Merge branch 'develop' into feature/dask-0

.github/workflows/gh-ci.yaml

@@ -127,7 +127,7 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.xml
-        fail_ci_if_error: True
+        fail_ci_if_error: False
         verbose: True
 
 
@@ -259,22 +259,22 @@ jobs:
 
     - name: check_package_build
       run: |
-        DISTRIBUTION=$(ls -t1 dist/MDAnalysis-*.tar.gz | head -n1)
+        DISTRIBUTION=$(ls -t1 dist/mdanalysis-*.tar.gz | head -n1)
         test -n "${DISTRIBUTION}" || { echo "no distribution dist/MDAnalysis-*.tar.gz found"; exit 1; }
         twine check $DISTRIBUTION
 
     - name: check_testsuite_build
       run: |
-        DISTRIBUTION=$(ls -t1 dist/MDAnalysisTests-*.tar.gz | head -n1)
+        DISTRIBUTION=$(ls -t1 dist/mdanalysistests-*.tar.gz | head -n1)
         test -n "${DISTRIBUTION}" || { echo "no distribution dist/MDAnalysisTests-*.tar.gz found"; exit 1; }
         twine check $DISTRIBUTION
 
     - name: install sdist
       working-directory: ./dist
       run: |
         ls -a .
-        python -m pip install MDAnalysis-*.tar.gz
-        python -m pip install MDAnalysisTests-*.tar.gz
+        python -m pip install mdanalysis-*.tar.gz
+        python -m pip install mdanalysistests-*.tar.gz
 
     - name: run tests
       working-directory: ./dist

README.rst

@@ -102,19 +102,18 @@ Citation
 When using MDAnalysis in published work, please cite the following
 two papers:
 
-*   R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy,
-    M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski,
-    S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis:
+*   R\. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy,
+    M\. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski,
+    S\. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis:
     A Python package for the rapid analysis of molecular
     dynamics simulations. In S. Benthall and S. Rostrup,
     editors, Proceedings of the 15th Python in Science
     Conference, pages 102-109, Austin, TX, 2016. SciPy.
-    doi:`10.25080/Majora-629e541a-00e`_    
-
+    doi: `10.25080/Majora-629e541a-00e`_    
 *   N. Michaud-Agrawal, E. J. Denning, T. B. Woolf,
     and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular
     Dynamics Simulations. *J. Comput. Chem.* **32** (2011), 2319--2327.
-    doi:`10.1002/jcc.21787`_
+    doi: `10.1002/jcc.21787`_
 
 For citations of included algorithms and sub-modules please see the references_.
 
@@ -194,4 +193,4 @@ For citations of included algorithms and sub-modules please see the references_.
 
 .. |discussions| image:: https://img.shields.io/github/discussions/MDAnalysis/MDAnalysis
    :alt: GitHub Discussions
-   :target: https://github.com/MDAnalysis/mdanalysis/discussions
+   :target: https://github.com/MDAnalysis/mdanalysis/discussions

package/MDAnalysis/analysis/helix_analysis.py

@@ -121,7 +121,7 @@ def vector_of_best_fit(coordinates):
     """
     centered = coordinates - coordinates.mean(axis=0)
     Mt_M = np.matmul(centered.T, centered)
-    u, s, vh = np.linalg.linalg.svd(Mt_M)
+    u, s, vh = np.linalg.svd(Mt_M)
     vector = vh[0]
 
     # does vector face first local helix origin?

package/MDAnalysis/lib/formats/cython_util.pyx

@@ -26,6 +26,8 @@ cimport numpy as cnp
 from libc.stdlib cimport free
 from cpython cimport PyObject, Py_INCREF
 
+from MDAnalysis.lib.util import no_copy_shim
+
 cnp.import_array()
 
 
@@ -71,7 +73,7 @@ cdef class ArrayWrapper:
         self.data_type = data_type
         self.ndim = ndim
 
-    def __array__(self):
+    def __array__(self, dtype=None, copy=None):
         """ Here we use the __array__ method, that is called when numpy
             tries to get an array from the object."""
         ndarray = cnp.PyArray_SimpleNewFromData(self.ndim,
@@ -110,7 +112,7 @@ cdef cnp.ndarray ptr_to_ndarray(void* data_ptr, cnp.int64_t[:] dim, int data_typ
     array_wrapper = ArrayWrapper()
     array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type)
 
-    cdef cnp.ndarray ndarray = np.array(array_wrapper, copy=False)
+    cdef cnp.ndarray ndarray = np.array(array_wrapper, copy=no_copy_shim)
     # Assign our object to the 'base' of the ndarray object
     ndarray[:] = array_wrapper.__array__()
     # Increment the reference count, as the above assignement was done in

package/MDAnalysis/lib/transformations.py

@@ -170,6 +170,7 @@
 from numpy.linalg import norm
 
 from .mdamath import angle as vecangle
+from MDAnalysis.lib.util import no_copy_shim
 
 def identity_matrix():
     """Return 4x4 identity/unit matrix.
@@ -326,7 +327,7 @@ def rotation_matrix(angle, direction, point=None):
     M[:3, :3] = R
     if point is not None:
         # rotation not around origin
-        point = np.array(point[:3], dtype=np.float64, copy=False)
+        point = np.array(point[:3], dtype=np.float64, copy=no_copy_shim)
         M[:3, 3] = point - np.dot(R, point)
     return M
 
@@ -497,7 +498,7 @@ def projection_matrix(point, normal, direction=None,
 
     """
     M = np.identity(4)
-    point = np.array(point[:3], dtype=np.float64, copy=False)
+    point = np.array(point[:3], dtype=np.float64, copy=no_copy_shim)
     normal = unit_vector(normal[:3])
     if perspective is not None:
         # perspective projection
@@ -515,7 +516,7 @@ def projection_matrix(point, normal, direction=None,
         M[3, 3] = np.dot(perspective, normal)
     elif direction is not None:
         # parallel projection
-        direction = np.array(direction[:3], dtype=np.float64, copy=False)
+        direction = np.array(direction[:3], dtype=np.float64, copy=no_copy_shim)
         scale = np.dot(direction, normal)
         M[:3, :3] -= np.outer(direction, normal) / scale
         M[:3, 3] = direction * (np.dot(point, normal) / scale)
@@ -970,8 +971,8 @@ def superimposition_matrix(v0, v1, scaling=False, usesvd=True):
     True
 
     """
-    v0 = np.array(v0, dtype=np.float64, copy=False)[:3]
-    v1 = np.array(v1, dtype=np.float64, copy=False)[:3]
+    v0 = np.array(v0, dtype=np.float64, copy=no_copy_shim)[:3]
+    v1 = np.array(v1, dtype=np.float64, copy=no_copy_shim)[:3]
 
     if v0.shape != v1.shape or v0.shape[1] < 3:
         raise ValueError("vector sets are of wrong shape or type")
@@ -1314,7 +1315,7 @@ def quaternion_from_matrix(matrix, isprecise=False):
     True
 
     """
-    M = np.array(matrix, dtype=np.float64, copy=False)[:4, :4]
+    M = np.array(matrix, dtype=np.float64, copy=no_copy_shim)[:4, :4]
     if isprecise:
         q = np.empty((4, ), dtype=np.float64)
         t = np.trace(M)

package/MDAnalysis/lib/util.py

@@ -2555,6 +2555,14 @@ def wrapper(self, *args, **kwargs):
     return wrapper
 
 
+def no_copy_shim():
+    if np.lib.NumpyVersion >= "2.0.0rc1":
+        copy = None
+    else:
+        copy = False
+    return copy
+
+
 def is_installed(modulename: str):
     """Checks if module is installed