Contributing

Contributions are welcome.

Submit contributions as a pull request on GitHub.

Standards

All contributions must be PEP complaint.
All modules, classes, and functions must have Sphinx style doc strings.
All parameters and variables should have type annotations.
A reasonable amount of code block documentation is expected as well.

Tests should be written first before implementing functionality. See https://en.wikipedia.org/wiki/Test-driven_development

Repo Maintainers

To create a new release for pypi and conda:

Clone this repository
Make sure all tests pass first by running ./setup.py test
Use git or the GitHub interface to tag the repository with the next version. Precede the version number with a 'v'. Follow symantic versioning rules https://semver.org/:

Given a version number MAJOR.MINOR.PATCH, increment the:

MAJOR version when you make incompatible API changes,

MINOR version when you add functionality in a backwards compatible manner, and

PATCH version when you make backwards compatible bug fixes.
Create a release via the GitHub interface for the new tag.

At this point the GitHub CI will kick in and automatically do the following steps

Build the package by running ./setup.py build sdist
Upload the new package to pypi by running twine upload -u brinkmanlab dist/<file with latest version number>.tar.gz

Bioconda will detect the upload and automatically update its recipe. A Bioconda maintainer will manually approve the update.