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Backport PR #4082 on branch 1.12.x (fix: limit Numba threads in Wilcoxon path of rank_genes_groups)#4088

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flying-sheep merged 1 commit into
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auto-backport-of-pr-4082-on-1.12.x
Apr 24, 2026
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Backport PR #4082 on branch 1.12.x (fix: limit Numba threads in Wilcoxon path of rank_genes_groups)#4088
flying-sheep merged 1 commit into
1.12.xfrom
auto-backport-of-pr-4082-on-1.12.x

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Backport PR #4082

@flying-sheep flying-sheep merged commit 8f30be6 into 1.12.x Apr 24, 2026
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@flying-sheep flying-sheep deleted the auto-backport-of-pr-4082-on-1.12.x branch April 24, 2026 14:25
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codecov Bot commented Apr 24, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.49%. Comparing base (cc62733) to head (e662e5f).
⚠️ Report is 11 commits behind head on 1.12.x.
✅ All tests successful. No failed tests found.

Additional details and impacted files
@@            Coverage Diff             @@
##           1.12.x    #4088      +/-   ##
==========================================
+ Coverage   78.45%   78.49%   +0.04%     
==========================================
  Files         118      120       +2     
  Lines       12608    12632      +24     
==========================================
+ Hits         9892     9916      +24     
  Misses       2716     2716              
Flag Coverage Δ
hatch-test.low-vers 77.79% <100.00%> (+0.04%) ⬆️
hatch-test.pre 78.38% <100.00%> (+0.04%) ⬆️

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

Files with missing lines Coverage Δ
src/scanpy/_utils/__init__.py 78.63% <100.00%> (+0.04%) ⬆️
src/scanpy/_utils/_numba.py 100.00% <100.00%> (ø)
src/scanpy/tools/_rank_genes_groups.py 92.77% <100.00%> (+0.02%) ⬆️

... and 8 files with indirect coverage changes

@zboldyga
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zboldyga commented Apr 25, 2026

hey @flying-sheep I was just doing some benchmarking of another change I'm suggesting to the library for wilcoxon DE and I noticed the default behavior of the library has changed (as compared with published v 1.12.0 -- it defaults to using a single thread for wilcoxon DE now when n_jobs is unspecified). I think it's this PR

I believe the prior default was to use all available threads, which seems to make more sense in the default case?

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3 participants