Remove zarr.Array monkey-patches, use ndim-based detection - #333
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h-mayorquin wants to merge 19 commits into
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Remove zarr.Array monkey-patches, use ndim-based detection#333h-mayorquin wants to merge 19 commits into
h-mayorquin wants to merge 19 commits into
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…cies' into improve_ci_dependencies
Improve dependencies
…ta (#328) Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com> Co-authored-by: Heberto Mayorquin <h.mayorquin@gmail.com>
Resolve conflicts: - backend.py: keep FsspecStore (v3 API), drop ConsolidatedMetadataStore unwrap (v2 only) - tox.ini: adopt uv --resolution lowest-direct approach from dev, keep py311 - requirements-min.txt: delete (replaced by uv resolution) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Replace the __len__ and __getitem__ monkey-patches on zarr.Array with proper fixes in hdmf-zarr's own code: - Add _is_collection() using ndim for array-like objects, falling back to __len__ for plain containers (lists, tuples) - Add _get_length() using shape[0] for array-like objects, falling back to len() for plain containers - Handle 0-d ndarrays in get_type() via data.item() extraction - Replace hasattr(data, "__len__") checks with _is_collection() calls This avoids globally modifying zarr.Array behavior, which would leak as side effects to other libraries in the same process. Related: - zarr-python #3740 (__len__ removal) - zarr-python #3741 (scalar indexing returns 0-d ndarray) - hdmf #1414 (ndim-based collection detection) - hdmf #1415 (0-d ndarray handling) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Point hdmf dependency to remove_duck_typing_for_type branch which includes both PRs #1414 and #1415 needed to avoid monkey-patching. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…tion Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## zarr-v3-migration #333 +/- ##
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+ Coverage 83.73% 84.08% +0.34%
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Files 5 5
Lines 1371 1376 +5
Branches 274 276 +2
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+ Hits 1148 1157 +9
+ Misses 147 144 -3
+ Partials 76 75 -1 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Fixes minimum CI jobs that use uv --resolution lowest-direct, which failed because ../hdmf doesn't exist on the CI runner. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
alejoe91
reviewed
Jun 25, 2026
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| Array.__getitem__ = _zarr_array_getitem_scalar_fix |
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In #349, I had to monkey patch __iter__ too: https://github.com/alejoe91/hdmf-zarr/blob/nwb-zarr-v2-io/src/hdmf_zarr/backend.py#L45-L55
@h-mayorquin maybe we can make a similar fix here? I think overall this PR has a better approach!
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Summary
Testing the approach proposed in #325 (comment).
zarr.Arraymonkey-patches (__len__and__getitem__)hasattr(data, "__len__")checks withndim-based collection detection (_is_collection)get_type()viadata.item()extraction (_resolve_scalarpattern)All 397 tests pass locally.
Related:
zarr.Array.__len__removed in v3 rewrite zarr-developers/zarr-python#3740,Array.__getitem__returns 0-d ndarray for scalar indexing on dimensioned arrays zarr-developers/zarr-python#3741hasattr(data, "__len__")duck typing withndim-based collection detection hdmf#1414, Handle 0-d ndarrays in scalar isinstance checks hdmf#1415Test plan
pytest tests/unit/test_zarrio.py— 397 passed, 0 failed