Python template repo

Template repository for both application and analysis repos in Python 3. Provides:

• A minimal Makefile
• Automatic setup of a pyenv virtualenv using Python 3.8.2 and named after the repo name (see make install/pyenv)
• pip-tools for requirements.txt management (see make requirements)
• pre-commit for linting (see make format)
• GitHub Actions for pre-commit and pytest

To get started

Just run:

make install

You can re-install just the Python dependencies with make install/requirements. Test with pytest or make test. Format per-file on commit or by running make format.

Customizing pre-commit behavior

If you'd like to enable pre-commit for a different set of hooks, you can set the PRE_COMMIT_HOOK_PREFERENCE environment variable before invoking make install, e.g., PRE_COMMIT_HOOK_PREFERENCE=pre-push make install. Note this will not work if you modify .pre-commit-config.yaml to have a default_stages directive (see the documentation for more info).

Adding badges

Unfortunately, Github badges need to have hardcoded paths. You can add this to the top of your REAMDE.md replacing $REPO as appropriate:

![test](https://github.com/onecodex/$REPORT/workflows/test/badge.svg) ![pre-commit](https://github.com/onecodex/$REPORT/workflows/pre-commit/badge.svg)

Initial GH Action status checks ⚠️

By default, creating a repository from this template will have a failing Github Action for tests. This is because pytest has an exit code of 5 when no tests are present. The best fix is to just write some tests!