File organization

The root directory / contains scripts and jupyter notebooks.
All module code lives in the /pyrocov/ package directory. As a rule of thumb, if you're importing a .py file an any other file, it should live in the /pyrocov/ directory; if your .py file has an if __name__ == "__main__" check, then it should live in the root directory.
Notebooks should be cleared of data before committing.
The /results/ directory (not under git control) contains large intermediate data including preprocessed input data and outputs from models and prediction.
The /paper/ directory contains git-controlled output for the paper, namely plots, .tsv files, and .fasta files for sharing outside of the dev team.

Committing code

The current policy is to allow pushing of code directly, without PRs.
If you would like code reviewed, please submit a PR and tag a reviewer.
Please run make format and make lint before committing code.
We'd like to resurrect make test but it is currently broken.
Each notebook has an owner (see git history); changes to notebooks by non-owners should be through pull request. This rule is intended to reduce difficult merge conflicts in jupyter notebooks.