_t_24 < __pyx_t_23; __pyx_t_24+=1) { + __pyx_v_d = __pyx_t_24; + + /* "MDAnalysis/lib/nsgrid.pyx":887 + * while probe[m] < 0: + * for d in range(m+1): + * probe[d] += self.box.c_pbcbox.box[m][d] # <<<<<<<<<<<<<< + * while probe[m] >= self.box.c_pbcbox.box[m][m]: + * for d in range(m+1): + */ + __pyx_t_25 = __pyx_v_d; + (__pyx_v_probe[__pyx_t_25]) = ((__pyx_v_probe[__pyx_t_25]) + ((__pyx_v_self->box->c_pbcbox.box[__pyx_v_m])[__pyx_v_d])); + } + } + + /* "MDAnalysis/lib/nsgrid.pyx":888 + * for d in range(m+1): + * probe[d] += self.box.c_pbcbox.box[m][d] + * while probe[m] >= self.box.c_pbcbox.box[m][m]: # <<<<<<<<<<<<<< + * for d in range(m+1): + * probe[d] -= self.box.c_pbcbox.box[m][d] + */ + while (1) { + __pyx_t_1 = (((__pyx_v_probe[__pyx_v_m]) >= ((__pyx_v_self->box->c_pbcbox.box[__pyx_v_m])[__pyx_v_m])) != 0); + if (!__pyx_t_1) break; + + /* "MDAnalysis/lib/nsgrid.pyx":889 + * probe[d] += self.box.c_pbcbox.box[m][d] + * while probe[m] >= self.box.c_pbcbox.box[m][m]: + * for d in range(m+1): # <<<<<<<<<<<<<< + * probe[d] -= self.box.c_pbcbox.box[m][d] + * else: + */ + __pyx_t_22 = (__pyx_v_m + 1); + __pyx_t_23 = __pyx_t_22; + for (__pyx_t_24 = 0; __pyx_t_24 < __pyx_t_23; __pyx_t_24+=1) { + __pyx_v_d = __pyx_t_24; + + /* "MDAnalysis/lib/nsgrid.pyx":890 + * while probe[m] >= self.box.c_pbcbox.box[m][m]: + * for d in range(m+1): + * probe[d] -= self.box.c_pbcbox.box[m][d] # <<<<<<<<<<<<<< + * else: + * for m in range(DIM -1, -1, -1): + */ + __pyx_t_25 = __pyx_v_d; 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+ + /* "MDAnalysis/lib/nsgrid.pyx":896 + * check = False + * break + * if probe[m] > self.box.c_pbcbox.box[m][m]: # <<<<<<<<<<<<<< + * check = False + * break + */ + } + } + __pyx_L29_break:; + } + __pyx_L17:; + + /* "MDAnalysis/lib/nsgrid.pyx":899 + * check = False + * break + * if not check: # <<<<<<<<<<<<<< + * continue + * # Get the cell index corresponding to the probe + */ + __pyx_t_1 = ((!(__pyx_v_check != 0)) != 0); + if (__pyx_t_1) { + + /* "MDAnalysis/lib/nsgrid.pyx":900 + * break + * if not check: + * continue # <<<<<<<<<<<<<< + * # Get the cell index corresponding to the probe + * cellindex_probe = self.grid.coord2cellid(probe) + */ + goto __pyx_L15_continue; + + /* "MDAnalysis/lib/nsgrid.pyx":899 + * check = False + * break + * if not check: # <<<<<<<<<<<<<< + * continue + * # Get the cell index corresponding to the probe + */ + } + + /* "MDAnalysis/lib/nsgrid.pyx":902 + * continue + * # Get the cell index corresponding to the probe + * cellindex_probe = self.grid.coord2cellid(probe) # <<<<<<<<<<<<<< + * # for this cellindex search in grid + * for j in range(self.grid.nbeads[cellindex_probe]): + */ + __pyx_v_cellindex_probe = ((struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSGrid *)__pyx_v_self->grid->__pyx_vtab)->coord2cellid(__pyx_v_self->grid, __pyx_v_probe); 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__pyx_t_7+=1) { + __pyx_v_i = __pyx_t_7; + + /* "MDAnalysis/lib/nsgrid.pyx":955 + * for i in range(size_search): + * # Start with first search coordinate + * current_beadid = i # <<<<<<<<<<<<<< + * # find the cellindex of the coordinate + * cellindex = self.grid.cellids[current_beadid] + */ + __pyx_v_current_beadid = __pyx_v_i; + + /* "MDAnalysis/lib/nsgrid.pyx":957 + * current_beadid = i + * # find the cellindex of the coordinate + * cellindex = self.grid.cellids[current_beadid] # <<<<<<<<<<<<<< + * for xi in range(DIM): + * for yi in range(DIM): + */ + __pyx_v_cellindex = (__pyx_v_self->grid->cellids[__pyx_v_current_beadid]); + + /* "MDAnalysis/lib/nsgrid.pyx":958 + * # find the cellindex of the coordinate + * cellindex = self.grid.cellids[current_beadid] + * for xi in range(DIM): # <<<<<<<<<<<<<< + * for yi in range(DIM): + * for zi in range(DIM): + */ + for (__pyx_t_8 = 0; __pyx_t_8 < 3; __pyx_t_8+=1) { + __pyx_v_xi = __pyx_t_8; + + /* "MDAnalysis/lib/nsgrid.pyx":959 + * cellindex = self.grid.cellids[current_beadid] + * for xi in range(DIM): + * for yi in range(DIM): # <<<<<<<<<<<<<< + * for zi in range(DIM): + * check = True + */ + for (__pyx_t_9 = 0; __pyx_t_9 < 3; __pyx_t_9+=1) { + __pyx_v_yi = __pyx_t_9; + + /* "MDAnalysis/lib/nsgrid.pyx":960 + * for xi in range(DIM): + * for yi in range(DIM): + * for zi in range(DIM): # <<<<<<<<<<<<<< + * check = True + * # Calculate and/or reinitialize shifted coordinates + */ + for (__pyx_t_10 = 0; __pyx_t_10 < 3; __pyx_t_10+=1) { + __pyx_v_zi = __pyx_t_10; + + /* "MDAnalysis/lib/nsgrid.pyx":961 + * for yi in range(DIM): + * for zi in range(DIM): + * check = True # <<<<<<<<<<<<<< + * # Calculate and/or reinitialize shifted coordinates + * # Probe the search coordinates in a brick shaped box + */ + __pyx_v_check = 1; + + /* "MDAnalysis/lib/nsgrid.pyx":964 + * # Calculate and/or reinitialize shifted coordinates + * # Probe the search coordinates in a brick shaped box + * probe[XX] = self.coords_bbox[current_beadid, XX] + (xi - 1) * self.grid.cellsize[XX] # <<<<<<<<<<<<<< + * probe[YY] = self.coords_bbox[current_beadid, YY] + (yi - 1) * self.grid.cellsize[YY] + * probe[ZZ] = self.coords_bbox[current_beadid, ZZ] + (zi - 1) * self.grid.cellsize[ZZ] + */ + __pyx_t_11 = __pyx_v_current_beadid; 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+ (__pyx_v_probe[2]) = ((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_self->coords_bbox.data + __pyx_t_15 * __pyx_v_self->coords_bbox.strides[0]) )) + __pyx_t_16)) ))) + ((__pyx_v_zi - 1) * (__pyx_v_self->grid->cellsize[2]))); + + /* "MDAnalysis/lib/nsgrid.pyx":968 + * probe[ZZ] = self.coords_bbox[current_beadid, ZZ] + (zi - 1) * self.grid.cellsize[ZZ] + * # Make sure the shifted coordinates is inside the brick-shaped box + * if self.periodic: # <<<<<<<<<<<<<< + * for m in range(DIM - 1, -1, -1): + * while probe[m] < 0: + */ + __pyx_t_17 = (__pyx_v_self->periodic != 0); + if (__pyx_t_17) { + + /* "MDAnalysis/lib/nsgrid.pyx":969 + * # Make sure the shifted coordinates is inside the brick-shaped box + * if self.periodic: + * for m in range(DIM - 1, -1, -1): # <<<<<<<<<<<<<< + * while probe[m] < 0: + * for d in range(m+1): + */ + for (__pyx_t_18 = 2; __pyx_t_18 > -1L; __pyx_t_18-=1) { + __pyx_v_m = __pyx_t_18; 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+ } + } + + /* "MDAnalysis/lib/nsgrid.pyx":973 + * for d in range(m+1): + * probe[d] += self.box.c_pbcbox.box[m][d] + * while probe[m] >= self.box.c_pbcbox.box[m][m]: # <<<<<<<<<<<<<< + * for d in range(m+1): + * probe[d] -= self.box.c_pbcbox.box[m][d] + */ + while (1) { + __pyx_t_17 = (((__pyx_v_probe[__pyx_v_m]) >= ((__pyx_v_self->box->c_pbcbox.box[__pyx_v_m])[__pyx_v_m])) != 0); + if (!__pyx_t_17) break; + + /* "MDAnalysis/lib/nsgrid.pyx":974 + * probe[d] += self.box.c_pbcbox.box[m][d] + * while probe[m] >= self.box.c_pbcbox.box[m][m]: + * for d in range(m+1): # <<<<<<<<<<<<<< + * probe[d] -= self.box.c_pbcbox.box[m][d] + * else: + */ + __pyx_t_19 = (__pyx_v_m + 1); + __pyx_t_20 = __pyx_t_19; + for (__pyx_t_21 = 0; __pyx_t_21 < __pyx_t_20; __pyx_t_21+=1) { + __pyx_v_d = __pyx_t_21; + + /* "MDAnalysis/lib/nsgrid.pyx":975 + * while probe[m] >= self.box.c_pbcbox.box[m][m]: + * for d in range(m+1): + * probe[d] -= self.box.c_pbcbox.box[m][d] # <<<<<<<<<<<<<< + * else: + * for m in range(DIM -1, -1, -1): + */ + __pyx_t_22 = __pyx_v_d; + (__pyx_v_probe[__pyx_t_22]) = ((__pyx_v_probe[__pyx_t_22]) - ((__pyx_v_self->box->c_pbcbox.box[__pyx_v_m])[__pyx_v_d])); + } + } + } + + /* "MDAnalysis/lib/nsgrid.pyx":968 + * probe[ZZ] = self.coords_bbox[current_beadid, ZZ] + (zi - 1) * self.grid.cellsize[ZZ] + * # Make sure the shifted coordinates is inside the brick-shaped box + * if self.periodic: # <<<<<<<<<<<<<< + * for m in range(DIM - 1, -1, -1): + * while probe[m] < 0: + */ + goto __pyx_L14; + } + + /* "MDAnalysis/lib/nsgrid.pyx":977 + * probe[d] -= self.box.c_pbcbox.box[m][d] + * else: + * for m in range(DIM -1, -1, -1): # <<<<<<<<<<<<<< + * if probe[m] < 0: + * check = False + */ + /*else*/ { + for (__pyx_t_18 = 2; __pyx_t_18 > -1L; __pyx_t_18-=1) { + __pyx_v_m = __pyx_t_18; + + /* "MDAnalysis/lib/nsgrid.pyx":978 + * else: + * for m in range(DIM -1, -1, -1): + * if probe[m] < 0: # <<<<<<<<<<<<<< + * check = False + * break + */ + __pyx_t_17 = (((__pyx_v_probe[__pyx_v_m]) < 0.0) != 0); + if (__pyx_t_17) { + + /* "MDAnalysis/lib/nsgrid.pyx":979 + * for m in range(DIM -1, -1, -1): + * if probe[m] < 0: + * check = False # <<<<<<<<<<<<<< + * break + * elif probe[m] >= self.box.c_pbcbox.box[m][m]: + */ + __pyx_v_check = 0; 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+ if (__pyx_t_2) { + + /* "View.MemoryView":1126 + * for i in range(ndim): + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< + * break + * + */ + __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); + + /* "View.MemoryView":1127 + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] + * break # <<<<<<<<<<<<<< + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + */ + goto __pyx_L7_break; + + /* "View.MemoryView":1125 + * + * for i in range(ndim): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * f_stride = mslice.strides[i] + * break + */ + } + } + __pyx_L7_break:; + + /* "View.MemoryView":1129 + * break + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< + * return 'C' + * else: + */ + __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1130 + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + * return 'C' # <<<<<<<<<<<<<< + * else: + * return 'F' + */ + __pyx_r = 'C'; + goto __pyx_L0; + + /* "View.MemoryView":1129 + * break + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< + * return 'C' + * else: + */ + } + + /* "View.MemoryView":1132 + * return 'C' + * else: + * return 'F' # <<<<<<<<<<<<<< + * + * @cython.cdivision(True) + */ + /*else*/ { + __pyx_r = 'F'; + goto __pyx_L0; + } + + /* "View.MemoryView":1111 + * + * @cname('__pyx_get_best_slice_order') + * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< + * """ + * Figure out the best memory access order for a given slice. + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1135 + * + * @cython.cdivision(True) + * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< + * char *dst_data, Py_ssize_t *dst_strides, + * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, + */ + +static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v_src_strides, char *__pyx_v_dst_data, Py_ssize_t *__pyx_v_dst_strides, Py_ssize_t *__pyx_v_src_shape, Py_ssize_t *__pyx_v_dst_shape, int __pyx_v_ndim, size_t __pyx_v_itemsize) { + CYTHON_UNUSED Py_ssize_t __pyx_v_i; + CYTHON_UNUSED Py_ssize_t __pyx_v_src_extent; + Py_ssize_t __pyx_v_dst_extent; + Py_ssize_t __pyx_v_src_stride; + Py_ssize_t __pyx_v_dst_stride; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + Py_ssize_t __pyx_t_4; + Py_ssize_t __pyx_t_5; + Py_ssize_t __pyx_t_6; + + /* "View.MemoryView":1142 + * + * cdef Py_ssize_t i + * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] + */ + __pyx_v_src_extent = (__pyx_v_src_shape[0]); + + /* "View.MemoryView":1143 + * cdef Py_ssize_t i + * cdef Py_ssize_t src_extent = src_shape[0] + * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t src_stride = src_strides[0] + * cdef Py_ssize_t dst_stride = dst_strides[0] + */ + __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); + + /* "View.MemoryView":1144 + * cdef Py_ssize_t src_extent = src_shape[0] + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + */ + __pyx_v_src_stride = (__pyx_v_src_strides[0]); + + /* "View.MemoryView":1145 + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] + * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< + * + * if ndim == 1: + */ + __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); + + /* "View.MemoryView":1147 + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + */ + __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1148 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ + __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L5_bool_binop_done; + } + __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L5_bool_binop_done; + } + + /* "View.MemoryView":1149 + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< + * memcpy(dst_data, src_data, itemsize * dst_extent) + * else: + */ + __pyx_t_2 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize); + if (__pyx_t_2) { + __pyx_t_2 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride)); + } + __pyx_t_3 = (__pyx_t_2 != 0); + __pyx_t_1 = __pyx_t_3; + __pyx_L5_bool_binop_done:; + + /* "View.MemoryView":1148 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ + if (__pyx_t_1) { + + /* "View.MemoryView":1150 + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< + * else: + * for i in range(dst_extent): + */ + (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent))); + + /* "View.MemoryView":1148 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ + goto __pyx_L4; + } + + /* "View.MemoryView":1152 + * memcpy(dst_data, src_data, itemsize * dst_extent) + * else: + * for i in range(dst_extent): # <<<<<<<<<<<<<< + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride + */ + /*else*/ { + __pyx_t_4 = __pyx_v_dst_extent; + __pyx_t_5 = __pyx_t_4; + for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { + __pyx_v_i = __pyx_t_6; + + /* "View.MemoryView":1153 + * else: + * for i in range(dst_extent): + * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< + * src_data += src_stride + * dst_data += dst_stride + */ + (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); + + /* "View.MemoryView":1154 + * for i in range(dst_extent): + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride # <<<<<<<<<<<<<< + * dst_data += dst_stride + * else: + */ + __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); + + /* "View.MemoryView":1155 + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride + * dst_data += dst_stride # <<<<<<<<<<<<<< + * else: + * for i in range(dst_extent): + */ + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L4:; + + /* "View.MemoryView":1147 + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + */ + goto __pyx_L3; + } + + /* "View.MemoryView":1157 + * dst_data += dst_stride + * else: + * for i in range(dst_extent): # <<<<<<<<<<<<<< + * _copy_strided_to_strided(src_data, src_strides + 1, + * dst_data, dst_strides + 1, + */ + /*else*/ { + __pyx_t_4 = __pyx_v_dst_extent; + __pyx_t_5 = __pyx_t_4; + for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { + __pyx_v_i = __pyx_t_6; + + /* "View.MemoryView":1158 + * else: + * for i in range(dst_extent): + * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< + * dst_data, dst_strides + 1, + * src_shape + 1, dst_shape + 1, + */ + _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); + + /* "View.MemoryView":1162 + * src_shape + 1, dst_shape + 1, + * ndim - 1, itemsize) + * src_data += src_stride # <<<<<<<<<<<<<< + * dst_data += dst_stride + * + */ + __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); + + /* "View.MemoryView":1163 + * ndim - 1, itemsize) + * src_data += src_stride + * dst_data += dst_stride # <<<<<<<<<<<<<< + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, + */ + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L3:; + + /* "View.MemoryView":1135 + * + * @cython.cdivision(True) + * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< + * char *dst_data, Py_ssize_t *dst_strides, + * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, + */ + + /* function exit code */ +} + +/* "View.MemoryView":1165 + * dst_data += dst_stride + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + */ + +static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { + + /* "View.MemoryView":1168 + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< + * src.shape, dst.shape, ndim, itemsize) + * + */ + _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1165 + * dst_data += dst_stride + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + */ + + /* function exit code */ +} + +/* "View.MemoryView":1172 + * + * @cname('__pyx_memoryview_slice_get_size') + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + */ + +static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { + int __pyx_v_i; + Py_ssize_t __pyx_v_size; + Py_ssize_t __pyx_r; + Py_ssize_t __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + + /* "View.MemoryView":1175 + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + __pyx_t_1 = __pyx_v_src->memview->view.itemsize; + __pyx_v_size = __pyx_t_1; + + /* "View.MemoryView":1177 + * cdef Py_ssize_t size = src.memview.view.itemsize + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * size *= src.shape[i] + * + */ + __pyx_t_2 = __pyx_v_ndim; + __pyx_t_3 = __pyx_t_2; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_i = __pyx_t_4; + + /* "View.MemoryView":1178 + * + * for i in range(ndim): + * size *= src.shape[i] # <<<<<<<<<<<<<< + * + * return size + */ + __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i])); + } + + /* "View.MemoryView":1180 + * size *= src.shape[i] + * + * return size # <<<<<<<<<<<<<< + * + * @cname('__pyx_fill_contig_strides_array') + */ + __pyx_r = __pyx_v_size; + goto __pyx_L0; + + /* "View.MemoryView":1172 + * + * @cname('__pyx_memoryview_slice_get_size') + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1183 + * + * @cname('__pyx_fill_contig_strides_array') + * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< + * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, + * int ndim, char order) nogil: + */ + +static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { + int __pyx_v_idx; + Py_ssize_t __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + + /* "View.MemoryView":1192 + * cdef int idx + * + * if order == 'F': # <<<<<<<<<<<<<< + * for idx in range(ndim): + * strides[idx] = stride + */ + __pyx_t_1 = ((__pyx_v_order == 'F') != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1193 + * + * if order == 'F': + * for idx in range(ndim): # <<<<<<<<<<<<<< + * strides[idx] = stride + * stride = stride * shape[idx] + */ + __pyx_t_2 = __pyx_v_ndim; + __pyx_t_3 = __pyx_t_2; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_idx = __pyx_t_4; + + /* "View.MemoryView":1194 + * if order == 'F': + * for idx in range(ndim): + * strides[idx] = stride # <<<<<<<<<<<<<< + * stride = stride * shape[idx] + * else: + */ + (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; + + /* "View.MemoryView":1195 + * for idx in range(ndim): + * strides[idx] = stride + * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * else: + * for idx in range(ndim - 1, -1, -1): + */ + __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); + } + + /* "View.MemoryView":1192 + * cdef int idx + * + * if order == 'F': # <<<<<<<<<<<<<< + * for idx in range(ndim): + * strides[idx] = stride + */ + goto __pyx_L3; + } + + /* "View.MemoryView":1197 + * stride = stride * shape[idx] + * else: + * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< + * strides[idx] = stride + * stride = stride * shape[idx] + */ + /*else*/ { + for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { + __pyx_v_idx = __pyx_t_2; + + /* "View.MemoryView":1198 + * else: + * for idx in range(ndim - 1, -1, -1): + * strides[idx] = stride # <<<<<<<<<<<<<< + * stride = stride * shape[idx] + * + */ + (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; + + /* "View.MemoryView":1199 + * for idx in range(ndim - 1, -1, -1): + * strides[idx] = stride + * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * + * return stride + */ + __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); + } + } + __pyx_L3:; + + /* "View.MemoryView":1201 + * stride = stride * shape[idx] + * + * return stride # <<<<<<<<<<<<<< + * + * @cname('__pyx_memoryview_copy_data_to_temp') + */ + __pyx_r = __pyx_v_stride; + goto __pyx_L0; + + /* "View.MemoryView":1183 + * + * @cname('__pyx_fill_contig_strides_array') + * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< + * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, + * int ndim, char order) nogil: + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1204 + * + * @cname('__pyx_memoryview_copy_data_to_temp') + * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *tmpslice, + * char order, + */ + +static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_tmpslice, char __pyx_v_order, int __pyx_v_ndim) { + int __pyx_v_i; + void *__pyx_v_result; + size_t __pyx_v_itemsize; + size_t __pyx_v_size; + void *__pyx_r; + Py_ssize_t __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + struct __pyx_memoryview_obj *__pyx_t_4; + int __pyx_t_5; + int __pyx_t_6; + + /* "View.MemoryView":1215 + * cdef void *result + * + * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< + * cdef size_t size = slice_get_size(src, ndim) + * + */ + __pyx_t_1 = __pyx_v_src->memview->view.itemsize; + __pyx_v_itemsize = __pyx_t_1; + + /* "View.MemoryView":1216 + * + * cdef size_t itemsize = src.memview.view.itemsize + * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<< + * + * result = malloc(size) + */ + __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim); + + /* "View.MemoryView":1218 + * cdef size_t size = slice_get_size(src, ndim) + * + * result = malloc(size) # <<<<<<<<<<<<<< + * if not result: + * _err(MemoryError, NULL) + */ + __pyx_v_result = malloc(__pyx_v_size); + + /* "View.MemoryView":1219 + * + * result = malloc(size) + * if not result: # <<<<<<<<<<<<<< + * _err(MemoryError, NULL) + * + */ + __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0); 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+ if (__pyx_t_2) { + + /* "View.MemoryView":1290 + * if src.shape[i] != dst.shape[i]: + * if src.shape[i] == 1: + * broadcasting = True # <<<<<<<<<<<<<< + * src.strides[i] = 0 + * else: + */ + __pyx_v_broadcasting = 1; + + /* "View.MemoryView":1291 + * if src.shape[i] == 1: + * broadcasting = True + * src.strides[i] = 0 # <<<<<<<<<<<<<< + * else: + * _err_extents(i, dst.shape[i], src.shape[i]) + */ + (__pyx_v_src.strides[__pyx_v_i]) = 0; + + /* "View.MemoryView":1289 + * for i in range(ndim): + * if src.shape[i] != dst.shape[i]: + * if src.shape[i] == 1: # <<<<<<<<<<<<<< + * broadcasting = True + * src.strides[i] = 0 + */ + goto __pyx_L7; + } + + /* "View.MemoryView":1293 + * src.strides[i] = 0 + * else: + * _err_extents(i, dst.shape[i], src.shape[i]) # <<<<<<<<<<<<<< + * + * if src.suboffsets[i] >= 0: + */ + /*else*/ { + __pyx_t_6 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(1, 1293, __pyx_L1_error) + } + __pyx_L7:; + + /* "View.MemoryView":1288 + * + * for i in range(ndim): + * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< + * if src.shape[i] == 1: + * broadcasting = True + */ + } + + /* "View.MemoryView":1295 + * _err_extents(i, dst.shape[i], src.shape[i]) + * + * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + */ + __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1296 + * + * if src.suboffsets[i] >= 0: + * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<< + * + * if slices_overlap(&src, &dst, ndim, itemsize): + */ + __pyx_t_6 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Dimension %d is not direct"), __pyx_v_i); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(1, 1296, __pyx_L1_error) + + /* "View.MemoryView":1295 + * _err_extents(i, dst.shape[i], src.shape[i]) + * + * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + */ + } + } + + /* "View.MemoryView":1298 + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< + * + * if not slice_is_contig(src, order, ndim): + */ + __pyx_t_2 = (__pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1300 + * if slices_overlap(&src, &dst, ndim, itemsize): + * + * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< + * order = get_best_order(&dst, ndim) + * + */ + __pyx_t_2 = ((!(__pyx_memviewslice_is_contig(__pyx_v_src, __pyx_v_order, __pyx_v_ndim) != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1301 + * + * if not slice_is_contig(src, order, ndim): + * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<< + * + * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) + */ + __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim); + + /* "View.MemoryView":1300 + * if slices_overlap(&src, &dst, ndim, itemsize): + * + * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< + * order = get_best_order(&dst, ndim) + * + */ + } + + /* "View.MemoryView":1303 + * order = get_best_order(&dst, ndim) + * + * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<< + * src = tmp + * + */ + __pyx_t_7 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_7 == ((void *)NULL))) __PYX_ERR(1, 1303, __pyx_L1_error) + __pyx_v_tmpdata = __pyx_t_7; + + /* "View.MemoryView":1304 + * + * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) + * src = tmp # <<<<<<<<<<<<<< + * + * if not broadcasting: + */ + __pyx_v_src = __pyx_v_tmp; + + /* "View.MemoryView":1298 + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< + * + * if not slice_is_contig(src, order, ndim): + */ + } + + /* "View.MemoryView":1306 + * src = tmp + * + * if not broadcasting: # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1309 + * + * + * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(dst, 'C', ndim) + * elif slice_is_contig(src, 'F', ndim): + */ + __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'C', __pyx_v_ndim) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1310 + * + * if slice_is_contig(src, 'C', ndim): + * direct_copy = slice_is_contig(dst, 'C', ndim) # <<<<<<<<<<<<<< + * elif slice_is_contig(src, 'F', ndim): + * direct_copy = slice_is_contig(dst, 'F', ndim) + */ + __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'C', __pyx_v_ndim); + + /* "View.MemoryView":1309 + * + * + * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(dst, 'C', ndim) + * elif slice_is_contig(src, 'F', ndim): + */ + goto __pyx_L12; + } + + /* "View.MemoryView":1311 + * if slice_is_contig(src, 'C', ndim): + * direct_copy = slice_is_contig(dst, 'C', ndim) + * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(dst, 'F', ndim) + * + */ + __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'F', __pyx_v_ndim) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1312 + * direct_copy = slice_is_contig(dst, 'C', ndim) + * elif slice_is_contig(src, 'F', ndim): + * direct_copy = slice_is_contig(dst, 'F', ndim) # <<<<<<<<<<<<<< + * + * if direct_copy: + */ + __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'F', __pyx_v_ndim); + + /* "View.MemoryView":1311 + * if slice_is_contig(src, 'C', ndim): + * direct_copy = slice_is_contig(dst, 'C', ndim) + * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(dst, 'F', ndim) + * + */ + } + __pyx_L12:; + + /* "View.MemoryView":1314 + * direct_copy = slice_is_contig(dst, 'F', ndim) + * + * if direct_copy: # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + __pyx_t_2 = (__pyx_v_direct_copy != