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Make all codecs pickleable#745

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d-v-b merged 23 commits intozarr-developers:mainfrom
TomNicholas:pickleable_all_codecs
May 14, 2025
Merged

Make all codecs pickleable#745
d-v-b merged 23 commits intozarr-developers:mainfrom
TomNicholas:pickleable_all_codecs

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@TomNicholas TomNicholas commented Apr 24, 2025 •
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Attempt to fix #744, using the __init_subclass__ approach suggested by @d-v-b.

I think this approach seems promising, but currently tests fail, and I don't know why. I get errors like

    def get_codec(config):
        """Obtain a codec for the given configuration.
    
        Parameters
        ----------
        config : dict-like
            Configuration object.
    
        Returns
        -------
        codec : Codec
    
        Examples
        --------
    
        >>> import numcodecs as codecs
        >>> codec = codecs.get_codec(dict(id='zlib', level=1))
        >>> codec
        Zlib(level=1)
    
        """
        config = dict(config)
        codec_id = config.pop('id', None)
        cls = codec_registry.get(codec_id)
        if cls is None and codec_id in entries:
            logger.debug("Auto loading codec '%s' from entrypoint", codec_id)
            cls = entries[codec_id].load()
            register_codec(cls, codec_id=codec_id)
        if cls:
            return cls.from_config(config)
>       raise UnknownCodecError(f"{codec_id!r}")
E       numcodecs.errors.UnknownCodecError: codec not available: ''Blosc''

TODO:

  • Unit tests and/or doctests in docstrings
  • Tests pass locally
  • Changes documented in docs/release.rst
  • GitHub Actions CI passes
  • Test coverage to 100% (Codecov passes)

TomNicholas
TomNicholas commented Apr 24, 2025
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numcodecs/tests/test_zarr3.py Outdated
Comment on lines +305 to +307
print(codec)
print(codec.codec_name)
print(codec.__doc__)
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for numcodecs.zarr3.Blosc this returns

Blosc(codec_name='numcodecs.Blosc', codec_config={})
numcodecs.Blosc

            See :class:`numcodecs.blosc.Blosc` for more details and parameters.

which all seems correct to me?

TomNicholas
TomNicholas commented Apr 24, 2025
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numcodecs/zarr3.py Outdated
@@ -184,30 +195,18 @@ async def _encode_single(self, chunk_ndbuffer: NDBuffer, chunk_spec: ArraySpec)


def _add_docstring(cls: type[T], ref_class_name: str) -> type[T]:
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All this can be deleted once the changes in this PR are applied to all the other codecs

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codecov bot commented Apr 24, 2025 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.96%. Comparing base (65e16c3) to head (1e66929).
⚠️ Report is 6 commits behind head on main.

Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #745      +/-   ##
==========================================
- Coverage   99.96%   99.96%   -0.01%     
==========================================
  Files          63       63              
  Lines        2736     2708      -28     
==========================================
- Hits         2735     2707      -28     
  Misses          1        1
Files with missing lines Coverage Δ
numcodecs/tests/test_zarr3.py 100.00% <100.00%> (ø)
numcodecs/zarr3.py 99.39% <100.00%> (-0.11%) ⬇️
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

chuckwondo
chuckwondo reviewed Apr 24, 2025
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@TomNicholas, I believe my suggested changes should get the tests to pass.

@TomNicholas @chuckwondo
Chuck's suggestions
5ef6a47 
Co-authored-by: Chuck Daniels <cjdaniels4@gmail.com>
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TomNicholas commented Apr 24, 2025

You legend @chuckwondo 🙇‍♂️

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TomNicholas commented Apr 24, 2025

pre-commit.ci autofix

TomNicholas
TomNicholas commented Apr 24, 2025
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numcodecs/zarr3.py


# bytes-to-bytes checksum codecs
CRC32 = _add_docstring(_make_checksum_codec("crc32", "CRC32"), "numcodecs.checksum32.CRC32")
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These codecs break the pattern of the ones above because they have "numcodecs.checksum32.<name>" instead of "numcodecs.<lowercasename>.<name>". I ignored that, but it doesn't seem to matter whatsoever?? Suspicious.

@TomNicholas TomNicholas marked this pull request as ready for review April 24, 2025 23:35
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TomNicholas commented Apr 24, 2025

@d-v-b @jakirkham this is ready for review. It would be nice to release it quickly if possible 😁

TomNicholas
TomNicholas commented Apr 24, 2025
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numcodecs/tests/test_zarr3.py
Comment on lines +9 to +10
import numcodecs.bitround

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@TomNicholas TomNicholas Apr 24, 2025 •
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I don't remember adding this - maybe the linter did??

@d-v-b d-v-b mentioned this pull request May 6, 2025
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@d-v-b d-v-b enabled auto-merge (squash) May 14, 2025 09:14
@d-v-b d-v-b merged commit 936f4d2 into zarr-developers:main May 14, 2025
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@d-v-b d-v-b mentioned this pull request Sep 5, 2025
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Can't pickle numcodecs codecs

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@TomNicholas @d-v-b @chuckwondo