numcodecs 0.16.0__tar.gz → 0.16.1__tar.gz

{numcodecs-0.16.0 → numcodecs-0.16.1}/.github/workflows/wheel.yaml

@@ -26,7 +26,7 @@ jobs:
         with:
           submodules: true
 
-      - uses: pypa/cibuildwheel@v2.23.0
+      - uses: pypa/cibuildwheel@v2.23.2
 
       - uses: actions/upload-artifact@v4
         with:

{numcodecs-0.16.0 → numcodecs-0.16.1}/.pre-commit-config.yaml

@@ -14,14 +14,14 @@ repos:
     - id: debug-statements
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.9
+    rev: v0.11.8
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
     - id: ruff-format
 
   - repo: https://github.com/scientific-python/cookie
-    rev: 2025.01.22
+    rev: 2025.05.02
     hooks:
     - id: sp-repo-review
 

{numcodecs-0.16.0/numcodecs.egg-info → numcodecs-0.16.1}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: numcodecs
-Version: 0.16.0
+Version: 0.16.1
 Summary: A Python package providing buffer compression and transformation codecs for use in data storage and communication applications.
 Maintainer-email: Alistair Miles <alimanfoo@googlemail.com>
-License: MIT
+License-Expression: MIT
 Project-URL: Bug Tracker, https://github.com/zarr-developers/numcodecs/issues
 Project-URL: Changelog, https://numcodecs.readthedocs.io/en/stable/release.html
 Project-URL: Documentation, https://numcodecs.readthedocs.io/
@@ -12,7 +12,6 @@ Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Information Technology
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Operating System :: Unix
@@ -21,6 +20,14 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Requires-Python: >=3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
+License-File: c-blosc/LICENSE.txt
+License-File: c-blosc/LICENSES/BITSHUFFLE.txt
+License-File: c-blosc/LICENSES/FASTLZ.txt
+License-File: c-blosc/LICENSES/LZ4.txt
+License-File: c-blosc/LICENSES/SNAPPY.txt
+License-File: c-blosc/LICENSES/STDINT.txt
+License-File: c-blosc/LICENSES/ZLIB-NG.txt
+License-File: c-blosc/LICENSES/ZLIB.txt
 Requires-Dist: numpy>=1.24
 Requires-Dist: typing_extensions
 Provides-Extra: docs

