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GenoPHI Test Suite

This directory contains the test suite for the GenoPHI package, organized into multiple tiers for different testing scenarios.

Test Organization

Test Tiers

Smoke Tests (test_smoke.py)

  • Quick package installation verification
  • Runtime: <5 seconds
  • Run with: pytest -m smoke

Unit Tests

  • Test individual functions with simple/mock data
  • Runtime: seconds
  • Run with: pytest -m unit

Integration Tests (tests/integration/)

  • Test module-to-module interactions
  • Use small test datasets (5-10 samples)
  • Runtime: ~30-45 minutes
  • Run with: pytest -m integration

End-to-End Tests (tests/e2e/)

  • Test complete workflows with reduced parameters
  • Runtime: ~60-90 minutes
  • Run with: pytest -m e2e

Full Regression Tests

  • Complete workflows with production parameters
  • Runtime: ~2-3 hours
  • Run with: pytest -m full

Running Tests

Quick Validation (Recommended for development)

# Run smoke tests only
pytest -m smoke -v

# Run smoke + unit tests
pytest -m "smoke or unit" -v

Standard Testing (Pre-commit/PR)

# Run integration tests (excludes slow tests)
pytest -m "integration and not slow" -v

# Run all integration tests
pytest tests/integration/ -v

Full Testing (Pre-release)

# Run all tests
pytest -v

# Run only tests that require MMSeqs2
pytest -m requires_mmseqs2 -v

# Run integration + E2E (skip full regression)
pytest -m "integration or e2e" -v

Selective Testing

# Skip tests that require MMSeqs2 (useful for quick checks)
pytest -m "not requires_mmseqs2" -v

# Run only slow tests
pytest -m slow -v

# Run specific test file
pytest tests/test_smoke.py -v

# Run specific test function
pytest tests/test_smoke.py::test_package_import -v

Test Markers

  • smoke: Quick installation verification (<5 sec)
  • unit: Unit tests for individual functions
  • integration: Module-to-module interaction tests (~30-45 min)
  • e2e: End-to-end workflow tests (~60-90 min)
  • slow: Long-running tests (>30 min)
  • full: Full regression tests (~2-3 hours)
  • requires_mmseqs2: Tests requiring MMSeqs2 installation

Test Data

Test data is located in /data/test_data/:

  • strain_AAs/: 25 E. coli strain proteomes (FASTA)
  • phage_AAs/: 25 phage proteomes (FASTA)
  • ecoli_test_interaction_matrix.csv: Interaction matrix (625 interactions)

Tests use subsets of this data:

  • Small dataset: 5 strains/phages
  • Medium dataset: 10 strains/phages
  • Full dataset: All 25 strains/phages

Continuous Integration Recommendations

On Every Commit

pytest -m smoke

On Pull Requests

pytest -m "integration and not slow"

On Release

pytest -v

Test Development Guidelines

  1. Write smoke tests for new modules/workflows
  2. Add integration tests for module interactions
  3. Mark tests appropriately with pytest markers
  4. Use fixtures from conftest.py for test data
  5. Keep tests isolated - each test should be independent
  6. Document test purpose in docstrings

Troubleshooting

Tests fail with "MMSeqs2 not found"

  • Ensure MMSeqs2 is installed and in PATH
  • Or skip these tests: pytest -m "not requires_mmseqs2"

Tests timeout

  • Increase timeout in pytest.ini
  • Or run with: pytest --timeout=1200

Structure

tests/
├── README.md                    # This file
├── pytest.ini                   # Pytest configuration
├── conftest.py                  # Shared fixtures
├── test_smoke.py               # Smoke tests
├── integration/                 # Integration tests
│   ├── test_clustering_to_features.py
│   ├── test_features_to_selection.py
│   ├── test_selection_to_modeling.py
│   └── test_kmer_pipeline.py
├── e2e/                        # End-to-end tests
│   └── test_protein_family_workflow.py
└── utils/                      # Test utilities
    └── test_helpers.py