.pre-commit-config.yaml

exclude: ^docs/

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.3.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: check-yaml
      - id: check-added-large-files
        args: ['--maxkb=92160']

  # - repo: https://github.com/psf/black
  #   rev: 24.10.0
  #   hooks:
  #     - id: black
  #       name: Format Python code with Black
  #       language_version: python3

  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.14.1
    hooks:
      - id: mypy
        name: Static type checking with MyPy
        exclude: ^bioneuralnet/network/pysmccnet/
        args: [
          --ignore-missing-imports,
          --follow-imports=silent,
        ]

  - repo: local
    hooks:
      - id: remove-pyc-and-pycache
        name: Remove .pyc files and __pycache__ directories
        entry: bash -c 'find . \( -path "./.enviroment" -o -path "./.testing" -o -path "./.venv" -o -path "./docs" -o -path "./node_modules" \) -prune -o -type f -name "*.pyc" -exec rm -f {} + -o -type d -name "__pycache__" -exec rm -rf {} +'
        pass_filenames: false
        language: system
        stages: [pre-commit]

      - id: clean-coverage-files
        name: Remove stale .coverage files
        entry: bash -c "find . -name '.coverage*' -exec rm -f {} + 2>/dev/null || true"
        language: system
        stages: [pre-commit]

      - id: check-forbidden-files
        name: Prevent adding forbidden file types except in allowed directory
        entry: |
          bash -c '
          FILES="$(git diff --cached --name-only)"
          if echo "$FILES" | grep -E "\.RData$"; then
            echo "Forbidden file types detected (RData)!"
            exit 1
          fi
          if echo "$FILES" | grep -E "\.csv$" | grep -vE "^bioneuralnet/datasets/(example|brca|monet)/"; then
            echo "Forbidden CSV files detected (outside allowed folders)!"
            exit 1
          fi
          '
        language: system
        stages: [pre-commit]

      - id: run-tests
        name: Run Tests with Pytest
        entry: bash -c "pytest tests"
        language: system
        types: [python]