Adds checksum flag to zstd codec (#519)

* expose checksum toggle for zstd

* fixes zstd checksumming

* less fixtures

* write_checksum -> checksum

* adds release notes

* set default clevel to 0

* release

* update fixtures

* fix checksum flag

* add test for checksum

* adds wrapper codecs for the v2 codec pipeline

* docstring

docs/release.rst

@@ -17,9 +17,10 @@ Maintenance
 
 Enhancements
 ~~~~~~~~~~~~
-
+* Add checksum flag to zstd and sets the default level to 0.
+  By :user:`Norman Rzepka <normanrz>`, :issue:`519`.
 * Add PCodec
-  By :user:`Ryan Abernathey <rabernat>`.
+  By :user:`Ryan Abernathey <rabernat>`, :issue:`501`.
 * Use PyData theme for docs
   By :user:`John Kirkham <jakirkham>`, :issue:`485`.
 

fixture/zstd/codec.00/config.json

@@ -1,4 +1,4 @@
 {
     "id": "zstd",
-    "level": 1
+    "level": 0
 }

fixture/zstd/codec.07/config.json

@@ -0,0 +1,5 @@
+{
+    "checksum": true,
+    "id": "zstd",
+    "level": 0
+}

fixture/zstd/codec.08/config.json

@@ -0,0 +1,5 @@
+{
+    "checksum": true,
+    "id": "zstd",
+    "level": 0
+}

fixture/zstd/codec.09/config.json

@@ -0,0 +1,5 @@
+{
+    "checksum": true,
+    "id": "zstd",
+    "level": 22
+}

numcodecs/tests/test_zstd.py

@@ -29,15 +29,18 @@
     Zstd(level=10),
     Zstd(level=22),
     Zstd(level=100),
+    Zstd(checksum=True),
+    Zstd(level=0, checksum=True),
+    Zstd(level=22, checksum=True),
 ]
 
 
 # mix of dtypes: integer, float, bool, string
 # mix of shapes: 1D, 2D, 3D
 # mix of orders: C, F
 arrays = [
-    np.arange(1000, dtype='i4'),
-    np.linspace(1000, 1001, 1000, dtype='f8'),
+    np.arange(1000, dtype="i4"),
+    np.linspace(1000, 1001, 1000, dtype="f8"),
     np.random.normal(loc=1000, scale=1, size=(100, 10)),
     np.random.randint(0, 2, size=1000, dtype=bool).reshape(100, 10, order='F'),
     np.random.choice([b'a', b'bb', b'ccc'], size=1000).reshape(10, 10, 10),
@@ -76,3 +79,17 @@ def test_err_decode_object_buffer():
 
 def test_err_encode_object_buffer():
     check_err_encode_object_buffer(Zstd())
+
+
+def test_checksum():
+    data = np.arange(0, 64, dtype="uint8")
+    assert len(Zstd(level=0, checksum=False).encode(data)) + 4 == len(
+        Zstd(level=0, checksum=True).encode(data)
+    )
+
+
+def test_native_functions():
+    # Note, these assertions might need to be changed for new versions of zstd
+    assert Zstd.default_level == 3
+    assert Zstd.min_level == -131072
+    assert Zstd.max_level == 22

numcodecs/zstd.pyx

@@ -19,21 +19,38 @@ cdef extern from "zstd.h":
 
     unsigned ZSTD_versionNumber() nogil
 
-    size_t ZSTD_compress(void* dst,
-                         size_t dstCapacity,
-                         const void* src,
-                         size_t srcSize,
-                         int compressionLevel) nogil
+    struct ZSTD_CCtx_s:
+        pass
+    ctypedef ZSTD_CCtx_s ZSTD_CCtx
+    cdef enum ZSTD_cParameter:
+        ZSTD_c_compressionLevel=100
+        ZSTD_c_checksumFlag=201
+
+    ZSTD_CCtx* ZSTD_createCCtx() nogil
+    size_t ZSTD_freeCCtx(ZSTD_CCtx* cctx) nogil
+    size_t ZSTD_CCtx_setParameter(ZSTD_CCtx* cctx, 
+                                  ZSTD_cParameter param, 
+                                  int value) nogil
+
+    size_t ZSTD_compress2(ZSTD_CCtx* cctx,
+                          void* dst,
+                          size_t dstCapacity,
+                          const void* src,
+                          size_t srcSize) nogil
 
     size_t ZSTD_decompress(void* dst,
                            size_t dstCapacity,
                            const void* src,
                            size_t compressedSize) nogil
 
-    unsigned long long ZSTD_getDecompressedSize(const void* src,
+    cdef long ZSTD_CONTENTSIZE_UNKNOWN
+    cdef long ZSTD_CONTENTSIZE_ERROR
+    unsigned long long ZSTD_getFrameContentSize(const void* src,
                                                 size_t srcSize) nogil
 
+    int ZSTD_minCLevel() nogil
     int ZSTD_maxCLevel() nogil
+    int ZSTD_defaultCLevel() nogil
 
     size_t ZSTD_compressBound(size_t srcSize) nogil
 
@@ -51,11 +68,11 @@ MICRO_VERSION_NUMBER = (
     (MINOR_VERSION_NUMBER * 100)
 )
 __version__ = '%s.%s.%s' % (MAJOR_VERSION_NUMBER, MINOR_VERSION_NUMBER, MICRO_VERSION_NUMBER)
-DEFAULT_CLEVEL = 1
+DEFAULT_CLEVEL = 0
 MAX_CLEVEL = ZSTD_maxCLevel()
 
 
-def compress(source, int level=DEFAULT_CLEVEL):
+def compress(source, int level=DEFAULT_CLEVEL, bint checksum=False):
     """Compress data.
 
     Parameters
@@ -64,7 +81,9 @@ def compress(source, int level=DEFAULT_CLEVEL):
         Data to be compressed. Can be any object supporting the buffer
         protocol.
     level : int
-        Compression level (1-22).
+        Compression level (-131072 to 22).
+    checksum : bool
+        Flag to enable checksums. The default is False.
 
     Returns
     -------
@@ -80,8 +99,6 @@ def compress(source, int level=DEFAULT_CLEVEL):
         bytes dest
 
     # check level
-    if level <= 0:
-        level = DEFAULT_CLEVEL
     if level > MAX_CLEVEL:
         level = MAX_CLEVEL
 
@@ -90,6 +107,19 @@ def compress(source, int level=DEFAULT_CLEVEL):
     source_ptr = source_buffer.ptr
     source_size = source_buffer.nbytes
 
+    cctx = ZSTD_createCCtx()
+    param_set_result = ZSTD_CCtx_setParameter(cctx, ZSTD_c_compressionLevel, level)
+
+    if ZSTD_isError(param_set_result):
+        error = ZSTD_getErrorName(param_set_result)
+        raise RuntimeError('Could not set zstd compression level: %s' % error)
+
+    param_set_result = ZSTD_CCtx_setParameter(cctx, ZSTD_c_checksumFlag, 1 if checksum else 0)
+
+    if ZSTD_isError(param_set_result):
+        error = ZSTD_getErrorName(param_set_result)
+        raise RuntimeError('Could not set zstd checksum flag: %s' % error)
+
     try:
 
         # setup destination
@@ -99,10 +129,11 @@ def compress(source, int level=DEFAULT_CLEVEL):
 
         # perform compression
         with nogil:
-            compressed_size = ZSTD_compress(dest_ptr, dest_size, source_ptr, source_size, level)
+            compressed_size = ZSTD_compress2(cctx, dest_ptr, dest_size, source_ptr, source_size)
 
     finally:
-
+        if cctx:
+            ZSTD_freeCCtx(cctx)
         # release buffers
         source_buffer.release()
 
@@ -148,8 +179,8 @@ def decompress(source, dest=None):
     try:
 
         # determine uncompressed size
-        dest_size = ZSTD_getDecompressedSize(source_ptr, source_size)
-        if dest_size == 0:
+        dest_size = ZSTD_getFrameContentSize(source_ptr, source_size)
+        if dest_size == 0 or dest_size == ZSTD_CONTENTSIZE_UNKNOWN or dest_size == ZSTD_CONTENTSIZE_ERROR:
             raise RuntimeError('Zstd decompression error: invalid input data')
 
         # setup destination buffer
@@ -193,7 +224,9 @@ class Zstd(Codec):
     Parameters
     ----------
     level : int
-        Compression level (1-22).
+        Compression level (-131072 to 22).
+    checksum : bool
+        Flag to enable checksums. The default is False.
 
     See Also
     --------
@@ -207,12 +240,13 @@ class Zstd(Codec):
     # practical limit on the size of buffers that Zstd can process and so we don't
     # enforce a max_buffer_size option here.
 
-    def __init__(self, level=DEFAULT_CLEVEL):
+    def __init__(self, level=DEFAULT_CLEVEL, checksum=False):
         self.level = level
+        self.checksum = checksum
 
     def encode(self, buf):
         buf = ensure_contiguous_ndarray(buf)
-        return compress(buf, self.level)
+        return compress(buf, self.level, self.checksum)
 
     def decode(self, buf, out=None):
         buf = ensure_contiguous_ndarray(buf)
@@ -223,3 +257,21 @@ class Zstd(Codec):
             (type(self).__name__,
              self.level)
         return r
+
+    @classmethod
+    @property
+    def default_level(cls):
+        """Returns the default compression level of the underlying zstd library."""
+        return ZSTD_defaultCLevel()
+
+    @classmethod
+    @property
+    def min_level(cls):
+        """Returns the minimum compression level of the underlying zstd library."""
+        return ZSTD_minCLevel()
+
+    @classmethod
+    @property
+    def max_level(cls):
+        """Returns the maximum compression level of the underlying zstd library."""
+        return ZSTD_maxCLevel()