.pre-commit-config.yaml

default_stages: [commit]

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.4.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: check-yaml

  - repo: https://github.com/commitizen-tools/commitizen
    rev: v3.25.0
    hooks:
      - id: commitizen

  - repo: https://github.com/adrienverge/yamllint.git
    rev: v1.32.0
    hooks:
      - id: yamllint
        args: ["-d relaxed"]

  - repo: https://github.com/executablebooks/mdformat
    rev: 0.7.17 # Use the ref you want to point at
    hooks:
      - id: mdformat
        # Optionally add plugins
        additional_dependencies:
          - mdformat-gfm
          - mdformat-black

  - repo: https://github.com/python-jsonschema/check-jsonschema
    rev: 0.26.3
    hooks:
      - id: check-github-workflows

  - repo: https://github.com/asottile/pyupgrade
    rev: v3.10.1
    hooks:
      - id: pyupgrade

  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.4.1
    hooks:
      # Run the linter.
      - id: ruff
        args: [ --fix ]
      # Run the formatter.
      - id: ruff-format

  - repo: https://github.com/kynan/nbstripout
    rev: 0.6.1
    hooks:
      - id: nbstripout
        args: ["--keep-output"]

  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.8.5
    hooks:
      - id: nbqa-black
      - id: nbqa-ruff
        args: ["--fix"]
      - id: nbqa-ruff

  - repo: https://github.com/snakemake/snakefmt
    rev: v0.8.4
    hooks:
      - id: snakefmt