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(fix): add convert_strings_to_categoricals to methods #1914

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flying-sheep merged 5 commits into
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pa/io
Mar 17, 2025
Merged

(fix): add convert_strings_to_categoricals to methods #1914
flying-sheep merged 5 commits into
mainfrom
pa/io

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@flying-sheep flying-sheep commented Mar 17, 2025

Also

  • fixes the Path types all over.
  • Exports anndata.io.write_{h5ad,zarr} in an understated manner

I added this to the 0.11.4 milestone as it mostly corrects an oversight in #1474, but if you want I can split this up instead.

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codecov Bot commented Mar 17, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 80.53%. Comparing base (45b796f) to head (591808e).
Report is 49 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1914      +/-   ##
==========================================
- Coverage   82.81%   80.53%   -2.28%     
==========================================
  Files          45       45              
  Lines        6774     6777       +3     
==========================================
- Hits         5610     5458     -152     
- Misses       1164     1319     +155     
Files with missing lines Coverage Δ
src/anndata/_core/anndata.py 82.51% <100.00%> (+0.04%) ⬆️
src/anndata/_core/file_backing.py 88.69% <100.00%> (ø)
src/anndata/_io/h5ad.py 92.68% <100.00%> (ø)
src/anndata/_io/read.py 81.48% <100.00%> (ø)
src/anndata/_io/specs/methods.py 84.27% <ø> (-1.47%) ⬇️
src/anndata/_io/write.py 77.77% <100.00%> (ø)
src/anndata/_io/zarr.py 82.02% <100.00%> (ø)
src/anndata/experimental/backed/_io.py 38.88% <100.00%> (+1.15%) ⬆️
src/anndata/experimental/merge.py 86.72% <100.00%> (ø)

... and 7 files with indirect coverage changes

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@flying-sheep flying-sheep added this to the 0.11.4 milestone Mar 17, 2025
@flying-sheep flying-sheep requested a review from ilan-gold March 17, 2025 10:24
@flying-sheep flying-sheep changed the title Pass through convert_strings_to_categoricals (fix): add convert_strings_to_categoricals to methods Mar 17, 2025
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fixes #1850 as well

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Definitely an oversight on the API's part, feel free to make a release

@flying-sheep flying-sheep linked an issue Mar 17, 2025 that may be closed by this pull request
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@flying-sheep flying-sheep enabled auto-merge (squash) March 17, 2025 12:15
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Clarify export status of anndata.io.write_* functions write_zarr fails if a column of floats is object type

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