.pre-commit-config.yaml

# See https://pre-commit.com for more information
# See https://pre-commit.com/hooks.html for more hooks
repos:
  - repo: https://github.com/ilsenatorov/pre-commit-jupyter
    rev: v1.3.2
    hooks:
      - id: jupyter-notebook-cleanup
        args: [--remove-cell-metadata, --remove-kernel-metadata]

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.4.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: mixed-line-ending
      - id: check-yaml
      - id: check-json
      - id: check-merge-conflict
      - id: check-case-conflict
  - repo: https://github.com/timothycrosley/isort
    rev: 5.12.0
    hooks:
      - id: isort
  - repo: https://github.com/ambv/black
    rev: 23.3.0
    hooks:
      - id: black
  - repo: https://github.com/pycqa/flake8
    rev: 6.0.0
    hooks:
      - id: flake8
  - repo: https://github.com/snakemake/snakefmt
    rev: v0.8.4
    hooks:
      - id: snakefmt
  - repo: https://github.com/econchick/interrogate
    rev: 1.5.0
    hooks:
      - id: interrogate
        args: [-vv]
        exclude: ^test/

ci:
  autofix_commit_msg: |
    [skip ci] auto fixes from pre-commit hooks