Note: Profiling durations of notebook cell executions

dominiquesydow commented 1 year ago

Currently, the CI takes 5-10 min to set up the environment and about 40 min to test about 30 notebooks. Keep here a list of cells that execute >5s.

Profiled on MacOS 13.1 with M1 chip:

PYTEST_ARGS="--nbval-lax --current-env --dist loadscope --numprocesses 2"
pytest $PYTEST_ARGS teachopencadd/talktorials/T*/talktorial.ipynb -v --durations=0

-v makes pytest more verbose
--durations=0 shows execution duration for all notebook cells
Report only cells with execution time >5s

dominiquesydow commented 1 year ago

Notebooks T00*

pytest $PYTEST_ARGS teachopencadd/talktorials/T00*/talktorial.ipynb -v --durations=0

Slowest cells (only >5s)

354.57s call     teachopencadd/talktorials/T001_query_chembl/talktorial.ipynb::Cell 11
         ---> Fetching ChEMBL data
226.98s call     teachopencadd/talktorials/T001_query_chembl/talktorial.ipynb::Cell 25
         ---> Fetching ChEMBL data
 36.61s call     teachopencadd/talktorials/T008_query_pdb/talktorial.ipynb::Cell 11
         ---> Fetching PDB data
 32.70s call     teachopencadd/talktorials/T006_compound_maximum_common_substructures/talktorial.ipynb::Cell 9
         ---> rdFMCS.FindMCS
 30.43s call     teachopencadd/talktorials/T006_compound_maximum_common_substructures/talktorial.ipynb::Cell 12
         ---> rdFMCS.FindMCS
 22.41s call     teachopencadd/talktorials/T008_query_pdb/talktorial.ipynb::Cell 4
         ---> Fetching PDB data
 20.50s call     teachopencadd/talktorials/T005_compound_clustering/talktorial.ipynb::Cell 13
         ---> Butina.ClusterData
 19.04s call     teachopencadd/talktorials/T008_query_pdb/talktorial.ipynb::Cell 9
 16.45s call     teachopencadd/talktorials/T007_compound_activity_machine_learning/talktorial.ipynb::Cell 25
 14.93s call     teachopencadd/talktorials/T007_compound_activity_machine_learning/talktorial.ipynb::Cell 22
 14.45s call     teachopencadd/talktorials/T008_query_pdb/talktorial.ipynb::Cell 8
 13.54s call     teachopencadd/talktorials/T003_compound_unwanted_substructures/talktorial.ipynb::Cell 10
 13.10s call     teachopencadd/talktorials/T007_compound_activity_machine_learning/talktorial.ipynb::Cell 8
 11.89s call     teachopencadd/talktorials/T003_compound_unwanted_substructures/talktorial.ipynb::Cell 5
 11.69s call     teachopencadd/talktorials/T007_compound_activity_machine_learning/talktorial.ipynb::Cell 24
  7.04s call     teachopencadd/talktorials/T007_compound_activity_machine_learning/talktorial.ipynb::Cell 0
  6.55s call     teachopencadd/talktorials/T005_compound_clustering/talktorial.ipynb::Cell 29
  5.65s call     teachopencadd/talktorials/T008_query_pdb/talktorial.ipynb::Cell 0

dominiquesydow commented 1 year ago

Notebooks T01*

(T019 fails, so durations for T019 cells not accurately included)

pytest $PYTEST_ARGS teachopencadd/talktorials/T01*/talktorial.ipynb -v --durations=0

Slowest cells (only >5s)

373.83s call     teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 61
         ---> Running full pipeline (LeadOptimizationPipeline.run)
119.94s call     teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 31
         ---> Docking (Docking)
 55.42s call     teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 25
         ---> Fetching PubChem data (LigandSimilaritySearch)
 36.69s call     teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 88
         ---> Fetching PubChem data (pubchem.similarity_search)
 32.84s call     teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 38
         ---> Docking (project1.Docking.visualize_all_poses())
 19.00s call     teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 117
 14.71s call     teachopencadd/talktorials/T015_protein_ligand_docking/talktorial.ipynb::Cell 12
 14.69s call     teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 42
 14.11s call     teachopencadd/talktorials/T013_query_pubchem/talktorial.ipynb::Cell 9
 10.72s call     teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 115
  9.91s call     teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 8
  8.65s call     teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 20
  8.55s call     teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 110
  7.69s call     teachopencadd/talktorials/T010_binding_site_comparison/talktorial.ipynb::Cell 25
  5.74s call     teachopencadd/talktorials/T010_binding_site_comparison/talktorial.ipynb::Cell 19
  5.10s call     teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 39
  5.04s call     teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 15

dominiquesydow commented 1 year ago

Notebooks T02*

pytest $PYTEST_ARGS teachopencadd/talktorials/T02*/talktorial.ipynb -v --durations=0

Slowest cells (only >5s)

20.76s call     teachopencadd/talktorials/T023_what_is_a_kinase/talktorial.ipynb::Cell 7
19.78s call     teachopencadd/talktorials/T027_kinase_similarity_ligand_profile/talktorial.ipynb::Cell 4
12.32s call     teachopencadd/talktorials/T022_ligand_based_screening_neural_network/talktorial.ipynb::Cell 11
 8.02s call     teachopencadd/talktorials/T022_ligand_based_screening_neural_network/talktorial.ipynb::Cell 7

dominiquesydow commented 1 year ago

Notebook T032

$ pytest $PYTEST_ARGS teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb -v --durations=0

Slowest cells (only >5s)

158.54s call     teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb::Cell 32
         ---> train_validate_qsar_model
 61.41s call     teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb::Cell 2
         ---> installation
 52.66s call     teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb::Cell 30
 51.01s call     teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb::Cell 6
 25.26s call     teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb::Cell 1
         ---> installation
 18.53s call     teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb::Cell 8
 14.55s call     teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb::Cell 21
  5.13s call     teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb::Cell 31

volkamerlab / teachopencadd