.pre-commit-config.yaml

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0  # Use the ref you want to point at
    hooks:
      - id: check-case-conflict
      - id: check-symlinks
      - id: check-docstring-first
      - id: check-merge-conflict
      - id: check-json
      - id: check-toml
      - id: check-yaml
      - id: destroyed-symlinks
      - id: end-of-file-fixer
        exclude: \.out$
      - id: fix-byte-order-marker
      - id: mixed-line-ending
      - id: name-tests-test
        args: ["--pytest-test-first"]
      - id: no-commit-to-branch # Protects main/master by default
      - id: pretty-format-json
        args: ["--autofix", "--no-sort-keys"]
        exclude: ^web/
      - id: requirements-txt-fixer
      - id: trailing-whitespace

  - repo: https://github.com/psf/black
    rev: 24.10.0
    hooks:
      - id: black
        types: [python]
        additional_dependencies: ['click==8.0.4']
        args: ["--extend-exclude", "topostats/plotting.py"]

  - repo: https://github.com/astral-sh/ruff-pre-commit
    # Ruff version.
    rev: v0.8.6
    hooks:
      - id: ruff
        args: [--fix, --exit-non-zero-on-fix]

ci:
  autofix_prs: true
  autofix_commit_msg: '[pre-commit.ci] Fixing issues with pre-commit'
  autoupdate_schedule: weekly
  autoupdate_commit_msg: '[pre-commit.ci] pre-commit automatically updated.'
  # skip: [] # Optionally list ids of hooks to skip on CI