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1316 + * if direct_copy: + * + * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); + + /* "View.MemoryView":1317 + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) + */ + (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim))); + + /* "View.MemoryView":1318 + * refcount_copying(&dst, dtype_is_object, ndim, False) + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * free(tmpdata) + * return 0 + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1319 + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) # <<<<<<<<<<<<<< + * return 0 + * + */ + free(__pyx_v_tmpdata); + + /* "View.MemoryView":1320 + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) + * return 0 # <<<<<<<<<<<<<< + * + * if order == 'F' == get_best_order(&dst, ndim): + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "View.MemoryView":1314 + * direct_copy = slice_is_contig(dst, 'F', ndim) + * + * if direct_copy: # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + } + + /* "View.MemoryView":1306 + * src = tmp + * + * if not broadcasting: # <<<<<<<<<<<<<< + * + * + */ + } + + /* "View.MemoryView":1322 + * return 0 + * + * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = (__pyx_v_order == 'F'); + if (__pyx_t_2) { + __pyx_t_2 = ('F' == __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim)); + } + __pyx_t_8 = (__pyx_t_2 != 0); + if (__pyx_t_8) { + + /* "View.MemoryView":1325 + * + * + * transpose_memslice(&src) # <<<<<<<<<<<<<< + * transpose_memslice(&dst) + * + */ + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(1, 1325, __pyx_L1_error) + + /* "View.MemoryView":1326 + * + * transpose_memslice(&src) + * transpose_memslice(&dst) # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(1, 1326, __pyx_L1_error) + + /* "View.MemoryView":1322 + * return 0 + * + * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< + * + * + */ + } + + /* "View.MemoryView":1328 + * transpose_memslice(&dst) + * + * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< + * copy_strided_to_strided(&src, &dst, ndim, itemsize) + * refcount_copying(&dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); + + /* "View.MemoryView":1329 + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<< + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + */ + copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1330 + * refcount_copying(&dst, dtype_is_object, ndim, False) + * copy_strided_to_strided(&src, &dst, ndim, itemsize) + * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * + * free(tmpdata) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1332 + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + * free(tmpdata) # <<<<<<<<<<<<<< + * return 0 + * + */ + free(__pyx_v_tmpdata); + + /* "View.MemoryView":1333 + * + * free(tmpdata) + * return 0 # <<<<<<<<<<<<<< + * + * @cname('__pyx_memoryview_broadcast_leading') + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "View.MemoryView":1264 + * + * @cname('__pyx_memoryview_copy_contents') + * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice dst, + * int src_ndim, int dst_ndim, + */ + + /* function exit code */ + __pyx_L1_error:; + { + #ifdef WITH_THREAD + PyGILState_STATE __pyx_gilstate_save = __Pyx_PyGILState_Ensure(); + #endif + __Pyx_AddTraceback("View.MemoryView.memoryview_copy_contents", __pyx_clineno, __pyx_lineno, __pyx_filename); + #ifdef WITH_THREAD + __Pyx_PyGILState_Release(__pyx_gilstate_save); + #endif + } + __pyx_r = -1; + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1336 + * + * @cname('__pyx_memoryview_broadcast_leading') + * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< + * int ndim, + * int ndim_other) nogil: + */ + +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslice, int __pyx_v_ndim, int __pyx_v_ndim_other) { + int __pyx_v_i; + int __pyx_v_offset; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":1340 + * int ndim_other) nogil: + * cdef int i + * cdef int offset = ndim_other - ndim # <<<<<<<<<<<<<< + * + * for i in range(ndim - 1, -1, -1): + */ + __pyx_v_offset = (__pyx_v_ndim_other - __pyx_v_ndim); + + /* "View.MemoryView":1342 + * cdef int offset = ndim_other - ndim + * + * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< + * mslice.shape[i + offset] = mslice.shape[i] + * mslice.strides[i + offset] = mslice.strides[i] + */ + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { + __pyx_v_i = __pyx_t_1; + + /* "View.MemoryView":1343 + * + * for i in range(ndim - 1, -1, -1): + * mslice.shape[i + offset] = mslice.shape[i] # <<<<<<<<<<<<<< + * mslice.strides[i + offset] = mslice.strides[i] + * mslice.suboffsets[i + offset] = mslice.suboffsets[i] + */ + (__pyx_v_mslice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->shape[__pyx_v_i]); + + /* "View.MemoryView":1344 + * for i in range(ndim - 1, -1, -1): + * mslice.shape[i + offset] = mslice.shape[i] + * mslice.strides[i + offset] = mslice.strides[i] # <<<<<<<<<<<<<< + * mslice.suboffsets[i + offset] = mslice.suboffsets[i] + * + */ + (__pyx_v_mslice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->strides[__pyx_v_i]); + + /* "View.MemoryView":1345 + * mslice.shape[i + offset] = mslice.shape[i] + * mslice.strides[i + offset] = mslice.strides[i] + * mslice.suboffsets[i + offset] = mslice.suboffsets[i] # <<<<<<<<<<<<<< + * + * for i in range(offset): + */ + (__pyx_v_mslice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->suboffsets[__pyx_v_i]); + } + + /* "View.MemoryView":1347 + * mslice.suboffsets[i + offset] = mslice.suboffsets[i] + * + * for i in range(offset): # <<<<<<<<<<<<<< + * mslice.shape[i] = 1 + * mslice.strides[i] = mslice.strides[0] + */ + __pyx_t_1 = __pyx_v_offset; + __pyx_t_2 = __pyx_t_1; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_i = __pyx_t_3; + + /* "View.MemoryView":1348 + * + * for i in range(offset): + * mslice.shape[i] = 1 # <<<<<<<<<<<<<< + * mslice.strides[i] = mslice.strides[0] + * mslice.suboffsets[i] = -1 + */ + (__pyx_v_mslice->shape[__pyx_v_i]) = 1; + + /* "View.MemoryView":1349 + * for i in range(offset): + * mslice.shape[i] = 1 + * mslice.strides[i] = mslice.strides[0] # <<<<<<<<<<<<<< + * mslice.suboffsets[i] = -1 + * + */ + (__pyx_v_mslice->strides[__pyx_v_i]) = (__pyx_v_mslice->strides[0]); 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+ p->__pyx_vtab = __pyx_vtabptr_10MDAnalysis_3lib_6nsgrid_PBCBox; + return o; +} + +static void __pyx_tp_dealloc_10MDAnalysis_3lib_6nsgrid_PBCBox(PyObject *o) { + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + (*Py_TYPE(o)->tp_free)(o); +} + +static PyMethodDef __pyx_methods_10MDAnalysis_3lib_6nsgrid_PBCBox[] = { + {"update", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_6PBCBox_3update, METH_O, __pyx_doc_10MDAnalysis_3lib_6nsgrid_6PBCBox_2update}, + {"__reduce_cython__", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_6PBCBox_5__reduce_cython__, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_6nsgrid_6PBCBox_4__reduce_cython__}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_6PBCBox_7__setstate_cython__, METH_O, __pyx_doc_10MDAnalysis_3lib_6nsgrid_6PBCBox_6__setstate_cython__}, + {0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type_10MDAnalysis_3lib_6nsgrid_PBCBox = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib.nsgrid.PBCBox", /*tp_name*/ + sizeof(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_10MDAnalysis_3lib_6nsgrid_PBCBox, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ + "PBCBox(__Pyx_memviewslice box, bool periodic)\n\n Cython implementation of\n `PBC-related `_\n operations. This class is used by classes :class:`FastNS`\n and :class:`NSGrid` to put all particles inside a brick-shaped box\n and to compute PBC-aware distance. The class can also handle\n non-PBC aware distance evaluations through ``periodic`` argument.\n\n .. warning::\n This class is not meant to be used by end users.\n\n .. warning::\n Even if MD triclinic boxes can be handled by this class,\n internal optimization is made based on the assumption that\n particles are inside a brick-shaped box. When this is not\n the case, calculated distances are not\n warranted to be exact.\n ", /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_10MDAnalysis_3lib_6nsgrid_PBCBox, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pw_10MDAnalysis_3lib_6nsgrid_6PBCBox_1__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_10MDAnalysis_3lib_6nsgrid_PBCBox, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSResults __pyx_vtable_10MDAnalysis_3lib_6nsgrid_NSResults; + +static PyObject *__pyx_tp_new_10MDAnalysis_3lib_6nsgrid_NSResults(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *p; + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + p = ((struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *)o); + p->__pyx_vtab = __pyx_vtabptr_10MDAnalysis_3lib_6nsgrid_NSResults; + new((void*)&(p->indices_buffer)) std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_intvec> (); + new((void*)&(p->distances_buffer)) std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_realvec> (); + new((void*)&(p->pairs_buffer)) std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int> (); + new((void*)&(p->pair_distances_buffer)) std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_real> (); + new((void*)&(p->pair_distances2_buffer)) std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_real> (); + p->coords.data = NULL; + p->coords.memview = NULL; + p->searchcoords.data = NULL; + p->searchcoords.memview = NULL; + return o; +} + +static void __pyx_tp_dealloc_10MDAnalysis_3lib_6nsgrid_NSResults(PyObject *o) { + struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *p = (struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *)o; + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + __Pyx_call_destructor(p->indices_buffer); + __Pyx_call_destructor(p->distances_buffer); + __Pyx_call_destructor(p->pairs_buffer); + __Pyx_call_destructor(p->pair_distances_buffer); + __Pyx_call_destructor(p->pair_distances2_buffer); + __PYX_XDEC_MEMVIEW(&p->coords, 1); + __PYX_XDEC_MEMVIEW(&p->searchcoords, 1); + (*Py_TYPE(o)->tp_free)(o); +} + +static PyObject *__pyx_getprop_10MDAnalysis_3lib_6nsgrid_9NSResults_cutoff(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10MDAnalysis_3lib_6nsgrid_9NSResults_6cutoff_1__get__(o); +} + +static PyMethodDef __pyx_methods_10MDAnalysis_3lib_6nsgrid_NSResults[] = { + {"get_pairs", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_9NSResults_3get_pairs, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_6nsgrid_9NSResults_2get_pairs}, + {"get_pair_distances", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_9NSResults_5get_pair_distances, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_6nsgrid_9NSResults_4get_pair_distances}, + {"get_indices", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_9NSResults_7get_indices, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_6nsgrid_9NSResults_6get_indices}, + {"get_distances", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_9NSResults_9get_distances, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_6nsgrid_9NSResults_8get_distances}, + {"__reduce_cython__", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_9NSResults_11__reduce_cython__, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_6nsgrid_9NSResults_10__reduce_cython__}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_9NSResults_13__setstate_cython__, METH_O, __pyx_doc_10MDAnalysis_3lib_6nsgrid_9NSResults_12__setstate_cython__}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_10MDAnalysis_3lib_6nsgrid_NSResults[] = { + {(char *)"cutoff", __pyx_getprop_10MDAnalysis_3lib_6nsgrid_9NSResults_cutoff, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type_10MDAnalysis_3lib_6nsgrid_NSResults = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib.nsgrid.NSResults", /*tp_name*/ + sizeof(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_10MDAnalysis_3lib_6nsgrid_NSResults, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ + "NSResults(real cutoff, __Pyx_memviewslice coords, __Pyx_memviewslice searchcoords)\nClass to store the results\n\n All the required outputs from :class:`FastNS` is stored in the\n instance of this class. All the methods of :class:`FastNS` returns\n an instance of this class, which can be used to generate the desired\n results on demand.\n ", /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_10MDAnalysis_3lib_6nsgrid_NSResults, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_10MDAnalysis_3lib_6nsgrid_NSResults, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pw_10MDAnalysis_3lib_6nsgrid_9NSResults_1__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_10MDAnalysis_3lib_6nsgrid_NSResults, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSGrid __pyx_vtable_10MDAnalysis_3lib_6nsgrid_NSGrid; + +static PyObject *__pyx_tp_new_10MDAnalysis_3lib_6nsgrid_NSGrid(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *p; + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + p = ((struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *)o); + p->__pyx_vtab = __pyx_vtabptr_10MDAnalysis_3lib_6nsgrid_NSGrid; + return o; +} + +static void __pyx_tp_dealloc_10MDAnalysis_3lib_6nsgrid_NSGrid(PyObject *o) { + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_pw_10MDAnalysis_3lib_6nsgrid_6NSGrid_3__dealloc__(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + (*Py_TYPE(o)->tp_free)(o); +} + +static PyObject *__pyx_getprop_10MDAnalysis_3lib_6nsgrid_6NSGrid_cutoff(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10MDAnalysis_3lib_6nsgrid_6NSGrid_6cutoff_1__get__(o); +} + +static PyMethodDef __pyx_methods_10MDAnalysis_3lib_6nsgrid_NSGrid[] = { + {"__reduce_cython__", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_6NSGrid_5__reduce_cython__, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_6nsgrid_6NSGrid_4__reduce_cython__}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_6NSGrid_7__setstate_cython__, METH_O, __pyx_doc_10MDAnalysis_3lib_6nsgrid_6NSGrid_6__setstate_cython__}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_10MDAnalysis_3lib_6nsgrid_NSGrid[] = { + {(char *)"cutoff", __pyx_getprop_10MDAnalysis_3lib_6nsgrid_6NSGrid_cutoff, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type_10MDAnalysis_3lib_6nsgrid_NSGrid = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib.nsgrid.NSGrid", /*tp_name*/ + sizeof(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_10MDAnalysis_3lib_6nsgrid_NSGrid, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ + "NSGrid(ncoords, cutoff, PBCBox box, max_size, force=False)\nConstructs a uniform cuboidal grid for a brick-shaped box\n\n This class uses :class:`PBCBox` to define the brick shaped box\n It is essential to initialize the box with :class:`PBCBox`\n inorder to form the grid.\n\n The domain is subdivided into number of cells based on the desired search\n radius. Ideally cellsize should be equal to the search radius, but small\n search radius leads to large cell-list data strucutres.\n An optimization of cutoff is imposed to limit the size of data\n structure such that the cellsize is always greater than or\n equal to cutoff distance.\n\n Note\n ----\n This class assumes that all the coordinates are already\n inside the brick shaped box. Care must be taken to ensure\n all the particles are within the brick shaped box as\n defined by :class:`PBCBox`. This can be ensured by using\n :func:`~MDAnalysis.lib.nsgrid.PBCBox.fast_put_atoms_in_bbox`\n\n .. warning::\n This class is not meant to be used by end users.\n\n ", /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_10MDAnalysis_3lib_6nsgrid_NSGrid, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_10MDAnalysis_3lib_6nsgrid_NSGrid, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pw_10MDAnalysis_3lib_6nsgrid_6NSGrid_1__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_10MDAnalysis_3lib_6nsgrid_NSGrid, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; + +static PyObject *__pyx_tp_new_10MDAnalysis_3lib_6nsgrid_FastNS(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *p; + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + p = ((struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *)o); + p->box = ((struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *)Py_None); Py_INCREF(Py_None); + p->grid = ((struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *)Py_None); Py_INCREF(Py_None); + p->coords.data = NULL; + p->coords.memview = NULL; + p->coords_bbox.data = NULL; + p->coords_bbox.memview = NULL; + return o; +} + +static void __pyx_tp_dealloc_10MDAnalysis_3lib_6nsgrid_FastNS(PyObject *o) { + struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *p = (struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *)o; + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + Py_CLEAR(p->box); + Py_CLEAR(p->grid); + __PYX_XDEC_MEMVIEW(&p->coords, 1); + __PYX_XDEC_MEMVIEW(&p->coords_bbox, 1); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_10MDAnalysis_3lib_6nsgrid_FastNS(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *p = (struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *)o; + if (p->box) { + e = (*v)(((PyObject *)p->box), a); if (e) return e; + } + if (p->grid) { + e = (*v)(((PyObject *)p->grid), a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_10MDAnalysis_3lib_6nsgrid_FastNS(PyObject *o) { + PyObject* tmp; + struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *p = (struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *)o; + tmp = ((PyObject*)p->box); + p->box = ((struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_PBCBox *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->grid); + p->grid = ((struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSGrid *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyObject *__pyx_getprop_10MDAnalysis_3lib_6nsgrid_6FastNS_cutoff(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10MDAnalysis_3lib_6nsgrid_6FastNS_6cutoff_1__get__(o); +} + +static PyMethodDef __pyx_methods_10MDAnalysis_3lib_6nsgrid_FastNS[] = { + {"search", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_6FastNS_3search, METH_O, __pyx_doc_10MDAnalysis_3lib_6nsgrid_6FastNS_2search}, + {"self_search", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_6FastNS_5self_search, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search}, + {"__reduce_cython__", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_6FastNS_7__reduce_cython__, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_6nsgrid_6FastNS_6__reduce_cython__}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_6nsgrid_6FastNS_9__setstate_cython__, METH_O, __pyx_doc_10MDAnalysis_3lib_6nsgrid_6FastNS_8__setstate_cython__}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_10MDAnalysis_3lib_6nsgrid_FastNS[] = { + {(char *)"cutoff", __pyx_getprop_10MDAnalysis_3lib_6nsgrid_6FastNS_cutoff, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type_10MDAnalysis_3lib_6nsgrid_FastNS = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib.nsgrid.FastNS", /*tp_name*/ + sizeof(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_10MDAnalysis_3lib_6nsgrid_FastNS, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + "FastNS(cutoff, coords, box, max_gridsize=5000, pbc=True)\nGrid based search between two group of atoms\n\n Instantiates a class object which uses :class:`PBCBox` and\n :class:`NSGrid` to construct a cuboidal\n grid in an orthogonal brick shaped box.\n\n Minimum image convention is used for distance evaluations\n if pbc is set to ``True``.\n ", /*tp_doc*/ + __pyx_tp_traverse_10MDAnalysis_3lib_6nsgrid_FastNS, /*tp_traverse*/ + __pyx_tp_clear_10MDAnalysis_3lib_6nsgrid_FastNS, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_10MDAnalysis_3lib_6nsgrid_FastNS, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_10MDAnalysis_3lib_6nsgrid_FastNS, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pw_10MDAnalysis_3lib_6nsgrid_6FastNS_1__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_10MDAnalysis_3lib_6nsgrid_FastNS, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct_array __pyx_vtable_array; + +static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_array_obj *p; + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + p = ((struct __pyx_array_obj *)o); + p->__pyx_vtab = __pyx_vtabptr_array; + p->mode = ((PyObject*)Py_None); Py_INCREF(Py_None); + p->_format = ((PyObject*)Py_None); Py_INCREF(Py_None); + if (unlikely(__pyx_array___cinit__(o, a, k) < 0)) goto bad; + return o; + bad: + Py_DECREF(o); o = 0; + return NULL; +} + +static void __pyx_tp_dealloc_array(PyObject *o) { + struct __pyx_array_obj *p = (struct __pyx_array_obj *)o; + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_array___dealloc__(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->mode); + Py_CLEAR(p->_format); + (*Py_TYPE(o)->tp_free)(o); +} +static PyObject *__pyx_sq_item_array(PyObject *o, Py_ssize_t i) { + PyObject *r; + PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; + r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); + Py_DECREF(x); + return r; +} + +static int __pyx_mp_ass_subscript_array(PyObject *o, PyObject *i, PyObject *v) { + if (v) { + return __pyx_array___setitem__(o, i, v); + } + else { + PyErr_Format(PyExc_NotImplementedError, + "Subscript deletion not supported by %.200s", Py_TYPE(o)->tp_name); + return -1; + } +} + +static PyObject *__pyx_tp_getattro_array(PyObject *o, PyObject *n) { + PyObject *v = __Pyx_PyObject_GenericGetAttr(o, n); + if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) { + PyErr_Clear(); + v = __pyx_array___getattr__(o, n); + } + return v; +} + +static PyObject *__pyx_getprop___pyx_array_memview(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_5array_7memview_1__get__(o); +} + +static PyMethodDef __pyx_methods_array[] = { + {"__getattr__", (PyCFunction)__pyx_array___getattr__, METH_O|METH_COEXIST, 0}, + {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_array_1__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_array_3__setstate_cython__, METH_O, 0}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_array[] = { + {(char *)"memview", __pyx_getprop___pyx_array_memview, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; + +static PySequenceMethods __pyx_tp_as_sequence_array = { + __pyx_array___len__, /*sq_length*/ + 0, /*sq_concat*/ + 0, /*sq_repeat*/ + __pyx_sq_item_array, /*sq_item*/ + 0, /*sq_slice*/ + 0, /*sq_ass_item*/ + 0, /*sq_ass_slice*/ + 0, /*sq_contains*/ + 0, /*sq_inplace_concat*/ + 0, /*sq_inplace_repeat*/ +}; + +static PyMappingMethods __pyx_tp_as_mapping_array = { + __pyx_array___len__, /*mp_length*/ + __pyx_array___getitem__, /*mp_subscript*/ + __pyx_mp_ass_subscript_array, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_array = { + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getreadbuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getwritebuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getsegcount*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getcharbuffer*/ + #endif + __pyx_array_getbuffer, /*bf_getbuffer*/ + 0, /*bf_releasebuffer*/ +}; + +static PyTypeObject __pyx_type___pyx_array = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib.nsgrid.array", /*tp_name*/ + sizeof(struct __pyx_array_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_array, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + &__pyx_tp_as_sequence_array, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_array, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + __pyx_tp_getattro_array, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_array, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ + 0, /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_array, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_array, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_array, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; + +static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_MemviewEnum_obj *p; + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + p = ((struct __pyx_MemviewEnum_obj *)o); + p->name = Py_None; Py_INCREF(Py_None); + return o; +} + +static void __pyx_tp_dealloc_Enum(PyObject *o) { + struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o; + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + Py_CLEAR(p->name); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_Enum(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o; + if (p->name) { + e = (*v)(p->name, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_Enum(PyObject *o) { + PyObject* tmp; + struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o; + tmp = ((PyObject*)p->name); + p->name = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_Enum[] = { + {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_MemviewEnum_1__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_MemviewEnum_3__setstate_cython__, METH_O, 0}, + {0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type___pyx_MemviewEnum = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib.nsgrid.Enum", /*tp_name*/ + sizeof(struct __pyx_MemviewEnum_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_Enum, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + __pyx_MemviewEnum___repr__, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + 0, /*tp_doc*/ + __pyx_tp_traverse_Enum, /*tp_traverse*/ + __pyx_tp_clear_Enum, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_Enum, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_MemviewEnum___init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_Enum, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct_memoryview __pyx_vtable_memoryview; + +static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_memoryview_obj *p; + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + p = ((struct __pyx_memoryview_obj *)o); + p->__pyx_vtab = __pyx_vtabptr_memoryview; + p->obj = Py_None; Py_INCREF(Py_None); + p->_size = Py_None; Py_INCREF(Py_None); + p->_array_interface = Py_None; Py_INCREF(Py_None); + p->view.obj = NULL; + if (unlikely(__pyx_memoryview___cinit__(o, a, k) < 0)) goto bad; + return o; + bad: + Py_DECREF(o); o = 0; + return NULL; +} + +static void __pyx_tp_dealloc_memoryview(PyObject *o) { + struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_memoryview___dealloc__(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->obj); + Py_CLEAR(p->_size); + Py_CLEAR(p->_array_interface); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_memoryview(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; + if (p->obj) { + e = (*v)(p->obj, a); if (e) return e; + } + if (p->_size) { + e = (*v)(p->_size, a); if (e) return e; + } + if (p->_array_interface) { + e = (*v)(p->_array_interface, a); if (e) return e; + } + if (p->view.obj) { + e = (*v)(p->view.obj, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_memoryview(PyObject *o) { + PyObject* tmp; + struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; + tmp = ((PyObject*)p->obj); + p->obj = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->_size); + p->_size = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->_array_interface); + p->_array_interface = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + Py_CLEAR(p->view.obj); + return 0; +} +static PyObject *__pyx_sq_item_memoryview(PyObject *o, Py_ssize_t i) { + PyObject *r; + PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; + r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); + Py_DECREF(x); + return r; +} + +static int __pyx_mp_ass_subscript_memoryview(PyObject *o, PyObject *i, PyObject *v) { + if (v) { + return __pyx_memoryview___setitem__(o, i, v); + } + else { + PyErr_Format(PyExc_NotImplementedError, + "Subscript deletion not supported by %.200s", Py_TYPE(o)->tp_name); + return -1; + } +} + +static PyObject *__pyx_getprop___pyx_memoryview_T(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_1T_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_base(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_4base_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_shape(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_5shape_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_strides(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_7strides_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_suboffsets(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_10suboffsets_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_ndim(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_4ndim_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_itemsize(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_8itemsize_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_nbytes(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_6nbytes_1__get__(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_size(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_10memoryview_4size_1__get__(o); +} + +static PyMethodDef __pyx_methods_memoryview[] = { + {"is_c_contig", (PyCFunction)__pyx_memoryview_is_c_contig, METH_NOARGS, 0}, + {"is_f_contig", (PyCFunction)__pyx_memoryview_is_f_contig, METH_NOARGS, 0}, + {"copy", (PyCFunction)__pyx_memoryview_copy, METH_NOARGS, 0}, + {"copy_fortran", (PyCFunction)__pyx_memoryview_copy_fortran, METH_NOARGS, 0}, + {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_memoryview_1__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_memoryview_3__setstate_cython__, METH_O, 0}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_memoryview[] = { + {(char *)"T", __pyx_getprop___pyx_memoryview_T, 0, (char *)0, 0}, + {(char *)"base", __pyx_getprop___pyx_memoryview_base, 0, (char *)0, 0}, + {(char *)"shape", __pyx_getprop___pyx_memoryview_shape, 0, (char *)0, 0}, + {(char *)"strides", __pyx_getprop___pyx_memoryview_strides, 0, (char *)0, 0}, + {(char *)"suboffsets", __pyx_getprop___pyx_memoryview_suboffsets, 0, (char *)0, 0}, + {(char *)"ndim", __pyx_getprop___pyx_memoryview_ndim, 0, (char *)0, 0}, + {(char *)"itemsize", __pyx_getprop___pyx_memoryview_itemsize, 0, (char *)0, 0}, + {(char *)"nbytes", __pyx_getprop___pyx_memoryview_nbytes, 0, (char *)0, 0}, + {(char *)"size", __pyx_getprop___pyx_memoryview_size, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; + +static PySequenceMethods __pyx_tp_as_sequence_memoryview = { + __pyx_memoryview___len__, /*sq_length*/ + 0, /*sq_concat*/ + 0, /*sq_repeat*/ + __pyx_sq_item_memoryview, /*sq_item*/ + 0, /*sq_slice*/ + 0, /*sq_ass_item*/ + 0, /*sq_ass_slice*/ + 0, /*sq_contains*/ + 0, /*sq_inplace_concat*/ + 0, /*sq_inplace_repeat*/ +}; + +static PyMappingMethods __pyx_tp_as_mapping_memoryview = { + __pyx_memoryview___len__, /*mp_length*/ + __pyx_memoryview___getitem__, /*mp_subscript*/ + __pyx_mp_ass_subscript_memoryview, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_memoryview = { + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getreadbuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getwritebuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getsegcount*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getcharbuffer*/ + #endif + __pyx_memoryview_getbuffer, /*bf_getbuffer*/ + 0, /*bf_releasebuffer*/ +}; + +static PyTypeObject __pyx_type___pyx_memoryview = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib.nsgrid.memoryview", /*tp_name*/ + sizeof(struct __pyx_memoryview_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_memoryview, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + __pyx_memoryview___repr__, /*tp_repr*/ + 0, /*tp_as_number*/ + &__pyx_tp_as_sequence_memoryview, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_memoryview, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + __pyx_memoryview___str__, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_memoryview, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + 0, /*tp_doc*/ + __pyx_tp_traverse_memoryview, /*tp_traverse*/ + __pyx_tp_clear_memoryview, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_memoryview, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_memoryview, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_memoryview, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct__memoryviewslice __pyx_vtable__memoryviewslice; + +static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_memoryviewslice_obj *p; + PyObject *o = __pyx_tp_new_memoryview(t, a, k); + if (unlikely(!o)) return 0; + p = ((struct __pyx_memoryviewslice_obj *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_memoryview*)__pyx_vtabptr__memoryviewslice; + p->from_object = Py_None; Py_INCREF(Py_None); + p->from_slice.memview = NULL; + return o; +} + +static void __pyx_tp_dealloc__memoryviewslice(PyObject *o) { + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_memoryviewslice___dealloc__(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->from_object); + PyObject_GC_Track(o); + __pyx_tp_dealloc_memoryview(o); +} + +static int __pyx_tp_traverse__memoryviewslice(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + e = __pyx_tp_traverse_memoryview(o, v, a); if (e) return e; + if (p->from_object) { + e = (*v)(p->from_object, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear__memoryviewslice(PyObject *o) { + PyObject* tmp; + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + __pyx_tp_clear_memoryview(o); + tmp = ((PyObject*)p->from_object); + p->from_object = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + __PYX_XDEC_MEMVIEW(&p->from_slice, 1); + return 0; +} + +static PyObject *__pyx_getprop___pyx_memoryviewslice_base(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_15View_dot_MemoryView_16_memoryviewslice_4base_1__get__(o); +} + +static PyMethodDef __pyx_methods__memoryviewslice[] = { + {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_memoryviewslice_1__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_memoryviewslice_3__setstate_cython__, METH_O, 0}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets__memoryviewslice[] = { + {(char *)"base", __pyx_getprop___pyx_memoryviewslice_base, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type___pyx_memoryviewslice = { + PyVarObject_HEAD_INIT(0, 0) + "MDAnalysis.lib.nsgrid._memoryviewslice", /*tp_name*/ + sizeof(struct __pyx_memoryviewslice_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc__memoryviewslice, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___repr__, /*tp_repr*/ + #else + 0, /*tp_repr*/ + #endif + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___str__, /*tp_str*/ + #else + 0, /*tp_str*/ + #endif + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + "Internal class for passing memoryview slices to Python", /*tp_doc*/ + __pyx_tp_traverse__memoryviewslice, /*tp_traverse*/ + 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*)modname); + if (!m) goto end; + p = PyObject_GetAttrString(m, (char *)"RefNannyAPI"); + if (!p) goto end; + r = PyLong_AsVoidPtr(p); +end: + Py_XDECREF(p); + Py_XDECREF(m); + return (__Pyx_RefNannyAPIStruct *)r; +} +#endif + +/* PyObjectGetAttrStr */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#endif + +/* GetBuiltinName */ +static PyObject *__Pyx_GetBuiltinName(PyObject *name) { + PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name); + if (unlikely(!result)) { + PyErr_Format(PyExc_NameError, +#if PY_MAJOR_VERSION >= 3 + "name '%U' is not defined", name); +#else + "name '%.200s' is not defined", PyString_AS_STRING(name)); +#endif + } + return result; +} + +/* RaiseArgTupleInvalid */ +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +/* RaiseDoubleKeywords */ +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +/* ParseKeywords */ +static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; +} + +/* PyCFunctionFastCall */ +#if CYTHON_FAST_PYCCALL +static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) { + PyCFunctionObject *func = (PyCFunctionObject*)func_obj; + PyCFunction meth = PyCFunction_GET_FUNCTION(func); + PyObject *self = PyCFunction_GET_SELF(func); + int flags = PyCFunction_GET_FLAGS(func); + assert(PyCFunction_Check(func)); + assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS))); + assert(nargs >= 0); + assert(nargs == 0 || args != NULL); + /* _PyCFunction_FastCallDict() must not be called with an exception set, + because it may clear it (directly or indirectly) and so the + caller loses its exception */ + assert(!PyErr_Occurred()); + if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) { + return (*((__Pyx_PyCFunctionFastWithKeywords)meth)) (self, args, nargs, NULL); + } else { + return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs); + } +} +#endif + +/* PyFunctionFastCall */ +#if CYTHON_FAST_PYCALL +#include "frameobject.h" +static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na, + PyObject *globals) { + PyFrameObject *f; + PyThreadState *tstate = __Pyx_PyThreadState_Current; + PyObject **fastlocals; + Py_ssize_t i; + PyObject *result; + assert(globals != NULL); + /* XXX Perhaps we should create a specialized + PyFrame_New() that doesn't take locals, but does + take builtins without sanity checking them. + */ + assert(tstate != NULL); + f = PyFrame_New(tstate, co, globals, NULL); + if (f == NULL) { + return NULL; + } + fastlocals = f->f_localsplus; + for (i = 0; i < na; i++) { + Py_INCREF(*args); + fastlocals[i] = *args++; + } + result = PyEval_EvalFrameEx(f,0); + ++tstate->recursion_depth; + Py_DECREF(f); + --tstate->recursion_depth; + return result; +} +#if 1 || PY_VERSION_HEX < 0x030600B1 +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs) { + PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); + PyObject *globals = PyFunction_GET_GLOBALS(func); + PyObject *argdefs = PyFunction_GET_DEFAULTS(func); + PyObject *closure; +#if PY_MAJOR_VERSION >= 3 + PyObject *kwdefs; +#endif + PyObject *kwtuple, **k; + PyObject **d; + Py_ssize_t nd; + Py_ssize_t nk; + PyObject *result; + assert(kwargs == NULL || PyDict_Check(kwargs)); + nk = kwargs ? PyDict_Size(kwargs) : 0; + if (Py_EnterRecursiveCall((char*)" while calling a Python object")) { + return NULL; + } + if ( +#if PY_MAJOR_VERSION >= 3 + co->co_kwonlyargcount == 0 && +#endif + likely(kwargs == NULL || nk == 0) && + co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { + if (argdefs == NULL && co->co_argcount == nargs) { + result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); + goto done; + } + else if (nargs == 0 && argdefs != NULL + && co->co_argcount == Py_SIZE(argdefs)) { + /* function called with no arguments, but all parameters have + a default value: use default values as arguments .*/ + args = &PyTuple_GET_ITEM(argdefs, 0); + result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); + goto done; + } + } + if (kwargs != NULL) { + Py_ssize_t pos, i; + kwtuple = PyTuple_New(2 * nk); + if (kwtuple == NULL) { + result = NULL; + goto done; + } + k = &PyTuple_GET_ITEM(kwtuple, 0); + pos = i = 0; + while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { + Py_INCREF(k[i]); + Py_INCREF(k[i+1]); + i += 2; + } + nk = i / 2; + } + else { + kwtuple = NULL; + k = NULL; + } + closure = PyFunction_GET_CLOSURE(func); +#if PY_MAJOR_VERSION >= 3 + kwdefs = PyFunction_GET_KW_DEFAULTS(func); +#endif + if (argdefs != NULL) { + d = &PyTuple_GET_ITEM(argdefs, 0); + nd = Py_SIZE(argdefs); + } + else { + d = NULL; + nd = 0; + } +#if PY_MAJOR_VERSION >= 3 + result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, + args, nargs, + k, (int)nk, + d, (int)nd, kwdefs, closure); +#else + result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, + args, nargs, + k, (int)nk, + d, (int)nd, closure); +#endif + Py_XDECREF(kwtuple); +done: + Py_LeaveRecursiveCall(); + return result; +} +#endif +#endif + +/* PyObjectCall */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *result; + ternaryfunc call = func->ob_type->tp_call; + if (unlikely(!call)) + return PyObject_Call(func, arg, kw); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = (*call)(func, arg, kw); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +/* PyObjectCallMethO */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = PyCFunction_GET_FUNCTION(func); + self = PyCFunction_GET_SELF(func); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +/* PyObjectCallOneArg */ +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#if CYTHON_FAST_PYCALL + if (PyFunction_Check(func)) { + return __Pyx_PyFunction_FastCall(func, &arg, 1); + } +#endif + if (likely(PyCFunction_Check(func))) { + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); +#if CYTHON_FAST_PYCCALL + } else if (PyCFunction_GET_FLAGS(func) & METH_FASTCALL) { + return __Pyx_PyCFunction_FastCall(func, &arg, 1); +#endif + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_Pack(1, arg); + if (unlikely(!args)) return NULL; + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +#endif + +/* MemviewSliceInit */ +static int +__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, + int ndim, + __Pyx_memviewslice *memviewslice, + int memview_is_new_reference) +{ + __Pyx_RefNannyDeclarations + int i, retval=-1; + Py_buffer *buf = &memview->view; + __Pyx_RefNannySetupContext("init_memviewslice", 0); + if (!buf) { + PyErr_SetString(PyExc_ValueError, + "buf is NULL."); + goto fail; + } else if (memviewslice->memview || memviewslice->data) { + PyErr_SetString(PyExc_ValueError, + "memviewslice is already initialized!"); + goto fail; + } + if (buf->strides) { + for (i = 0; i < ndim; i++) { + memviewslice->strides[i] = buf->strides[i]; + } + } else { + Py_ssize_t stride = buf->itemsize; + for (i = ndim - 1; i >= 0; i--) { + memviewslice->strides[i] = stride; + stride *= buf->shape[i]; + } + } + for (i = 0; i < ndim; i++) { + memviewslice->shape[i] = buf->shape[i]; + if (buf->suboffsets) { + memviewslice->suboffsets[i] = buf->suboffsets[i]; + } else { + memviewslice->suboffsets[i] = -1; + } + } + memviewslice->memview = memview; + memviewslice->data = (char *)buf->buf; + if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { + Py_INCREF(memview); + } + retval = 0; + goto no_fail; +fail: + memviewslice->memview = 0; + memviewslice->data = 0; + retval = -1; +no_fail: + __Pyx_RefNannyFinishContext(); + return retval; +} +#ifndef Py_NO_RETURN +#define Py_NO_RETURN +#endif +static void __pyx_fatalerror(const char *fmt, ...) Py_NO_RETURN { + va_list vargs; + char msg[200]; +#ifdef HAVE_STDARG_PROTOTYPES + va_start(vargs, fmt); +#else + va_start(vargs); +#endif + vsnprintf(msg, 200, fmt, vargs); + va_end(vargs); + Py_FatalError(msg); +} +static CYTHON_INLINE int +__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock) +{ + int result; + PyThread_acquire_lock(lock, 1); + result = (*acquisition_count)++; + PyThread_release_lock(lock); + return result; +} +static CYTHON_INLINE int +__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock) +{ + int result; + PyThread_acquire_lock(lock, 1); + result = (*acquisition_count)--; + PyThread_release_lock(lock); + return result; +} +static CYTHON_INLINE void +__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) +{ + int first_time; + struct __pyx_memoryview_obj *memview = memslice->memview; + if (!memview || (PyObject *) memview == Py_None) + return; + if (__pyx_get_slice_count(memview) < 0) + __pyx_fatalerror("Acquisition count is %d (line %d)", + __pyx_get_slice_count(memview), lineno); + first_time = __pyx_add_acquisition_count(memview) == 0; + if (first_time) { + if (have_gil) { + Py_INCREF((PyObject *) memview); + } else { + PyGILState_STATE _gilstate = PyGILState_Ensure(); + Py_INCREF((PyObject *) memview); + PyGILState_Release(_gilstate); + } + } +} +static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, + int have_gil, int lineno) { + int last_time; + struct __pyx_memoryview_obj *memview = memslice->memview; + if (!memview ) { + return; + } else if ((PyObject *) memview == Py_None) { + memslice->memview = NULL; + return; + } + if (__pyx_get_slice_count(memview) <= 0) + __pyx_fatalerror("Acquisition count is %d (line %d)", + __pyx_get_slice_count(memview), lineno); + last_time = __pyx_sub_acquisition_count(memview) == 1; + memslice->data = NULL; + if (last_time) { + if (have_gil) { + Py_CLEAR(memslice->memview); + } else { + PyGILState_STATE _gilstate = PyGILState_Ensure(); + Py_CLEAR(memslice->memview); + PyGILState_Release(_gilstate); + } + } else { + memslice->memview = NULL; + } +} + +/* PyErrFetchRestore */ +#if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +} +static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +} +#endif + +/* RaiseException */ +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + __Pyx_PyThreadState_declare + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_PyThreadState_assign + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + int is_subclass = PyObject_IsSubclass(instance_class, type); + if (!is_subclass) { + instance_class = NULL; + } else if (unlikely(is_subclass == -1)) { + goto bad; + } else { + type = instance_class; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } + if (cause) { + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { +#if CYTHON_COMPILING_IN_PYPY + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); + Py_INCREF(tb); + PyErr_Restore(tmp_type, tmp_value, tb); + Py_XDECREF(tmp_tb); +#else + PyThreadState *tstate = __Pyx_PyThreadState_Current; + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } +#endif + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +/* WriteUnraisableException */ +static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, + CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, + int full_traceback, CYTHON_UNUSED int nogil) { + PyObject *old_exc, *old_val, *old_tb; + PyObject *ctx; + __Pyx_PyThreadState_declare +#ifdef WITH_THREAD + PyGILState_STATE state; + if (nogil) + state = PyGILState_Ensure(); +#ifdef _MSC_VER + else state = (PyGILState_STATE)-1; +#endif +#endif + __Pyx_PyThreadState_assign + __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); + if (full_traceback) { + Py_XINCREF(old_exc); + Py_XINCREF(old_val); + Py_XINCREF(old_tb); + __Pyx_ErrRestore(old_exc, old_val, old_tb); + PyErr_PrintEx(1); + } + #if PY_MAJOR_VERSION < 3 + ctx = PyString_FromString(name); + #else + ctx = PyUnicode_FromString(name); + #endif + __Pyx_ErrRestore(old_exc, old_val, old_tb); + if (!ctx) { + PyErr_WriteUnraisable(Py_None); + } else { + PyErr_WriteUnraisable(ctx); + Py_DECREF(ctx); + } +#ifdef WITH_THREAD + if (nogil) + PyGILState_Release(state); +#endif +} + +/* GetModuleGlobalName */ +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { + PyObject *result; +#if !CYTHON_AVOID_BORROWED_REFS +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 + result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash); + if (likely(result)) { + Py_INCREF(result); + } else if (unlikely(PyErr_Occurred())) { + result = NULL; + } else { +#else + result = PyDict_GetItem(__pyx_d, name); + if (likely(result)) { + Py_INCREF(result); + } else { +#endif +#else + result = PyObject_GetItem(__pyx_d, name); + if (!result) { + PyErr_Clear(); +#endif + result = __Pyx_GetBuiltinName(name); + } + return result; +} + +/* PyErrExceptionMatches */ + #if CYTHON_FAST_THREAD_STATE +static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; icurexc_type; + if (exc_type == err) return 1; + if (unlikely(!exc_type)) return 0; + if (unlikely(PyTuple_Check(err))) + return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); + return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); +} +#endif + +/* GetAttr */ + static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { +#if CYTHON_USE_TYPE_SLOTS +#if PY_MAJOR_VERSION >= 3 + if (likely(PyUnicode_Check(n))) +#else + if (likely(PyString_Check(n))) +#endif + return __Pyx_PyObject_GetAttrStr(o, n); +#endif + return PyObject_GetAttr(o, n); +} + +/* GetAttr3 */ + static PyObject *__Pyx_GetAttr3Default(PyObject *d) { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) + return NULL; + __Pyx_PyErr_Clear(); + Py_INCREF(d); + return d; +} +static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { + PyObject *r = __Pyx_GetAttr(o, n); + return (likely(r)) ? r : __Pyx_GetAttr3Default(d); +} + +/* ArgTypeTest */ + static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) +{ + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + else if (exact) { + #if PY_MAJOR_VERSION == 2 + if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; + #endif + } + else { + if (likely(__Pyx_TypeCheck(obj, type))) return 1; + } + PyErr_Format(PyExc_TypeError, + "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", + name, type->tp_name, Py_TYPE(obj)->tp_name); + return 0; +} + +/* Import */ + static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_MAJOR_VERSION < 3 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_MAJOR_VERSION < 3 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + +/* ImportFrom */ + static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { + PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); + if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { + PyErr_Format(PyExc_ImportError, + #if PY_MAJOR_VERSION < 3 + "cannot import name %.230s", PyString_AS_STRING(name)); + #else + "cannot import name %S", name); + #endif + } + return value; +} + +/* GetItemInt */ + static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { + PyObject *r; + if (!j) return NULL; + r = PyObject_GetItem(o, j); + Py_DECREF(j); + return r; +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyList_GET_SIZE(o); + } + if ((!boundscheck) || likely((0 <= wrapped_i) & (wrapped_i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, wrapped_i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyTuple_GET_SIZE(o); + } + if ((!boundscheck) || likely((0 <= wrapped_i) & (wrapped_i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS + if (is_list || PyList_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); + if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) { + PyObject *r = PyList_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } + else if (PyTuple_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } else { + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_item)) { + if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (likely(l >= 0)) { + i += l; + } else { + if (!PyErr_ExceptionMatches(PyExc_OverflowError)) + return NULL; + PyErr_Clear(); + } + } + return m->sq_item(o, i); + } + } +#else + if (is_list || PySequence_Check(o)) { + return PySequence_GetItem(o, i); + } +#endif + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +} + +/* SliceObject */ + static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj, + Py_ssize_t cstart, Py_ssize_t cstop, + PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, + int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { +#if CYTHON_USE_TYPE_SLOTS + PyMappingMethods* mp; +#if PY_MAJOR_VERSION < 3 + PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence; + if (likely(ms && ms->sq_slice)) { + if (!has_cstart) { + if (_py_start && (*_py_start != Py_None)) { + cstart = __Pyx_PyIndex_AsSsize_t(*_py_start); + if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; + } else + cstart = 0; + } + if (!has_cstop) { + if (_py_stop && (*_py_stop != Py_None)) { + cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop); + if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; + } else + cstop = PY_SSIZE_T_MAX; + } + if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) { + Py_ssize_t l = ms->sq_length(obj); + if (likely(l >= 0)) { + if (cstop < 0) { + cstop += l; + if (cstop < 0) cstop = 0; + } + if (cstart < 0) { + cstart += l; + if (cstart < 0) cstart = 0; + } + } else { + if (!PyErr_ExceptionMatches(PyExc_OverflowError)) + goto bad; + PyErr_Clear(); + } + } + return ms->sq_slice(obj, cstart, cstop); + } +#endif + mp = Py_TYPE(obj)->tp_as_mapping; + if (likely(mp && mp->mp_subscript)) +#endif + { + PyObject* result; + PyObject *py_slice, *py_start, *py_stop; + if (_py_slice) { + py_slice = *_py_slice; + } else { + PyObject* owned_start = NULL; + PyObject* owned_stop = NULL; + if (_py_start) { + py_start = *_py_start; + } else { + if (has_cstart) { + owned_start = py_start = PyInt_FromSsize_t(cstart); + if (unlikely(!py_start)) goto bad; + } else + py_start = Py_None; + } + if (_py_stop) { + py_stop = *_py_stop; + } else { + if (has_cstop) { + owned_stop = py_stop = PyInt_FromSsize_t(cstop); + if (unlikely(!py_stop)) { + Py_XDECREF(owned_start); + goto bad; + } + } else + py_stop = Py_None; + } + py_slice = PySlice_New(py_start, py_stop, Py_None); + Py_XDECREF(owned_start); + Py_XDECREF(owned_stop); + if (unlikely(!py_slice)) goto bad; + } +#if CYTHON_USE_TYPE_SLOTS + result = mp->mp_subscript(obj, py_slice); +#else + result = PyObject_GetItem(obj, py_slice); +#endif + if (!_py_slice) { + Py_DECREF(py_slice); + } + return result; + } + PyErr_Format(PyExc_TypeError, + "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name); +bad: + return NULL; +} + +/* HasAttr */ + static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { + PyObject *r; + if (unlikely(!__Pyx_PyBaseString_Check(n))) { + PyErr_SetString(PyExc_TypeError, + "hasattr(): attribute name must be string"); + return -1; + } + r = __Pyx_GetAttr(o, n); + if (unlikely(!r)) { + PyErr_Clear(); + return 0; + } else { + Py_DECREF(r); + return 1; + } +} + +/* ExtTypeTest */ + static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(__Pyx_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + +/* DictGetItem */ + #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { + PyObject *value; + value = PyDict_GetItemWithError(d, key); + if (unlikely(!value)) { + if (!PyErr_Occurred()) { + PyObject* args = PyTuple_Pack(1, key); + if (likely(args)) + PyErr_SetObject(PyExc_KeyError, args); + Py_XDECREF(args); + } + return NULL; + } + Py_INCREF(value); + return value; +} +#endif + +/* RaiseTooManyValuesToUnpack */ + static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +/* RaiseNeedMoreValuesToUnpack */ + static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +/* RaiseNoneIterError */ + static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +/* SaveResetException */ + #if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + #if PY_VERSION_HEX >= 0x030700A3 + *type = tstate->exc_state.exc_type; + *value = tstate->exc_state.exc_value; + *tb = tstate->exc_state.exc_traceback; + #else + *type = tstate->exc_type; + *value = tstate->exc_value; + *tb = tstate->exc_traceback; + #endif + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); +} +static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + #if PY_VERSION_HEX >= 0x030700A3 + tmp_type = tstate->exc_state.exc_type; + tmp_value = tstate->exc_state.exc_value; + tmp_tb = tstate->exc_state.exc_traceback; + tstate->exc_state.exc_type = type; + tstate->exc_state.exc_value = value; + tstate->exc_state.exc_traceback = tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = type; + tstate->exc_value = value; + tstate->exc_traceback = tb; + #endif + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +} +#endif + +/* GetException */ + #if CYTHON_FAST_THREAD_STATE +static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { +#else +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { +#endif + PyObject *local_type, *local_value, *local_tb; +#if CYTHON_FAST_THREAD_STATE + PyObject *tmp_type, *tmp_value, *tmp_tb; + local_type = tstate->curexc_type; + local_value = tstate->curexc_value; + local_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif + PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_FAST_THREAD_STATE + if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif + goto bad; + #if PY_MAJOR_VERSION >= 3 + if (local_tb) { + if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) + goto bad; + } + #endif + Py_XINCREF(local_tb); + Py_XINCREF(local_type); + Py_XINCREF(local_value); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_FAST_THREAD_STATE + #if PY_VERSION_HEX >= 0x030700A3 + tmp_type = tstate->exc_state.exc_type; + tmp_value = tstate->exc_state.exc_value; + tmp_tb = tstate->exc_state.exc_traceback; + tstate->exc_state.exc_type = local_type; + tstate->exc_state.exc_value = local_value; + tstate->exc_state.exc_traceback = local_tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = local_type; + tstate->exc_value = local_value; + tstate->exc_traceback = local_tb; + #endif + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif + return 0; +bad: + *type = 0; + *value = 0; + *tb = 0; + Py_XDECREF(local_type); + Py_XDECREF(local_value); + Py_XDECREF(local_tb); + return -1; +} + +/* BytesEquals */ + static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else + if (s1 == s2) { + return (equals == Py_EQ); + } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { + const char *ps1, *ps2; + Py_ssize_t length = PyBytes_GET_SIZE(s1); + if (length != PyBytes_GET_SIZE(s2)) + return (equals == Py_NE); + ps1 = PyBytes_AS_STRING(s1); + ps2 = PyBytes_AS_STRING(s2); + if (ps1[0] != ps2[0]) { + return (equals == Py_NE); + } else if (length == 1) { + return (equals == Py_EQ); + } else { + int result; +#if CYTHON_USE_UNICODE_INTERNALS + Py_hash_t hash1, hash2; + hash1 = ((PyBytesObject*)s1)->ob_shash; + hash2 = ((PyBytesObject*)s2)->ob_shash; + if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { + return (equals == Py_NE); + } +#endif + result = memcmp(ps1, ps2, (size_t)length); + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { + return (equals == Py_NE); + } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { + return (equals == Py_NE); + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +#endif +} + +/* UnicodeEquals */ + static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else +#if PY_MAJOR_VERSION < 3 + PyObject* owned_ref = NULL; +#endif + int s1_is_unicode, s2_is_unicode; + if (s1 == s2) { + goto return_eq; + } + s1_is_unicode = PyUnicode_CheckExact(s1); + s2_is_unicode = PyUnicode_CheckExact(s2); +#if PY_MAJOR_VERSION < 3 + if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { + owned_ref = PyUnicode_FromObject(s2); + if (unlikely(!owned_ref)) + return -1; + s2 = owned_ref; + s2_is_unicode = 1; + } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { + owned_ref = PyUnicode_FromObject(s1); + if (unlikely(!owned_ref)) + return -1; + s1 = owned_ref; + s1_is_unicode = 1; + } else if (((!s2_is_unicode) & (!s1_is_unicode))) { + return __Pyx_PyBytes_Equals(s1, s2, equals); + } +#endif + if (s1_is_unicode & s2_is_unicode) { + Py_ssize_t length; + int kind; + void *data1, *data2; + if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) + return -1; + length = __Pyx_PyUnicode_GET_LENGTH(s1); + if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { + goto return_ne; + } +#if CYTHON_USE_UNICODE_INTERNALS + { + Py_hash_t hash1, hash2; + #if CYTHON_PEP393_ENABLED + hash1 = ((PyASCIIObject*)s1)->hash; + hash2 = ((PyASCIIObject*)s2)->hash; + #else + hash1 = ((PyUnicodeObject*)s1)->hash; + hash2 = ((PyUnicodeObject*)s2)->hash; + #endif + if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { + goto return_ne; + } + } +#endif + kind = __Pyx_PyUnicode_KIND(s1); + if (kind != __Pyx_PyUnicode_KIND(s2)) { + goto return_ne; + } + data1 = __Pyx_PyUnicode_DATA(s1); + data2 = __Pyx_PyUnicode_DATA(s2); + if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { + goto return_ne; + } else if (length == 1) { + goto return_eq; + } else { + int result = memcmp(data1, data2, (size_t)(length * kind)); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & s2_is_unicode) { + goto return_ne; + } else if ((s2 == Py_None) & s1_is_unicode) { + goto return_ne; + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +return_eq: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ); +return_ne: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_NE); +#endif +} + +/* ObjectGetItem */ + #if CYTHON_USE_TYPE_SLOTS +static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { + PyObject *runerr; + Py_ssize_t key_value; + PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; + if (unlikely(!