.pre-commit-config.yaml

default_stages: ["commit", "commit-msg", "push"]
default_language_version:
  python: python3

exclude: ^openfold/|^ProteinMPNN/
repos:
  - repo: https://github.com/charliermarsh/ruff-pre-commit
    rev: "v0.0.269"
    hooks:
      - id: ruff
        name: "Linting (ruff)"
        args: [--fix, --exit-non-zero-on-fix]

  - repo: https://github.com/timothycrosley/isort
    rev: 5.12.0
    hooks:
      - id: isort
        name: "Import sorting (isort)"

  - repo: https://github.com/psf/black
    rev: 23.3.0
    hooks:
      - id: black
        name: "Code formatting (black)"

  - repo: local
    hooks:
      - id: mypy
        name: "Static type checking (mypy)"
        entry: python -m mypy .
        language: system
        types: [python]
        pass_filenames: false

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.1.0
    hooks:
      - id: check-added-large-files
        args: ['--maxkb=1400']
        name: "Verify no large files have been added (pre-commit)"
      - id: check-case-conflict
        name: "Check for file collisions on case-insensitive filesystems (pre-commit)"
      - id: check-merge-conflict
        name: "Verify no merge conflict markers (pre-commit)"
      - id: check-symlinks
        name: "Verify no missing symlink targets (pre-commit)"
      - id: check-toml
        name: "Verify TOML syntax (pre-commit)"
      - id: check-yaml
        name: "Verify YAML syntax (pre-commit)"
      - id: debug-statements
        name: "Verify no debugger imports or breakpoint() calls (pre-commit)"
      - id: destroyed-symlinks
        name: "Check for symlinks that have been converted to regular files (pre-commit)"
      - id: end-of-file-fixer
        name: "Verify files end with a newline (pre-commit)"
      - id: fix-byte-order-marker
        name: "Remove UTF-8 byte order marker (pre-commit)"
      - id: mixed-line-ending
        name: "Fix potential line mismatches caused by Windows (pre-commit)"
      - id: trailing-whitespace
        name: "Trim trailing whitespace (pre-commit)"
        args: [ --markdown-linebreak-ext=md ] # Trailing whitespaces are part of Markdown syntax
      - id: requirements-txt-fixer
        name: "Requirements txt sorting (pre-commit)"

  - repo: https://github.com/pycqa/pydocstyle
    rev: 6.3.0
    hooks:
      - id: pydocstyle
        name: "Check docstring formatting (pydocstyle)"
        additional_dependencies:
          - "tomli" # To avoid warning when pydocstyle reads from pyproject.toml
        args:
          - --convention=google
          - --match='(.*(?<!_test)\.py)$' # Exclude test files

  - repo: https://github.com/asottile/pyupgrade
    rev: v3.4.0
    hooks:
      - id: pyupgrade
        name: "Check for Python 3.9 syntax upgrades (pyupgrade)"
        args:
          - --py39-plus

  - repo: https://github.com/pre-commit/mirrors-pylint
    rev: v3.0.0a5
    hooks:
      - id: pylint
        name: "Static code analysis (pylint)"

  - repo: https://github.com/codespell-project/codespell
    rev: v2.2.6
    hooks:
      - id: codespell
        name: codespell
        description: Checks for common misspellings in text files.
        entry: codespell --ignore-words=.codespell-ignore.txt
        language: python
        types: [text]