scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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lets umap run in parallel #3295

Open Intron7 opened 1 month ago

Intron7 commented 1 month ago

Closes #3211

Lets you run all parts of UMAP in Parallel. Default will still be False for reproducibility. Benchmarks (95k Cells AMD5950X) parallel = False 33 s parallel = True 18 s

I copied the doc string from UMAP to explain the impact of parallel execution.

Intron7 commented 1 month ago

I didn't add release note yet because I'm not sure if this should already go into 1.10.4

codecov[bot] commented 1 month ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 77.04%. Comparing base (bbcd4b1) to head (4eba4a8). Report is 2 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #3295 +/- ## ========================================== + Coverage 76.95% 77.04% +0.09% ========================================== Files 109 110 +1 Lines 12465 12494 +29 ========================================== + Hits 9592 9626 +34 + Misses 2873 2868 -5 ``` | [Files with missing lines](https://app.codecov.io/gh/scverse/scanpy/pull/3295?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse) | Coverage Δ | | |---|---|---| | [src/scanpy/tools/\_umap.py](https://app.codecov.io/gh/scverse/scanpy/pull/3295?src=pr&el=tree&filepath=src%2Fscanpy%2Ftools%2F_umap.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS90b29scy9fdW1hcC5weQ==) | `74.19% <100.00%> (+2.52%)` | :arrow_up: | ... and [4 files with indirect coverage changes](https://app.codecov.io/gh/scverse/scanpy/pull/3295/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse)