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Remove grouping bottleneck (#42) #150

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Remove grouping bottleneck (#42)

Remove grouping bottleneck (#42) #150

Run time

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Job Run time
test / List components to test
40s
test / Test (embed_cell_types_jittered, control_methods, src/control_methods/embed_cell_types_jittered/c...
59s
test / Test (embed_cell_types, control_methods, src/control_methods/embed_cell_types/config.vsh.yaml, sr...
58s
test / Test (no_integration, control_methods, src/control_methods/no_integration/config.vsh.yaml, src/co...
59s
test / Test (shuffle_integration_by_batch, control_methods, src/control_methods/shuffle_integration_by_b...
1m 4s
test / Test (shuffle_integration, control_methods, src/control_methods/shuffle_integration/config.vsh.ya...
2m 6s
test / Test (shuffle_integration_by_cell_type, control_methods, src/control_methods/shuffle_integration_...
58s
test / Test (no_integration_batch, control_methods, src/control_methods/no_integration_batch/config.vsh....
1m 3s
test / Test (isolated_label_asw, metrics, src/metrics/isolated_label_asw/config.vsh.yaml, src/metrics/is...
1m 4s
test / Test (isolated_label_f1, metrics, src/metrics/isolated_label_f1/config.vsh.yaml, src/metrics/isol...
2m 2s
test / Test (clustering_overlap, metrics, src/metrics/clustering_overlap/config.vsh.yaml, src/metrics/cl...
1m 5s
test / Test (asw_batch, metrics, src/metrics/asw_batch/config.vsh.yaml, src/metrics/asw_batch/, python_s...
1m 7s
test / Test (graph_connectivity, metrics, src/metrics/graph_connectivity/config.vsh.yaml, src/metrics/gr...
1m 48s
test / Test (kbet, metrics, src/metrics/kbet/config.vsh.yaml, src/metrics/kbet/, python_script, metrics/...
1m 36s
test / Test (pcr, metrics, src/metrics/pcr/config.vsh.yaml, src/metrics/pcr/, python_script, metrics/pcr)
1m 5s
test / Test (cell_cycle_conservation, metrics, src/metrics/cell_cycle_conservation/config.vsh.yaml, src/...
1m 13s
test / Test (hvg_overlap, metrics, src/metrics/hvg_overlap/config.vsh.yaml, src/metrics/hvg_overlap/, py...
1m 59s
test / Test (asw_label, metrics, src/metrics/asw_label/config.vsh.yaml, src/metrics/asw_label/, python_s...
1m 9s
test / Test (lisi, metrics, src/metrics/lisi/config.vsh.yaml, src/metrics/lisi/, python_script, metrics/...
1m 15s
test / Test (transform, data_processors, src/data_processors/transform/config.vsh.yaml, src/data_process...
1m 48s
test / Test (precompute_clustering_run, data_processors, src/data_processors/precompute_clustering_run/c...
1m 9s
test / Test (precompute_clustering_merge, data_processors, src/data_processors/precompute_clustering_mer...
1m 39s
test / Test (process_dataset, data_processors, src/data_processors/process_dataset/config.vsh.yaml, src/...
1m 17s
test / Test (scanvi, methods, src/methods/scanvi/config.vsh.yaml, src/methods/scanvi/, python_script, me...
5m 52s
test / Test (batchelor_fastmnn, methods, src/methods/batchelor_fastmnn/config.vsh.yaml, src/methods/batc...
1m 58s
test / Test (mnnpy, methods, src/methods/mnnpy/config.vsh.yaml, src/methods/mnnpy/, python_script, metho...
1m 48s
test / Test (scalex, methods, src/methods/scalex/config.vsh.yaml, src/methods/scalex/, python_script, me...
2m 48s
test / Test (uce, methods, src/methods/uce/config.vsh.yaml, src/methods/uce/, python_script, methods/uce)
4m 17s
test / Test (scprint, methods, src/methods/scprint/config.vsh.yaml, src/methods/scprint/, python_script,...
13m 45s
test / Test (scgpt_finetuned, methods, src/methods/scgpt_finetuned/config.vsh.yaml, src/methods/scgpt_fi...
6m 46s
test / Test (harmonypy, methods, src/methods/harmonypy/config.vsh.yaml, src/methods/harmonypy/, python_s...
1m 3s
test / Test (scgpt_zeroshot, methods, src/methods/scgpt_zeroshot/config.vsh.yaml, src/methods/scgpt_zero...
7m 17s
test / Test (liger, methods, src/methods/liger/config.vsh.yaml, src/methods/liger/, r_script, methods/li...
2m 30s
test / Test (batchelor_mnn_correct, methods, src/methods/batchelor_mnn_correct/config.vsh.yaml, src/meth...
2m 20s
test / Test (scimilarity, methods, src/methods/scimilarity/config.vsh.yaml, src/methods/scimilarity/, py...
5m 18s
test / Test (pyliger, methods, src/methods/pyliger/config.vsh.yaml, src/methods/pyliger/, python_script,...
2m 31s
test / Test (bbknn, methods, src/methods/bbknn/config.vsh.yaml, src/methods/bbknn/, python_script, metho...
1m 23s
test / Test (scvi, methods, src/methods/scvi/config.vsh.yaml, src/methods/scvi/, python_script, methods/...
6m 40s
test / Test (combat, methods, src/methods/combat/config.vsh.yaml, src/methods/combat/, python_script, me...
1m 3s
test / Test (geneformer, methods, src/methods/geneformer/config.vsh.yaml, src/methods/geneformer/, pytho...
4m 53s
test / Test (scanorama, methods, src/methods/scanorama/config.vsh.yaml, src/methods/scanorama/, python_s...
2m 5s
test / Test (harmony, methods, src/methods/harmony/config.vsh.yaml, src/methods/harmony/, r_script, meth...
1m 11s
1h 45m 31s