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chore: add in accessors to silence deprecation warnings#3974

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flying-sheep merged 16 commits into
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ig/deprecate_obs_vector
Feb 16, 2026
Merged

chore: add in accessors to silence deprecation warnings#3974
flying-sheep merged 16 commits into
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ig/deprecate_obs_vector

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@ilan-gold ilan-gold commented Feb 13, 2026

  • Release notes not necessary because: deprecation warning removal

@ilan-gold ilan-gold added this to the 1.12.1 milestone Feb 13, 2026
@ilan-gold ilan-gold force-pushed the ig/deprecate_obs_vector branch from d234850 to 28c3e44 Compare February 13, 2026 10:54
@ilan-gold ilan-gold marked this pull request as ready for review February 13, 2026 10:55
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codecov Bot commented Feb 13, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.28%. Comparing base (182d863) to head (0096ee3).
⚠️ Report is 63 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3974      +/-   ##
==========================================
+ Coverage   78.26%   78.28%   +0.01%     
==========================================
  Files         117      117              
  Lines       12634    12634              
==========================================
+ Hits         9888     9890       +2     
+ Misses       2746     2744       -2     
Flag Coverage Δ
hatch-test.low-vers 77.56% <66.66%> (-0.04%) ⬇️
hatch-test.pre 77.22% <88.88%> (ø)

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

Files with missing lines Coverage Δ
src/scanpy/plotting/_anndata.py 85.63% <100.00%> (+0.05%) ⬆️
src/scanpy/plotting/_tools/scatterplots.py 83.52% <100.00%> (ø)
src/scanpy/plotting/_utils.py 78.90% <100.00%> (+0.47%) ⬆️


adata.obs["1_missing"] = adata.obs_vector("1")
# TODO: If we don't `copy`, something about this being an ArrayView means that all values get set to nan?
adata.obs["1_missing"] = adata[:, "1"].X.flatten().copy()
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We need to get rid of views

@ilan-gold ilan-gold changed the title chore: add in accessors for deprecation warnings chore: add in accessors to silence deprecation warnings Feb 13, 2026
Comment thread src/scanpy/plotting/_tools/scatterplots.py Outdated
@flying-sheep flying-sheep enabled auto-merge (squash) February 16, 2026 15:18
@flying-sheep flying-sheep enabled auto-merge (squash) February 16, 2026 15:55
@flying-sheep flying-sheep merged commit 274ede8 into main Feb 16, 2026
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@flying-sheep flying-sheep deleted the ig/deprecate_obs_vector branch February 16, 2026 16:06
meeseeksmachine pushed a commit to meeseeksmachine/scanpy that referenced this pull request Feb 16, 2026
flying-sheep pushed a commit that referenced this pull request Feb 16, 2026
…e deprecation warnings) (#3976)

Co-authored-by: Ilan Gold <ilanbassgold@gmail.com>
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Integration Testing CI Test Failure on python 3.13 with prerelease dependencies

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