Test notebooks

[schallerdavid]

Description

This PR aims to include notebooks found in examples in CI testing.

Todos

• [x] enable pytests of notebooks
• planned notebooks:
  • [ ] basic KinoML concepts (i.e. DataSetProviders, Featurizers etc.)
  • [ ] workflow example including ingesting data, featurization, model training and testing
  • [ ] structure preparation
  • [ ] docking
• [ ] all notebooks pass

Hints

• nbval has a default timeout for cell execution of 2000 s (~33 min) (--nbval-cell-timeout), in case there is no way to make a cell finish within this time, we could think about increasing this threshold
• depracated notebooks were removed, but can be found in this commit

Status

• [ ] Ready to go

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[codecov-commenter]

Codecov Report

Merging #66 (2e34a55) into master (065b4b9) will decrease coverage by 0.02%. The diff coverage is n/a.

[schallerdavid]

It appears that many of the notebooks are kind of WIP examples that are out of data and repetitive (e.g. featurizing ChEMBL and PKIS datasets). Since we agreed on providing example notebooks, that are more application-focused, we could think about a new set of notebooks and build them from scratch with some inspiration from the old notebooks.