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chore: stale AnnData.concatenate references#4201

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ilan-gold merged 2 commits into
scverse:mainfrom
rwbaber:doc/fix-stale-concatenate-links
Jul 8, 2026
Merged

chore: stale AnnData.concatenate references#4201
ilan-gold merged 2 commits into
scverse:mainfrom
rwbaber:doc/fix-stale-concatenate-links

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@rwbaber

@rwbaber rwbaber commented Jul 8, 2026

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This PR fixes stale references to AnnData.concatenate, which was removed from anndata (scverse/anndata#2370) and is no longer available in the hosted intersphinx inventory. These stale references were causing the Read the Docs build to fail.

Changes:

  • Replace broken Sphinx AnnData.concatenate method links with plain literal text.
  • Update the Harmony time-series example and test to use anndata.concat.
  • Preserve the previous unique-index behavior with index_unique="-".
  • Closes #
  • Tests included or not required because:
  • Release notes not necessary because: this is just a fix for stale historical references caused by an upstream anndata API removal.

@codecov

codecov Bot commented Jul 8, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 79.87%. Comparing base (af6de2e) to head (860ac8f).
✅ All tests successful. No failed tests found.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #4201      +/-   ##
==========================================
- Coverage   79.87%   79.87%   -0.01%     
==========================================
  Files         121      121              
  Lines       12932    12932              
==========================================
- Hits        10330    10329       -1     
- Misses       2602     2603       +1     
Flag Coverage Δ
hatch-test.low-vers 78.97% <ø> (-0.04%) ⬇️
hatch-test.pre 79.82% <ø> (-0.01%) ⬇️

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

Files with missing lines Coverage Δ
src/scanpy/external/pp/_mnn_correct.py 22.22% <ø> (ø)
src/scanpy/external/tl/_harmony_timeseries.py 28.57% <ø> (ø)

... and 1 file with indirect coverage changes

@ilan-gold ilan-gold changed the title Fix stale AnnData.concatenate references chore: stale AnnData.concatenate references Jul 8, 2026
@ilan-gold ilan-gold added this to the 1.12.3 milestone Jul 8, 2026
@ilan-gold ilan-gold enabled auto-merge (squash) July 8, 2026 14:04
@ilan-gold ilan-gold merged commit a7868fe into scverse:main Jul 8, 2026
16 of 18 checks passed
flying-sheep pushed a commit that referenced this pull request Jul 8, 2026
…references) (#4203)

Co-authored-by: rwbaber <97636743+rwbaber@users.noreply.github.com>
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2 participants