(m && m->sq_item))) { + PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); + return NULL; + } + key_value = __Pyx_PyIndex_AsSsize_t(index); + if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { + return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); + } + if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { + PyErr_Clear(); + PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); + } + return NULL; +} +static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { + PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; + if (likely(m && m->mp_subscript)) { + return m->mp_subscript(obj, key); + } + return __Pyx_PyObject_GetIndex(obj, key); +} +#endif + +/* decode_c_string */ + static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { + Py_ssize_t length; + if (unlikely((start < 0) | (stop < 0))) { + size_t slen = strlen(cstring); + if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { + PyErr_SetString(PyExc_OverflowError, + "c-string too long to convert to Python"); + return NULL; + } + length = (Py_ssize_t) slen; + if (start < 0) { + start += length; + if (start < 0) + start = 0; + } + if (stop < 0) + stop += length; + } + length = stop - start; + if (unlikely(length <= 0)) + return PyUnicode_FromUnicode(NULL, 0); + cstring += start; + if (decode_func) { + return decode_func(cstring, length, errors); + } else { + return PyUnicode_Decode(cstring, length, encoding, errors); + } +} + +/* SwapException */ + #if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + #if PY_VERSION_HEX >= 0x030700A3 + tmp_type = tstate->exc_state.exc_type; + tmp_value = tstate->exc_state.exc_value; + tmp_tb = tstate->exc_state.exc_traceback; + tstate->exc_state.exc_type = *type; + tstate->exc_state.exc_value = *value; + tstate->exc_state.exc_traceback = *tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = *type; + tstate->exc_value = *value; + tstate->exc_traceback = *tb; + #endif + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} +#else +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); + PyErr_SetExcInfo(*type, *value, *tb); + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} +#endif + +/* FastTypeChecks */ + #if CYTHON_COMPILING_IN_CPYTHON +static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { + while (a) { + a = a->tp_base; + if (a == b) + return 1; + } + return b == &PyBaseObject_Type; +} +static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { + PyObject *mro; + if (a == b) return 1; + mro = a->tp_mro; + if (likely(mro)) { + Py_ssize_t i, n; + n = PyTuple_GET_SIZE(mro); + for (i = 0; i < n; i++) { + if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) + return 1; + } + return 0; + } + return __Pyx_InBases(a, b); +} +#if PY_MAJOR_VERSION == 2 +static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { + PyObject *exception, *value, *tb; + int res; + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ErrFetch(&exception, &value, &tb); + res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; + if (unlikely(res == -1)) { + PyErr_WriteUnraisable(err); + res = 0; + } + if (!res) { + res = PyObject_IsSubclass(err, exc_type2); + if (unlikely(res == -1)) { + PyErr_WriteUnraisable(err); + res = 0; + } + } + __Pyx_ErrRestore(exception, value, tb); + return res; +} +#else +static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { + int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; + if (!res) { + res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); + } + return res; +} +#endif +static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + assert(PyExceptionClass_Check(exc_type)); + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i= 0 || (x^b) >= 0)) + return PyInt_FromLong(x); + return PyLong_Type.tp_as_number->nb_add(op1, op2); + } + #endif + #if CYTHON_USE_PYLONG_INTERNALS + if (likely(PyLong_CheckExact(op1))) { + const long b = intval; + long a, x; +#ifdef HAVE_LONG_LONG + const PY_LONG_LONG llb = intval; + PY_LONG_LONG lla, llx; +#endif + const digit* digits = ((PyLongObject*)op1)->ob_digit; + const Py_ssize_t size = Py_SIZE(op1); + if (likely(__Pyx_sst_abs(size) <= 1)) { + a = likely(size) ? digits[0] : 0; + if (size == -1) a = -a; + } else { + switch (size) { + case -2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case 2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case -3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case 3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case -4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case 4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + default: return PyLong_Type.tp_as_number->nb_add(op1, op2); + } + } + x = a + b; + return PyLong_FromLong(x); +#ifdef HAVE_LONG_LONG + long_long: + llx = lla + llb; + return PyLong_FromLongLong(llx); +#endif + + + } + #endif + if (PyFloat_CheckExact(op1)) { + const long b = intval; + double a = PyFloat_AS_DOUBLE(op1); + double result; + PyFPE_START_PROTECT("add", return NULL) + result = ((double)a) + (double)b; + PyFPE_END_PROTECT(result) + return PyFloat_FromDouble(result); + } + return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); +} +#endif + +/* None */ + static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); +} + +/* PyObject_GenericGetAttrNoDict */ + #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { + PyErr_Format(PyExc_AttributeError, +#if PY_MAJOR_VERSION >= 3 + "'%.50s' object has no attribute '%U'", + tp->tp_name, attr_name); +#else + "'%.50s' object has no attribute '%.400s'", + tp->tp_name, PyString_AS_STRING(attr_name)); +#endif + return NULL; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { + PyObject *descr; + PyTypeObject *tp = Py_TYPE(obj); + if (unlikely(!PyString_Check(attr_name))) { + return PyObject_GenericGetAttr(obj, attr_name); + } + assert(!tp->tp_dictoffset); + descr = _PyType_Lookup(tp, attr_name); + if (unlikely(!descr)) { + return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); + } + Py_INCREF(descr); + #if PY_MAJOR_VERSION < 3 + if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) + #endif + { + descrgetfunc f = Py_TYPE(descr)->tp_descr_get; + if (unlikely(f)) { + PyObject *res = f(descr, obj, (PyObject *)tp); + Py_DECREF(descr); + return res; + } + } + return descr; +} +#endif + +/* PyObject_GenericGetAttr */ + #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { + if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { + return PyObject_GenericGetAttr(obj, attr_name); + } + return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); +} +#endif + +/* SetVTable */ + static int __Pyx_SetVtable(PyObject *dict, void *vtable) { +#if PY_VERSION_HEX >= 0x02070000 + PyObject *ob = PyCapsule_New(vtable, 0, 0); +#else + PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); +#endif + if (!ob) + goto bad; + if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) + goto bad; + Py_DECREF(ob); + return 0; +bad: + Py_XDECREF(ob); + return -1; +} + +/* SetupReduce */ + static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { + int ret; + PyObject *name_attr; + name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2); + if (likely(name_attr)) { + ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); + } else { + ret = -1; + } + if (unlikely(ret < 0)) { + PyErr_Clear(); + ret = 0; + } + Py_XDECREF(name_attr); + return ret; +} +static int __Pyx_setup_reduce(PyObject* type_obj) { + int ret = 0; + PyObject *object_reduce = NULL; + PyObject *object_reduce_ex = NULL; + PyObject *reduce = NULL; + PyObject *reduce_ex = NULL; + PyObject *reduce_cython = NULL; + PyObject *setstate = NULL; + PyObject *setstate_cython = NULL; +#if CYTHON_USE_PYTYPE_LOOKUP + if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto GOOD; +#else + if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto GOOD; +#endif +#if CYTHON_USE_PYTYPE_LOOKUP + object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; +#else + object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; +#endif + reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto BAD; + if (reduce_ex == object_reduce_ex) { +#if CYTHON_USE_PYTYPE_LOOKUP + object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; +#else + object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; +#endif + reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto BAD; + if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { + reduce_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_cython); if (unlikely(!reduce_cython)) goto BAD; + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto BAD; + setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); + if (!setstate) PyErr_Clear(); + if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { + setstate_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate_cython); if (unlikely(!setstate_cython)) goto BAD; + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto BAD; + } + PyType_Modified((PyTypeObject*)type_obj); + } + } + goto GOOD; +BAD: + if (!PyErr_Occurred()) + PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); + ret = -1; +GOOD: +#if !CYTHON_USE_PYTYPE_LOOKUP + Py_XDECREF(object_reduce); + Py_XDECREF(object_reduce_ex); +#endif + Py_XDECREF(reduce); + Py_XDECREF(reduce_ex); + Py_XDECREF(reduce_cython); + Py_XDECREF(setstate); + Py_XDECREF(setstate_cython); + return ret; +} + +/* CLineInTraceback */ + #ifndef CYTHON_CLINE_IN_TRACEBACK +static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { + PyObject *use_cline; + PyObject *ptype, *pvalue, *ptraceback; +#if CYTHON_COMPILING_IN_CPYTHON + PyObject **cython_runtime_dict; +#endif + if (unlikely(!__pyx_cython_runtime)) { + return c_line; + } + __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); +#if CYTHON_COMPILING_IN_CPYTHON + cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); + if (likely(cython_runtime_dict)) { + use_cline = __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback); + } else +#endif + { + PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); + if (use_cline_obj) { + use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; + Py_DECREF(use_cline_obj); + } else { + PyErr_Clear(); + use_cline = NULL; + } + } + if (!use_cline) { + c_line = 0; + PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); + } + else if (PyObject_Not(use_cline) != 0) { + c_line = 0; + } + __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); + return c_line; +} +#endif + +/* CodeObjectCache */ + static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = start + (end - start) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} + +/* AddTraceback */ + #include "compile.h" +#include "frameobject.h" +#include "traceback.h" +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + #if PY_MAJOR_VERSION < 3 + py_srcfile = PyString_FromString(filename); + #else + py_srcfile = PyUnicode_FromString(filename); + #endif + if (!py_srcfile) goto bad; + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #endif + } + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + #else + py_funcname = PyUnicode_FromString(funcname); + #endif + } + if (!py_funcname) goto bad; + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + PyThreadState *tstate = __Pyx_PyThreadState_Current; + if (c_line) { + c_line = __Pyx_CLineForTraceback(tstate, c_line); + } + py_code = __pyx_find_code_object(c_line ? -c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); + } + py_frame = PyFrame_New( + tstate, /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + __Pyx_PyFrame_SetLineNumber(py_frame, py_line); + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} + +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (__Pyx_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); + if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if ((0)) {} + else if (__Pyx_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); + view->obj = NULL; + Py_DECREF(obj); +} +#endif + + + /* MemviewSliceIsContig */ + static int +__pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim) +{ + int i, index, step, start; + Py_ssize_t itemsize = mvs.memview->view.itemsize; + if (order == 'F') { + step = 1; + start = 0; + } else { + step = -1; + start = ndim - 1; + } + for (i = 0; i < ndim; i++) { + index = start + step * i; + if (mvs.suboffsets[index] >= 0 || mvs.strides[index] != itemsize) + return 0; + itemsize *= mvs.shape[index]; + } + return 1; +} + +/* OverlappingSlices */ + static void +__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, + void **out_start, void **out_end, + int ndim, size_t itemsize) +{ + char *start, *end; + int i; + start = end = slice->data; + for (i = 0; i < ndim; i++) { + Py_ssize_t stride = slice->strides[i]; + Py_ssize_t extent = slice->shape[i]; + if (extent == 0) { + *out_start = *out_end = start; + return; + } else { + if (stride > 0) + end += stride * (extent - 1); + else + start += stride * (extent - 1); + } + } + *out_start = start; + *out_end = end + itemsize; +} +static int +__pyx_slices_overlap(__Pyx_memviewslice *slice1, + __Pyx_memviewslice *slice2, + int ndim, size_t itemsize) +{ + void *start1, *end1, *start2, *end2; + __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); + __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); + return (start1 < end2) && (start2 < end1); +} + +/* Capsule */ + static CYTHON_INLINE PyObject * +__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) +{ + PyObject *cobj; +#if PY_VERSION_HEX >= 0x02070000 + cobj = PyCapsule_New(p, sig, NULL); +#else + cobj = PyCObject_FromVoidPtr(p, NULL); +#endif + return cobj; +} + +/* MemviewDtypeToObject */ + static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real(const char *itemp) { + return (PyObject *) PyFloat_FromDouble(*(__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) itemp); +} +static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real(const char *itemp, PyObject *obj) { + __pyx_t_10MDAnalysis_3lib_6nsgrid_real value = __pyx_PyFloat_AsFloat(obj); + if ((value == ((npy_float32)-1)) && PyErr_Occurred()) + return 0; + *(__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) itemp = value; + return 1; +} + +/* IsLittleEndian */ + static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) +{ + union { + uint32_t u32; + uint8_t u8[4]; + } S; + S.u32 = 0x01020304; + return S.u8[0] == 4; +} + +/* BufferFormatCheck */ + static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type) { + stack[0].field = &ctx->root; + stack[0].parent_offset = 0; + ctx->root.type = type; + ctx->root.name = "buffer dtype"; + ctx->root.offset = 0; + ctx->head = stack; + ctx->head->field = &ctx->root; + ctx->fmt_offset = 0; + ctx->head->parent_offset = 0; + ctx->new_packmode = '@'; + ctx->enc_packmode = '@'; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->is_complex = 0; + ctx->is_valid_array = 0; + ctx->struct_alignment = 0; + while (type->typegroup == 'S') { + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = 0; + type = type->fields->type; + } +} +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; + } else { + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; + } + } + *ts = t; + return count; +} +static int __Pyx_BufFmt_ExpectNumber(const char **ts) { + int number = __Pyx_BufFmt_ParseNumber(ts); + if (number == -1) + PyErr_Format(PyExc_ValueError,\ + "Does not understand character buffer dtype format string ('%c')", **ts); + return number; +} +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + PyErr_Format(PyExc_ValueError, + "Unexpected format string character: '%c'", ch); +} +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'c': return "'char'"; + case 'b': return "'signed char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 's': case 'p': return "a string"; + case 0: return "end"; + default: return "unparseable format string"; + } +} +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; + } + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +/* These are for computing the padding at the end of the struct to align + on the first member of the struct. This will probably the same as above, + but we don't have any guarantees. + */ +typedef struct { short x; char c; } __Pyx_pad_short; +typedef struct { int x; char c; } __Pyx_pad_int; +typedef struct { long x; char c; } __Pyx_pad_long; +typedef struct { float x; char c; } __Pyx_pad_float; +typedef struct { double x; char c; } __Pyx_pad_double; +typedef struct { long double x; char c; } __Pyx_pad_longdouble; +typedef struct { void *x; char c; } __Pyx_pad_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); + case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); + case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': + return 'H'; + case 'b': case 'h': case 'i': + case 'l': case 'q': case 's': case 'p': + return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': + return 'U'; + case 'f': case 'd': case 'g': + return (is_complex ? 'C' : 'R'); + case 'O': + return 'O'; + case 'P': + return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; + } + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset, arraysize = 1; + if (ctx->enc_type == 0) return 0; + if (ctx->head->field->type->arraysize[0]) { + int i, ndim = 0; + if (ctx->enc_type == 's' || ctx->enc_type == 'p') { + ctx->is_valid_array = ctx->head->field->type->ndim == 1; + ndim = 1; + if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { + PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %zu", + ctx->head->field->type->arraysize[0], ctx->enc_count); + return -1; + } + } + if (!ctx->is_valid_array) { + PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", + ctx->head->field->type->ndim, ndim); + return -1; + } + for (i = 0; i < ctx->head->field->type->ndim; i++) { + arraysize *= ctx->head->field->type->arraysize[i]; + } + ctx->is_valid_array = 0; + ctx->enc_count = 1; + } + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + } + if (ctx->enc_packmode == '@') { + size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + size_t align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + if (ctx->struct_alignment == 0) + ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, + ctx->is_complex); + } + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + if ((type->typegroup == 'H' || group == 'H') && type->size == size) { + } else { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + } + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", + (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); + return -1; + } + ctx->fmt_offset += size; + if (arraysize) + ctx->fmt_offset += (arraysize - 1) * size; + --ctx->enc_count; + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + break; + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } + } + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} +static PyObject * +__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) +{ + const char *ts = *tsp; + int i = 0, number; + int ndim = ctx->head->field->type->ndim; +; + ++ts; + if (ctx->new_count != 1) { + PyErr_SetString(PyExc_ValueError, + "Cannot handle repeated arrays in format string"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + while (*ts && *ts != ')') { + switch (*ts) { + case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; + default: break; + } + number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) + return PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %d", + ctx->head->field->type->arraysize[i], number); + if (*ts != ',' && *ts != ')') + return PyErr_Format(PyExc_ValueError, + "Expected a comma in format string, got '%c'", *ts); + if (*ts == ',') ts++; + i++; + } + if (i != ndim) + return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", + ctx->head->field->type->ndim, i); + if (!*ts) { + PyErr_SetString(PyExc_ValueError, + "Unexpected end of format string, expected ')'"); + return NULL; + } + ctx->is_valid_array = 1; + ctx->new_count = 1; + *tsp = ++ts; + return Py_None; +} +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case '\r': + case '\n': + ++ts; + break; + case '<': + if (!__Pyx_Is_Little_Endian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_Is_Little_Endian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + ctx->new_packmode = *ts++; + break; + case 'T': + { + const char* ts_after_sub; + size_t i, struct_count = ctx->new_count; + size_t struct_alignment = ctx->struct_alignment; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + ctx->enc_count = 0; + ctx->struct_alignment = 0; + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + if (struct_alignment) ctx->struct_alignment = struct_alignment; + } + break; + case '}': + { + size_t alignment = ctx->struct_alignment; + ++ts; + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + if (alignment && ctx->fmt_offset % alignment) { + ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); + } + } + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->enc_packmode = ctx->new_packmode; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } + CYTHON_FALLTHROUGH; + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': case 'p': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex && + ctx->enc_packmode == ctx->new_packmode) { + ctx->enc_count += ctx->new_count; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; + } + CYTHON_FALLTHROUGH; + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + case ':': + ++ts; + while(*ts != ':') ++ts; + ++ts; + break; + case '(': + if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; + break; + default: + { + int number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + ctx->new_count = (size_t)number; + } + } + } +} + +/* TypeInfoCompare */ + static int +__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) +{ + int i; + if (!a || !b) + return 0; + if (a == b) + return 1; + if (a->size != b->size || a->typegroup != b->typegroup || + a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { + if (a->typegroup == 'H' || b->typegroup == 'H') { + return a->size == b->size; + } else { + return 0; + } + } + if (a->ndim) { + for (i = 0; i < a->ndim; i++) + if (a->arraysize[i] != b->arraysize[i]) + return 0; + } + if (a->typegroup == 'S') { + if (a->flags != b->flags) + return 0; + if (a->fields || b->fields) { + if (!(a->fields && b->fields)) + return 0; + for (i = 0; a->fields[i].type && b->fields[i].type; i++) { + __Pyx_StructField *field_a = a->fields + i; + __Pyx_StructField *field_b = b->fields + i; + if (field_a->offset != field_b->offset || + !__pyx_typeinfo_cmp(field_a->type, field_b->type)) + return 0; + } + return !a->fields[i].type && !b->fields[i].type; + } + } + return 1; +} + +/* MemviewSliceValidateAndInit */ + static int +__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) +{ + if (buf->shape[dim] <= 1) + return 1; + if (buf->strides) { + if (spec & __Pyx_MEMVIEW_CONTIG) { + if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { + if (buf->strides[dim] != sizeof(void *)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly contiguous " + "in dimension %d.", dim); + goto fail; + } + } else if (buf->strides[dim] != buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_FOLLOW) { + Py_ssize_t stride = buf->strides[dim]; + if (stride < 0) + stride = -stride; + if (stride < buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } + } + } else { + if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not contiguous in " + "dimension %d", dim); + goto fail; + } else if (spec & (__Pyx_MEMVIEW_PTR)) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not indirect in " + "dimension %d", dim); + goto fail; + } else if (buf->suboffsets) { + PyErr_SetString(PyExc_ValueError, + "Buffer exposes suboffsets but no strides"); + goto fail; + } + } + return 1; +fail: + return 0; +} +static int +__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) +{ + if (spec & __Pyx_MEMVIEW_DIRECT) { + if (buf->suboffsets && buf->suboffsets[dim] >= 0) { + PyErr_Format(PyExc_ValueError, + "Buffer not compatible with direct access " + "in dimension %d.", dim); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_PTR) { + if (!buf->suboffsets || (buf->suboffsets && buf->suboffsets[dim] < 0)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly accessible " + "in dimension %d.", dim); + goto fail; + } + } + return 1; +fail: + return 0; +} +static int +__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) +{ + int i; + if (c_or_f_flag & __Pyx_IS_F_CONTIG) { + Py_ssize_t stride = 1; + for (i = 0; i < ndim; i++) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) + { + PyErr_SetString(PyExc_ValueError, + "Buffer not fortran contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { + Py_ssize_t stride = 1; + for (i = ndim - 1; i >- 1; i--) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) { + PyErr_SetString(PyExc_ValueError, + "Buffer not C contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } + return 1; +fail: + return 0; +} +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj) +{ + struct __pyx_memoryview_obj *memview, *new_memview; + __Pyx_RefNannyDeclarations + Py_buffer *buf; + int i, spec = 0, retval = -1; + __Pyx_BufFmt_Context ctx; + int from_memoryview = __pyx_memoryview_check(original_obj); + __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); + if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) + original_obj)->typeinfo)) { + memview = (struct __pyx_memoryview_obj *) original_obj; + new_memview = NULL; + } else { + memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + original_obj, buf_flags, 0, dtype); + new_memview = memview; + if (unlikely(!memview)) + goto fail; + } + buf = &memview->view; + if (buf->ndim != ndim) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + ndim, buf->ndim); + goto fail; + } + if (new_memview) { + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned) buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " + "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", + buf->itemsize, + (buf->itemsize > 1) ? "s" : "", + dtype->name, + dtype->size, + (dtype->size > 1) ? "s" : ""); + goto fail; + } + for (i = 0; i < ndim; i++) { + spec = axes_specs[i]; + if (!__pyx_check_strides(buf, i, ndim, spec)) + goto fail; + if (!