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Handle numcodecs bug for encoding read-only string array #1421

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merged 3 commits into from
Mar 13, 2024

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@ivirshup ivirshup commented Mar 13, 2024

Workaround for:

If and when that is resolved we should probably change the code to look more like:

    # Workaround for https://github.com/zarr-developers/numcodecs/issues/514
    if Version(numcodecs.__version__) =< Version("0.12.1") and not elem.flags.writeable:
        warn(
            "Making a copy of string array as workaround for numcodecs bug, upgrade numcodecs to avoid this warning",
        )
        elem = elem.copy()
  • Closes #
  • Tests added
  • Release note added (or unnecessary)

@ivirshup ivirshup added this to the 0.10.7 milestone Mar 13, 2024
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codecov bot commented Mar 13, 2024

Codecov Report

Attention: Patch coverage is 50.00000% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 86.29%. Comparing base (9d0d272) to head (d97411b).

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1421      +/-   ##
==========================================
- Coverage   86.31%   86.29%   -0.02%     
==========================================
  Files          36       36              
  Lines        5610     5612       +2     
==========================================
+ Hits         4842     4843       +1     
- Misses        768      769       +1     
Flag Coverage Δ
gpu-tests 52.42% <0.00%> (-0.02%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Coverage Δ
anndata/_io/specs/methods.py 88.22% <50.00%> (-0.18%) ⬇️

@ivirshup ivirshup merged commit 20adb70 into scverse:main Mar 13, 2024
15 of 16 checks passed
meeseeksmachine pushed a commit to meeseeksmachine/anndata that referenced this pull request Mar 13, 2024
flying-sheep pushed a commit that referenced this pull request Mar 14, 2024
… read-only string array) (#1422)

Co-authored-by: Isaac Virshup <[email protected]>
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