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chore: disable zarr v2 writing (at least as far as we can control it) - #2628

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ilan-gold wants to merge 12 commits into
mainfrom
ig/no_zarr_v2_writes
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chore: disable zarr v2 writing (at least as far as we can control it)#2628
ilan-gold wants to merge 12 commits into
mainfrom
ig/no_zarr_v2_writes

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@ilan-gold

@ilan-gold ilan-gold commented Sep 1, 2026

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2 reasons to do this:

  1. Fewer tests mean faster completion
  2. No one should be writing v2 data anymore given that all reasonable data is in-spec writable and spatial data has upgraded (and anndataR can now read v3 data as well: https://anndatar.scverse.org/reference/write_zarr.html?q=v3#zarr-format)

I'm setting this as a 0.13.4 to remind myself to backport the functionality by deprecating instead of removing the setting. I will then add a test for that as well as a sensible release note for the 0.13.4 release.

  • Closes #
  • Tests added
  • Release note not necessary because:

@ilan-gold ilan-gold added this to the 0.13.4 milestone Sep 1, 2026
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codecov Bot commented Sep 1, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.80%. Comparing base (d75540e) to head (f30a494).
✅ All tests successful. No failed tests found.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #2628      +/-   ##
==========================================
- Coverage   87.66%   85.80%   -1.86%     
==========================================
  Files          49       49              
  Lines        8121     8114       -7     
==========================================
- Hits         7119     6962     -157     
- Misses       1002     1152     +150     
Files with missing lines Coverage Δ
src/anndata/_io/zarr.py 86.25% <ø> (-0.31%) ⬇️
src/anndata/_settings.py 100.00% <100.00%> (ø)

... and 8 files with indirect coverage changes

@ilan-gold
ilan-gold marked this pull request as ready for review September 3, 2026 21:00
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