__pyx_check_suboffsets(buf, i, ndim, spec)) + goto fail; + } + if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, + new_memview != NULL) == -1)) { + goto fail; + } + retval = 0; + goto no_fail; +fail: + Py_XDECREF(new_memview); + retval = -1; +no_fail: + __Pyx_RefNannyFinishContext(); + return retval; +} + +/* ObjectToMemviewSlice */ + static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real(PyObject *obj, int writable_flag) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_FOLLOW), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, + (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 2, + &__Pyx_TypeInfo_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_long(npy_long value) { + const npy_long neg_one = (npy_long) -1, const_zero = (npy_long) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(npy_long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(npy_long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(npy_long) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(npy_long) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(npy_long) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(npy_long), + little, !is_unsigned); + } +} + +/* CIntFromPyVerify */ + #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) +#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) +#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ + {\ + func_type value = func_value;\ + if (sizeof(target_type) < sizeof(func_type)) {\ + if (unlikely(value != (func_type) (target_type) value)) {\ + func_type zero = 0;\ + if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ + return (target_type) -1;\ + if (is_unsigned && unlikely(value < zero))\ + goto raise_neg_overflow;\ + else\ + goto raise_overflow;\ + }\ + }\ + return (target_type) value;\ + } + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = (long) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + +/* Declarations */ + #if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +/* Arithmetic */ + #if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + #if 1 + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + if (b.imag == 0) { + return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); + } else if (fabsf(b.real) >= fabsf(b.imag)) { + if (b.real == 0 && b.imag == 0) { + return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); + } else { + float r = b.imag / b.real; + float s = 1.0 / (b.real + b.imag * r); + return __pyx_t_float_complex_from_parts( + (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); + } + } else { + float r = b.real / b.imag; + float s = 1.0 / (b.imag + b.real * r); + return __pyx_t_float_complex_from_parts( + (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); + } + } + #else + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + if (b.imag == 0) { + return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); + } else { + float denom = b.real * b.real + b.imag * b.imag; + return __pyx_t_float_complex_from_parts( + (a.real * b.real + a.imag * b.imag) / denom, + (a.imag * b.real - a.real * b.imag) / denom); + } + } + #endif + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod_float(a, a); + return __Pyx_c_prod_float(a, a); + case 3: + z = __Pyx_c_prod_float(a, a); + return __Pyx_c_prod_float(z, a); + case 4: + z = __Pyx_c_prod_float(a, a); + return __Pyx_c_prod_float(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } else if (b.imag == 0) { + z.real = powf(a.real, b.real); + z.imag = 0; + return z; + } else if (a.real > 0) { + r = a.real; + theta = 0; + } else { + r = -a.real; + theta = atan2f(0, -1); + } + } else { + r = __Pyx_c_abs_float(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +/* Declarations */ + #if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +/* Arithmetic */ + #if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + #if 1 + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + if (b.imag == 0) { + return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } else if (fabs(b.real) >= fabs(b.imag)) { + if (b.real == 0 && b.imag == 0) { + return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); + } else { + double r = b.imag / b.real; + double s = 1.0 / (b.real + b.imag * r); + return __pyx_t_double_complex_from_parts( + (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); + } + } else { + double r = b.real / b.imag; + double s = 1.0 / (b.imag + b.real * r); + return __pyx_t_double_complex_from_parts( + (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); + } + } + #else + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + if (b.imag == 0) { + return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); + } else { + double denom = b.real * b.real + b.imag * b.imag; + return __pyx_t_double_complex_from_parts( + (a.real * b.real + a.imag * b.imag) / denom, + (a.imag * b.real - a.real * b.imag) / denom); + } + } + #endif + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod_double(a, a); + return __Pyx_c_prod_double(a, a); + case 3: + z = __Pyx_c_prod_double(a, a); + return __Pyx_c_prod_double(z, a); + case 4: + z = __Pyx_c_prod_double(a, a); + return __Pyx_c_prod_double(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } else if (b.imag == 0) { + z.real = pow(a.real, b.real); + z.imag = 0; + return z; + } else if (a.real > 0) { + r = a.real; + theta = 0; + } else { + r = -a.real; + theta = atan2(0, -1); + } + } else { + r = __Pyx_c_abs_double(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { + const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum NPY_TYPES) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(enum NPY_TYPES) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), + little, !is_unsigned); + } +} + +/* MemviewSliceCopyTemplate */ + static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object) +{ + __Pyx_RefNannyDeclarations + int i; + __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; + struct __pyx_memoryview_obj *from_memview = from_mvs->memview; + Py_buffer *buf = &from_memview->view; + PyObject *shape_tuple = NULL; + PyObject *temp_int = NULL; + struct __pyx_array_obj *array_obj = NULL; + struct __pyx_memoryview_obj *memview_obj = NULL; + __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); + for (i = 0; i < ndim; i++) { + if (from_mvs->suboffsets[i] >= 0) { + PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " + "indirect dimensions (axis %d)", i); + goto fail; + } + } + shape_tuple = PyTuple_New(ndim); + if (unlikely(!shape_tuple)) { + goto fail; + } + __Pyx_GOTREF(shape_tuple); + for(i = 0; i < ndim; i++) { + temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); + if(unlikely(!temp_int)) { + goto fail; + } else { + PyTuple_SET_ITEM(shape_tuple, i, temp_int); + temp_int = NULL; + } + } + array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); + if (unlikely(!array_obj)) { + goto fail; + } + __Pyx_GOTREF(array_obj); + memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + (PyObject *) array_obj, contig_flag, + dtype_is_object, + from_mvs->memview->typeinfo); + if (unlikely(!memview_obj)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) + goto fail; + if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, + dtype_is_object) < 0)) + goto fail; + goto no_fail; +fail: + __Pyx_XDECREF(new_mvs.memview); + new_mvs.memview = NULL; + new_mvs.data = NULL; +no_fail: + __Pyx_XDECREF(shape_tuple); + __Pyx_XDECREF(temp_int); + __Pyx_XDECREF(array_obj); + __Pyx_RefNannyFinishContext(); + return new_mvs; +} + +/* CIntFromPy */ + static CYTHON_INLINE npy_long __Pyx_PyInt_As_npy_long(PyObject *x) { + const npy_long neg_one = (npy_long) -1, const_zero = (npy_long) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(npy_long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(npy_long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (npy_long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (npy_long) 0; + case 1: __PYX_VERIFY_RETURN_INT(npy_long, digit, digits[0]) + case 2: + if (8 * sizeof(npy_long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_long) >= 2 * PyLong_SHIFT) { + return (npy_long) (((((npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(npy_long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_long) >= 3 * PyLong_SHIFT) { + return (npy_long) (((((((npy_long)digits[2]) << PyLong_SHIFT) | (npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(npy_long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_long) >= 4 * PyLong_SHIFT) { + return (npy_long) (((((((((npy_long)digits[3]) << PyLong_SHIFT) | (npy_long)digits[2]) << PyLong_SHIFT) | (npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (npy_long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(npy_long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_long, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(npy_long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (npy_long) 0; + case -1: __PYX_VERIFY_RETURN_INT(npy_long, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(npy_long, digit, +digits[0]) + case -2: + if (8 * sizeof(npy_long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_long) - 1 > 2 * PyLong_SHIFT) { + return (npy_long) (((npy_long)-1)*(((((npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(npy_long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_long) - 1 > 2 * PyLong_SHIFT) { + return (npy_long) ((((((npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(npy_long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_long) - 1 > 3 * PyLong_SHIFT) { + return (npy_long) (((npy_long)-1)*(((((((npy_long)digits[2]) << PyLong_SHIFT) | (npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(npy_long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_long) - 1 > 3 * PyLong_SHIFT) { + return (npy_long) ((((((((npy_long)digits[2]) << PyLong_SHIFT) | (npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(npy_long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_long) - 1 > 4 * PyLong_SHIFT) { + return (npy_long) (((npy_long)-1)*(((((((((npy_long)digits[3]) << PyLong_SHIFT) | (npy_long)digits[2]) << PyLong_SHIFT) | (npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(npy_long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(npy_long) - 1 > 4 * PyLong_SHIFT) { + return (npy_long) ((((((((((npy_long)digits[3]) << PyLong_SHIFT) | (npy_long)digits[2]) << PyLong_SHIFT) | (npy_long)digits[1]) << PyLong_SHIFT) | (npy_long)digits[0]))); + } + } + break; + } +#endif + if (sizeof(npy_long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_long, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(npy_long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_long, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + npy_long val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (npy_long) -1; + } + } else { + npy_long val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (npy_long) -1; + val = __Pyx_PyInt_As_npy_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to npy_long"); + return (npy_long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to npy_long"); + return (npy_long) -1; +} + +/* CIntFromPy */ + static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = (long) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + case -2: + if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + } +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +/* CIntFromPy */ + static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + case -2: + if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + } +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; + } + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +/* CIntFromPy */ + static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *x) { + const size_t neg_one = (size_t) -1, const_zero = (size_t) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(size_t) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(size_t, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (size_t) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (size_t) 0; + case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, digits[0]) + case 2: + if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) >= 2 * PyLong_SHIFT) { + return (size_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) >= 3 * PyLong_SHIFT) { + return (size_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) >= 4 * PyLong_SHIFT) { + return (size_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (size_t) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(size_t) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(size_t) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (size_t) 0; + case -1: __PYX_VERIFY_RETURN_INT(size_t, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, +digits[0]) + case -2: + if (8 * sizeof(size_t) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { + return (size_t) (((size_t)-1)*(((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { + return (size_t) ((((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { + return (size_t) (((size_t)-1)*(((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { + return (size_t) ((((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) { + return (size_t) (((size_t)-1)*(((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) { + return (size_t) ((((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + } +#endif + if (sizeof(size_t) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(size_t) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + size_t val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (size_t) -1; + } + } else { + size_t val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (size_t) -1; + val = __Pyx_PyInt_As_size_t(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to size_t"); + return (size_t) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to size_t"); + return (size_t) -1; +} + +/* CIntFromPy */ + static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { + const char neg_one = (char) -1, const_zero = (char) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(char) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (char) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (char) 0; + case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) + case 2: + if (8 * sizeof(char) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { + return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(char) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { + return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(char) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { + return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (char) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(char) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (char) 0; + case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) + case -2: + if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(char) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(char) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(char) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { + return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + } +#endif + if (sizeof(char) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + char val; + PyObject *v = __Pyx_PyNumber_IntOrLong(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (char) -1; + } + } else { + char val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (char) -1; + val = __Pyx_PyInt_As_char(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to char"); + return (char) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to char"); + return (char) -1; +} + +/* ObjectToMemviewSlice */ + static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int(PyObject *obj, int writable_flag) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS_RO | writable_flag, 1, + &__Pyx_TypeInfo_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +/* CheckBinaryVersion */ + static int __Pyx_check_binary_version(void) { + char ctversion[4], rtversion[4]; + PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); + if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + return PyErr_WarnEx(NULL, message, 1); + } + return 0; +} + +/* ModuleImport */ + #ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + +/* TypeImport */ + #ifndef __PYX_HAVE_RT_ImportType +#define __PYX_HAVE_RT_ImportType +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, + size_t size, int strict) +{ + PyObject *py_module = 0; + PyObject *result = 0; + PyObject *py_name = 0; + char warning[200]; + Py_ssize_t basicsize; +#ifdef Py_LIMITED_API + PyObject *py_basicsize; +#endif + py_module = __Pyx_ImportModule(module_name); + if (!py_module) + goto bad; + py_name = __Pyx_PyIdentifier_FromString(class_name); + if (!py_name) + goto bad; + result = PyObject_GetAttr(py_module, py_name); + Py_DECREF(py_name); + py_name = 0; + Py_DECREF(py_module); + py_module = 0; + if (!result) + goto bad; + if (!PyType_Check(result)) { + PyErr_Format(PyExc_TypeError, + "%.200s.%.200s is not a type object", + module_name, class_name); + goto bad; + } +#ifndef Py_LIMITED_API + basicsize = ((PyTypeObject *)result)->tp_basicsize; +#else + py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); + if (!py_basicsize) + goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; +#endif + if (!strict && (size_t)basicsize > size) { + PyOS_snprintf(warning, sizeof(warning), + "%s.%s size changed, may indicate binary incompatibility. Expected %zd, got %zd", + module_name, class_name, basicsize, size); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; + } + else if ((size_t)basicsize != size) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s has the wrong size, try recompiling. Expected %zd, got %zd", + module_name, class_name, basicsize, size); + goto bad; + } + return (PyTypeObject *)result; +bad: + Py_XDECREF(py_module); + Py_XDECREF(result); + return NULL; +} +#endif + +/* InitStrings */ + static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + if (t->is_unicode) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + #else + if (t->is_unicode | t->is_str) { + if (t->intern) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->encoding) { + *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); + } else { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + if (PyObject_Hash(*t->p) == -1) + return -1; + ++t; + } + return 0; +} + +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); +} +static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { + Py_ssize_t ignore; + return __Pyx_PyObject_AsStringAndSize(o, &ignore); +} +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +#if !CYTHON_PEP393_ENABLED +static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { + char* defenc_c; + PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); + if (!defenc) return NULL; + defenc_c = PyBytes_AS_STRING(defenc); +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + { + char* end = defenc_c + PyBytes_GET_SIZE(defenc); + char* c; + for (c = defenc_c; c < end; c++) { + if ((unsigned char) (*c) >= 128) { + PyUnicode_AsASCIIString(o); + return NULL; + } + } + } +#endif + *length = PyBytes_GET_SIZE(defenc); + return defenc_c; +} +#else +static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { + if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL; +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + if (likely(PyUnicode_IS_ASCII(o))) { + *length = PyUnicode_GET_LENGTH(o); + return PyUnicode_AsUTF8(o); + } else { + PyUnicode_AsASCIIString(o); + return NULL; + } +#else + return PyUnicode_AsUTF8AndSize(o, length); +#endif +} +#endif +#endif +static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT + if ( +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + __Pyx_sys_getdefaultencoding_not_ascii && +#endif + PyUnicode_Check(o)) { + return __Pyx_PyUnicode_AsStringAndSize(o, length); + } else +#endif +#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) + if (PyByteArray_Check(o)) { + *length = PyByteArray_GET_SIZE(o); + return PyByteArray_AS_STRING(o); + } else +#endif + { + char* result; + int r = PyBytes_AsStringAndSize(o, &result, length); + if (unlikely(r < 0)) { + return NULL; + } else { + return result; + } + } +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + int is_true = x == Py_True; + if (is_true | (x == Py_False) | (x == Py_None)) return is_true; + else return PyObject_IsTrue(x); +} +static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) { +#if PY_MAJOR_VERSION >= 3 + if (PyLong_Check(result)) { + if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, + "__int__ returned non-int (type %.200s). " + "The ability to return an instance of a strict subclass of int " + "is deprecated, and may be removed in a future version of Python.", + Py_TYPE(result)->tp_name)) { + Py_DECREF(result); + return NULL; + } + return result; + } +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type %.200s)", + type_name, type_name, Py_TYPE(result)->tp_name); + Py_DECREF(result); + return NULL; +} +static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { +#if CYTHON_USE_TYPE_SLOTS + PyNumberMethods *m; +#endif + const char *name = NULL; + PyObject *res = NULL; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x) || PyLong_Check(x))) +#else + if (likely(PyLong_Check(x))) +#endif + return __Pyx_NewRef(x); +#if CYTHON_USE_TYPE_SLOTS + m = Py_TYPE(x)->tp_as_number; + #if PY_MAJOR_VERSION < 3 + if (m && m->nb_int) { + name = "int"; + res = m->nb_int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = m->nb_long(x); + } + #else + if (likely(m && m->nb_int)) { + name = "int"; + res = m->nb_int(x); + } + #endif +#else + if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) { + res = PyNumber_Int(x); + } +#endif + if (likely(res)) { +#if PY_MAJOR_VERSION < 3 + if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) { +#else + if (unlikely(!PyLong_CheckExact(res))) { +#endif + return __Pyx_PyNumber_IntOrLongWrongResultType(res, name); + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject *x; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(b))) { + if (sizeof(Py_ssize_t) >= sizeof(long)) + return PyInt_AS_LONG(b); + else + return PyInt_AsSsize_t(x); + } +#endif + if (likely(PyLong_CheckExact(b))) { + #if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)b)->ob_digit; + const Py_ssize_t size = Py_SIZE(b); + if (likely(__Pyx_sst_abs(size) <= 1)) { + ival = likely(size) ? digits[0] : 0; + if (size == -1) ival = -ival; + return ival; + } else { + switch (size) { + case 2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + } + } + #endif + return PyLong_AsSsize_t(b); + } + x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) { + return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False); +} +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { + return PyInt_FromSize_t(ival); +} + + +#endif /* Py_PYTHON_H */ diff --git a/package/MDAnalysis/lib/qcprot.c b/package/MDAnalysis/lib/qcprot.c index 049857b3a93..c268ef9be1d 100644 --- a/package/MDAnalysis/lib/qcprot.c +++ b/package/MDAnalysis/lib/qcprot.c @@ -1,11 +1,11 @@ -/* Generated by Cython 0.28.2 */ +/* Generated by Cython 0.28.5 */ /* BEGIN: Cython Metadata { "distutils": { "depends": [ - "/home/richard/miniconda2/envs/mda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h", - "/home/richard/miniconda2/envs/mda3/lib/python3.6/site-packages/numpy/core/include/numpy/ufuncobject.h" + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h", + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include/numpy/ufuncobject.h" ], "extra_compile_args": [ "-std=c99", @@ -14,7 +14,7 @@ "-funroll-loops" ], "include_dirs": [ - "/home/richard/miniconda2/envs/mda3/lib/python3.6/site-packages/numpy/core/include" + "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include" ], "name": "MDAnalysis.lib.qcprot", "sources": [ @@ -32,7 +32,7 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) #error Cython requires Python 2.6+ or Python 3.3+. #else -#define CYTHON_ABI "0_28_2" +#define CYTHON_ABI "0_28_5" #define CYTHON_FUTURE_DIVISION 0 #include #ifndef offsetof @@ -478,6 +478,7 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact + #define PyObject_Unicode PyObject_Str #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) @@ -675,7 +676,7 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); #define __Pyx_PySequence_Tuple(obj)\ @@ -783,7 +784,7 @@ static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } static PyObject *__pyx_m = NULL; static PyObject *__pyx_d; static PyObject *__pyx_b; -static PyObject *__pyx_cython_runtime; +static PyObject *__pyx_cython_runtime = NULL; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static PyObject *__pyx_empty_unicode; @@ -857,7 +858,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":730 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -866,7 +867,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":731 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -875,7 +876,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":732 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -884,7 +885,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":733 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -893,7 +894,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":737 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -902,7 +903,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":738 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -911,7 +912,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":739 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -920,7 +921,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":740 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -929,7 +930,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -938,7 +939,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -947,7 +948,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":754 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -956,7 +957,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":755 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -965,7 +966,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":756 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -974,7 +975,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -983,7 +984,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -992,7 +993,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1001,7 +1002,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1010,7 +1011,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":763 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1019,7 +1020,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":765 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1028,7 +1029,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":766 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1037,7 +1038,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1072,7 +1073,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do /*--- Type declarations ---*/ -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1081,7 +1082,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":770 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1090,7 +1091,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1099,7 +1100,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -1354,6 +1355,9 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /* Import.proto */ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); +/* ImportFrom.proto */ +static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); + /* CLineInTraceback.proto */ #ifdef CYTHON_CLINE_IN_TRACEBACK #define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0) @@ -1623,6 +1627,7 @@ static const char __pyx_k_yz[] = "yz"; static const char __pyx_k_z1[] = "z1"; static const char __pyx_k_z2[] = "z2"; static const char __pyx_k_zx[] = "zx"; +static const char __pyx_k_Doi[] = "Doi"; static const char __pyx_k_Sxx[] = "Sxx"; static const char __pyx_k_Sxy[] = "Sxy"; static const char __pyx_k_Sxz[] = "Sxz"; @@ -1648,6 +1653,7 @@ static const char __pyx_k_a41[] = "a41"; static const char __pyx_k_a42[] = "a42"; static const char __pyx_k_a43[] = "a43"; static const char __pyx_k_a44[] = "a44"; +static const char __pyx_k_due[] = "due"; static const char __pyx_k_ref[] = "ref"; static const char __pyx_k_rms[] = "rms"; static const char __pyx_k_rot[] = "rot"; @@ -1660,18 +1666,22 @@ static const char __pyx_k_Syz2[] = "Syz2"; static const char __pyx_k_Szx2[] = "Szx2"; static const char __pyx_k_Szy2[] = "Szy2"; static const char __pyx_k_Szz2[] = "Szz2"; +static const char __pyx_k_cite[] = "cite"; static const char __pyx_k_conf[] = "conf"; static const char __pyx_k_main[] = "__main__"; static const char __pyx_k_oldg[] = "oldg"; +static const char __pyx_k_path[] = "path"; static const char __pyx_k_qsqr[] = "qsqr"; static const char __pyx_k_rmsd[] = "rmsd"; static const char __pyx_k_test[] = "__test__"; +static const char __pyx_k_QCBIB[] = "_QCBIB"; static const char __pyx_k_delta[] = "delta"; static const char __pyx_k_dtype[] = "dtype"; static const char __pyx_k_normq[] = "normq"; static const char __pyx_k_numpy[] = "numpy"; static const char __pyx_k_range[] = "range"; static const char __pyx_k_zeros[] = "zeros"; +static const char __pyx_k_BibTeX[] = "BibTeX"; static const char __pyx_k_import[] = "__import__"; static const char __pyx_k_weight[] = "weight"; static const char __pyx_k_SxxmSyy[] = "SxxmSyy"; @@ -1703,6 +1713,8 @@ static const char __pyx_k_a3243_4233[] = "a3243_4233"; static const char __pyx_k_a3244_4234[] = "a3244_4234"; static const char __pyx_k_a3344_4334[] = "a3344_4334"; static const char __pyx_k_ImportError[] = "ImportError"; +static const char __pyx_k_cite_module[] = "cite_module"; +static const char __pyx_k_description[] = "description"; static const char __pyx_k_InnerProduct[] = "InnerProduct"; static const char __pyx_k_RuntimeError[] = "RuntimeError"; static const char __pyx_k_SyzSzymSyySzz2[] = "SyzSzymSyySzz2"; @@ -1710,11 +1722,14 @@ static const char __pyx_k_Sxy2Sxz2Syx2Szx2[] = "Sxy2Sxz2Syx2Szx2"; static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; static const char __pyx_k_Sxx2Syy2Szz2Syz2Szy2[] = "Sxx2Syy2Szz2Syz2Szy2"; static const char __pyx_k_MDAnalysis_lib_qcprot[] = "MDAnalysis.lib.qcprot"; +static const char __pyx_k_QCProt_implementation[] = "QCProt implementation"; static const char __pyx_k_FastCalcRMSDAndRotation[] = "FastCalcRMSDAndRotation"; static const char __pyx_k_CalcRMSDRotationalMatrix[] = "CalcRMSDRotationalMatrix"; +static const char __pyx_k_10_1107_s0108767305015266[] = "10.1107/s0108767305015266"; static const char __pyx_k_MDAnalysis_lib_qcprot_pyx[] = "MDAnalysis/lib/qcprot.pyx"; static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static const char __pyx_k_Fast_QCP_RMSD_structure_alignme[] = "\nFast QCP RMSD structure alignment --- :mod:`MDAnalysis.lib.qcprot`\n==================================================================\n\n:Author: Joshua L. Adelman, University of Pittsburgh\n:Author: Robert R. Delgado, Cornell University and Arizona State University\n:Contact: jla65@pitt.edu\n:Year: 2011, 2016\n:Licence: BSD\n\nPyQCPROT_ is a python/cython implementation of Douglas Theobald's QCP\nmethod for calculating the minimum RMSD between two structures\n[Theobald2005]_ and determining the optimal least-squares rotation\nmatrix [Liu2010]_.\n\nA full description of the method, along with the original C implementation can\nbe found at http://theobald.brandeis.edu/qcp/\n\nSee Also\n--------\nMDAnalysis.analysis.align:\n Align structures using :func:`CalcRMSDRotationalMatrix`\nMDAnalysis.analysis.rms.rmsd:\n Calculate the RMSD between two structures using\n :func:`CalcRMSDRotationalMatrix`\n\n\n.. versionchanged:: 0.16.0\n Call signatures were changed to directly interface with MDAnalysis\n coordinate arrays: shape (N, 3)\n\nReferences\n----------\n\nIf you use this QCP rotation calculation method in a publication, please\nreference:\n\n.. [Theobald2005] Douglas L. Theobald (2005)\n \"Rapid calculation of RMSD using a quaternion-based characteristic\n polynomial.\" Acta Crystallographica A 61(4):478-480.\n\n.. [Liu2010] Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2010)\n \"Fast determination of the optimal rotational matrix for macromolecular\n superpositions.\" J. Comput. Chem. 31, 1561-1563.\n\n.. _PyQCPROT: https://github.com/synapticarbors/pyqcprot\n\n\nFunctions\n---------\n\nUsers will typically use the :func:`CalcRMSDRotationalMatrix` function.