blastdock/.pre-commit-config.yaml at main · BlastDock/blastdock · GitHub

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repos:
  # General file cleanup
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.5.0
    hooks:
      - id: trailing-whitespace
        exclude: \.md$
      - id: end-of-file-fixer
        exclude: \.md$
      - id: check-yaml
        args: ['--unsafe']  # Allow custom YAML tags in templates
      - id: check-json
      - id: check-added-large-files
        args: ['--maxkb=1000']
      - id: check-merge-conflict
      - id: check-case-conflict
      - id: detect-private-key
      - id: mixed-line-ending
        args: ['--fix=lf']

  # Python code formatting
  - repo: https://github.com/psf/black
    rev: 24.10.0
    hooks:
      - id: black
        language_version: python3.8
        args: ['--line-length=88']
        exclude: ^(build/|dist/|\.eggs/|\.git/|\.venv/|venv/)

  # Python import sorting
  - repo: https://github.com/pycqa/isort
    rev: 5.13.2
    hooks:
      - id: isort
        args: ['--profile', 'black']
        exclude: ^(build/|dist/|\.eggs/|\.git/|\.venv/|venv/)

  # Python linting
  - repo: https://github.com/pycqa/flake8
    rev: 7.0.0
    hooks:
      - id: flake8
        args: ['--max-line-length=127', '--extend-ignore=E203,W503']
        exclude: ^(build/|dist/|\.eggs/|\.git/|\.venv/|venv/)

  # Python type checking (optional - can be slow)
  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.8.0
    hooks:
      - id: mypy
        additional_dependencies: [types-all]
        args: ['--ignore-missing-imports', '--no-strict-optional']
        exclude: ^(tests/|build/|dist/|\.eggs/|\.git/|\.venv/|venv/)

  # Security checks
  - repo: https://github.com/PyCQA/bandit
    rev: 1.7.6
    hooks:
      - id: bandit
        args: ['-ll', '-i']  # Low severity, ignore informational
        exclude: ^(tests/|build/|dist/)

  # Markdown linting
  - repo: https://github.com/igorshubovych/markdownlint-cli
    rev: v0.38.0
    hooks:
      - id: markdownlint
        args: ['--fix']
        exclude: ^(CHANGELOG\.md|node_modules/)

# Configuration
default_language_version:
  python: python3.11

fail_fast: false

# CI configuration
ci:
  autofix_commit_msg: |
    [pre-commit.ci] auto fixes from pre-commit hooks
  autofix_prs: true
  autoupdate_branch: ''
  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
  autoupdate_schedule: weekly
  skip: []
  submodules: false