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Testing Guide

Quick guide for running tests in this project.

Note

Integration and full pipeline tests likely requires specific neuroimaging tools that can be called with niwrap. To perform these tests, also pass the --runner flag to pytest.

Quick Start

# Install dependencies
pip install -e ".[dev]"

# Run fast tests (recommended during development)
pytest -m unit

# Run all tests (except slow ones)
pytest -m "not slow and not full_pipeline" --runner <local|docker|singularity>

# Run everything
pytest --runner <local|docker|singularity>

Test Categories

Marker Speed
unit <1s per test
integration 1-5 min
slow >5 min
full_pipeline 30+ min

Common Commands

Development Workflow

# Fast feedback loop (unit tests only)
pytest -m unit

# Test specific file
pytest tests/unit/test_bids_parsing.py

# Test specific function
pytest tests/unit/test_bids_parsing.py::test_parse_subject_id

Useful Options

 
# Stop on first failure
pytest -x

# Show which tests are slowest
pytest --durations=10

# Run tests matching a pattern
pytest -k "motion_correction"

Test Data

Test data is stored in tests/data/.

Coverage Requirements

  • Overall: >85%
  • Unit tests: >90%
  • Integration tests: >80%
# Check coverage
pytest --cov=src --cov-report=term-missing

# Generate HTML report
pytest --cov=src --cov-report=html

CI/CD

Tests run automatically on GitHub Actions:

  • On every push: Unit tests + fast integration tests
  • Manual trigger: Full pipeline tests (slow)

To run the same tests as CI locally:

pytest -m "not slow and not full_pipeline" \
  --cov=src \
  --cov-report=xml \
  --junitxml=pytest.xml

Directory Structure

tests/
├── conftest.py              # Shared fixtures
├── unit/                    # Fast tests (<1s)
├── integration/             # Medium tests (1-5 min)
├── full_pipeline/           # Slow tests (30+ min)
└── data/                    # Test datasets

Best Practices

  1. Run unit tests frequently - They're fast (<1s)
  2. Run integration tests before committing - Catch issues early
  3. Use appropriate markers - Auto-applied based on file location
  4. Write descriptive test names - test_motion_correction_preserves_dimensions
  5. One assertion per test - When practical
  6. Use fixtures - Don't repeat setup code
  7. Keep tests independent - No shared state between tests