\n\n.. autofunction:: CalcRMSDRotationalMatrix\n\n.. autofunction:: InnerProduct\n\n.. autofunction:: FastCalcRMSDAndRotation\n\n"; +static const char __pyx_k_article_qcprot2_author_Pu_Liu_a[] = "@article{qcprot2,\nauthor = {Pu Liu and Dimitris K. Agrafiotis and Douglas L. Theobald},\ntitle = {Fast determination of the optimal rotational matrix for macromolecular superpositions},\njournal = {Journal of Computational Chemistry},\nvolume = {31},\nnumber = {7},\npages = {1561-1563},\ndoi = {10.1002/jcc.21439},\n}\n"; static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; static const char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; @@ -1722,9 +1737,12 @@ static const char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; static const char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_kp_s_10_1107_s0108767305015266; static PyObject *__pyx_n_s_A; +static PyObject *__pyx_n_s_BibTeX; static PyObject *__pyx_n_s_C; static PyObject *__pyx_n_s_CalcRMSDRotationalMatrix; +static PyObject *__pyx_n_s_Doi; static PyObject *__pyx_n_s_E0; static PyObject *__pyx_n_s_FastCalcRMSDAndRotation; static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; @@ -1733,10 +1751,12 @@ static PyObject *__pyx_n_s_G1; static PyObject *__pyx_n_s_G2; static PyObject *__pyx_n_s_ImportError; static PyObject *__pyx_n_s_InnerProduct; -static PyObject *__pyx_n_s_MDAnalysis_lib_qcprot; +static PyObject *__pyx_kp_s_MDAnalysis_lib_qcprot; static PyObject *__pyx_kp_s_MDAnalysis_lib_qcprot_pyx; static PyObject *__pyx_n_s_N; static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_n_s_QCBIB; +static PyObject *__pyx_kp_s_QCProt_implementation; static PyObject *__pyx_n_s_RuntimeError; static PyObject *__pyx_n_s_Sxx; static PyObject *__pyx_n_s_Sxx2; @@ -1798,16 +1818,21 @@ static PyObject *__pyx_n_s_a41; static PyObject *__pyx_n_s_a42; static PyObject *__pyx_n_s_a43; static PyObject *__pyx_n_s_a44; +static PyObject *__pyx_kp_s_article_qcprot2_author_Pu_Liu_a; static PyObject *__pyx_n_s_ax; static PyObject *__pyx_n_s_ay; static PyObject *__pyx_n_s_az; static PyObject *__pyx_n_s_b; +static PyObject *__pyx_n_s_cite; +static PyObject *__pyx_n_s_cite_module; static PyObject *__pyx_n_s_cline_in_traceback; static PyObject *__pyx_n_s_conf; static PyObject *__pyx_n_s_coords1; static PyObject *__pyx_n_s_coords2; static PyObject *__pyx_n_s_delta; +static PyObject *__pyx_n_s_description; static PyObject *__pyx_n_s_dtype; +static PyObject *__pyx_n_s_due; static PyObject *__pyx_n_s_evalprec; static PyObject *__pyx_n_s_evecprec; static PyObject *__pyx_n_s_float64; @@ -1823,6 +1848,7 @@ static PyObject *__pyx_n_s_numpy; static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to; static PyObject *__pyx_kp_s_numpy_core_umath_failed_to_impor; static PyObject *__pyx_n_s_oldg; +static PyObject *__pyx_n_s_path; static PyObject *__pyx_n_s_q1; static PyObject *__pyx_n_s_q2; static PyObject *__pyx_n_s_q3; @@ -1866,14 +1892,15 @@ static PyObject *__pyx_tuple__9; static PyObject *__pyx_tuple__10; static PyObject *__pyx_tuple__11; static PyObject *__pyx_tuple__12; -static PyObject *__pyx_tuple__14; -static PyObject *__pyx_tuple__16; -static PyObject *__pyx_codeobj__13; -static PyObject *__pyx_codeobj__15; -static PyObject *__pyx_codeobj__17; +static PyObject *__pyx_tuple__13; +static PyObject *__pyx_tuple__15; +static PyObject *__pyx_tuple__17; +static PyObject *__pyx_codeobj__14; +static PyObject *__pyx_codeobj__16; +static PyObject *__pyx_codeobj__18; /* Late includes */ -/* "MDAnalysis/lib/qcprot.pyx":150 +/* "MDAnalysis/lib/qcprot.pyx":175 * @cython.boundscheck(False) * @cython.wraparound(False) * def InnerProduct(np.ndarray[np.float64_t, ndim=1] A, # <<<<<<<<<<<<<< @@ -1923,29 +1950,29 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_6qcprot_1InnerProduct(PyObject *__py case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coords1)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 1); __PYX_ERR(0, 150, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 1); __PYX_ERR(0, 175, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coords2)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 2); __PYX_ERR(0, 150, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 2); __PYX_ERR(0, 175, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 3: if (likely((values[3] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_N)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 3); __PYX_ERR(0, 150, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 3); __PYX_ERR(0, 175, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 4: if (likely((values[4] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_weight)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 4); __PYX_ERR(0, 150, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 4); __PYX_ERR(0, 175, __pyx_L3_error) } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "InnerProduct") < 0)) __PYX_ERR(0, 150, __pyx_L3_error) + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "InnerProduct") < 0)) __PYX_ERR(0, 175, __pyx_L3_error) } } else if (PyTuple_GET_SIZE(__pyx_args) != 5) { goto __pyx_L5_argtuple_error; @@ -1959,21 +1986,21 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_6qcprot_1InnerProduct(PyObject *__py __pyx_v_A = ((PyArrayObject *)values[0]); __pyx_v_coords1 = ((PyArrayObject *)values[1]); __pyx_v_coords2 = ((PyArrayObject *)values[2]); - __pyx_v_N = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_N == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 153, __pyx_L3_error) + __pyx_v_N = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_N == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 178, __pyx_L3_error) __pyx_v_weight = ((PyArrayObject *)values[4]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - 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/* "MDAnalysis/lib/qcprot.pyx":192 + /* "MDAnalysis/lib/qcprot.pyx":217 * cdef double G1, G2 * * G1 = 0.0 # <<<<<<<<<<<<<< @@ -2119,7 +2146,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P */ __pyx_v_G1 = 0.0; - /* "MDAnalysis/lib/qcprot.pyx":193 + /* "MDAnalysis/lib/qcprot.pyx":218 * * G1 = 0.0 * G2 = 0.0 # <<<<<<<<<<<<<< @@ -2128,7 +2155,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P */ __pyx_v_G2 = 0.0; - /* "MDAnalysis/lib/qcprot.pyx":195 + /* "MDAnalysis/lib/qcprot.pyx":220 * G2 = 0.0 * * A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0 # <<<<<<<<<<<<<< @@ -2154,7 +2181,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_9 = 8; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_9, __pyx_pybuffernd_A.diminfo[0].strides) = 0.0; - /* "MDAnalysis/lib/qcprot.pyx":197 + /* "MDAnalysis/lib/qcprot.pyx":222 * A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0 * * if (weight is not None): # <<<<<<<<<<<<<< @@ -2165,7 +2192,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_11 = (__pyx_t_10 != 0); if (__pyx_t_11) { - /* "MDAnalysis/lib/qcprot.pyx":198 + /* "MDAnalysis/lib/qcprot.pyx":223 * * if (weight is not None): * for i in range(N): # <<<<<<<<<<<<<< @@ -2177,7 +2204,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) { __pyx_v_i = __pyx_t_14; - /* "MDAnalysis/lib/qcprot.pyx":199 + /* "MDAnalysis/lib/qcprot.pyx":224 * if (weight is not None): * for i in range(N): * x1 = weight[i] * coords1[i, 0] # <<<<<<<<<<<<<< @@ -2189,7 +2216,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_17 = 0; __pyx_v_x1 = ((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_weight.rcbuffer->pybuffer.buf, __pyx_t_15, __pyx_pybuffernd_weight.diminfo[0].strides)) * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_17, __pyx_pybuffernd_coords1.diminfo[1].strides))); - /* "MDAnalysis/lib/qcprot.pyx":200 + /* "MDAnalysis/lib/qcprot.pyx":225 * for i in range(N): * x1 = weight[i] * coords1[i, 0] * y1 = weight[i] * coords1[i, 1] # <<<<<<<<<<<<<< @@ -2201,7 +2228,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_20 = 1; __pyx_v_y1 = ((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_weight.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_weight.diminfo[0].strides)) * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_20, __pyx_pybuffernd_coords1.diminfo[1].strides))); - /* "MDAnalysis/lib/qcprot.pyx":201 + /* "MDAnalysis/lib/qcprot.pyx":226 * x1 = weight[i] * coords1[i, 0] * y1 = weight[i] * coords1[i, 1] * z1 = weight[i] * coords1[i, 2] # <<<<<<<<<<<<<< @@ -2213,7 +2240,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_23 = 2; __pyx_v_z1 = ((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_weight.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_weight.diminfo[0].strides)) * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_22, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_23, __pyx_pybuffernd_coords1.diminfo[1].strides))); - /* "MDAnalysis/lib/qcprot.pyx":203 + /* "MDAnalysis/lib/qcprot.pyx":228 * z1 = weight[i] * coords1[i, 2] * * G1 += x1 * coords1[i, 0] + y1 * coords1[i, 1] + z1 * coords1[i, 2] # <<<<<<<<<<<<<< @@ -2228,7 +2255,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_29 = 2; __pyx_v_G1 = (__pyx_v_G1 + (((__pyx_v_x1 * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_24, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_25, __pyx_pybuffernd_coords1.diminfo[1].strides))) + (__pyx_v_y1 * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_26, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_27, __pyx_pybuffernd_coords1.diminfo[1].strides)))) + (__pyx_v_z1 * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_28, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_29, __pyx_pybuffernd_coords1.diminfo[1].strides))))); - /* "MDAnalysis/lib/qcprot.pyx":205 + /* "MDAnalysis/lib/qcprot.pyx":230 * G1 += x1 * coords1[i, 0] + y1 * coords1[i, 1] + z1 * coords1[i, 2] * * x2 = coords2[i, 0] # <<<<<<<<<<<<<< @@ -2239,7 +2266,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_31 = 0; __pyx_v_x2 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords2.rcbuffer->pybuffer.buf, __pyx_t_30, __pyx_pybuffernd_coords2.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_coords2.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":206 + /* "MDAnalysis/lib/qcprot.pyx":231 * * x2 = coords2[i, 0] * y2 = coords2[i, 1] # <<<<<<<<<<<<<< @@ -2250,7 +2277,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_33 = 1; __pyx_v_y2 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords2.rcbuffer->pybuffer.buf, __pyx_t_32, __pyx_pybuffernd_coords2.diminfo[0].strides, __pyx_t_33, __pyx_pybuffernd_coords2.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":207 + /* "MDAnalysis/lib/qcprot.pyx":232 * x2 = coords2[i, 0] * y2 = coords2[i, 1] * z2 = coords2[i, 2] # <<<<<<<<<<<<<< @@ -2261,7 +2288,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_35 = 2; __pyx_v_z2 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords2.rcbuffer->pybuffer.buf, __pyx_t_34, __pyx_pybuffernd_coords2.diminfo[0].strides, __pyx_t_35, __pyx_pybuffernd_coords2.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":209 + /* "MDAnalysis/lib/qcprot.pyx":234 * z2 = coords2[i, 2] * * G2 += weight[i] * (x2 * x2 + y2 * y2 + z2 * z2) # <<<<<<<<<<<<<< @@ -2271,7 +2298,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_36 = __pyx_v_i; __pyx_v_G2 = (__pyx_v_G2 + ((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_weight.rcbuffer->pybuffer.buf, __pyx_t_36, __pyx_pybuffernd_weight.diminfo[0].strides)) * (((__pyx_v_x2 * __pyx_v_x2) + (__pyx_v_y2 * __pyx_v_y2)) + (__pyx_v_z2 * __pyx_v_z2)))); - /* "MDAnalysis/lib/qcprot.pyx":211 + /* "MDAnalysis/lib/qcprot.pyx":236 * G2 += weight[i] * (x2 * x2 + y2 * y2 + z2 * z2) * * A[0] += (x1 * x2) # <<<<<<<<<<<<<< @@ -2281,7 +2308,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_37 = 0; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_37, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_x1 * __pyx_v_x2); - /* "MDAnalysis/lib/qcprot.pyx":212 + /* "MDAnalysis/lib/qcprot.pyx":237 * * A[0] += (x1 * x2) * A[1] += (x1 * y2) # <<<<<<<<<<<<<< @@ -2291,7 +2318,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_38 = 1; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_38, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_x1 * __pyx_v_y2); - /* "MDAnalysis/lib/qcprot.pyx":213 + /* "MDAnalysis/lib/qcprot.pyx":238 * A[0] += (x1 * x2) * A[1] += (x1 * y2) * A[2] += (x1 * z2) # <<<<<<<<<<<<<< @@ -2301,7 +2328,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_39 = 2; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_39, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_x1 * __pyx_v_z2); - /* "MDAnalysis/lib/qcprot.pyx":215 + /* "MDAnalysis/lib/qcprot.pyx":240 * A[2] += (x1 * z2) * * A[3] += (y1 * x2) # <<<<<<<<<<<<<< @@ -2311,7 +2338,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_40 = 3; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_40, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_y1 * __pyx_v_x2); - /* "MDAnalysis/lib/qcprot.pyx":216 + /* "MDAnalysis/lib/qcprot.pyx":241 * * A[3] += (y1 * x2) * A[4] += (y1 * y2) # <<<<<<<<<<<<<< @@ -2321,7 +2348,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_41 = 4; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_41, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_y1 * __pyx_v_y2); - /* "MDAnalysis/lib/qcprot.pyx":217 + /* "MDAnalysis/lib/qcprot.pyx":242 * A[3] += (y1 * x2) * A[4] += (y1 * y2) * A[5] += (y1 * z2) # <<<<<<<<<<<<<< @@ -2331,7 +2358,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_42 = 5; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_42, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_y1 * __pyx_v_z2); - /* "MDAnalysis/lib/qcprot.pyx":219 + /* "MDAnalysis/lib/qcprot.pyx":244 * A[5] += (y1 * z2) * * A[6] += (z1 * x2) # <<<<<<<<<<<<<< @@ -2341,7 +2368,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_43 = 6; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_43, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_z1 * __pyx_v_x2); - /* "MDAnalysis/lib/qcprot.pyx":220 + /* "MDAnalysis/lib/qcprot.pyx":245 * * A[6] += (z1 * x2) * A[7] += (z1 * y2) # <<<<<<<<<<<<<< @@ -2351,7 +2378,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_44 = 7; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_44, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_z1 * __pyx_v_y2); - /* "MDAnalysis/lib/qcprot.pyx":221 + /* "MDAnalysis/lib/qcprot.pyx":246 * A[6] += (z1 * x2) * A[7] += (z1 * y2) * A[8] += (z1 * z2) # <<<<<<<<<<<<<< @@ -2362,7 +2389,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_45, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_z1 * __pyx_v_z2); } - /* "MDAnalysis/lib/qcprot.pyx":197 + /* "MDAnalysis/lib/qcprot.pyx":222 * A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0 * * if (weight is not None): # <<<<<<<<<<<<<< @@ -2372,7 +2399,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P goto __pyx_L3; } - /* "MDAnalysis/lib/qcprot.pyx":224 + /* "MDAnalysis/lib/qcprot.pyx":249 * * else: * for i in range(N): # <<<<<<<<<<<<<< @@ -2385,7 +2412,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) { __pyx_v_i = __pyx_t_14; - /* "MDAnalysis/lib/qcprot.pyx":225 + /* "MDAnalysis/lib/qcprot.pyx":250 * else: * for i in range(N): * x1 = coords1[i, 0] # <<<<<<<<<<<<<< @@ -2396,7 +2423,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_47 = 0; __pyx_v_x1 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_46, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_47, __pyx_pybuffernd_coords1.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":226 + /* "MDAnalysis/lib/qcprot.pyx":251 * for i in range(N): * x1 = coords1[i, 0] * y1 = coords1[i, 1] # <<<<<<<<<<<<<< @@ -2407,7 +2434,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_49 = 1; __pyx_v_y1 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_48, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_49, __pyx_pybuffernd_coords1.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":227 + /* "MDAnalysis/lib/qcprot.pyx":252 * x1 = coords1[i, 0] * y1 = coords1[i, 1] * z1 = coords1[i, 2] # <<<<<<<<<<<<<< @@ -2418,7 +2445,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_51 = 2; __pyx_v_z1 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_50, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_51, __pyx_pybuffernd_coords1.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":229 + /* "MDAnalysis/lib/qcprot.pyx":254 * z1 = coords1[i, 2] * * G1 += (x1 * x1 + y1 * y1 + z1 * z1) # <<<<<<<<<<<<<< @@ -2427,7 +2454,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P */ __pyx_v_G1 = (__pyx_v_G1 + (((__pyx_v_x1 * __pyx_v_x1) + (__pyx_v_y1 * __pyx_v_y1)) + (__pyx_v_z1 * __pyx_v_z1))); - /* "MDAnalysis/lib/qcprot.pyx":231 + /* "MDAnalysis/lib/qcprot.pyx":256 * G1 += (x1 * x1 + y1 * y1 + z1 * z1) * * x2 = coords2[i, 0] # <<<<<<<<<<<<<< @@ -2438,7 +2465,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_53 = 0; __pyx_v_x2 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords2.rcbuffer->pybuffer.buf, __pyx_t_52, __pyx_pybuffernd_coords2.diminfo[0].strides, __pyx_t_53, __pyx_pybuffernd_coords2.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":232 + /* "MDAnalysis/lib/qcprot.pyx":257 * * x2 = coords2[i, 0] * y2 = coords2[i, 1] # <<<<<<<<<<<<<< @@ -2449,7 +2476,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_55 = 1; __pyx_v_y2 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords2.rcbuffer->pybuffer.buf, __pyx_t_54, __pyx_pybuffernd_coords2.diminfo[0].strides, __pyx_t_55, __pyx_pybuffernd_coords2.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":233 + /* "MDAnalysis/lib/qcprot.pyx":258 * x2 = coords2[i, 0] * y2 = coords2[i, 1] * z2 = coords2[i, 2] # <<<<<<<<<<<<<< @@ -2460,7 +2487,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_57 = 2; __pyx_v_z2 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords2.rcbuffer->pybuffer.buf, __pyx_t_56, __pyx_pybuffernd_coords2.diminfo[0].strides, __pyx_t_57, __pyx_pybuffernd_coords2.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":235 + /* "MDAnalysis/lib/qcprot.pyx":260 * z2 = coords2[i, 2] * * G2 += (x2 * x2 + y2 * y2 + z2 * z2) # <<<<<<<<<<<<<< @@ -2469,7 +2496,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P */ __pyx_v_G2 = (__pyx_v_G2 + (((__pyx_v_x2 * __pyx_v_x2) + (__pyx_v_y2 * __pyx_v_y2)) + (__pyx_v_z2 * __pyx_v_z2))); - /* "MDAnalysis/lib/qcprot.pyx":237 + /* "MDAnalysis/lib/qcprot.pyx":262 * G2 += (x2 * x2 + y2 * y2 + z2 * z2) * * A[0] += (x1 * x2) # <<<<<<<<<<<<<< @@ -2479,7 +2506,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_58 = 0; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_58, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_x1 * __pyx_v_x2); - /* "MDAnalysis/lib/qcprot.pyx":238 + /* "MDAnalysis/lib/qcprot.pyx":263 * * A[0] += (x1 * x2) * A[1] += (x1 * y2) # <<<<<<<<<<<<<< @@ -2489,7 +2516,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_59 = 1; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_59, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_x1 * __pyx_v_y2); - /* "MDAnalysis/lib/qcprot.pyx":239 + /* "MDAnalysis/lib/qcprot.pyx":264 * A[0] += (x1 * x2) * A[1] += (x1 * y2) * A[2] += (x1 * z2) # <<<<<<<<<<<<<< @@ -2499,7 +2526,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_60 = 2; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_60, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_x1 * __pyx_v_z2); - /* "MDAnalysis/lib/qcprot.pyx":241 + /* "MDAnalysis/lib/qcprot.pyx":266 * A[2] += (x1 * z2) * * A[3] += (y1 * x2) # <<<<<<<<<<<<<< @@ -2509,7 +2536,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_61 = 3; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_61, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_y1 * __pyx_v_x2); - /* "MDAnalysis/lib/qcprot.pyx":242 + /* "MDAnalysis/lib/qcprot.pyx":267 * * A[3] += (y1 * x2) * A[4] += (y1 * y2) # <<<<<<<<<<<<<< @@ -2519,7 +2546,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_62 = 4; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_62, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_y1 * __pyx_v_y2); - /* "MDAnalysis/lib/qcprot.pyx":243 + /* "MDAnalysis/lib/qcprot.pyx":268 * A[3] += (y1 * x2) * A[4] += (y1 * y2) * A[5] += (y1 * z2) # <<<<<<<<<<<<<< @@ -2529,7 +2556,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_63 = 5; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_63, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_y1 * __pyx_v_z2); - /* "MDAnalysis/lib/qcprot.pyx":245 + /* "MDAnalysis/lib/qcprot.pyx":270 * A[5] += (y1 * z2) * * A[6] += (z1 * x2) # <<<<<<<<<<<<<< @@ -2539,7 +2566,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_64 = 6; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_64, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_z1 * __pyx_v_x2); - /* "MDAnalysis/lib/qcprot.pyx":246 + /* "MDAnalysis/lib/qcprot.pyx":271 * * A[6] += (z1 * x2) * A[7] += (z1 * y2) # <<<<<<<<<<<<<< @@ -2549,7 +2576,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_65 = 7; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_65, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_z1 * __pyx_v_y2); - /* "MDAnalysis/lib/qcprot.pyx":247 + /* "MDAnalysis/lib/qcprot.pyx":272 * A[6] += (z1 * x2) * A[7] += (z1 * y2) * A[8] += (z1 * z2) # <<<<<<<<<<<<<< @@ -2562,7 +2589,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P } __pyx_L3:; - /* "MDAnalysis/lib/qcprot.pyx":249 + /* "MDAnalysis/lib/qcprot.pyx":274 * A[8] += (z1 * z2) * * return (G1 + G2) * 0.5 # <<<<<<<<<<<<<< @@ -2570,13 +2597,13 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P * @cython.boundscheck(False) */ __Pyx_XDECREF(__pyx_r); - __pyx_t_67 = PyFloat_FromDouble(((__pyx_v_G1 + __pyx_v_G2) * 0.5)); if (unlikely(!__pyx_t_67)) __PYX_ERR(0, 249, __pyx_L1_error) + __pyx_t_67 = PyFloat_FromDouble(((__pyx_v_G1 + __pyx_v_G2) * 0.5)); if (unlikely(!__pyx_t_67)) __PYX_ERR(0, 274, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_67); __pyx_r = __pyx_t_67; __pyx_t_67 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/qcprot.pyx":150 + /* "MDAnalysis/lib/qcprot.pyx":175 * @cython.boundscheck(False) * @cython.wraparound(False) * def InnerProduct(np.ndarray[np.float64_t, ndim=1] A, # <<<<<<<<<<<<<< @@ -2610,7 +2637,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P return __pyx_r; } -/* "MDAnalysis/lib/qcprot.pyx":253 +/* "MDAnalysis/lib/qcprot.pyx":278 * @cython.boundscheck(False) * @cython.wraparound(False) * def CalcRMSDRotationalMatrix(np.ndarray[np.float64_t, ndim=2] ref, # <<<<<<<<<<<<<< @@ -2660,29 +2687,29 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_6qcprot_3CalcRMSDRotationalMatrix(Py case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_conf)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("CalcRMSDRotationalMatrix", 1, 5, 5, 1); __PYX_ERR(0, 253, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("CalcRMSDRotationalMatrix", 1, 5, 5, 1); __PYX_ERR(0, 278, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_N)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("CalcRMSDRotationalMatrix", 1, 5, 5, 2); __PYX_ERR(0, 253, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("CalcRMSDRotationalMatrix", 1, 5, 5, 2); __PYX_ERR(0, 278, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 3: if (likely((values[3] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_rot)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("CalcRMSDRotationalMatrix", 1, 5, 5, 3); __PYX_ERR(0, 253, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("CalcRMSDRotationalMatrix", 1, 5, 5, 3); __PYX_ERR(0, 278, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 4: if (likely((values[4] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_weights)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("CalcRMSDRotationalMatrix", 1, 5, 5, 4); __PYX_ERR(0, 253, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("CalcRMSDRotationalMatrix", 1, 5, 5, 4); __PYX_ERR(0, 278, __pyx_L3_error) } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "CalcRMSDRotationalMatrix") < 0)) __PYX_ERR(0, 253, __pyx_L3_error) + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "CalcRMSDRotationalMatrix") < 0)) __PYX_ERR(0, 278, __pyx_L3_error) } } else if (PyTuple_GET_SIZE(__pyx_args) != 5) { goto __pyx_L5_argtuple_error; @@ -2695,22 +2722,22 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_6qcprot_3CalcRMSDRotationalMatrix(Py } __pyx_v_ref = ((PyArrayObject *)values[0]); __pyx_v_conf = ((PyArrayObject *)values[1]); - 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__PYX_ERR(0, 342, __pyx_L1_error) + __PYX_ERR(0, 367, __pyx_L1_error) } __pyx_v_Szx = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_A.diminfo[0].strides)); - /* "MDAnalysis/lib/qcprot.pyx":343 + /* "MDAnalysis/lib/qcprot.pyx":368 * Syz = A[5] * Szx = A[6] * Szy = A[7] # <<<<<<<<<<<<<< @@ -3474,11 +3501,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_12 >= __pyx_pybuffernd_A.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 343, __pyx_L1_error) + __PYX_ERR(0, 368, __pyx_L1_error) } __pyx_v_Szy = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_A.diminfo[0].strides)); - /* "MDAnalysis/lib/qcprot.pyx":344 + /* "MDAnalysis/lib/qcprot.pyx":369 * Szx = A[6] * Szy = A[7] * Szz = A[8] # <<<<<<<<<<<<<< @@ -3493,11 +3520,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_13 >= __pyx_pybuffernd_A.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 344, __pyx_L1_error) + __PYX_ERR(0, 369, __pyx_L1_error) } __pyx_v_Szz = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_13, __pyx_pybuffernd_A.diminfo[0].strides)); - /* "MDAnalysis/lib/qcprot.pyx":346 + /* "MDAnalysis/lib/qcprot.pyx":371 * Szz = A[8] * * Sxx2 = Sxx * Sxx # <<<<<<<<<<<<<< @@ -3506,7 +3533,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Sxx2 = (__pyx_v_Sxx * __pyx_v_Sxx); - /* "MDAnalysis/lib/qcprot.pyx":347 + /* "MDAnalysis/lib/qcprot.pyx":372 * * Sxx2 = Sxx * Sxx * Syy2 = Syy * Syy # <<<<<<<<<<<<<< @@ -3515,7 +3542,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Syy2 = (__pyx_v_Syy * __pyx_v_Syy); - /* "MDAnalysis/lib/qcprot.pyx":348 + /* "MDAnalysis/lib/qcprot.pyx":373 * Sxx2 = Sxx * Sxx * Syy2 = Syy * Syy * Szz2 = Szz * Szz # <<<<<<<<<<<<<< @@ -3524,7 +3551,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Szz2 = (__pyx_v_Szz * __pyx_v_Szz); - /* "MDAnalysis/lib/qcprot.pyx":350 + /* "MDAnalysis/lib/qcprot.pyx":375 * Szz2 = Szz * Szz * * Sxy2 = Sxy * Sxy # <<<<<<<<<<<<<< @@ -3533,7 +3560,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Sxy2 = (__pyx_v_Sxy * __pyx_v_Sxy); - /* "MDAnalysis/lib/qcprot.pyx":351 + /* "MDAnalysis/lib/qcprot.pyx":376 * * Sxy2 = Sxy * Sxy * Syz2 = Syz * Syz # <<<<<<<<<<<<<< @@ -3542,7 +3569,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Syz2 = (__pyx_v_Syz * __pyx_v_Syz); - /* "MDAnalysis/lib/qcprot.pyx":352 + /* "MDAnalysis/lib/qcprot.pyx":377 * Sxy2 = Sxy * Sxy * Syz2 = Syz * Syz * Sxz2 = Sxz * Sxz # <<<<<<<<<<<<<< @@ -3551,7 +3578,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Sxz2 = (__pyx_v_Sxz * __pyx_v_Sxz); - /* "MDAnalysis/lib/qcprot.pyx":354 + /* "MDAnalysis/lib/qcprot.pyx":379 * Sxz2 = Sxz * Sxz * * Syx2 = Syx * Syx # <<<<<<<<<<<<<< @@ -3560,7 +3587,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Syx2 = (__pyx_v_Syx * __pyx_v_Syx); - /* "MDAnalysis/lib/qcprot.pyx":355 + /* "MDAnalysis/lib/qcprot.pyx":380 * * Syx2 = Syx * Syx * Szy2 = Szy * Szy # <<<<<<<<<<<<<< @@ -3569,7 +3596,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Szy2 = (__pyx_v_Szy * __pyx_v_Szy); - /* "MDAnalysis/lib/qcprot.pyx":356 + /* "MDAnalysis/lib/qcprot.pyx":381 * Syx2 = Syx * Syx * Szy2 = Szy * Szy * Szx2 = Szx * Szx # <<<<<<<<<<<<<< @@ -3578,7 +3605,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Szx2 = (__pyx_v_Szx * __pyx_v_Szx); - /* "MDAnalysis/lib/qcprot.pyx":358 + /* "MDAnalysis/lib/qcprot.pyx":383 * Szx2 = Szx * Szx * * SyzSzymSyySzz2 = 2.0 * (Syz*Szy - Syy*Szz) # <<<<<<<<<<<<<< @@ -3587,7 +3614,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SyzSzymSyySzz2 = (2.0 * ((__pyx_v_Syz * __pyx_v_Szy) - (__pyx_v_Syy * __pyx_v_Szz))); - /* "MDAnalysis/lib/qcprot.pyx":359 + /* "MDAnalysis/lib/qcprot.pyx":384 * * SyzSzymSyySzz2 = 2.0 * (Syz*Szy - Syy*Szz) * Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2 # <<<<<<<<<<<<<< @@ -3596,7 +3623,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Sxx2Syy2Szz2Syz2Szy2 = ((((__pyx_v_Syy2 + __pyx_v_Szz2) - __pyx_v_Sxx2) + __pyx_v_Syz2) + __pyx_v_Szy2); - /* "MDAnalysis/lib/qcprot.pyx":361 + /* "MDAnalysis/lib/qcprot.pyx":386 * Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2 * * C[2] = -2.0 * (Sxx2 + Syy2 + Szz2 + Sxy2 + Syx2 + Sxz2 + Szx2 + Syz2 + Szy2) # <<<<<<<<<<<<<< @@ -3611,11 +3638,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_14 >= __pyx_pybuffernd_C.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 361, __pyx_L1_error) + __PYX_ERR(0, 386, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_C.rcbuffer->pybuffer.buf, __pyx_t_14, __pyx_pybuffernd_C.diminfo[0].strides) = (-2.0 * ((((((((__pyx_v_Sxx2 + __pyx_v_Syy2) + __pyx_v_Szz2) + __pyx_v_Sxy2) + __pyx_v_Syx2) + __pyx_v_Sxz2) + __pyx_v_Szx2) + __pyx_v_Syz2) + __pyx_v_Szy2)); - /* "MDAnalysis/lib/qcprot.pyx":362 + /* "MDAnalysis/lib/qcprot.pyx":387 * * C[2] = -2.0 * (Sxx2 + Syy2 + Szz2 + Sxy2 + Syx2 + Sxz2 + Szx2 + Syz2 + Szy2) * C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz) # <<<<<<<<<<<<<< @@ -3630,11 +3657,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_15 >= __pyx_pybuffernd_C.