.pre-commit-config.yaml

repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
  rev: v5.0.0
  hooks:
    - id: check-added-large-files
    - id: check-case-conflict
    - id: check-executables-have-shebangs
    - id: check-json
    - id: check-merge-conflict
    - id: check-shebang-scripts-are-executable
    - id: check-symlinks
    - id: check-yaml
    - id: debug-statements
    - id: destroyed-symlinks
    - id: end-of-file-fixer
      files: \.(py|sh|smk|md|yml|yaml)$
    - id: mixed-line-ending
    - id: trailing-whitespace
      files: \.(py|sh|smk|md|yml|yaml)$
- repo: https://github.com/scop/pre-commit-shfmt
  rev: v3.10.0-2
  hooks:
    - id: shfmt  # prebuilt upstream executable
      args: [
        '-sr',  # redirect operators will be followed by a space
        '-i=4',  # indent with four spaces
        '-w',  # write changes in place
      ]
- repo: https://github.com/shellcheck-py/shellcheck-py
  rev: v0.10.0.1
  hooks:
    - id: shellcheck
      args: [
        '--severity=info',
      ]
- repo: https://github.com/asottile/pyupgrade
  rev: v3.19.1
  hooks:
    - id: pyupgrade
- repo: https://github.com/astral-sh/ruff-pre-commit
  # Ruff version.
  rev: v0.8.6
  hooks:
    # Run the formatter.
    - id: ruff-format
      types_or: [ python, pyi, jupyter ]
      args: [
        '--config=format.docstring-code-format=true'
      ]
    # Run the linter.
    - id: ruff
      types_or: [ python, pyi, jupyter ]
      args: [ --fix ]
- repo: https://github.com/snakemake/snakefmt
  rev: v0.10.2
  hooks:
    - id: snakefmt
- repo: https://github.com/codespell-project/codespell
  rev: v2.3.0
  hooks:
    - id: codespell
      files: \.(py|smk|md)$
- repo: https://github.com/pre-commit/mirrors-mypy
  rev: v1.14.1
  hooks:
    - id: mypy
      # equivalent to "files" in .mypy.ini
      files: '^(pyani_plus|tests)/'
- repo: https://github.com/Lucas-C/pre-commit-hooks
  rev: v1.5.5
  hooks:
    - id: insert-license
      name: Check MIT license
      files: \.(py|sh|smk)$
      args:
        - "--license-filepath=LICENSE"
        - "--use-current-year"
        - "--detect-license-in-X-top-lines=20"
        - "--no-extra-eol"