Handle tables via pip as pandas extra instead of separate conda install (and update installation instructions)#3214
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deruyter92 wants to merge 4 commits intomainfrom
Open
Handle tables via pip as pandas extra instead of separate conda install (and update installation instructions)#3214deruyter92 wants to merge 4 commits intomainfrom
deruyter92 wants to merge 4 commits intomainfrom
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deruyter92
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C-Achard
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Feb 26, 2026
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Let's try and get this merged & released ASAP; let me know if anything needs to be updated/released on the napari-DLC side as well and I will work on that @deruyter92
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Is the failing CI a drift due to the requirements.txt file ? This may need adjustment in #3184 as well |
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@C-Achard the failing CircleCI is a result of the caching setup in the workflow: by default it loads the cached environment, and compares it against the new requirements, failing if there is a mismatch. I verified that removing the caching step from the CircleCI resolves the problem. |
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Motivation:
The separate conda installation of pytables, and it's potential mismatch with the pandas version has been causing some problems in the past (e.g. see recent issues and PRs #3111, #3162, #3163, #3171). Installing pytables from PyPI as dependency of pandas via the [hdf5] extra, would resolve these issues.
PR #3184 already addresses this issue by updating the pyproject.toml to the newest PEP standards, but untill that PR is merged, this could PR provide a bridging alternative. Also, the installation instructions with respect to the tables requirement need to be adjusted anyway, so this is addressed in the current PR.
Changes:
NOTE: CircleCI is expected to fail on this PR, since the current workflow is set up to explicitly fail when the requirements.txt change with respect to the cached environment. I verified that the tests pass when I temporarily remove this caching restriction (succeeds👍).
I am keeping the CI workflow in the original state now. @MMathisLab Let me know in case you prefer me to remove the caching restriction for the future (see example in commit bc3ff85).