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 362, __pyx_L1_error) + __PYX_ERR(0, 387, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_C.rcbuffer->pybuffer.buf, __pyx_t_15, __pyx_pybuffernd_C.diminfo[0].strides) = (8.0 * (((((((__pyx_v_Sxx * __pyx_v_Syz) * __pyx_v_Szy) + ((__pyx_v_Syy * __pyx_v_Szx) * __pyx_v_Sxz)) + ((__pyx_v_Szz * __pyx_v_Sxy) * __pyx_v_Syx)) - ((__pyx_v_Sxx * __pyx_v_Syy) * __pyx_v_Szz)) - ((__pyx_v_Syz * __pyx_v_Szx) * __pyx_v_Sxy)) - ((__pyx_v_Szy * __pyx_v_Syx) * __pyx_v_Sxz))); - /* "MDAnalysis/lib/qcprot.pyx":364 + /* "MDAnalysis/lib/qcprot.pyx":389 * C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz) * * SxzpSzx = Sxz + Szx # <<<<<<<<<<<<<< @@ -3643,7 +3670,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SxzpSzx = (__pyx_v_Sxz + __pyx_v_Szx); - /* "MDAnalysis/lib/qcprot.pyx":365 + /* "MDAnalysis/lib/qcprot.pyx":390 * * SxzpSzx = Sxz + Szx * SyzpSzy = Syz + Szy # <<<<<<<<<<<<<< @@ -3652,7 +3679,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SyzpSzy = (__pyx_v_Syz + __pyx_v_Szy); - /* "MDAnalysis/lib/qcprot.pyx":366 + /* "MDAnalysis/lib/qcprot.pyx":391 * SxzpSzx = Sxz + Szx * SyzpSzy = Syz + Szy * SxypSyx = Sxy + Syx # <<<<<<<<<<<<<< @@ -3661,7 +3688,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SxypSyx = (__pyx_v_Sxy + __pyx_v_Syx); - /* "MDAnalysis/lib/qcprot.pyx":367 + /* "MDAnalysis/lib/qcprot.pyx":392 * SyzpSzy = Syz + Szy * SxypSyx = Sxy + Syx * SyzmSzy = Syz - Szy # <<<<<<<<<<<<<< @@ -3670,7 +3697,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SyzmSzy = (__pyx_v_Syz - __pyx_v_Szy); - /* "MDAnalysis/lib/qcprot.pyx":368 + /* "MDAnalysis/lib/qcprot.pyx":393 * SxypSyx = Sxy + Syx * SyzmSzy = Syz - Szy * SxzmSzx = Sxz - Szx # <<<<<<<<<<<<<< @@ -3679,7 +3706,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SxzmSzx = (__pyx_v_Sxz - __pyx_v_Szx); - /* "MDAnalysis/lib/qcprot.pyx":369 + /* "MDAnalysis/lib/qcprot.pyx":394 * SyzmSzy = Syz - Szy * SxzmSzx = Sxz - Szx * SxymSyx = Sxy - Syx # <<<<<<<<<<<<<< @@ -3688,7 +3715,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SxymSyx = (__pyx_v_Sxy - __pyx_v_Syx); - /* "MDAnalysis/lib/qcprot.pyx":370 + /* "MDAnalysis/lib/qcprot.pyx":395 * SxzmSzx = Sxz - Szx * SxymSyx = Sxy - Syx * SxxpSyy = Sxx + Syy # <<<<<<<<<<<<<< @@ -3697,7 +3724,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SxxpSyy = (__pyx_v_Sxx + __pyx_v_Syy); - /* "MDAnalysis/lib/qcprot.pyx":371 + /* "MDAnalysis/lib/qcprot.pyx":396 * SxymSyx = Sxy - Syx * SxxpSyy = Sxx + Syy * SxxmSyy = Sxx - Syy # <<<<<<<<<<<<<< @@ -3706,7 +3733,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SxxmSyy = (__pyx_v_Sxx - __pyx_v_Syy); - /* "MDAnalysis/lib/qcprot.pyx":372 + /* "MDAnalysis/lib/qcprot.pyx":397 * SxxpSyy = Sxx + Syy * SxxmSyy = Sxx - Syy * Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2 # <<<<<<<<<<<<<< @@ -3715,7 +3742,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Sxy2Sxz2Syx2Szx2 = (((__pyx_v_Sxy2 + __pyx_v_Sxz2) - __pyx_v_Syx2) - __pyx_v_Szx2); - /* "MDAnalysis/lib/qcprot.pyx":374 + /* "MDAnalysis/lib/qcprot.pyx":399 * Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2 * * C[0] = (Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2 # <<<<<<<<<<<<<< @@ -3730,11 +3757,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_C.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 374, __pyx_L1_error) + __PYX_ERR(0, 399, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_C.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_C.diminfo[0].strides) = ((((((__pyx_v_Sxy2Sxz2Syx2Szx2 * __pyx_v_Sxy2Sxz2Syx2Szx2) + ((__pyx_v_Sxx2Syy2Szz2Syz2Szy2 + __pyx_v_SyzSzymSyySzz2) * (__pyx_v_Sxx2Syy2Szz2Syz2Szy2 - __pyx_v_SyzSzymSyySzz2))) + ((((-__pyx_v_SxzpSzx) * __pyx_v_SyzmSzy) + (__pyx_v_SxymSyx * (__pyx_v_SxxmSyy - __pyx_v_Szz))) * (((-__pyx_v_SxzmSzx) * __pyx_v_SyzpSzy) + (__pyx_v_SxymSyx * (__pyx_v_SxxmSyy + __pyx_v_Szz))))) + ((((-__pyx_v_SxzpSzx) * __pyx_v_SyzpSzy) - (__pyx_v_SxypSyx * (__pyx_v_SxxpSyy - __pyx_v_Szz))) * (((-__pyx_v_SxzmSzx) * __pyx_v_SyzmSzy) - (__pyx_v_SxypSyx * (__pyx_v_SxxpSyy + __pyx_v_Szz))))) + (((__pyx_v_SxypSyx * __pyx_v_SyzpSzy) + (__pyx_v_SxzpSzx * (__pyx_v_SxxmSyy + __pyx_v_Szz))) * (((-__pyx_v_SxymSyx) * __pyx_v_SyzmSzy) + (__pyx_v_SxzpSzx * (__pyx_v_SxxpSyy + __pyx_v_Szz))))) + (((__pyx_v_SxypSyx * __pyx_v_SyzmSzy) + (__pyx_v_SxzmSzx * (__pyx_v_SxxmSyy - __pyx_v_Szz))) * (((-__pyx_v_SxymSyx) * __pyx_v_SyzpSzy) + (__pyx_v_SxzmSzx * (__pyx_v_SxxpSyy - __pyx_v_Szz))))); - /* "MDAnalysis/lib/qcprot.pyx":381 + /* "MDAnalysis/lib/qcprot.pyx":406 * + (+(SxypSyx)*(SyzmSzy)+(SxzmSzx)*(SxxmSyy-Szz)) * (-(SxymSyx)*(SyzpSzy)+(SxzmSzx)*(SxxpSyy-Szz))) * * mxEigenV = E0 # <<<<<<<<<<<<<< @@ -3743,7 +3770,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_mxEigenV = __pyx_v_E0; - /* "MDAnalysis/lib/qcprot.pyx":382 + /* "MDAnalysis/lib/qcprot.pyx":407 * * mxEigenV = E0 * for i in range(50): # <<<<<<<<<<<<<< @@ -3753,7 +3780,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT for (__pyx_t_17 = 0; __pyx_t_17 < 50; __pyx_t_17+=1) { __pyx_v_i = __pyx_t_17; - /* "MDAnalysis/lib/qcprot.pyx":383 + /* "MDAnalysis/lib/qcprot.pyx":408 * mxEigenV = E0 * for i in range(50): * oldg = mxEigenV # <<<<<<<<<<<<<< @@ -3762,7 +3789,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_oldg = __pyx_v_mxEigenV; - /* "MDAnalysis/lib/qcprot.pyx":384 + /* "MDAnalysis/lib/qcprot.pyx":409 * for i in range(50): * oldg = mxEigenV * x2 = mxEigenV*mxEigenV # <<<<<<<<<<<<<< @@ -3771,7 +3798,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_x2 = (__pyx_v_mxEigenV * __pyx_v_mxEigenV); - /* "MDAnalysis/lib/qcprot.pyx":385 + /* "MDAnalysis/lib/qcprot.pyx":410 * oldg = mxEigenV * x2 = mxEigenV*mxEigenV * b = (x2 + C[2])*mxEigenV # <<<<<<<<<<<<<< @@ -3786,11 +3813,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_18 >= __pyx_pybuffernd_C.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 385, __pyx_L1_error) + __PYX_ERR(0, 410, __pyx_L1_error) } __pyx_v_b = ((__pyx_v_x2 + (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_C.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_C.diminfo[0].strides))) * __pyx_v_mxEigenV); - /* "MDAnalysis/lib/qcprot.pyx":386 + /* "MDAnalysis/lib/qcprot.pyx":411 * x2 = mxEigenV*mxEigenV * b = (x2 + C[2])*mxEigenV * a = b + C[1] # <<<<<<<<<<<<<< @@ -3805,11 +3832,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_19 >= __pyx_pybuffernd_C.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 386, __pyx_L1_error) + __PYX_ERR(0, 411, __pyx_L1_error) } __pyx_v_a = (__pyx_v_b + (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_C.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_C.diminfo[0].strides))); - /* "MDAnalysis/lib/qcprot.pyx":387 + /* "MDAnalysis/lib/qcprot.pyx":412 * b = (x2 + C[2])*mxEigenV * a = b + C[1] * delta = ((a*mxEigenV + C[0])/(2.0*x2*mxEigenV + b + a)) # <<<<<<<<<<<<<< @@ -3824,17 +3851,17 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_C.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 387, __pyx_L1_error) + __PYX_ERR(0, 412, __pyx_L1_error) } __pyx_t_21 = ((__pyx_v_a * __pyx_v_mxEigenV) + (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_C.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_C.diminfo[0].strides))); __pyx_t_22 = ((((2.0 * __pyx_v_x2) * __pyx_v_mxEigenV) + __pyx_v_b) + __pyx_v_a); if (unlikely(__pyx_t_22 == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "float division"); - __PYX_ERR(0, 387, __pyx_L1_error) + __PYX_ERR(0, 412, __pyx_L1_error) } __pyx_v_delta = (__pyx_t_21 / __pyx_t_22); - /* "MDAnalysis/lib/qcprot.pyx":388 + /* "MDAnalysis/lib/qcprot.pyx":413 * a = b + C[1] * delta = ((a*mxEigenV + C[0])/(2.0*x2*mxEigenV + b + a)) * mxEigenV -= delta # <<<<<<<<<<<<<< @@ -3843,7 +3870,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_mxEigenV = (__pyx_v_mxEigenV - __pyx_v_delta); - /* "MDAnalysis/lib/qcprot.pyx":389 + /* "MDAnalysis/lib/qcprot.pyx":414 * delta = ((a*mxEigenV + C[0])/(2.0*x2*mxEigenV + b + a)) * mxEigenV -= delta * if (fabs(mxEigenV - oldg) < fabs((evalprec)*mxEigenV)): # <<<<<<<<<<<<<< @@ -3853,7 +3880,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_23 = ((fabs((__pyx_v_mxEigenV - __pyx_v_oldg)) < fabs((__pyx_v_evalprec * __pyx_v_mxEigenV))) != 0); if (__pyx_t_23) { - /* "MDAnalysis/lib/qcprot.pyx":390 + /* "MDAnalysis/lib/qcprot.pyx":415 * mxEigenV -= delta * if (fabs(mxEigenV - oldg) < fabs((evalprec)*mxEigenV)): * break # <<<<<<<<<<<<<< @@ -3862,7 +3889,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ goto __pyx_L4_break; - /* "MDAnalysis/lib/qcprot.pyx":389 + /* "MDAnalysis/lib/qcprot.pyx":414 * delta = ((a*mxEigenV + C[0])/(2.0*x2*mxEigenV + b + a)) * mxEigenV -= delta * if (fabs(mxEigenV - oldg) < fabs((evalprec)*mxEigenV)): # <<<<<<<<<<<<<< @@ -3873,7 +3900,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } __pyx_L4_break:; - /* "MDAnalysis/lib/qcprot.pyx":397 + /* "MDAnalysis/lib/qcprot.pyx":422 * # the fabs() is to guard against extremely small, * # but *negative* numbers due to floating point error * rms = sqrt(fabs(2.0 * (E0 - mxEigenV)/N)) # <<<<<<<<<<<<<< @@ -3883,11 +3910,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_22 = (2.0 * (__pyx_v_E0 - __pyx_v_mxEigenV)); if (unlikely(__pyx_v_N == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "float division"); - __PYX_ERR(0, 397, __pyx_L1_error) + __PYX_ERR(0, 422, __pyx_L1_error) } __pyx_v_rms = sqrt(fabs((__pyx_t_22 / __pyx_v_N))); - /* "MDAnalysis/lib/qcprot.pyx":399 + /* "MDAnalysis/lib/qcprot.pyx":424 * rms = sqrt(fabs(2.0 * (E0 - mxEigenV)/N)) * * if (rot is None): # <<<<<<<<<<<<<< @@ -3898,7 +3925,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_24 = (__pyx_t_23 != 0); if (__pyx_t_24) { - /* "MDAnalysis/lib/qcprot.pyx":400 + /* "MDAnalysis/lib/qcprot.pyx":425 * * if (rot is None): * return rms # Don't bother with rotation. # <<<<<<<<<<<<<< @@ -3906,13 +3933,13 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT * a11 = SxxpSyy + Szz-mxEigenV */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyFloat_FromDouble(__pyx_v_rms); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 400, __pyx_L1_error) + __pyx_t_1 = PyFloat_FromDouble(__pyx_v_rms); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 425, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/qcprot.pyx":399 + /* "MDAnalysis/lib/qcprot.pyx":424 * rms = sqrt(fabs(2.0 * (E0 - mxEigenV)/N)) * * if (rot is None): # <<<<<<<<<<<<<< @@ -3921,7 +3948,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ } - /* "MDAnalysis/lib/qcprot.pyx":402 + /* "MDAnalysis/lib/qcprot.pyx":427 * return rms # Don't bother with rotation. * * a11 = SxxpSyy + Szz-mxEigenV # <<<<<<<<<<<<<< @@ -3930,7 +3957,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a11 = ((__pyx_v_SxxpSyy + __pyx_v_Szz) - __pyx_v_mxEigenV); - /* "MDAnalysis/lib/qcprot.pyx":403 + /* "MDAnalysis/lib/qcprot.pyx":428 * * a11 = SxxpSyy + Szz-mxEigenV * a12 = SyzmSzy # <<<<<<<<<<<<<< @@ -3939,7 +3966,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a12 = __pyx_v_SyzmSzy; - /* "MDAnalysis/lib/qcprot.pyx":404 + /* "MDAnalysis/lib/qcprot.pyx":429 * a11 = SxxpSyy + Szz-mxEigenV * a12 = SyzmSzy * a13 = - SxzmSzx # <<<<<<<<<<<<<< @@ -3948,7 +3975,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a13 = (-__pyx_v_SxzmSzx); - /* "MDAnalysis/lib/qcprot.pyx":405 + /* "MDAnalysis/lib/qcprot.pyx":430 * a12 = SyzmSzy * a13 = - SxzmSzx * a14 = SxymSyx # <<<<<<<<<<<<<< @@ -3957,7 +3984,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a14 = __pyx_v_SxymSyx; - /* "MDAnalysis/lib/qcprot.pyx":406 + /* "MDAnalysis/lib/qcprot.pyx":431 * a13 = - SxzmSzx * a14 = SxymSyx * a21 = SyzmSzy # <<<<<<<<<<<<<< @@ -3966,7 +3993,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a21 = __pyx_v_SyzmSzy; - /* "MDAnalysis/lib/qcprot.pyx":407 + /* "MDAnalysis/lib/qcprot.pyx":432 * a14 = SxymSyx * a21 = SyzmSzy * a22 = SxxmSyy - Szz-mxEigenV # <<<<<<<<<<<<<< @@ -3975,7 +4002,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a22 = ((__pyx_v_SxxmSyy - __pyx_v_Szz) - __pyx_v_mxEigenV); - /* "MDAnalysis/lib/qcprot.pyx":408 + /* "MDAnalysis/lib/qcprot.pyx":433 * a21 = SyzmSzy * a22 = SxxmSyy - Szz-mxEigenV * a23 = SxypSyx # <<<<<<<<<<<<<< @@ -3984,7 +4011,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a23 = __pyx_v_SxypSyx; - /* "MDAnalysis/lib/qcprot.pyx":409 + /* "MDAnalysis/lib/qcprot.pyx":434 * a22 = SxxmSyy - Szz-mxEigenV * a23 = SxypSyx * a24= SxzpSzx # <<<<<<<<<<<<<< @@ -3993,7 +4020,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a24 = __pyx_v_SxzpSzx; - /* "MDAnalysis/lib/qcprot.pyx":410 + /* "MDAnalysis/lib/qcprot.pyx":435 * a23 = SxypSyx * a24= SxzpSzx * a31 = a13 # <<<<<<<<<<<<<< @@ -4002,7 +4029,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a31 = __pyx_v_a13; - /* "MDAnalysis/lib/qcprot.pyx":411 + /* "MDAnalysis/lib/qcprot.pyx":436 * a24= SxzpSzx * a31 = a13 * a32 = a23 # <<<<<<<<<<<<<< @@ -4011,7 +4038,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a32 = __pyx_v_a23; - /* "MDAnalysis/lib/qcprot.pyx":412 + /* "MDAnalysis/lib/qcprot.pyx":437 * a31 = a13 * a32 = a23 * a33 = Syy-Sxx-Szz - mxEigenV # <<<<<<<<<<<<<< @@ -4020,7 +4047,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a33 = (((__pyx_v_Syy - __pyx_v_Sxx) - __pyx_v_Szz) - __pyx_v_mxEigenV); - /* "MDAnalysis/lib/qcprot.pyx":413 + /* "MDAnalysis/lib/qcprot.pyx":438 * a32 = a23 * a33 = Syy-Sxx-Szz - mxEigenV * a34 = SyzpSzy # <<<<<<<<<<<<<< @@ -4029,7 +4056,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a34 = __pyx_v_SyzpSzy; - /* "MDAnalysis/lib/qcprot.pyx":414 + /* "MDAnalysis/lib/qcprot.pyx":439 * a33 = Syy-Sxx-Szz - mxEigenV * a34 = SyzpSzy * a41 = a14 # <<<<<<<<<<<<<< @@ -4038,7 +4065,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a41 = __pyx_v_a14; - /* "MDAnalysis/lib/qcprot.pyx":415 + /* "MDAnalysis/lib/qcprot.pyx":440 * a34 = SyzpSzy * a41 = a14 * a42 = a24 # <<<<<<<<<<<<<< @@ -4047,7 +4074,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a42 = __pyx_v_a24; - /* "MDAnalysis/lib/qcprot.pyx":416 + /* "MDAnalysis/lib/qcprot.pyx":441 * a41 = a14 * a42 = a24 * a43 = a34 # <<<<<<<<<<<<<< @@ -4056,7 +4083,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a43 = __pyx_v_a34; - /* "MDAnalysis/lib/qcprot.pyx":417 + /* "MDAnalysis/lib/qcprot.pyx":442 * a42 = a24 * a43 = a34 * a44 = Szz - SxxpSyy - mxEigenV # <<<<<<<<<<<<<< @@ -4065,7 +4092,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a44 = ((__pyx_v_Szz - __pyx_v_SxxpSyy) - __pyx_v_mxEigenV); - /* "MDAnalysis/lib/qcprot.pyx":418 + /* "MDAnalysis/lib/qcprot.pyx":443 * a43 = a34 * a44 = Szz - SxxpSyy - mxEigenV * a3344_4334 = a33 * a44 - a43 * a34 # <<<<<<<<<<<<<< @@ -4074,7 +4101,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a3344_4334 = ((__pyx_v_a33 * __pyx_v_a44) - (__pyx_v_a43 * __pyx_v_a34)); - /* "MDAnalysis/lib/qcprot.pyx":419 + /* "MDAnalysis/lib/qcprot.pyx":444 * a44 = Szz - SxxpSyy - mxEigenV * a3344_4334 = a33 * a44 - a43 * a34 * a3244_4234 = a32 * a44-a42*a34 # <<<<<<<<<<<<<< @@ -4083,7 +4110,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a3244_4234 = ((__pyx_v_a32 * __pyx_v_a44) - (__pyx_v_a42 * __pyx_v_a34)); - /* "MDAnalysis/lib/qcprot.pyx":420 + /* "MDAnalysis/lib/qcprot.pyx":445 * a3344_4334 = a33 * a44 - a43 * a34 * a3244_4234 = a32 * a44-a42*a34 * a3243_4233 = a32 * a43 - a42 * a33 # <<<<<<<<<<<<<< @@ -4092,7 +4119,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a3243_4233 = ((__pyx_v_a32 * __pyx_v_a43) - (__pyx_v_a42 * __pyx_v_a33)); - /* "MDAnalysis/lib/qcprot.pyx":421 + /* "MDAnalysis/lib/qcprot.pyx":446 * a3244_4234 = a32 * a44-a42*a34 * a3243_4233 = a32 * a43 - a42 * a33 * a3143_4133 = a31 * a43-a41*a33 # <<<<<<<<<<<<<< @@ -4101,7 +4128,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a3143_4133 = ((__pyx_v_a31 * __pyx_v_a43) - (__pyx_v_a41 * __pyx_v_a33)); - /* "MDAnalysis/lib/qcprot.pyx":422 + /* "MDAnalysis/lib/qcprot.pyx":447 * a3243_4233 = a32 * a43 - a42 * a33 * a3143_4133 = a31 * a43-a41*a33 * a3144_4134 = a31 * a44 - a41 * a34 # <<<<<<<<<<<<<< @@ -4110,7 +4137,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a3144_4134 = ((__pyx_v_a31 * __pyx_v_a44) - (__pyx_v_a41 * __pyx_v_a34)); - /* "MDAnalysis/lib/qcprot.pyx":423 + /* "MDAnalysis/lib/qcprot.pyx":448 * a3143_4133 = a31 * a43-a41*a33 * a3144_4134 = a31 * a44 - a41 * a34 * a3142_4132 = a31 * a42-a41*a32 # <<<<<<<<<<<<<< @@ -4119,7 +4146,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a3142_4132 = ((__pyx_v_a31 * __pyx_v_a42) - (__pyx_v_a41 * __pyx_v_a32)); - /* "MDAnalysis/lib/qcprot.pyx":424 + /* "MDAnalysis/lib/qcprot.pyx":449 * a3144_4134 = a31 * a44 - a41 * a34 * a3142_4132 = a31 * a42-a41*a32 * q1 = a22*a3344_4334-a23*a3244_4234+a24*a3243_4233 # <<<<<<<<<<<<<< @@ -4128,7 +4155,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q1 = (((__pyx_v_a22 * __pyx_v_a3344_4334) - (__pyx_v_a23 * __pyx_v_a3244_4234)) + (__pyx_v_a24 * __pyx_v_a3243_4233)); - /* "MDAnalysis/lib/qcprot.pyx":425 + /* "MDAnalysis/lib/qcprot.pyx":450 * a3142_4132 = a31 * a42-a41*a32 * q1 = a22*a3344_4334-a23*a3244_4234+a24*a3243_4233 * q2 = -a21*a3344_4334+a23*a3144_4134-a24*a3143_4133 # <<<<<<<<<<<<<< @@ -4137,7 +4164,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q2 = ((((-__pyx_v_a21) * __pyx_v_a3344_4334) + (__pyx_v_a23 * __pyx_v_a3144_4134)) - (__pyx_v_a24 * __pyx_v_a3143_4133)); - /* "MDAnalysis/lib/qcprot.pyx":426 + /* "MDAnalysis/lib/qcprot.pyx":451 * q1 = a22*a3344_4334-a23*a3244_4234+a24*a3243_4233 * q2 = -a21*a3344_4334+a23*a3144_4134-a24*a3143_4133 * q3 = a21*a3244_4234-a22*a3144_4134+a24*a3142_4132 # <<<<<<<<<<<<<< @@ -4146,7 +4173,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q3 = (((__pyx_v_a21 * __pyx_v_a3244_4234) - (__pyx_v_a22 * __pyx_v_a3144_4134)) + (__pyx_v_a24 * __pyx_v_a3142_4132)); - /* "MDAnalysis/lib/qcprot.pyx":427 + /* "MDAnalysis/lib/qcprot.pyx":452 * q2 = -a21*a3344_4334+a23*a3144_4134-a24*a3143_4133 * q3 = a21*a3244_4234-a22*a3144_4134+a24*a3142_4132 * q4 = -a21*a3243_4233+a22*a3143_4133-a23*a3142_4132 # <<<<<<<<<<<<<< @@ -4155,7 +4182,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q4 = ((((-__pyx_v_a21) * __pyx_v_a3243_4233) + (__pyx_v_a22 * __pyx_v_a3143_4133)) - (__pyx_v_a23 * __pyx_v_a3142_4132)); - /* "MDAnalysis/lib/qcprot.pyx":429 + /* "MDAnalysis/lib/qcprot.pyx":454 * q4 = -a21*a3243_4233+a22*a3143_4133-a23*a3142_4132 * * qsqr = q1 * q1 + q2 * q2 + q3 * q3 + q4 * q4 # <<<<<<<<<<<<<< @@ -4164,7 +4191,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_qsqr = ((((__pyx_v_q1 * __pyx_v_q1) + (__pyx_v_q2 * __pyx_v_q2)) + (__pyx_v_q3 * __pyx_v_q3)) + (__pyx_v_q4 * __pyx_v_q4)); - /* "MDAnalysis/lib/qcprot.pyx":436 + /* "MDAnalysis/lib/qcprot.pyx":461 * # uncommented, but it is most likely unnecessary. * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4174,7 +4201,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_24 = ((__pyx_v_qsqr < __pyx_v_evecprec) != 0); if (__pyx_t_24) { - /* "MDAnalysis/lib/qcprot.pyx":437 + /* "MDAnalysis/lib/qcprot.pyx":462 * * if (qsqr < evecprec): * q1 = a12*a3344_4334 - a13*a3244_4234 + a14*a3243_4233 # <<<<<<<<<<<<<< @@ -4183,7 +4210,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q1 = (((__pyx_v_a12 * __pyx_v_a3344_4334) - (__pyx_v_a13 * __pyx_v_a3244_4234)) + (__pyx_v_a14 * __pyx_v_a3243_4233)); - /* "MDAnalysis/lib/qcprot.pyx":438 + /* "MDAnalysis/lib/qcprot.pyx":463 * if (qsqr < evecprec): * q1 = a12*a3344_4334 - a13*a3244_4234 + a14*a3243_4233 * q2 = -a11*a3344_4334 + a13*a3144_4134 - a14*a3143_4133 # <<<<<<<<<<<<<< @@ -4192,7 +4219,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q2 = ((((-__pyx_v_a11) * __pyx_v_a3344_4334) + (__pyx_v_a13 * __pyx_v_a3144_4134)) - (__pyx_v_a14 * __pyx_v_a3143_4133)); - /* "MDAnalysis/lib/qcprot.pyx":439 + /* "MDAnalysis/lib/qcprot.pyx":464 * q1 = a12*a3344_4334 - a13*a3244_4234 + a14*a3243_4233 * q2 = -a11*a3344_4334 + a13*a3144_4134 - a14*a3143_4133 * q3 = a11*a3244_4234 - a12*a3144_4134 + a14*a3142_4132 # <<<<<<<<<<<<<< @@ -4201,7 +4228,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q3 = (((__pyx_v_a11 * __pyx_v_a3244_4234) - (__pyx_v_a12 * __pyx_v_a3144_4134)) + (__pyx_v_a14 * __pyx_v_a3142_4132)); - /* "MDAnalysis/lib/qcprot.pyx":440 + /* "MDAnalysis/lib/qcprot.pyx":465 * q2 = -a11*a3344_4334 + a13*a3144_4134 - a14*a3143_4133 * q3 = a11*a3244_4234 - a12*a3144_4134 + a14*a3142_4132 * q4 = -a11*a3243_4233 + a12*a3143_4133 - a13*a3142_4132 # <<<<<<<<<<<<<< @@ -4210,7 +4237,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q4 = ((((-__pyx_v_a11) * __pyx_v_a3243_4233) + (__pyx_v_a12 * __pyx_v_a3143_4133)) - (__pyx_v_a13 * __pyx_v_a3142_4132)); - /* "MDAnalysis/lib/qcprot.pyx":441 + /* "MDAnalysis/lib/qcprot.pyx":466 * q3 = a11*a3244_4234 - a12*a3144_4134 + a14*a3142_4132 * q4 = -a11*a3243_4233 + a12*a3143_4133 - a13*a3142_4132 * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 # <<<<<<<<<<<<<< @@ -4219,7 +4246,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_qsqr = ((((__pyx_v_q1 * __pyx_v_q1) + (__pyx_v_q2 * __pyx_v_q2)) + (__pyx_v_q3 * __pyx_v_q3)) + (__pyx_v_q4 * __pyx_v_q4)); - /* "MDAnalysis/lib/qcprot.pyx":443 + /* "MDAnalysis/lib/qcprot.pyx":468 * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4229,7 +4256,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_24 = ((__pyx_v_qsqr < __pyx_v_evecprec) != 0); if (__pyx_t_24) { - /* "MDAnalysis/lib/qcprot.pyx":444 + /* "MDAnalysis/lib/qcprot.pyx":469 * * if (qsqr < evecprec): * a1324_1423 = a13 * a24 - a14 * a23 # <<<<<<<<<<<<<< @@ -4238,7 +4265,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a1324_1423 = ((__pyx_v_a13 * __pyx_v_a24) - (__pyx_v_a14 * __pyx_v_a23)); - /* "MDAnalysis/lib/qcprot.pyx":445 + /* "MDAnalysis/lib/qcprot.pyx":470 * if (qsqr < evecprec): * a1324_1423 = a13 * a24 - a14 * a23 * a1224_1422 = a12 * a24 - a14 * a22 # <<<<<<<<<<<<<< @@ -4247,7 +4274,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a1224_1422 = ((__pyx_v_a12 * __pyx_v_a24) - (__pyx_v_a14 * __pyx_v_a22)); - /* "MDAnalysis/lib/qcprot.pyx":446 + /* "MDAnalysis/lib/qcprot.pyx":471 * a1324_1423 = a13 * a24 - a14 * a23 * a1224_1422 = a12 * a24 - a14 * a22 * a1223_1322 = a12 * a23 - a13 * a22 # <<<<<<<<<<<<<< @@ -4256,7 +4283,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a1223_1322 = ((__pyx_v_a12 * __pyx_v_a23) - (__pyx_v_a13 * __pyx_v_a22)); - /* "MDAnalysis/lib/qcprot.pyx":447 + /* "MDAnalysis/lib/qcprot.pyx":472 * a1224_1422 = a12 * a24 - a14 * a22 * a1223_1322 = a12 * a23 - a13 * a22 * a1124_1421 = a11 * a24 - a14 * a21 # <<<<<<<<<<<<<< @@ -4265,7 +4292,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a1124_1421 = ((__pyx_v_a11 * __pyx_v_a24) - (__pyx_v_a14 * __pyx_v_a21)); - /* "MDAnalysis/lib/qcprot.pyx":448 + /* "MDAnalysis/lib/qcprot.pyx":473 * a1223_1322 = a12 * a23 - a13 * a22 * a1124_1421 = a11 * a24 - a14 * a21 * a1123_1321 = a11 * a23 - a13 * a21 # <<<<<<<<<<<<<< @@ -4274,7 +4301,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a1123_1321 = ((__pyx_v_a11 * __pyx_v_a23) - (__pyx_v_a13 * __pyx_v_a21)); - /* "MDAnalysis/lib/qcprot.pyx":449 + /* "MDAnalysis/lib/qcprot.pyx":474 * a1124_1421 = a11 * a24 - a14 * a21 * a1123_1321 = a11 * a23 - a13 * a21 * a1122_1221 = a11 * a22 - a12 * a21 # <<<<<<<<<<<<<< @@ -4283,7 +4310,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a1122_1221 = ((__pyx_v_a11 * __pyx_v_a22) - (__pyx_v_a12 * __pyx_v_a21)); - /* "MDAnalysis/lib/qcprot.pyx":451 + /* "MDAnalysis/lib/qcprot.pyx":476 * a1122_1221 = a11 * a22 - a12 * a21 * * q1 = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322 # <<<<<<<<<<<<<< @@ -4292,7 +4319,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q1 = (((__pyx_v_a42 * __pyx_v_a1324_1423) - (__pyx_v_a43 * __pyx_v_a1224_1422)) + (__pyx_v_a44 * __pyx_v_a1223_1322)); - /* "MDAnalysis/lib/qcprot.pyx":452 + /* "MDAnalysis/lib/qcprot.pyx":477 * * q1 = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322 * q2 = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321 # <<<<<<<<<<<<<< @@ -4301,7 +4328,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q2 = ((((-__pyx_v_a41) * __pyx_v_a1324_1423) + (__pyx_v_a43 * __pyx_v_a1124_1421)) - (__pyx_v_a44 * __pyx_v_a1123_1321)); - /* "MDAnalysis/lib/qcprot.pyx":453 + /* "MDAnalysis/lib/qcprot.pyx":478 * q1 = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322 * q2 = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321 * q3 = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221 # <<<<<<<<<<<<<< @@ -4310,7 +4337,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q3 = (((__pyx_v_a41 * __pyx_v_a1224_1422) - (__pyx_v_a42 * __pyx_v_a1124_1421)) + (__pyx_v_a44 * __pyx_v_a1122_1221)); - /* "MDAnalysis/lib/qcprot.pyx":454 + /* "MDAnalysis/lib/qcprot.pyx":479 * q2 = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321 * q3 = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221 * q4 = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221 # <<<<<<<<<<<<<< @@ -4319,7 +4346,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q4 = ((((-__pyx_v_a41) * __pyx_v_a1223_1322) + (__pyx_v_a42 * __pyx_v_a1123_1321)) - (__pyx_v_a43 * __pyx_v_a1122_1221)); - /* "MDAnalysis/lib/qcprot.pyx":455 + /* "MDAnalysis/lib/qcprot.pyx":480 * q3 = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221 * q4 = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221 * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 # <<<<<<<<<<<<<< @@ -4328,7 +4355,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_qsqr = ((((__pyx_v_q1 * __pyx_v_q1) + (__pyx_v_q2 * __pyx_v_q2)) + (__pyx_v_q3 * __pyx_v_q3)) + (__pyx_v_q4 * __pyx_v_q4)); - /* "MDAnalysis/lib/qcprot.pyx":457 + /* "MDAnalysis/lib/qcprot.pyx":482 * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4338,7 +4365,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_24 = ((__pyx_v_qsqr < __pyx_v_evecprec) != 0); if (__pyx_t_24) { - /* "MDAnalysis/lib/qcprot.pyx":458 + /* "MDAnalysis/lib/qcprot.pyx":483 * * if (qsqr < evecprec): * q1 = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322 # <<<<<<<<<<<<<< @@ -4347,7 +4374,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q1 = (((__pyx_v_a32 * __pyx_v_a1324_1423) - (__pyx_v_a33 * __pyx_v_a1224_1422)) + (__pyx_v_a34 * __pyx_v_a1223_1322)); - /* "MDAnalysis/lib/qcprot.pyx":459 + /* "MDAnalysis/lib/qcprot.pyx":484 * if (qsqr < evecprec): * q1 = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322 * q2 = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321 # <<<<<<<<<<<<<< @@ -4356,7 +4383,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q2 = ((((-__pyx_v_a31) * __pyx_v_a1324_1423) + (__pyx_v_a33 * __pyx_v_a1124_1421)) - (__pyx_v_a34 * __pyx_v_a1123_1321)); - /* "MDAnalysis/lib/qcprot.pyx":460 + /* "MDAnalysis/lib/qcprot.pyx":485 * q1 = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322 * q2 = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321 * q3 = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221 # <<<<<<<<<<<<<< @@ -4365,7 +4392,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q3 = (((__pyx_v_a31 * __pyx_v_a1224_1422) - (__pyx_v_a32 * __pyx_v_a1124_1421)) + (__pyx_v_a34 * __pyx_v_a1122_1221)); - /* "MDAnalysis/lib/qcprot.pyx":461 + /* "MDAnalysis/lib/qcprot.pyx":486 * q2 = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321 * q3 = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221 * q4 = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221 # <<<<<<<<<<<<<< @@ -4374,7 +4401,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q4 = ((((-__pyx_v_a31) * __pyx_v_a1223_1322) + (__pyx_v_a32 * __pyx_v_a1123_1321)) - (__pyx_v_a33 * __pyx_v_a1122_1221)); - /* "MDAnalysis/lib/qcprot.pyx":462 + /* "MDAnalysis/lib/qcprot.pyx":487 * q3 = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221 * q4 = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221 * qsqr = q1*q1 + q2 *q2 + q3*q3 + q4*q4 # <<<<<<<<<<<<<< @@ -4383,7 +4410,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_qsqr = ((((__pyx_v_q1 * __pyx_v_q1) + (__pyx_v_q2 * __pyx_v_q2)) + (__pyx_v_q3 * __pyx_v_q3)) + (__pyx_v_q4 * __pyx_v_q4)); - /* "MDAnalysis/lib/qcprot.pyx":464 + /* "MDAnalysis/lib/qcprot.pyx":489 * qsqr = q1*q1 + q2 *q2 + q3*q3 + q4*q4 * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4393,7 +4420,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_24 = ((__pyx_v_qsqr < __pyx_v_evecprec) != 0); if (__pyx_t_24) { - /* "MDAnalysis/lib/qcprot.pyx":466 + /* "MDAnalysis/lib/qcprot.pyx":491 * if (qsqr < evecprec): * # if qsqr is still too small, return the identity matrix. # * rot[0] = rot[4] = rot[8] = 1.0 # <<<<<<<<<<<<<< @@ -4408,7 +4435,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_25 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 466, __pyx_L1_error) + __PYX_ERR(0, 491, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_25, __pyx_pybuffernd_rot.diminfo[0].strides) = 1.0; __pyx_t_26 = 4; @@ -4419,7 +4446,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_26 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 466, __pyx_L1_error) + __PYX_ERR(0, 491, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_26, __pyx_pybuffernd_rot.diminfo[0].strides) = 1.0; __pyx_t_27 = 8; @@ -4430,11 +4457,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_27 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 466, __pyx_L1_error) + __PYX_ERR(0, 491, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_27, __pyx_pybuffernd_rot.diminfo[0].strides) = 1.0; - /* "MDAnalysis/lib/qcprot.pyx":467 + /* "MDAnalysis/lib/qcprot.pyx":492 * # if qsqr is still too small, return the identity matrix. # * rot[0] = rot[4] = rot[8] = 1.0 * rot[1] = rot[2] = rot[3] = rot[5] = rot[6] = rot[7] = 0.0 # <<<<<<<<<<<<<< @@ -4449,7 +4476,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_28 