openkinome / kinoml

Structure-informed machine learning for kinase modeling

https://openkinome.org/kinoml/

MIT License

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Add klifs data to CI cache #83

Closed schallerdavid closed 3 years ago

schallerdavid commented 3 years ago

Description

Currently, testing the KLIFS complex featurizers in the CI takes quite some time, since the KLIFS queries in the _pre_featurize method will need to download all data on every push. This PR aims to enable persistent caching of the results for the CI.

Todos

[x] update docking notebook to specify cache_dir
[x] increase notebook cell timeout to allow finishing of the cells, when cached files are not present yet
[x] include cache in CI
[x] CI execution time improves

Status

[x] Ready to go

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codecov-commenter commented 3 years ago

Codecov Report

Merging #83 (7bacc71) into master (7c039be) will increase coverage by 0.64%. The diff coverage is n/a.

schallerdavid commented 3 years ago

Hey @jchodera and @t-kimber ,

I found a solution to cache the data from querying KLIFS. However, MacOS is super slow compared to the others (but still faster than without caching).

If you think this is fine, I would merge this into #66. This PR just targets the master branch to trigger the CI.

schallerdavid commented 3 years ago

Thanks for the review @jchodera, tracking execution times seems super useful. However, tracking jupyter notebook cell execution times is not possible with nbval. Also, googling for alternative packages didn't give an easy solution. I could open an issue, so we don't forget about it.