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