.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-docstring-first
      - id: check-merge-conflict
      - id: check-toml
      - id: check-yaml
      - id: debug-statements
      - id: end-of-file-fixer
        types: [python]
      - id: fix-byte-order-marker
      - id: name-tests-test
        args: ["--pytest-test-first"]
      - id: no-commit-to-branch # Protects main/master by default
      - id: requirements-txt-fixer
      - id: trailing-whitespace
        types: [python, yaml, markdown]

  - repo: https://github.com/DavidAnson/markdownlint-cli2
    rev: v0.16.0
    hooks:
      - id: markdownlint-cli2
        args: []

  - repo: https://github.com/asottile/pyupgrade
    rev: v3.19.0
    hooks:
      - id: pyupgrade
        args: [--py38-plus]

  - repo: https://github.com/astral-sh/ruff-pre-commit
    # Ruff version.
    rev: v0.8.2
    hooks:
      - id: ruff
        args: [ --fix, --exit-non-zero-on-fix ]

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

  - repo: https://github.com/kynan/nbstripout
    rev: 0.8.1
    hooks:
      - id: nbstripout

  - repo: https://github.com/numpy/numpydoc
    rev: v1.8.0
    hooks:
      - id: numpydoc-validation

  - repo: local
    hooks:
      - id: pylint
        args: ["--rcfile=.pylintrc"]
        name: Pylint
        entry: python -m pylint
        language: system
        files: \.py$

  - repo: local
    hooks:
      - id: pytest
        name: Pytest (testmon)
        entry: pytest --testmon
        language: system
        files: \.py$

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-autoupdate'
  skip: [pylint, pytest] # Optionally list ids of hooks to skip on CI