.pre-commit-config.yaml

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.4.0
    hooks:
      - id: check-merge-conflict
      - id: debug-statements
      - id: mixed-line-ending
      - id: detect-private-key
      - id: check-case-conflict
      - id: check-yaml
      - id: trailing-whitespace
  - repo: https://github.com/asottile/reorder_python_imports
    rev: v3.9.0
    hooks:
      - id: reorder-python-imports
        args:
          [
            --application-directories=python,
            --unclassifiable-application-module=_tskit,
          ]
  - repo: https://github.com/charliermarsh/ruff-pre-commit
    rev: "v0.0.262"
    hooks:
      - id: ruff
        args:
          [
            "--per-file-ignores=tests/test_utils.py:E501,manticore/tests/wm/snakemake.py:E501",
          ]
  - repo: https://github.com/psf/black
    rev: 23.3.0
    hooks:
      - id: black
        language_version: python3
  - repo: https://github.com/asottile/blacken-docs
    rev: 1.13.0
    hooks:
      - id: blacken-docs
        args: [--skip-errors]
        additional_dependencies: [black==22.3.0]
        language_version: python3
  - repo: https://github.com/DavidAnson/markdownlint-cli2
    rev: v0.7.0
    hooks:
      - id: markdownlint-cli2
        files: \.(md|qmd)$
        types: [file]
        exclude: LICENSE.md
      - id: markdownlint-cli2-fix
        files: \.(md|qmd)$
        types: [file]
        exclude: LICENSE.md