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dscim tests seem to fail when using zarr >= v3.x package #369

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brews opened this issue Jan 14, 2025 · 0 comments
Open

dscim tests seem to fail when using zarr >= v3.x package #369

brews opened this issue Jan 14, 2025 · 0 comments
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bug Something isn't working help wanted Extra attention is needed

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brews commented Jan 14, 2025

dscim directly depends on the zarr package. When dependabot tried to bump the zarr-python package to the new v3.0.0 release, it failed CI checks.

See the PR here: #368

Cut-n-pasted from CI logs:

==================================== ERRORS ====================================
_________________ ERROR collecting tests/test_input_damages.py _________________
ImportError while importing test module '/home/runner/work/dscim/dscim/tests/test_input_damages.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_input_damages.py:10: in <module>
    from dscim.preprocessing.input_damages import (
/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/site-packages/dscim/preprocessing/input_damages.py:17: in <module>
    from zarr.errors import GroupNotFoundError
E   ImportError: cannot import name 'GroupNotFoundError' from 'zarr.errors' (/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/site-packages/zarr/errors.py)

From a quick look it looks like it's failing to even collect test_input_damages.py because it's importing something that's now missing from the zarr package in this input_damages.py

@brews brews added bug Something isn't working help wanted Extra attention is needed labels Jan 14, 2025
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