.pre-commit-config.yaml

repos:
  - repo: https://github.com/PyCQA/isort
    rev: 5.13.2
    hooks:
      - id: isort
        args: ["--profile", "black"]
        types: [python]
        exclude: '^data|^src/bio_datasets/structure/pdbx'

  - repo: https://github.com/psf/black
    rev: 22.10.0
    hooks:
      - id: black
        types: [python]
        exclude: '^data|.*\.pdb$|.*\.cif|.*\.bcif|^src/bio_datasets/structure/pdbx'
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v2.3.0
    hooks:
      - id: check-yaml
        exclude: '^data|.*\.pdb$|.*\.cif$|.*\.bcif|^src/bio_datasets/structure/protein/library|^src/bio_datasets/structure/pdbx'
      - id: end-of-file-fixer
        exclude: '^data|.*\.pdb$|.*\.cif$|.*\.bcif|^src/bio_datasets/structure/protein/library|^src/bio_datasets/structure/pdbx'
      - id: trailing-whitespace
        exclude: '^data|.*\.pdb$|.*\.cif$|.*\.bcif|^src/bio_datasets/structure/protein/library|^src/bio_datasets/structure/pdbx'
        # exclude: '^data|^scripts/gvp'
  - repo: https://github.com/pycqa/flake8
    rev: 6.0.0  # Use the latest stable version
    hooks:
      - id: flake8
        exclude: '^examples|^src/bio_datasets/structure/pdbx'
        name: "Linter"
        types: [python]
        args:
          # - --config=pyproject.toml  # TODO: fix this
          - --ignore=E501,W503,W391,E203,N806,E266
          - --max-cognitive-complexity=13
          - --max-line-length=88
        additional_dependencies:
          - pep8-naming
          - flake8-builtins
          - flake8-comprehensions
          - flake8-bugbear
          - flake8-pytest-style
          - flake8-cognitive-complexity