README.md

Testing

Note

Integration and full pipeline tests require neuroimaging tools via niwrap. Pass --runner <local|docker|singularity> to select how they run.

Running tests

# Unit tests only (fast, no runner needed)
pytest -m unit

# Quick integration tests
pytest -m "integration and not slow" --runner docker

# All integration tests (including slow)
pytest -m integration --runner docker

# Full pipeline
pytest -m full_pipeline --runner docker

# Everything
pytest --runner docker

Test tiers

Directory-based markers (unit, integration, full_pipeline) are auto-applied by conftest.py. The slow marker is applied manually on individual long-running integration tests.

Marker	Source	Typical duration
unit	auto (dir)	< 1 s per test
integration	auto (dir)	1–5 min
slow	manual	5–30 min
full_pipeline	auto (dir)	30+ min

Directory structure

tests/
├── conftest.py        # Shared fixtures (auto-markers, niwrap runner, test subject)
├── unit/              # Pure logic: BIDS parsing, file helpers
├── integration/       # Single-tool runs with real data (@slow on long ones)
├── full_pipeline/     # End-to-end workflow tests
└── data/              # Test datasets (not in version control)

Coverage

pytest --cov=src --cov-report=term-missing