diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index a82417d..2ff4409 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -2,49 +2,6 @@ ## CI -Checks are automatically run on certain pushed commits for testing and linting -purposes. Some are defined by [.github/workflows/ci.yaml][] while others are -configured outside of this repository. +Tests are run through GitHub Actions when triggered by events as defined by [.github/workflows/ci.yaml][] [.github/workflows/ci.yaml]: ./.github/workflows/ci.yaml - -## Pre-commit - -[pre-commit][] is used for various checks (see [configuration][]). - -You can either [install it yourself][] to catch issues before pushing or look -for the [pre-commit.ci run][] after pushing. - -[pre-commit]: https://pre-commit.com/ -[configuration]: ./.pre-commit-config.yaml -[install it yourself]: https://pre-commit.com/#install -[pre-commit.ci run]: https://results.pre-commit.ci/repo/github/493877605 - -## Snakemake formatting - -We use [`snakefmt`](https://github.com/snakemake/snakefmt) to ensure consistency in style across Snakemake files in this project. - -### Installing - -- Using mamba/bioconda: - -```bash -mamba install -c bioconda snakefmt -``` - -- Using pip: - -```bash -pip install snakefmt -``` - -### IDE-independent - -1. Check for styling issues with `snakefmt --check .` -1. Automatically fix styling issues with `snakefmt .` - -### Using VSCode extension - -1. Install the [VSCode extension](https://marketplace.visualstudio.com/items?itemName=tfehlmann.snakefmt) -1. Check for styling issues with `Ctrl+Shift+P` and select `snakefmt: Check` -1. Automatically fix styling issues with `Ctrl+Shift+P` and select `Format document`