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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~ 35.63% faster filtering #3330

Open kaushalprasadhial opened 4 weeks ago

kaushalprasadhial commented 4 weeks ago
We are submitting PR for speed up of the filtering Time
Original 290.59
Updated 187.03
Speedup 35.63%

Experiment was done on AWS r7i.24xlarge

codecov[bot] commented 4 weeks ago

Codecov Report

Attention: Patch coverage is 22.44898% with 38 lines in your changes missing coverage. Please review.

Project coverage is 72.25%. Comparing base (a70582e) to head (25e7cd4). Report is 103 commits behind head on main.

Files with missing lines Patch % Lines
src/scanpy/preprocessing/_simple.py 22.44% 38 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #3330 +/- ## ========================================== - Coverage 76.27% 72.25% -4.03% ========================================== Files 117 111 -6 Lines 12795 12639 -156 ========================================== - Hits 9760 9132 -628 - Misses 3035 3507 +472 ``` | [Files with missing lines](https://app.codecov.io/gh/scverse/scanpy/pull/3330?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/3330?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=) | `61.67% <22.44%> (ø)` | | ... and [65 files with indirect coverage changes](https://app.codecov.io/gh/scverse/scanpy/pull/3330/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse)