Fix test function name in test_score2.py

[fbraza]

Summary

• Renamed test function from test_phenoage to test_score2 to match what it's actually testing
• Fixes Fix test function name in test_score2.py #4

Changes

• Updated function name in tests/test_score2.py:17 from test_phenoage to test_score2
• The function tests the SCORE2 cardiovascular risk algorithm, not PhenoAge

Test plan

• Run uv run pytest tests/test_score2.py -v to ensure tests still pass
• Verified that both test cases pass with the renamed function

🤖 Generated with opencode

[claude]

Claude finished @fbraza's task —— View job

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Code Review Complete ✅

I've thoroughly analyzed this pull request and provide the following feedback:

Review Tasks:

• Analyze the changed files to understand full scope
• Review the test function rename (test_phenoage → test_score2)
• Check for code quality and best practices
• Identify potential bugs or issues
• Assess performance considerations
• Review security concerns
• Evaluate test coverage

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Summary

This is a well-executed and necessary fix that correctly addresses the mismatch between the test function name and its actual purpose.

✅ Positive Aspects

1. Correct Fix: The rename from test_phenoage to test_score2 aligns the function name with its actual behavior - testing the SCORE2 cardiovascular risk algorithm in tests/test_score2.py:17.

2. Good Test Structure:

   • Uses proper pytest parametrization for multiple test cases
   • Tests realistic patient scenarios (patients 25 & 26)
   • Validates all key outputs: age, risk score, and risk category
   • Uses appropriate floating-point comparison with pytest.approx()

3. Code Quality:

   • Clean, readable code structure
   • Proper type annotations throughout the codebase
   • Well-documented functions with clear docstrings
   • Consistent code style and formatting

4. Robust Implementation: The SCORE2 algorithm implementation follows medical guidelines correctly with proper sex-specific coefficients, baseline survival rates, and regional calibration.

🔍 Observations

1. Test Coverage: The tests cover the main happy path but could be enhanced with edge cases (boundary ages, extreme biomarker values).

2. Minor Code Patterns:

   • The biomarker extraction logic in helpers.py:147-190 is well-designed and reusable
   • Good separation of concerns between data processing and algorithm implementation

🛡️ Security & Performance

• Security: ✅ No security concerns - code handles file I/O safely with proper error handling
• Performance: ✅ Efficient - uses NumPy for mathematical operations and avoids unnecessary computations
• Error Handling: ✅ Proper validation with informative error messages

🧪 Test Assessment

The test validates:

• ✅ Correct age extraction (50.00)
• ✅ Risk score calculation with appropriate tolerance (±0.1)
• ✅ Risk categorization ("Low to moderate", "High")

Test data appears valid for 50-year-old patients with risk scores of 4.34% and 6.31%.

📋 Recommendations

1. Consider adding edge case tests:

   # Test boundary ages (40, 49, 50, 69)
   # Test extreme biomarker values
   # Test invalid input handling

2. The PR scope is appropriate - focused on the specific issue without unnecessary changes.

✅ Final Assessment

This is a clean, focused fix that resolves issue #4 correctly. The code quality is high, tests are well-structured, and the change is exactly what was needed - no more, no less.

Recommendation: APPROVE ✅

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