scverse / pertpy

Perturbation Analysis in the scverse ecosystem.
https://pertpy.readthedocs.io/en/latest/
MIT License
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Improve pytest speed #430

Open Zethson opened 1 year ago

Zethson commented 1 year ago

Description of feature

Currently, starting pytest takes ages because it doesn't collect the tests that fast or seems to download something. I don't really know what's going on.

I think this was introduced when we merged the CellLineMetaData PR.

Zethson commented 1 year ago

@Lilly-May @wxicu this is for later. Please ignore it for now - you have other things to do that are currently more important.

Zethson commented 6 months ago

716.87s call tests/tools/test_augur.py::test_differential_prioritization 265.23s call tests/tools/_distances/test_distance_tests.py::test_distancetest[wasserstein] 91.72s call tests/tools/test_mixscape.py::test_perturbation_signature 88.49s call tests/metadata/test_cell_line.py::test_bulk_rna_expression_annotation 48.50s call tests/tools/test_mixscape.py::test_lda 46.60s call tests/tools/test_augur.py::test_random_forest_classifier 44.65s setup tests/tools/_distances/test_distances.py::test_distance_axioms 42.71s setup tests/tools/_distances/test_distances.py::test_distance_layers 42.25s setup tests/tools/_distances/test_distances.py::test_triangle_inequality 42.06s setup tests/tools/_distances/test_distances.py::test_distance_pairwise 41.77s setup tests/tools/_distances/test_distances.py::test_distance_output_type 39.17s setup tests/tools/_distances/test_distances.py::test_distance_counts 30.01s call tests/tools/_coda/test_sccoda.py::test_make_arviz 26.42s call tests/tools/test_dialogue.py::test_dialogue_pipeline 25.98s call tests/tools/_coda/test_sccoda.py::test_credible_effects 20.37s call tests/tools/_coda/test_tasccoda.py::test_run_nuts 16.22s call tests/tools/_perturbation_space/test_simple_perturbation_space.py::test_label_transfer 14.47s call tests/tools/_coda/test_sccoda.py::test_run_nuts