pre-commit-hooks

Local policy hooks shared across Marc-commits' bioinformatics repos, consumed via pre-commit's remote-hook resolution.

Usage

- repo: https://github.com/Marc-commits/pre-commit-hooks
  rev: v0.4.0
  hooks:
    - id: readme-url-check
    - id: sh-strict-mode
    # ... any other id from .pre-commit-hooks.yaml

Hooks

• Repo/config: version-sync, validate-config
• README: readme-no-local-paths, readme-url-check
• R: r-script-shebang, r-script-runnable, r-script-tldr, r-script-stdin-stdout, r-metadata, r-script-startup-banner, r-script-quiet-banner, r-script-no-pkg-startup, r-script-session-info
• Python: py-shebang, py-marimo-check, py-help-version, py-tldr, py-metadata
• Shell: sh-bash-shebang, sh-usage-banner, sh-strict-mode, sh-help-version, sh-tldr, sh-metadata
• Docker: docker-build-check, docker-metadata
• Snakemake/conda: snakemake-lint, workflow-sh-strict-mode, conda-env-validate, snakemake-rulegraph

Full hook definitions live in .pre-commit-hooks.yaml.

readme-url-check and private GitHub repos

By default this hook only confirms URLs are reachable anonymously. To also confirm private-repo URLs are valid (rather than just flagging them as unreachable), export GITHUB_TOKEN_PC_CHECK_README_URLS with a token that can see those repos before running pre-commit. The variable is intentionally not named GITHUB_TOKEN/GH_TOKEN — those names are read by the gh CLI itself, and exporting a token under those names silently overrides gh auth login's stored credentials wherever it's set.