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scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
1.93k stars 603 forks source link

Backport PR #3284 on branch 1.10.x (Speedup (~20x) of scanpy.pp.regress_out function using Linear Least Square method.) #3350

Closed meeseeksmachine closed 1 week ago

meeseeksmachine commented 1 week ago

Backport PR #3284: Speedup (~20x) of scanpy.pp.regress_out function using Linear Least Square method.

codecov[bot] commented 1 week ago

Codecov Report

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

Project coverage is 76.97%. Comparing base (8d692c5) to head (f4ff2fe). Report is 3 commits behind head on 1.10.x.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## 1.10.x #3350 +/- ## ========================================== + Coverage 76.94% 76.97% +0.03% ========================================== Files 109 109 Lines 12463 12484 +21 ========================================== + Hits 9590 9610 +20 - Misses 2873 2874 +1 ``` | [Files with missing lines](https://app.codecov.io/gh/scverse/scanpy/pull/3350?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/preprocessing/\_simple.py](https://app.codecov.io/gh/scverse/scanpy/pull/3350?src=pr&el=tree&filepath=src%2Fscanpy%2Fpreprocessing%2F_simple.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9wcmVwcm9jZXNzaW5nL19zaW1wbGUucHk=) | `88.67% <100.00%> (+0.13%)` | :arrow_up: | | [src/scanpy/preprocessing/\_utils.py](https://app.codecov.io/gh/scverse/scanpy/pull/3350?src=pr&el=tree&filepath=src%2Fscanpy%2Fpreprocessing%2F_utils.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9wcmVwcm9jZXNzaW5nL191dGlscy5weQ==) | `97.87% <100.00%> (+0.43%)` | :arrow_up: |