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(feat): benchmarking #176

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scverse-benchmark / benchmark failed Apr 1, 2025 in 23m 39s

Benchmark

Benchmark run successful

Details

All benchmarks:

Change Before [8ddfdb2] After [a433b79] Ratio Benchmark (Parameter)
2.46±0.02ms 2.37±0.01ms 0.97 preprocessing.PreprocessingSuite.time_calculate_qc_metrics('pbmc68k_reduced')
failed failed n/a preprocessing.PreprocessingSuite.time_filter_cells('pbmc68k_reduced')
failed failed n/a preprocessing.PreprocessingSuite.time_filter_genes('pbmc68k_reduced')
9.85±0.2ms 9.45±0.08ms 0.96 preprocessing.PreprocessingSuite.time_highly_variable_genes('pbmc68k_reduced')
472±0.3μs 478±2μs 1.01 preprocessing.PreprocessingSuite.time_log1p('pbmc68k_reduced')
7.57±0.07ms 7.55±0.07ms 1.00 preprocessing.PreprocessingSuite.time_neighbors('pbmc68k_reduced')
62.6±20μs 62.9±20μs 1.00 preprocessing.PreprocessingSuite.time_normalize_total('pbmc68k_reduced')
9.91±0.1ms 9.94±0.08ms 1.00 preprocessing.PreprocessingSuite.time_pca('pbmc68k_reduced')
4.14±0.09ms 4.12±0.06ms 1.00 preprocessing.PreprocessingSuite.time_regress_out('pbmc68k_reduced')
- 1.90±0.05ms 1.48±0.01ms 0.78 preprocessing.PreprocessingSuite.time_scale('pbmc68k_reduced')
27072 27072 1.00 preprocessing.PreprocessingSuite.track_peakmem_calculate_qc_metrics('pbmc68k_reduced')
failed failed n/a preprocessing.PreprocessingSuite.track_peakmem_filter_cells('pbmc68k_reduced')
failed failed n/a preprocessing.PreprocessingSuite.track_peakmem_filter_genes('pbmc68k_reduced')
4284000 4284000 1.00 preprocessing.PreprocessingSuite.track_peakmem_highly_variable_genes('pbmc68k_reduced')
1207104 1207104 1.00 preprocessing.PreprocessingSuite.track_peakmem_neighbors('pbmc68k_reduced')
0 0 n/a preprocessing.PreprocessingSuite.track_peakmem_normalize_total('pbmc68k_reduced')
3932144 3932144 1.00 preprocessing.PreprocessingSuite.track_peakmem_pca('pbmc68k_reduced')
4319248 4319248 1.00 preprocessing.PreprocessingSuite.track_peakmem_regress_out('pbmc68k_reduced')
27328 27328 1.00 preprocessing.PreprocessingSuite.track_peakmem_scale('pbmc68k_reduced')
4284000 4284000 1.00 preprocessing.PreprocessingSuite.track_peakmem_time_log1p('pbmc68k_reduced')
failed failed n/a preprocessing.track_peakmem
16.9±0.7μs 17.0±0.4μs 1.01 readwrite.ToGPUSuite.time_to_gpu('obmc68k_reduced')
2142000 2142000 1.00 readwrite.ToGPUSuite.track_peakmem_to_gpu('obmc68k_reduced')
failed failed n/a readwrite.track_peakmem
11.2±0.3ms 11.4±0.3ms 1.02 squidpy.ToolsSuite.time_autocorr_geary('pbmc68k_reduced')
10.6±0.3ms 10.7±0.3ms 1.01 squidpy.ToolsSuite.time_autocorr_moran('pbmc68k_reduced')
50.6±0.5ms 52.1±0.8ms 1.03 squidpy.ToolsSuite.time_ligrec('pbmc68k_reduced')
3549552 3549552 1.00 squidpy.ToolsSuite.track_peakmem_autocorr_geary('pbmc68k_reduced')
3549552 3549552 1.00 squidpy.ToolsSuite.track_peakmem_autocorr_moran('pbmc68k_reduced')
53168 53168 1.00 squidpy.ToolsSuite.track_peakmem_ligrec('pbmc68k_reduced')
failed failed n/a squidpy.track_peakmem
78.9±4ms 78.9±3ms 1.00 tools.ToolsSuite.time_diffmap('pbmc68k_reduced')
8.84±0.09ms 8.81±0.08ms 1.00 tools.ToolsSuite.time_embedding_denity('pbmc68k_reduced')
89.8±5ms 84.3±0.3ms 0.94 tools.ToolsSuite.time_leiden('pbmc68k_reduced')
26.7±0.3ms 26.2±0.7ms 0.98 tools.ToolsSuite.time_umap('pbmc68k_reduced')
754928 754928 1.00 tools.ToolsSuite.track_peakmem_diffmap('pbmc68k_reduced')
7879216 7879216 1.00 tools.ToolsSuite.track_peakmem_embedding_denity('pbmc68k_reduced')
1056376 1056376 1.00 tools.ToolsSuite.track_peakmem_leiden('pbmc68k_reduced')
655904 655904 1.00 tools.ToolsSuite.track_peakmem_umap('pbmc68k_reduced')
failed failed n/a tools.track_peakmem
failed failed n/a utils.track_peakmem
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