.pre-commit-config.yaml

default_stages: [ "pre-commit", "commit-msg", "pre-push" ]
default_language_version:
  python: python3.12

repos:
  - repo: https://github.com/timothycrosley/isort
    rev: 5.12.0
    hooks:
      - id: isort

  - repo: https://github.com/psf/black
    rev: 24.2.0
    hooks:
      - id: black
        name: "Code formatter"
        exclude: notebooks/

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
      - id: end-of-file-fixer
        name: "End of file fixer"
        exclude: docker/template.env *.fasta
      - id: debug-statements
        name: "Debug imports and breakpoints checker"
      - id: requirements-txt-fixer
        name: "Requirements txt fixer"
      - id: mixed-line-ending
        name: "Mixed line ending fixer"
      - id: check-yaml
        name: "Yaml checker"
        args: [ '--unsafe' ]
      - id: trailing-whitespace
        name: "Trailing whitespace fixer"

  - repo: https://github.com/PyCQA/flake8
    rev: 7.3.0
    hooks:
      - id: flake8
        # E203 - ":" with whitespace before it
        # W503 - line break before binary operator (conflicts with other pre-commit hooks).
        # CCR001 - Cognitive complexity (it's too annoying - write the functions you want ;)).
        # C408 - allow to write dict() instead of rewriting as literal
        name: "Linter"
        args:
          - --config=setup.cfg
          - --ignore=E203,W503,CCR001,C408
          - --max-line-length=88
        additional_dependencies:
          - pep8-naming
          - flake8-builtins
          - flake8-comprehensions
          - flake8-bugbear
          - flake8-pytest-style
          - flake8-cognitive-complexity

  - repo: https://github.com/compilerla/conventional-pre-commit
    rev: v2.3.0
    hooks:
      - id: conventional-pre-commit
        name: "Commit linter"
        stages: [ commit-msg ]
        args: [ ci, build, docs, feat, fix, perf, refactor, style, test, EXP, revert, chore, config, release, cleanup]