repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v2.3.0
    hooks:
      - id: end-of-file-fixer
      - id: trailing-whitespace
      - id: check-yaml
        exclude: "mkdocs.yml"
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.9.10
    hooks:
      - id: ruff
        # 1. Attempt to automatically fix any lint issues.
        args: ["--fix"]
      - id: ruff-format
  - repo: https://github.com/Yelp/detect-secrets
    rev: v1.5.0
    hooks:
      - id: detect-secrets
        name: detect-secrets (everything but notebooks)
        args: ['--baseline', '.secrets.baseline', '--exclude-files', '(.*\.ipynb|.*\.baseline)$', ]
        exclude: package.lock.json
      - id: detect-secrets
        name: detect-secrets (notebooks only)
        args: ['--baseline', '.secrets-nb.baseline', '--exclude-files', '^.(?!.*\.ipynb)', '--exclude-lines', '"(hash|id|image/\w+)":.*|<.*at 0x[0-9a-f]+>|object at 0x[0-9a-f]+', ]
  - repo: local
    hooks:
      - id: license-header-check
        name: Run license-check script
        entry: python internal/infra-bionemo/src/infra_bionemo/license_check.py -c scripts -c sub-packages -c docs -c internal --license-header ./license_header --modify
        language: python
        additional_dependencies: ["click==8.1.7"]
        pass_filenames: false
        always_run: true