github actions and publishing releases

[aryarm]

It would be nice if we could automate everything!

Some things that our github actions could do

on every pull request, we should...

• [x] check that we follow the conventional commits spec for that PR title so that we can automatically figure out how to bump the version number later on (see for ex, this)
• [x] run black (and isort?) to check that we follow proper style
• [x] check that the docs can be built but this is already handled by readthedocs, anyway
• [x] check that large files aren't included in the PR via this github action
• [x] run pytest to check that...
  • all the tests pass
  • the code coverage doesn't decrease?

every so often, when we want to create a new release, it should...

• [x] bump the version number
• [x] build the changelog
• [x] build the newest release
• [x] publish it to pypi (and bioconda?)

nox

• [x] we should install and configure nox to have it run all of our checks
• [ ] incorporate a type checker like mypy?

version constraints

• [x] we should test our version constraints using nox to ensure they're not being too picky
  • [x] also, do we really need to depend on brewer2mpl? can we find an alternative?
• [x] and we should remove the upper-limit caps that get added by default by poetry
  • I just read this article about it, and it was eye opening
• [x] also we should make sure we're configuring our loggers properly (see here, here, and here)

Some relevant links

• https://cookiecutter-hypermodern-python.readthedocs.io/
• https://github.com/snakemake/snakemake/tree/main/.github/workflows
• https://github.com/googleapis/release-please#release-please
• https://mestrak.com/blog/semantic-release-with-python-poetry-github-actions-20nn
• https://github.com/amannn/action-semantic-pull-request
• https://github.com/elgohr/Publish-Docker-Github-Action
• https://about.codecov.io/blog/python-code-coverage-using-github-actions-and-codecov/

[aryarm]

• [x] we should also document our process for publishing a new release:

1. we merge the most recent haptools PR labeled "chore(main)" created by the github actions bot
2. the bot automatically creates a new version on PyPI and tags a release on Github
3. bioconda automatically detects the new release on PyPI and creates a PR on their end to have the version updated on bioconda
4. we have to comment on the PR with "@BiocondaBot please add label"
5. someone from the bioconda team merges our PR and the version gets updated on bioconda (which usually takes ~1-2 days)