.pre-commit-config.yaml

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.5.0
    hooks:
      - id: check-merge-conflict
      - id: check-added-large-files
      - id: debug-statements
      - id: mixed-line-ending
      - id: check-case-conflict
      - id: check-yaml
      - id: trailing-whitespace
      - id: end-of-file-fixer
  - repo: https://github.com/asottile/reorder_python_imports
    rev: v3.12.0
    hooks:
      - id: reorder-python-imports
        args: [--application-directories=python, --unclassifiable-application-module=_tskit]
  - repo: https://github.com/asottile/pyupgrade
    rev: v3.15.0
    hooks:
      - id: pyupgrade
        args: [--py3-plus, --py37-plus]
  - repo: https://github.com/psf/black
    rev: 23.3.0
    hooks:
      - id: black
        language_version: python3
  - repo: https://github.com/charliermarsh/ruff-pre-commit
    rev: "v0.1.11"
    hooks:
      - id: ruff
        args:
          [
          "--ignore=F821",
          ]
  - repo: https://github.com/asottile/blacken-docs
    rev: 1.16.0
    hooks:
      - id: blacken-docs
        additional_dependencies: [black==22.12.0]
        language_version: python3
  - repo: https://github.com/snakemake/snakefmt
    rev: v0.8.5
    hooks:
      - id: snakefmt
  - repo: local
    hooks:
      - id: lint
        name: Snakemake lint
        entry: snakemake --configfile config/config.yaml --configfile config/envmodules.yaml --lint text -v -s
        language: system
        log_file: 'snakemake-lint.txt'
        files: '.*\.smk$|Snakefile'
        exclude: .*/test-.*\.smk$
  - repo: https://github.com/DavidAnson/markdownlint-cli2
    rev: v0.11.0
    hooks:
      - id: markdownlint-cli2
        files: \.(md|qmd)$
        types: [file]
        exclude: LICENSE.md
      - id: markdownlint-cli2-fix
        files: \.(md|qmd)$
        types: [file]
        exclude: LICENSE.md