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bids-utils — Project Instructions

Pre-Commit Gate: tox Must Pass

MANDATORY: Before committing ANY code changes, run tox and verify ALL environments pass. Never auto-commit if tox fails.

# Run full tox suite
tox

# Or run individual envs to iterate faster
tox -e py312        # tests
tox -e lint         # ruff
tox -e type         # mypy
tox -e duplication  # pylint duplicate-code

If any environment fails:

  1. Fix the issue
  2. Re-run the failing environment to confirm the fix
  3. Run the full tox suite once more
  4. Only then commit

Project Layout

  • src/bids_utils/ — library code (private modules prefixed with _)
  • src/bids_utils/cli/ — CLI commands (thin wrappers over library)
  • tests/ — pytest test suite
  • tests/integration/ — integration tests requiring bids-examples

Testing

  • pytest orchestrated by tox with tox-uv
  • bids-examples is a git submodule used for integration tests
  • AI-generated tests must be marked @pytest.mark.ai_generated

Dependencies

  • bidsschematools — BIDS schema access (core dep)
  • click — CLI framework (core dep)
  • packaging — version comparison for migration (core dep)
  • All version specs live in pyproject.toml (single source of truth)