.pre-commit-config.yaml

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.5.0
    hooks:
      - id: check-merge-conflict
      - id: check-added-large-files
      - id: debug-statements
      - id: mixed-line-ending
      - id: check-case-conflict
      - id: check-yaml
      - id: trailing-whitespace
      - id: end-of-file-fixer
  - repo: https://github.com/asottile/pyupgrade
    rev: v3.15.1
    hooks:
      - id: pyupgrade
        args: [--py3-plus, --py37-plus]
  - repo: https://github.com/pycqa/isort
    rev: 5.13.2
    hooks:
      - id: isort
        name: "isort (python)"
        args: ["--profile", "black", "--force-single-line"]
  - repo: https://github.com/psf/black
    rev: 24.2.0
    hooks:
      - id: black
        language_version: python3
  - repo: https://github.com/charliermarsh/ruff-pre-commit
    rev: "v0.3.0"
    hooks:
      - id: ruff
  - repo: https://github.com/asottile/blacken-docs
    rev: 1.16.0
    hooks:
      - id: blacken-docs
        args: [--skip-errors]
        additional_dependencies: [black==22.12.0]
        language_version: python3
  - repo: https://github.com/snakemake/snakefmt
    rev: v0.10.0
    hooks:
      - id: snakefmt
  - repo: local
    hooks:
      - id: lint
        name: Snakemake lint
        entry: snakemake --lint text -s
        language: system
        files: ".*.smk$|.*Snakefile$"
  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: "v4.0.0-alpha.8"
    hooks:
      - id: prettier
  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
    rev: 2.7.3
    hooks:
      - id: editorconfig-checker
        alias: ec
  - repo: https://github.com/DavidAnson/markdownlint-cli2
    rev: v0.12.1
    hooks:
      - id: markdownlint-cli2
        files: \.(md|qmd)$
        types: [file]
        exclude: LICENSE.md
  - repo: local
    hooks:
      - id: pylint
        name: pylint
        entry: pylint
        language: system
        types: [python]
        args: [
            "-rn", # Only display messages
            "-sn", # Don't display the score
          ]