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performance optimization of stats code for rank_genes_groups#4204

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performance optimization of stats code for rank_genes_groups#4204
zboldyga wants to merge 3 commits into
scverse:mainfrom
zboldyga:zb/rank-genes-groups-stats

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@zboldyga

@zboldyga zboldyga commented Jul 8, 2026

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  • Closes #
  • [x ] Tests included or not required because:

@ilan-gold replayed changes of #4118 onto main

@zboldyga

zboldyga commented Jul 8, 2026

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@ilan-gold regarding these points, perhaps I open separate PR(s):

  • addressing the scanpy 2.0 change in how cells with group NaN/unassigned are handled (uniform treatment across aggregate, rank_genes_groups, anywhere else relevant?, + docs update for this).

  • adding benchmark code for rank_genes_groups paths that are fast-enough to run quickly (e.g. < 1 min).

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codecov Bot commented Jul 8, 2026

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Codecov Report

❌ Patch coverage is 97.16981% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.93%. Comparing base (eea0015) to head (304a1b5).
✅ All tests successful. No failed tests found.

Files with missing lines Patch % Lines
src/scanpy/tools/_rank_genes_groups.py 97.16% 3 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #4204      +/-   ##
==========================================
+ Coverage   79.90%   79.93%   +0.03%     
==========================================
  Files         121      121              
  Lines       12949    12976      +27     
==========================================
+ Hits        10347    10373      +26     
- Misses       2602     2603       +1     
Flag Coverage Δ
hatch-test.low-vers 79.06% <97.16%> (+0.03%) ⬆️
hatch-test.pre 79.90% <97.16%> (+0.03%) ⬆️

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

Files with missing lines Coverage Δ
src/scanpy/tools/_rank_genes_groups.py 93.81% <97.16%> (-0.36%) ⬇️

... and 1 file with indirect coverage changes

@zboldyga zboldyga marked this pull request as ready for review July 9, 2026 01:23
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