Add tests (essentially the same ones as in my other greenelab/pancancer-evaluation repo) and set up GitHub actions to run them for new PRs. Closes #27.
Add the data types that are being used to decide which samples to use to the metadata being saved in the output directory for each experiment. This addresses the first half of #26.
Clean up a hack I was using to use non-compressed data to select the sample set for certain compressed data experiments. Closes #26.
No new results in this PR, but this should make it easier to add new functionality in the future and be more confident that nothing is breaking.
Files to review:
All the large .tsv files can safely be ignored, they need to be tracked in git so the tests can run but they don't require any review. Most of the testing code was copied over from the pancancer-evaluation repo, so it doesn't necessarily need to be reviewed closely, but feel free to spend as much or as little time as you want looking at it.
PR description:
This PR addresses a few small outstanding issues:
Add tests (essentially the same ones as in my other
greenelab/pancancer-evaluationrepo) and set up GitHub actions to run them for new PRs. Closes #27.Add the data types that are being used to decide which samples to use to the metadata being saved in the output directory for each experiment. This addresses the first half of #26.
Clean up a hack I was using to use non-compressed data to select the sample set for certain compressed data experiments. Closes #26.
No new results in this PR, but this should make it easier to add new functionality in the future and be more confident that nothing is breaking.
Files to review:
All the large
.tsvfiles can safely be ignored, they need to be tracked in git so the tests can run but they don't require any review. Most of the testing code was copied over from thepancancer-evaluationrepo, so it doesn't necessarily need to be reviewed closely, but feel free to spend as much or as little time as you want looking at it.