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fix: limit Numba threads in Wilcoxon path of rank_genes_groups#4082

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Apr 24, 2026
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fix: limit Numba threads in Wilcoxon path of rank_genes_groups#4082
flying-sheep merged 8 commits into
scverse:mainfrom
JhonatanFelix:main

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@JhonatanFelix JhonatanFelix commented Apr 23, 2026 •
edited by flying-sheep
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Summary

This PR limits Numba thread usage during the wilcoxon path of scanpy.tl.rank_genes_groups by temporarily applying scanpy.settings.n_jobs via numba.set_num_threads(.....) and restoring the previous value afterward.

Implementation

  • added a private _numba_thread_limit(....) context manager in scanpy.tools._rank_genes_groups
  • used numba.get_num_threads() / numba.set_num_threads(...)
  • clamped the requested value to the valid range
  • restored the previous thread count in a finally block
  • applied the limit only when method == "wilcoxon"

Required checks

Added some focused tests for the new numba thread-limiting behavior in rank_genes_groups:

  • temporary restoration of the previous numba thread count
  • restoration on exception
  • clamping to the configured numba maximum
  • applying the thread limit for method="wilcoxon" using scanpy.settings.n_jobs
  • not applying the thread limit for unrelated methods
  • Release notes not necessary because: It is a small internal behavior fix, it does not change the public API or user workflow.

@JhonatanFelix JhonatanFelix marked this pull request as ready for review April 23, 2026 10:09
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codecov Bot commented Apr 23, 2026 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.63%. Comparing base (44cfc6e) to head (6be0d40).
⚠️ Report is 1 commits behind head on main.
✅ All tests successful. No failed tests found.

Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #4082      +/-   ##
==========================================
+ Coverage   78.59%   78.63%   +0.03%     
==========================================
  Files         118      119       +1     
  Lines       12745    12762      +17     
==========================================
+ Hits        10017    10035      +18     
+ Misses       2728     2727       -1
Flag Coverage Δ
hatch-test.low-vers 77.93% <100.00%> (+0.03%) ⬆️
hatch-test.pre 78.51% <100.00%> (+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/_utils/__init__.py 75.11% <100.00%> (+0.05%) ⬆️
src/scanpy/_utils/_numba.py 100.00% <100.00%> (ø)
src/scanpy/tools/_rank_genes_groups.py 92.85% <100.00%> (+0.02%) ⬆️

... and 1 file with indirect coverage changes

@flying-sheep flying-sheep mentioned this pull request Apr 24, 2026
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@flying-sheep flying-sheep added this to the 1.12.2 milestone Apr 24, 2026
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flying-sheep commented Apr 24, 2026

Looks great! Please merge JhonatanFelix#1

@JhonatanFelix JhonatanFelix reopened this Apr 24, 2026
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JhonatanFelix commented Apr 24, 2026

Done! @flying-sheep

@flying-sheep flying-sheep merged commit 2b60935 into scverse:main Apr 24, 2026
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flying-sheep commented Apr 24, 2026

wonderful, thank you!

flying-sheep pushed a commit that referenced this pull request Apr 24, 2026
@JhonatanFelix @flying-sheep
Backport PR #4082: fix: limit Numba threads in Wilcoxon path of rank_…
e662e5f 
…genes_groups
@flying-sheep flying-sheep mentioned this pull request Apr 24, 2026
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@scverse scverse deleted a comment from lumberbot-app Bot Apr 24, 2026
flying-sheep added a commit that referenced this pull request Apr 24, 2026
@flying-sheep @JhonatanFelix
Backport PR #4082 on branch 1.12.x (fix: limit Numba threads in Wilco…
8f30be6 
…xon path of rank_genes_groups) (#4088)

Co-authored-by: Jhonatan Felix <108437587+JhonatanFelix@users.noreply.github.com>
flying-sheep added a commit that referenced this pull request Apr 26, 2026
@JhonatanFelix @flying-sheep
fix: limit Numba threads in Wilcoxon path of rank_genes_groups (#4082)
c1e67ce 
Co-authored-by: Philipp A. <flying-sheep@web.de>
@flying-sheep flying-sheep mentioned this pull request Apr 28, 2026
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Call numba.set_num_threads when n_jobs is specified (e.g. in scanpy.tl.rank_genes_group)

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