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Unit test failures under Zarr Python 3.0.2 #1290

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tomwhite opened this issue Feb 10, 2025 · 0 comments
Open

Unit test failures under Zarr Python 3.0.2 #1290

tomwhite opened this issue Feb 10, 2025 · 0 comments
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IO Issues related to reading and writing common third-party file formats upstream Used when our build breaks due to upstream changes

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@tomwhite
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From https://github.com/sgkit-dev/sgkit/actions/runs/13239074156/job/36950197009:

sgkit/tests/test_regenie.py:326: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
sgkit/tests/test_regenie.py:265: in check_simulation_result
    with ZipStore(str(dataset_dir / "genotypes.zarr.zip"), mode="r") as store:
/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/abc/store.py:97: in __exit__
    self.close()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = ZipStore('zip:///tmp/pytest-of-runner/pytest-0/test_regenie__glow_comparison_0/test_regenie/dataset/sim_sm_01/genotypes.zarr.zip')

    def close(self) -> None:
        # docstring inherited
        super().close()
>       with self._lock:
E       AttributeError: 'ZipStore' object has no attribute '_lock'

/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/storage/_zip.py:124: AttributeError
=========================== short test summary info ============================
FAILED sgkit/tests/test_association.py::test_regenie_loco_regression[True-numpy] - AttributeError: 'ZipStore' object has no attribute '_lock'
FAILED sgkit/tests/test_association.py::test_regenie_loco_regression[False-numpy] - AttributeError: 'ZipStore' object has no attribute '_lock'
FAILED sgkit/tests/test_regenie.py::test_regenie__glow_comparison[numpy] - AttributeError: 'ZipStore' object has no attribute '_lock'

I manually verified that this is fixed by zarr-developers/zarr-python#2807, so it will be fixed in the next release of Zarr Python.

@tomwhite tomwhite added IO Issues related to reading and writing common third-party file formats upstream Used when our build breaks due to upstream changes labels Feb 10, 2025
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