.pre-commit-config.yaml

minimum_pre_commit_version: '2.18.0'
default_install_hook_types: [pre-commit, commit-msg]
default_stages: [commit, push]

repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
  rev: v4.3.0
  hooks:
  - id: no-commit-to-branch  # prevent direct commits to main branch
    alias: no-commit-to-main
  - id: check-yaml
    args: ['--unsafe']
  # - id: check-toml
  - id: end-of-file-fixer
  - id: trailing-whitespace
  - id: no-commit-to-branch
    alias: validate-branch-name
    args: ['--pattern', '^(?!((fix|feat|style|ci|test|docs)\/[a-zA-Z0-9\-]+)$).*']

- repo: https://github.com/codespell-project/codespell
  rev: v2.2.4
  hooks:
  - id: codespell
    additional_dependencies:
      - tomli
    exclude: '^pdm\.lock$'

- repo: https://github.com/astral-sh/ruff-pre-commit
  # Ruff version.
  rev: v0.1.8
  hooks:
  # Run the linter.
  - id: ruff
    types_or: [ python, pyi, jupyter ]
  # Run the linter and fix the errors.
  - id: ruff
    alias: ruff-fix
    types_or: [ python, pyi, jupyter ]
    args: [ --fix ]
    stages: [manual]
  # Run the formatter.
  - id: ruff-format
    types_or: [ python, pyi, jupyter ]
    args: [ --check ]
  # Run the formatter and fix the errors.
  - id: ruff-format
    alias: ruff-format-fix
    types_or: [ python, pyi, jupyter ]
    stages: [manual]

- repo: https://github.com/commitizen-tools/commitizen
  rev: v3.13.0
  hooks:
    - id: commitizen
      stages: [commit-msg]
    - id: commitizen-branch
      stages: [push]

- repo: https://github.com/pre-commit/mirrors-mypy
  rev: 'v1.7.1'
  hooks:
  - id: mypy
    args: [--strict, --ignore-missing-imports]
    additional_dependencies: [tokenize-rt==3.2.0]
    stages: [manual]

- repo: local
  hooks:
  - id: miniwdl-check
    name: miniwdl check
    language: system
    files: ".+\\.wdl"
    verbose: true
    entry: .venv/bin/miniwdl
    args: [check]