Run notebooks in CI #122
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Run notebooks in CI #122
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Adds GitHub action for running selected notebooks. Not all notebooks are run to keep the execution time in reasonable boundaries.
On top of the main item, the PR improves logging by not complaining about missing protein annotations for additional classes of non-coding variants (see the
NONCODING_EFFECTSattribute ofVepFunctionalAnnotator.Furthermore, the PR ensures we sort the phenotype features by first the corrected p value, and then the uncorrected value. Previously, the data frame was sorted by the corrected values only, which is sub-optimal if all values are equal to
1.0.Last, I went through the notebooks and simplified the code, while preserving as much of the original content as possible. In result, all notebooks should be runnable. However, the results still need to be worked on to ensure we ask the proper questions - the questions from the respective papers.
Fixes #86