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Improve pytest speed #430

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1 of 5 tasks
Zethson opened this issue Nov 9, 2023 · 2 comments
Open
1 of 5 tasks

Improve pytest speed #430

Zethson opened this issue Nov 9, 2023 · 2 comments
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enhancement New feature or request performance Performance

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@Zethson
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Zethson commented Nov 9, 2023

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.

  • Figure out why test collection takes so long. Are we checking too many folders? Is it downloading things? Why are these not cached? What's happening?
  • Move more fixtures/anndata object creations into conftest fixtures
  • Cache cachedir on Github Actions tests
  • Benchmark which tests take too long. Which functions take too long? Document them.
  • Discuss with @Zethson how we'll speed everything up
@Zethson Zethson added the enhancement New feature or request label Nov 9, 2023
@Zethson
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Zethson commented Nov 9, 2023

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

@Zethson Zethson added the performance Performance label Nov 9, 2023
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Zethson commented May 21, 2024

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

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