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 467, __pyx_L1_error) + __PYX_ERR(0, 492, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_28, __pyx_pybuffernd_rot.diminfo[0].strides) = 0.0; __pyx_t_29 = 2; @@ -4460,7 +4487,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 467, __pyx_L1_error) + __PYX_ERR(0, 492, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_rot.diminfo[0].strides) = 0.0; __pyx_t_30 = 3; @@ -4471,7 +4498,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 467, __pyx_L1_error) + __PYX_ERR(0, 492, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_30, __pyx_pybuffernd_rot.diminfo[0].strides) = 0.0; __pyx_t_31 = 5; @@ -4482,7 +4509,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - 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/* "MDAnalysis/lib/qcprot.pyx":443 + /* "MDAnalysis/lib/qcprot.pyx":468 * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4546,7 +4573,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ } - /* "MDAnalysis/lib/qcprot.pyx":436 + /* "MDAnalysis/lib/qcprot.pyx":461 * # uncommented, but it is most likely unnecessary. * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4555,7 +4582,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ } - /* "MDAnalysis/lib/qcprot.pyx":472 + /* "MDAnalysis/lib/qcprot.pyx":497 * * * normq = sqrt(qsqr) # <<<<<<<<<<<<<< @@ -4564,7 +4591,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_normq = sqrt(__pyx_v_qsqr); - /* "MDAnalysis/lib/qcprot.pyx":473 + /* "MDAnalysis/lib/qcprot.pyx":498 * * normq = sqrt(qsqr) * q1 /= normq # <<<<<<<<<<<<<< @@ -4573,11 +4600,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ if (unlikely(__pyx_v_normq == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "float division"); - 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/* "MDAnalysis/lib/qcprot.pyx":481 + /* "MDAnalysis/lib/qcprot.pyx":506 * x2 = q2 * q2 * y2 = q3 * q3 * z2 = q4 * q4 # <<<<<<<<<<<<<< @@ -4652,7 +4679,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_z2 = (__pyx_v_q4 * __pyx_v_q4); - /* "MDAnalysis/lib/qcprot.pyx":483 + /* "MDAnalysis/lib/qcprot.pyx":508 * z2 = q4 * q4 * * xy = q2 * q3 # <<<<<<<<<<<<<< @@ -4661,7 +4688,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_xy = (__pyx_v_q2 * __pyx_v_q3); - /* "MDAnalysis/lib/qcprot.pyx":484 + /* "MDAnalysis/lib/qcprot.pyx":509 * * xy = q2 * q3 * az = q1 * q4 # <<<<<<<<<<<<<< @@ -4670,7 +4697,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_az = (__pyx_v_q1 * __pyx_v_q4); - /* "MDAnalysis/lib/qcprot.pyx":485 + /* "MDAnalysis/lib/qcprot.pyx":510 * xy = q2 * q3 * az = q1 * q4 * zx = q4 * q2 # <<<<<<<<<<<<<< @@ -4679,7 +4706,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_zx = (__pyx_v_q4 * __pyx_v_q2); - 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y2 - z2 * rot[1] = 2 * (xy + az) * rot[2] = 2 * (zx - ay) # <<<<<<<<<<<<<< @@ -4759,11 +4786,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 492, __pyx_L1_error) + __PYX_ERR(0, 517, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_36, __pyx_pybuffernd_rot.diminfo[0].strides) = (2.0 * (__pyx_v_zx - __pyx_v_ay)); - /* "MDAnalysis/lib/qcprot.pyx":493 + /* "MDAnalysis/lib/qcprot.pyx":518 * rot[1] = 2 * (xy + az) * rot[2] = 2 * (zx - ay) * rot[3] = 2 * (xy - az) # <<<<<<<<<<<<<< @@ -4778,11 +4805,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - 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az) * rot[4] = a2 - x2 + y2 - z2 * rot[5] = 2 * (yz + ax) # <<<<<<<<<<<<<< @@ -4816,11 +4843,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 495, __pyx_L1_error) + __PYX_ERR(0, 520, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_39, __pyx_pybuffernd_rot.diminfo[0].strides) = (2.0 * (__pyx_v_yz + __pyx_v_ax)); - /* "MDAnalysis/lib/qcprot.pyx":496 + /* "MDAnalysis/lib/qcprot.pyx":521 * rot[4] = a2 - x2 + y2 - z2 * rot[5] = 2 * (yz + ax) * rot[6] = 2 * (zx + ay) # <<<<<<<<<<<<<< @@ -4835,11 +4862,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 496, __pyx_L1_error) + __PYX_ERR(0, 521, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_40, __pyx_pybuffernd_rot.diminfo[0].strides) = (2.0 * (__pyx_v_zx + __pyx_v_ay)); - /* "MDAnalysis/lib/qcprot.pyx":497 + /* "MDAnalysis/lib/qcprot.pyx":522 * rot[5] = 2 * (yz + ax) * rot[6] = 2 * (zx + ay) * rot[7] = 2 * (yz - ax) # <<<<<<<<<<<<<< @@ -4854,11 +4881,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 497, __pyx_L1_error) + __PYX_ERR(0, 522, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_41, __pyx_pybuffernd_rot.diminfo[0].strides) = (2.0 * (__pyx_v_yz - __pyx_v_ax)); - /* "MDAnalysis/lib/qcprot.pyx":498 + /* "MDAnalysis/lib/qcprot.pyx":523 * rot[6] = 2 * (zx + ay) * rot[7] = 2 * (yz - ax) * rot[8] = a2 - x2 - y2 + z2 # <<<<<<<<<<<<<< @@ -4873,24 +4900,24 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_42 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 498, __pyx_L1_error) + __PYX_ERR(0, 523, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_42, __pyx_pybuffernd_rot.diminfo[0].strides) = (((__pyx_v_a2 - __pyx_v_x2) - __pyx_v_y2) + __pyx_v_z2); - /* "MDAnalysis/lib/qcprot.pyx":500 + /* "MDAnalysis/lib/qcprot.pyx":525 * rot[8] = a2 - x2 - y2 + z2 * * return rms # <<<<<<<<<<<<<< * */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyFloat_FromDouble(__pyx_v_rms); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 500, __pyx_L1_error) + __pyx_t_1 = PyFloat_FromDouble(__pyx_v_rms); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 525, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/qcprot.pyx":288 + /* "MDAnalysis/lib/qcprot.pyx":313 * return FastCalcRMSDAndRotation(rot, A, E0, N) * * def FastCalcRMSDAndRotation(np.ndarray[np.float64_t, ndim=1] rot, # <<<<<<<<<<<<<< @@ -4924,7 +4951,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -4972,7 +4999,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); __Pyx_GIVEREF(__pyx_v_info->obj); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":222 * * cdef int i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -4981,7 +5008,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":223 * cdef int i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -4990,7 +5017,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":225 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -4999,7 +5026,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -5013,7 +5040,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":228 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -5024,7 +5051,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L4_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -5033,7 +5060,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":229 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -5046,7 +5073,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 229, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":227 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -5055,7 +5082,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -5069,7 +5096,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L7_bool_binop_done; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":232 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -5080,7 +5107,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -5089,7 +5116,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":233 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -5102,7 +5129,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 233, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":231 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -5111,7 +5138,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":235 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -5120,7 +5147,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":236 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -5129,7 +5156,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -5139,7 +5166,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":240 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) # <<<<<<<<<<<<<< @@ -5148,7 +5175,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyObject_Malloc((((sizeof(Py_ssize_t)) * 2) * ((size_t)__pyx_v_ndim)))); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":241 * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -5157,7 +5184,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":242 * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -5169,7 +5196,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":243 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -5178,7 +5205,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":244 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -5188,7 +5215,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -5198,7 +5225,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":246 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -5208,7 +5235,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":247 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -5219,7 +5246,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L9:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":248 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -5228,7 +5255,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":249 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -5237,7 +5264,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":250 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -5246,7 +5273,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":253 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -5255,7 +5282,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":254 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -5267,7 +5294,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":257 * cdef int offset * * info.obj = self # <<<<<<<<<<<<<< @@ -5280,7 +5307,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -5290,7 +5317,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(PyDataType_HASFIELDS(__pyx_v_descr) != 0)) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":260 * * if not PyDataType_HASFIELDS(descr): * t = descr.type_num # <<<<<<<<<<<<<< @@ -5300,7 +5327,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -5320,7 +5347,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L15_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":262 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -5337,7 +5364,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L14_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -5346,7 +5373,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -5359,7 +5386,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 263, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":261 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -5368,7 +5395,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":264 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -5380,7 +5407,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"b"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -5391,7 +5418,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"B"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -5402,7 +5429,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"h"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -5413,7 +5440,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"H"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -5424,7 +5451,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"i"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -5435,7 +5462,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"I"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -5446,7 +5473,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"l"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -5457,7 +5484,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"L"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -5468,7 +5495,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -5479,7 +5506,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Q"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -5490,7 +5517,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"f"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -5501,7 +5528,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"d"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -5512,7 +5539,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"g"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":277 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -5523,7 +5550,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zf"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -5534,7 +5561,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zd"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -5545,7 +5572,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = ((char *)"Zg"); break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -5557,7 +5584,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":282 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -5578,7 +5605,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -5587,7 +5614,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -5597,7 +5624,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":259 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -5606,7 +5633,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 * return * else: * info.format = PyObject_Malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -5616,7 +5643,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)PyObject_Malloc(0xFF)); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 * else: * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -5625,7 +5652,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":288 * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -5634,7 +5661,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -5644,7 +5671,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_8 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_8 == ((char *)NULL))) __PYX_ERR(1, 289, __pyx_L1_error) __pyx_v_f = __pyx_t_8; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -5654,7 +5681,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":215 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -5686,7 +5713,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":294 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -5710,7 +5737,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -5720,7 +5747,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) # <<<<<<<<<<<<<< @@ -5729,7 +5756,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->format); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":295 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -5738,7 +5765,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -5748,7 +5775,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":298 * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * PyObject_Free(info.strides) # <<<<<<<<<<<<<< @@ -5757,7 +5784,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->strides); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -5766,7 +5793,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - 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/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":784 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":784 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< @@ -5966,7 +5993,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":787 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":787 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -5980,7 +6007,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":788 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":788 * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): * return PyArray_MultiIterNew(5, a, b, c, d, e) # <<<<<<<<<<<<<< @@ -5994,7 +6021,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":787 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":787 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -6013,7 +6040,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< @@ -6027,7 +6054,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ int __pyx_t_1; __Pyx_RefNannySetupContext("PyDataType_SHAPE", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":791 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":791 * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< @@ -6037,7 +6064,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ __pyx_t_1 = (PyDataType_HASSUBARRAY(__pyx_v_d) != 0); if (__pyx_t_1) { - 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/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< @@ -6087,7 +6114,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -6116,7 +6143,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx char *__pyx_t_9; __Pyx_RefNannySetupContext("_util_dtypestring", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":801 * * cdef dtype child * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -6125,7 +6152,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_endian_detector = 1; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":802 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":802 * cdef dtype child * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -6134,7 +6161,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -6157,7 +6184,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":806 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":806 * * for childname in descr.names: * fields = descr.fields[childname] # <<<<<<<<<<<<<< @@ -6174,7 +6201,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3)); __pyx_t_3 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":807 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":807 * for childname in descr.names: * fields = descr.fields[childname] * child, new_offset = fields # <<<<<<<<<<<<<< @@ -6209,7 +6236,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -6226,7 +6253,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -6239,7 +6266,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 810, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":809 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -6248,7 +6275,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -6268,7 +6295,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L8_next_or:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":813 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":813 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -6285,7 +6312,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = __pyx_t_7; __pyx_L7_bool_binop_done:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -6294,7 +6321,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -6307,7 +6334,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 814, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -6316,7 +6343,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":824 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -6332,7 +6359,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":825 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -6341,7 +6368,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":826 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -6350,7 +6377,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":827 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -6361,7 +6388,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":829 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -6371,7 +6398,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -6381,7 +6408,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":832 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -6393,7 +6420,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -6403,7 +6430,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":834 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -6416,7 +6443,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __PYX_ERR(1, 834, __pyx_L1_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":833 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -6425,7 +6452,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":837 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -6443,7 +6470,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":838 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -6461,7 +6488,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":839 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -6479,7 +6506,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -6497,7 +6524,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -6515,7 +6542,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -6533,7 +6560,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":843 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -6551,7 +6578,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -6569,7 +6596,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":845 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -6587,7 +6614,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":846 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -6605,7 +6632,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":847 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -6623,7 +6650,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":848 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -6641,7 +6668,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":849 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -6659,7 +6686,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -6679,7 +6706,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":851 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -6699,7 +6726,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":852 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -6719,7 +6746,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":853 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -6737,7 +6764,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -6756,7 +6783,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":856 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -6765,7 +6792,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":831 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -6775,7 +6802,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":860 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -6788,7 +6815,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -6798,7 +6825,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":861 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -6808,7 +6835,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":796 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -6833,7 +6860,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -6848,7 +6875,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -6859,7 +6886,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":980 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -6868,7 +6895,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_baseptr = NULL; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":979 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -6878,7 +6905,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a goto __pyx_L3; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":982 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -6888,7 +6915,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a /*else*/ { Py_INCREF(__pyx_v_base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":983 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -6899,7 +6926,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":984 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -6908,7 +6935,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -6917,7 +6944,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -6929,7 +6956,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -6943,7 +6970,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -6953,7 +6980,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); if (__pyx_t_1) { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":989 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< @@ -6964,7 +6991,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":988 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -6973,7 +7000,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 * return None * else: * return arr.base # <<<<<<<<<<<<<< @@ -6987,7 +7014,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py goto __pyx_L0; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":987 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -7002,7 +7029,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -7023,7 +7050,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_array", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -7039,7 +7066,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 * cdef inline int import_array() except -1: * try: * _import_array() # <<<<<<<<<<<<<< @@ -7048,7 +7075,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { */ __pyx_t_4 = _import_array(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 998, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -7062,7 +7089,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":999 * try: * _import_array() * except Exception: # <<<<<<<<<<<<<< @@ -7077,7 +7104,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1000 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -7093,7 +7120,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -7108,7 +7135,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":996 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -7131,7 +7158,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -7152,7 +7179,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_umath", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -7168,7 +7195,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1004 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1004 * cdef inline int import_umath() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -7177,7 +7204,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1004, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -7191,7 +7218,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1005 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -7206,7 +7233,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1006 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -7222,7 +7249,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1003 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -7237,7 +7264,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1002 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -7260,7 +7287,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 +/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -7281,7 +7308,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_ufunc", 0); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -7297,7 +7324,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1010 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1010 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -7306,7 +7333,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1010, __pyx_L3_error) - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -7320,7 +7347,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1011 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1011 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -7334,7 +7361,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1012 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -7348,7 +7375,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1009 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -7363,7 +7390,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_L8_try_end:; } - /* "../../../miniconda2/envs/mda3/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 + /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1008 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -7423,9 +7450,12 @@ static struct PyModuleDef __pyx_moduledef = { #endif static __Pyx_StringTabEntry __pyx_string_tab[] = { + {&__pyx_kp_s_10_1107_s0108767305015266, __pyx_k_10_1107_s0108767305015266, sizeof(__pyx_k_10_1107_s0108767305015266), 0, 0, 1, 0}, {&__pyx_n_s_A, __pyx_k_A, sizeof(__pyx_k_A), 0, 0, 1, 1}, + {&__pyx_n_s_BibTeX, __pyx_k_BibTeX, sizeof(__pyx_k_BibTeX), 0, 0, 1, 1}, {&__pyx_n_s_C, __pyx_k_C, sizeof(__pyx_k_C), 0, 0, 1, 1}, {&__pyx_n_s_CalcRMSDRotationalMatrix, __pyx_k_CalcRMSDRotationalMatrix, sizeof(__pyx_k_CalcRMSDRotationalMatrix), 0, 0, 1, 1}, + {&__pyx_n_s_Doi, __pyx_k_Doi, sizeof(__pyx_k_Doi), 0, 0, 1, 1}, {&__pyx_n_s_E0, __pyx_k_E0, sizeof(__pyx_k_E0), 0, 0, 1, 1}, {&__pyx_n_s_FastCalcRMSDAndRotation, __pyx_k_FastCalcRMSDAndRotation, sizeof(__pyx_k_FastCalcRMSDAndRotation), 0, 0, 1, 1}, {&__pyx_kp_u_Format_string_allocated_too_shor, __pyx_k_Format_string_allocated_too_shor, sizeof(__pyx_k_Format_string_allocated_too_shor), 0, 1, 0, 0}, @@ -7434,10 +7464,12 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_G2, __pyx_k_G2, sizeof(__pyx_k_G2), 0, 0, 1, 1}, {&__pyx_n_s_ImportError, __pyx_k_ImportError, sizeof(__pyx_k_ImportError), 0, 0, 1, 1}, {&__pyx_n_s_InnerProduct, __pyx_k_InnerProduct, sizeof(__pyx_k_InnerProduct), 0, 0, 1, 1}, - 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