Testing Guide¶

Running Tests¶

All Tests (Local Development)¶

make test

Unit Tests Only (Excluding Integration Tests)¶

uv run python -m pytest tests -m "not integration"

Integration Tests Only¶

uv run python -m pytest tests -m "integration"

Test Categories¶

Unit Tests¶

Run without external API calls
Fast and reliable
Always run in CI

Integration Tests¶

Make real API calls to external services (PubMed, cBioPortal, etc.)
Marked with @pytest.mark.integration
May fail due to:
Network issues
API rate limiting
Service availability
Run separately in CI with continue-on-error: true

CI/CD Testing Strategy¶

Pull Requests & Main Branch:
Run unit tests only (-m "not integration")
Ensures fast, reliable CI runs
Prevents flaky test failures
Integration Tests:
Run in a separate optional job
Allowed to fail without blocking CI
Useful for monitoring API availability

Writing New Tests¶

Unit Test Example¶

@pytest.mark.asyncio
async def test_search_articles():
    """Test article search functionality."""
    # Mock external API calls
    with patch("biomcp.articles.search.fetch_articles") as mock_fetch:
        mock_fetch.return_value = {"results": [...]}
        # Test code here

Integration Test Example¶

@pytest.mark.asyncio
@pytest.mark.integration  # This marks it as an integration test
async def test_real_api_call():
    """Test real API interaction."""
    # Makes actual API calls
    result = await fetch_from_pubmed("BRAF")
    assert result is not None

Troubleshooting Test Failures¶

Integration Test Failures¶

If integration tests fail in CI:

Check if the external API is available
Look for rate limiting messages
Verify network connectivity
These failures don't block merges

Running Tests with Coverage¶

make cov

This generates an HTML coverage report in htmlcov/.