omni-medical-suite/.pre-commit-config.yaml at main · DrAbdulmalek/omni-medical-suite · GitHub

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repos:
  # ===================================================================
  # ruff — Python linter + formatter (replaces flake8, black, isort)
  # ===================================================================
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.8.6
    hooks:
      - id: ruff
        args: [--fix, --config=ruff.toml]
        files: ^(src|packages|app|tests|scripts)/.*\.py$
        exclude: ^(packages/omniparse|packages/omni-ocr)/
      - id: ruff-format
        args: [--config=ruff.toml]
        files: ^(src|packages|app|tests|scripts)/.*\.py$
        exclude: ^(packages/omniparse|packages/omni-ocr)/

  # ===================================================================
  # Standard pre-commit hooks
  # ===================================================================
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0
    hooks:
      - id: trailing-whitespace
        exclude: \.(png|jpg|jpeg|gif|svg|ico)$
      - id: end-of-file-fixer
        exclude: \.(png|jpg|jpeg|gif|svg|ico)$
      - id: check-yaml
        args: [--unsafe]
      - id: check-json
      - id: check-toml
      - id: check-added-large-files
        args: [--maxkb=500]
      - id: check-merge-conflict
      - id: check-case-conflict
      - id: detect-private-key
      - id: check-executables-have-shebangs
      - id: no-commit-to-branch
        args: [--branch, main, --branch, develop]

  # ===================================================================
  # Security: detect secrets
  # ===================================================================
  - repo: https://github.com/Yelp/detect-secrets
    rev: v1.5.0
    hooks:
      - id: detect-secrets
        args: [--baseline, .secrets.baseline, --exclude-files, '.*/samples/.*']
        exclude: package-lock\.json

  # ===================================================================
  # Security: bandit (Python security linter)
  # ===================================================================
  - repo: https://github.com/PyCQA/bandit
    rev: 1.8.0
    hooks:
      - id: bandit
        args: [-ll, -x, tests, packages/omniparse, packages/omni-ocr]
        additional_dependencies: ["bandit[toml]"]

  # ===================================================================
  # Docstring enforcement (optional — enable incrementally)
  # ===================================================================
  # - repo: https://github.com/pycqa/pydocstyle
  #   rev: 6.3.0
  #   hooks:
  #     - id: pydocstyle
  #       args: [--convention=pep257, --add-ignore=D100,D104,D105,D107]
  #       files: ^(src|packages|app)/.*\.py$
  #       exclude: ^(packages/omniparse|packages/omni-ocr)/

# ===================================================================
# Global settings
# ===================================================================
ci:
  autoupdate_schedule: weekly
  skip: [bandit]  # bandit is slow; run in CI only
  autofix_commit_msg: "style: auto-fix by pre-commit hooks"
  fail_fast: false

default_stages: [pre-commit, pre-push]

minimum_pre_commit_version: "3.0.0"