.pre-commit-config.yaml

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.1.0
    hooks:
      - id: check-merge-conflict
      - id: debug-statements
      - id: mixed-line-ending
      - id: check-case-conflict
      - id: check-yaml
      - id: trailing-whitespace
  - repo: https://github.com/asottile/reorder_python_imports
    rev: v3.0.1
    hooks:
      - id: reorder-python-imports
        args: [--application-directories=python,
               --unclassifiable-application-module=_tskit]
  - repo: https://github.com/asottile/pyupgrade
    rev: v2.31.1
    hooks:
      - id: pyupgrade
        args: [--py3-plus, --py37-plus]
  - repo: https://github.com/psf/black
    rev: 22.3.0
    hooks:
      - id: black
        language_version: python3
  - repo: https://github.com/PyCQA/flake8
    rev: 4.0.1
    hooks:
    - id: flake8
      args: [--max-line-length=89]
      additional_dependencies: ["flake8-bugbear==22.3.23", "flake8-builtins==1.5.3"]
      exclude: src/datasources/workflow/scripts
  - repo: https://github.com/asottile/blacken-docs
    rev: v1.12.1
    hooks:
      - id: blacken-docs
        args: [--skip-errors]
        additional_dependencies: [black==22.3.0]
        language_version: python3
  - repo: https://github.com/snakemake/snakefmt
    rev: 0.4.4
    hooks:
      - id: snakefmt
  - repo: local
    hooks:
      - id: lint
        name: Snakemake lint
        entry: snakemake --lint text --snakefile src/datasources/workflow/Snakefile --directory src/datasources/
        language: system
        files: ''