add pre-commit config & run pre-commit on all files - Githubissues

dieterich-lab / rp-bp

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.

MIT License

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add pre-commit config & run pre-commit on all files #115

Closed lkeegan closed 1 year ago

lkeegan commented 1 year ago

What it does:

formats python .py files with black
strips jupyter notebooks of outputs and formats with black
runs flake8 linter
- note: all errors have initially been added to --ignore list in .pre-commit-config.yaml
various other useful formatters/linters

To use locally:

ensure pre-commit is installed: pip install pre-commit
run pre-commit install in the root directory of the repository
pre-commit will now run automatically on any changed files with every commit
you can also run it manually on all files with pre-commit run -a

To enable CI:

go to https://pre-commit.ci/ and enable it for this github repo
it will run pre-commit on any PRs and automatically push any necessary fixes
it will also occasionally make a PR updating the version of the pre-commit hooks to the latest ones