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Backport PR #2628 on branch 0.13.x (chore: disable zarr v2 writing (at least as far as we can control it)) - #2643

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Backport PR #2628 on branch 0.13.x (chore: disable zarr v2 writing (at least as far as we can control it))#2643
ilan-gold wants to merge 3 commits into
0.13.xfrom
auto-backport-of-pr-2628-on-0.13.x

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@ilan-gold

@ilan-gold ilan-gold commented Sep 8, 2026

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This PR:

  1. leaves the setting in place and deprecates it
  2. Tests that setting and then using it triggers a warning with v2
  3. Leaves v3 untouched

Hopefully I got that right!

See:
https://github.com/scverse/anndata/pull/2643/changes#diff-e4676cccdf29fdbe5cfd0a760aaf30a1408f2efd19aa0889871bf505f759663b
and
https://github.com/scverse/anndata/pull/2643/changes#diff-fc69accdad779387bbaf2b952adcff99c96d09fd6416011b319b6887d5a5498e

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

@codecov

codecov Bot commented Sep 8, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.00%. Comparing base (d38f76a) to head (5639ef4).
✅ All tests successful. No failed tests found.

Additional details and impacted files
@@            Coverage Diff             @@
##           0.13.x    #2643      +/-   ##
==========================================
- Coverage   88.01%   86.00%   -2.02%     
==========================================
  Files          49       49              
  Lines        7879     7882       +3     
==========================================
- Hits         6935     6779     -156     
- Misses        944     1103     +159     
Files with missing lines Coverage Δ
src/anndata/_io/zarr.py 87.31% <100.00%> (+0.39%) ⬆️
src/anndata/_settings.py 100.00% <100.00%> (ø)
src/anndata/tests/helpers.py 83.24% <100.00%> (-9.08%) ⬇️

... and 8 files with indirect coverage changes

@flying-sheep flying-sheep left a comment

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Looks good to me. One small nitpick.

Comment thread src/anndata/_settings.py Outdated
@ilan-gold
ilan-gold enabled auto-merge (squash) September 8, 2026 16:46
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