Add basic project structure #1
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Looks good! Just a few small comments.
One thing you might mention in the environment README is that your script environment/scripts/setup_environment.sh requires Conda version >=4.9.0 for the --no-capture-output argument (I was on an older version and had to upgrade to get it to work, before that it threw an error). Otherwise the environment setup worked fine for me!
Thank you for your review, @jjc2718!
That's awesome! I'm very glad that it worked for you because it failed for @ben-heil before, so maybe this is related to a channel priority issue. I'm not entirely sure how to fix this, because having custom configurations per user might be common, and it should be addressed here. I will add a comment regarding this aspect in the README.md file. I also added a note regarding the required conda version. |
Co-authored-by: Jake Crawford <[email protected]>
This PR copies most of the project structure from PhenoPLIER into this new project. It adds Github Actions workflows, unit tests, and code coverage. Most of the files here were already reviewed, and it would be great if the reviewer can follow the instructions (see below) to create the conda environment without problems.
The main files that need review are:
.github/workflows/pytest.yaml: it is similar to the PhenoPLIER's one, but here 1) I add support to cache the entire conda environment (which significantly reduces workflow time), 2) tests are run also in macOS and MS Windows, and 3) code coverage reports are submitted to codecov.README.md: this file was already mostly reviewed, but this version includes some "TODOs" since the project is just starting (for instance, no description available yet).environment/README.md: if possible, it would be great if the reviewer can follow the instructions to create the conda environment. It won't take much time, and we found some issues previously in some contexts (my guess is that it is related to a channel priority problem). After installing the environment, follow the instructions intests/README.mdto run the unit tests.The rest of the files were mostly entirely copied from PhenoPLIER (which were already reviewed), but the reviewer is welcome to take a look again of course.