micos-2024/.pre-commit-config.yaml at master · open-genomics/micos-2024 · GitHub

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# Pre-commit hooks for MICOS-2024
# 代码质量检查和格式化配置

repos:
  # Python代码格式化
  - repo: https://github.com/psf/black
    rev: 26.5.1
    hooks:
      - id: black
        language_version: python3
        args: [--line-length=88]

  # Python导入排序
  # 注: isort 9.x 为 beta，保持 5.13.2 稳定末版
  - repo: https://github.com/pycqa/isort
    rev: 5.13.2
    hooks:
      - id: isort
        args: [--profile=black, --line-length=88]

  # Python代码质量检查
  # 注: E501 忽略策略与 .flake8 保持一致
  - repo: https://github.com/pycqa/flake8
    rev: 7.3.0
    hooks:
      - id: flake8
        args: [--max-line-length=88, --extend-ignore=E203,W503,E501]

  # Python类型检查
  # 注: mypy 2.x 不支持 python_version=3.9，保持 v1.8.0 以兼容项目声明
  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.8.0
    hooks:
      - id: mypy
        additional_dependencies: [types-PyYAML, types-requests]
        args: [--ignore-missing-imports]

  # 通用文件检查
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: check-yaml
      - id: check-json
      - id: check-toml
      - id: check-xml
      - id: check-merge-conflict
      - id: check-case-conflict
      - id: check-added-large-files
        args: [--maxkb=10240]  # 10MB limit
      - id: check-executables-have-shebangs
      - id: check-shebang-scripts-are-executable

  # Shell脚本检查
  - repo: https://github.com/shellcheck-py/shellcheck-py
    rev: v0.11.0.1
    hooks:
      - id: shellcheck
        args: [--severity=warning]

  # Markdown格式检查
  - repo: https://github.com/igorshubovych/markdownlint-cli
    rev: v0.49.1
    hooks:
      - id: markdownlint
        args: [--fix]

  # YAML格式化
  # 注: mirrors-prettier 最新 tag 为 alpha (v4.0.0-alpha.8)，已移除。
  #     YAML 语法正确性由 pre-commit-hooks.check-yaml 保证。

  # 安全性检查
  # 注: 仅检查不输出报告文件，避免污染工作区。CI 中有独立 bandit 步骤输出报告。
  - repo: https://github.com/PyCQA/bandit
    rev: 1.9.4
    hooks:
      - id: bandit
        args: [-r, micos/]
        exclude: ^tests/

  # 文档字符串检查
  - repo: https://github.com/pycqa/pydocstyle
    rev: 6.3.0
    hooks:
      - id: pydocstyle
        args: [--convention=google]

# 配置选项
default_language_version:
  python: python3

# 排除的文件和目录
exclude: |
  (?x)^(
    .*\.min\.js|
    .*\.min\.css|
    node_modules/|
    .git/|
    .tox/|
    .venv/|
    venv/|
    env/|
    build/|
    dist/|
    .*\.egg-info/|
    data/|
    results/|
    logs/|
    temp/|
    tmp/|
    .*\.log|
    .*\.tmp|
    .*\.temp|
  )$

# 安装说明:
# 1. 安装pre-commit: pip install pre-commit
# 2. 安装hooks: pre-commit install
# 3. 运行所有文件检查: pre-commit run --all-files
# 4. 更新hooks: pre-commit autoupdate