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perf: run umap in parallel when rng=None is passed#4036

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flying-sheep wants to merge 3 commits intomainfrom
pa/parallel-umap
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perf: run umap in parallel when rng=None is passed#4036
flying-sheep wants to merge 3 commits intomainfrom
pa/parallel-umap

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@flying-sheep flying-sheep commented Apr 7, 2026

milestone 1.13.0, since 1.12.x doesn’t have rng.

scanpy 2.0 will have rng=None by default and therefore the speedup.

@flying-sheep flying-sheep marked this pull request as ready for review April 7, 2026 12:39
@flying-sheep flying-sheep modified the milestones: 1.12.1, 1.13.0 Apr 7, 2026
@flying-sheep flying-sheep changed the title perf: run umap in parallel perf: run umap in parallel when rng=None is passed Apr 7, 2026
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codecov bot commented Apr 7, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.50%. Comparing base (9bc2c1e) to head (f51185e).
✅ All tests successful. No failed tests found.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #4036      +/-   ##
==========================================
- Coverage   78.51%   78.50%   -0.01%     
==========================================
  Files         117      117              
  Lines       12753    12750       -3     
==========================================
- Hits        10013    10010       -3     
  Misses       2740     2740              
Flag Coverage Δ
hatch-test.low-vers 77.80% <100.00%> (-0.01%) ⬇️
hatch-test.pre 77.46% <100.00%> (+12.62%) ⬆️

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

Files with missing lines Coverage Δ
src/scanpy/tools/_umap.py 70.96% <100.00%> (-1.34%) ⬇️

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scverse-benchmark bot commented Apr 7, 2026

Benchmark changes

Change Before [9bc2c1e] After [f51185e] Ratio Benchmark (Parameter)
- 1.04±0s 340±2ms 0.33 tools.ToolsSuite.time_umap

Comparison: https://github.com/scverse/scanpy/compare/9bc2c1ed1bd1cf6f6c06cec71cce99916d048163..f51185ef4c38bd72b9f6e6647c4d74515507dfb8
Last changed: Tue, 7 Apr 2026 13:55:40 +0000

More details: https://github.com/scverse/scanpy/pull/4036/checks?check_run_id=70245416359

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Umap parallel

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