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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 604 forks source link

Benchmark dask #3319

Open mikelkou opened 1 month ago

mikelkou commented 1 month ago

draft benchmarks with dask

codecov[bot] commented 1 month ago

Codecov Report

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

Project coverage is 77.26%. Comparing base (8e64165) to head (ca9b8f6). Report is 13 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #3319 +/- ## ========================================== + Coverage 77.22% 77.26% +0.04% ========================================== Files 111 111 Lines 12600 12630 +30 ========================================== + Hits 9730 9759 +29 - Misses 2870 2871 +1 ``` [see 11 files with indirect coverage changes](https://app.codecov.io/gh/scverse/scanpy/pull/3319/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse)
scverse-benchmark[bot] commented 1 month ago

Benchmark changes

Change Before [3d220a93] After [ca9b8f67] Ratio Benchmark (Parameter)
- 63.0±0.9ms 53.7±0.2ms 0.85 preprocessing_counts.FastSuite.time_calculate_qc_metrics('pbmc3k', 'counts')
- 60.4±0.5ms 46.4±1ms 0.77 preprocessing_counts.time_filter_cells('pbmc3k', 'counts')

[!WARNING] Some benchmarks failed

Comparison: https://github.com/scverse/scanpy/compare/3d220a93c83fdd60ee3220c94db3dd8d5533c60d..ca9b8f671ae4403a89d775707498c7422e0384a3 Last changed:

More details: https://github.com/scverse/scanpy/pull/3319/checks?check_run_id=32663197935