{numcodecs-0.16.0 → numcodecs-0.16.1}/docs/contributing.rst

@@ -203,12 +203,11 @@ contributors.
 Merging pull requests
 ~~~~~~~~~~~~~~~~~~~~~
 
-Pull requests submitted by an external contributor should be reviewed and approved by at least
-one core developers before being merged. Ideally, pull requests submitted by a core developer
-should be reviewed and approved by at least one other core developers before being merged.
+Pull requests should be reviewed and approved by at least one core developer
+(other than the pull request author) before being merged.
 
-Pull requests should not be merged until all CI checks have passed (Travis, AppVeyor,
-Codecov) against code that has had the latest main merged in.
+Pull requests should not be merged until all CI checks have passed against code
+that has had the latest main merged in.
 
 Compatibility and versioning policies
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -278,6 +277,10 @@ hard-and-fast rules, e.g., it is fine to make a minor release to make a single n
 feature available; equally, it is fine to make a minor release that includes a number of
 changes.
 
+When making a minor release, open an issue stating your intention so other developers
+know that a release is planned. At least a week's notice should be given for other
+developers to be aware of and possibly add to the contents of the release.
+
 Major releases obviously need to be given careful consideration, and should be done as
 infrequently as possible, as they will break existing code and/or affect data
 compatibility in some way.

{numcodecs-0.16.0 → numcodecs-0.16.1}/docs/release.rst

@@ -14,6 +14,39 @@ Release notes
 
 .. _unreleased:
 
+Unreleased
+----------
+
+Enhancements
+~~~~~~~~~~~~
+
+Improvements
+~~~~~~~~~~~~
+
+* In ``vlen``, define and use ``const`` ``HEADER_LENGTH``.
+  By :user:`John Kirkham <jakirkham>`, :issue:`723`
+* All codecs are now pickleable.
+  By :user:`Tom Nicholas <TomNicholas>`, :issue:`744`
+
+Fixes
+~~~~~
+
+* Fix ``const`` discard warnings in ``fletcher32``.
+  By :user:`John Kirkham <jakirkham>`, :issue:`728`
+
+* Update ``license*`` metadata and include third-party licenses.
+  By :user:`John Kirkham <jakirkham>`, :issue:`729`
+
+* Add ``#ifndef`` guard around ``PyBytes_RESIZE``.
+  By :user:`John Kirkham <jakirkham>`, :issue:`732`
+
+* Remove ``typesize`` from ``Blosc.get_config`` output
+  By :user:`Ilan Gold <ilan-gold>`
+
+Maintenance
+~~~~~~~~~~~
+
+
 0.16.0
 ------
 

{numcodecs-0.16.0 → numcodecs-0.16.1}/numcodecs/blosc.pyx

@@ -489,11 +489,11 @@ class Blosc(Codec):
         self.clevel = clevel
         self.shuffle = shuffle
         self.blocksize = blocksize
-        self.typesize = typesize
+        self._typesize = typesize
 
     def encode(self, buf):
         buf = ensure_contiguous_ndarray(buf, self.max_buffer_size)
-        return compress(buf, self._cname_bytes, self.clevel, self.shuffle, self.blocksize, self.typesize)
+        return compress(buf, self._cname_bytes, self.clevel, self.shuffle, self.blocksize, self._typesize)
 
     def decode(self, buf, out=None):
         buf = ensure_contiguous_ndarray(buf, self.max_buffer_size)

{numcodecs-0.16.0 → numcodecs-0.16.1}/numcodecs/compat_ext.pxd

@@ -3,7 +3,9 @@
 
 cdef extern from *:
     """
+    #ifndef PyBytes_RESIZE
     #define PyBytes_RESIZE(b, n) _PyBytes_Resize(&b, n)
+    #endif
     """
     int PyBytes_RESIZE(object b, Py_ssize_t n) except -1
 

{numcodecs-0.16.0 → numcodecs-0.16.1}/numcodecs/fletcher32.pyx

@@ -76,7 +76,7 @@ class Fletcher32(Codec):
         """Return buffer plus a footer with the fletcher checksum (4-bytes)"""
         buf = ensure_contiguous_ndarray(buf).ravel().view('uint8')
         cdef const uint8_t[::1] b_mv = buf
-        cdef uint8_t* b_ptr = &b_mv[0]
+        cdef const uint8_t* b_ptr = &b_mv[0]
         cdef Py_ssize_t b_len = len(b_mv)
 
         cdef Py_ssize_t out_len = b_len + FOOTER_LENGTH
@@ -92,7 +92,7 @@ class Fletcher32(Codec):
         """Check fletcher checksum, and return buffer without it"""
         b = ensure_contiguous_ndarray(buf).view('uint8')
         cdef const uint8_t[::1] b_mv = b
-        cdef uint8_t* b_ptr = &b_mv[0]
+        cdef const uint8_t* b_ptr = &b_mv[0]
         cdef Py_ssize_t b_len = len(b_mv)
 
         val = _fletcher32(b_mv[:-FOOTER_LENGTH])

{numcodecs-0.16.0 → numcodecs-0.16.1}/numcodecs/tests/common.py

@@ -202,7 +202,7 @@ def check_backwards_compatibility(codec_id, arrays, codecs, precision=None, pref
 
         for j, codec in enumerate(codecs):
             if codec is None:
-                pytest.skip("codec has been removed")
+                continue
 
             # setup a directory to hold encoded data
             codec_dir = os.path.join(fixture_dir, f'codec.{j:02d}')

{numcodecs-0.16.0 → numcodecs-0.16.1}/numcodecs/tests/test_blosc.py

@@ -245,20 +245,20 @@ def test_err_encode_object_buffer():
     check_err_encode_object_buffer(Blosc())
 
 
-def test_decompression_error_handling():
-    for codec in codecs:
-        _skip_null(codec)
-        with pytest.raises(RuntimeError):
-            codec.decode(bytearray())
-        with pytest.raises(RuntimeError):
-            codec.decode(bytearray(0))
+@pytest.mark.parametrize('codec', codecs)
+def test_decompression_error_handling(codec):
+    _skip_null(codec)
+    with pytest.raises(RuntimeError):
+        codec.decode(bytearray())
+    with pytest.raises(RuntimeError):
+        codec.decode(bytearray(0))
 
 
-def test_max_buffer_size():
-    for codec in codecs:
-        _skip_null(codec)
-        assert codec.max_buffer_size == 2**31 - 1
-        check_max_buffer_size(codec)
+@pytest.mark.parametrize('codec', codecs)
+def test_max_buffer_size(codec):
+    _skip_null(codec)
+    assert codec.max_buffer_size == 2**31 - 1
+    check_max_buffer_size(codec)
 
 
 def test_typesize_explicit():
@@ -278,7 +278,13 @@ def test_typesize_less_than_1():
         Blosc(shuffle=Blosc.SHUFFLE, typesize=0)
     compressor = Blosc(shuffle=Blosc.SHUFFLE)
     # not really something that should be done in practice, but good for testing.
-    compressor.typesize = 0
+    compressor._typesize = 0
     arr = np.arange(100)
     with pytest.raises(ValueError, match=r"Cannot use typesize"):
         compressor.encode(arr.tobytes())
+
+
+def test_config_no_typesize():
+    codec = Blosc(shuffle=Blosc.SHUFFLE, typesize=5)
+    config = codec.get_config()
+    assert "typesize" not in config

{numcodecs-0.16.0 → numcodecs-0.16.1}/numcodecs/tests/test_vlen_bytes.py

@@ -1,4 +1,3 @@
-import sys
 import unittest
 
 import numpy as np
@@ -85,9 +84,6 @@ def test_decode_errors():
         codec.decode(enc, out=np.zeros(10, dtype='i4'))
 
 
-# TODO: fix this test on GitHub actions somehow...
-# See https://github.com/zarr-developers/numcodecs/issues/683
-@pytest.mark.skipif(sys.platform == "darwin", reason="Test is failing on macOS on GitHub actions.")
 def test_encode_none():
     a = np.array([b'foo', None, b'bar'], dtype=object)
     codec = VLenBytes()

{numcodecs-0.16.0 → numcodecs-0.16.1}/numcodecs/tests/test_zarr3.py

@@ -1,10 +1,13 @@
 from __future__ import annotations
 
+import pickle
 from typing import TYPE_CHECKING
 
 import numpy as np
 import pytest
 
+import numcodecs.bitround
+
 if TYPE_CHECKING:  # pragma: no cover
     import zarr
 else:
@@ -260,7 +263,7 @@ def test_delta_astype(store: StorePath):
             dtype=data.dtype,
             fill_value=0,
             filters=[
-                numcodecs.zarr3.Delta(dtype="i8", astype="i2"),  # type: ignore[arg-type]
+                numcodecs.zarr3.Delta(dtype="i8", astype="i2"),
             ],
         )
 
@@ -277,3 +280,39 @@ def test_repr():
 def test_to_dict():
     codec = numcodecs.zarr3.LZ4(level=5)
     assert codec.to_dict() == {"name": "numcodecs.lz4", "configuration": {"level": 5}}
+
+
+@pytest.mark.parametrize(
+    "codec_cls",
+    [
+        numcodecs.zarr3.Blosc,
+        numcodecs.zarr3.LZ4,
+        numcodecs.zarr3.Zstd,
+        numcodecs.zarr3.Zlib,
+        numcodecs.zarr3.GZip,
+        numcodecs.zarr3.BZ2,
+        numcodecs.zarr3.LZMA,
+        numcodecs.zarr3.Shuffle,
+        numcodecs.zarr3.BitRound,
+        numcodecs.zarr3.Delta,
+        numcodecs.zarr3.FixedScaleOffset,
+        numcodecs.zarr3.Quantize,
+        numcodecs.zarr3.PackBits,
+        numcodecs.zarr3.AsType,
+        numcodecs.zarr3.CRC32,
+        numcodecs.zarr3.CRC32C,
+        numcodecs.zarr3.Adler32,
+        numcodecs.zarr3.Fletcher32,
+        numcodecs.zarr3.JenkinsLookup3,
+        numcodecs.zarr3.PCodec,
+        numcodecs.zarr3.ZFPY,
+    ],
+)
+def test_codecs_pickleable(codec_cls):
+    codec = codec_cls()
+
+    expected = codec
+
+    p = pickle.dumps(codec)
+    actual = pickle.loads(p)
+    assert actual == expected

{numcodecs-0.16.0 → numcodecs-0.16.1}/numcodecs/version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.16.0'
-__version_tuple__ = version_tuple = (0, 16, 0)
+__version__ = version = '0.16.1'
+__version_tuple__ = version_tuple = (0, 16, 1)