Scientific Test-Driven Development

Scientific Test-Driven Development

Overview

Pragmatic test-driven development for scientific code: write tests first for new features and complex changes, verify with tests for simple bug fixes.

Core principle: Tests before implementation for new behavior, tests verify implementation for known bugs.

Announce at start: "I'm using the scientific-tdd skill to implement this feature."

When to Use This Skill

MUST use for:

• New features or algorithms
• Complex modifications to existing code
• Adding new mathematical models
• Implementing new likelihood functions or state transitions

Can skip test-first for:

• Simple bug fixes where existing tests already cover the behavior
• Documentation changes
• Refactoring with existing comprehensive tests (use safe-refactoring instead)

Process Checklist

Copy to TodoWrite:

Scientific TDD Progress:
- [ ] Understand existing behavior (read code and tests)
- [ ] Write test capturing desired new behavior
- [ ] Run test to confirm RED (fails as expected)
- [ ] Implement minimal code to pass test
- [ ] Run test to confirm GREEN (passes)
- [ ] Run full test suite (check for regressions)
- [ ] Run numerical validation if mathematical code changed
- [ ] Run code-reviewer agent (and/​or ux-reviewer when appropriate)
- [ ] Refactor if needed (keep tests green)
- [ ] Commit with descriptive message

Detailed Steps

Step 1: Understand Existing Behavior

Before writing new tests, understand current state:

• Read relevant source files
• Read existing tests for similar functionality
• Run existing tests to see current behavior
• Identify what needs to change

Commands:

# Find relevant tests
pytest --collect-only -q | grep <relevant_term>

# Run specific test file
/​Users/​edeno/​miniconda3/​envs/​non_local_detector/​bin/​pytest src/​non_local_detector/​tests/<test_file>.py -v

Step 2: Write Failing Test (RED)

Write test that captures desired behavior:

Test Structure:

def test_descriptive_name_of_behavior():
    """Test that [specific behavior] works correctly.

    This test verifies that [explain what you're testing] when [condition].
    """
    # Arrange: Set up test data
    input_data = create_test_input()

    # Act: Call the function/​method
    result = function_under_test(input_data)

    # Assert: Verify behavior
    assert result.shape == expected_shape
    assert np.allclose(result.sum(), 1.0, atol=1e-10)  # Probabilities sum to 1

For mathematical code, verify:

• Correct output shapes
• Mathematical invariants (probabilities sum to 1, matrices are stochastic)
• Expected numerical values (with appropriate tolerances)
• Edge cases (empty inputs, single element, boundary conditions)

Step 3: Run Test - Confirm RED

CRITICAL: Test MUST fail before implementing:

/​Users/​edeno/​miniconda3/​envs/​non_local_detector/​bin/​pytest src/​non_local_detector/​tests/<test_file>.py::test_name -v

Expected output: Test fails with clear error (function not defined, wrong output, etc.)

If test passes: The test isn't testing new behavior - reconsider what you're testing.

Step 4: Implement Minimal Code

Write simplest code that makes test pass:

• Don't over-engineer
• Don't add features not tested
• Follow YAGNI (You Aren't Gonna Need It)
• Use existing patterns from codebase

For scientific code:

• Maintain numerical stability
• Use JAX operations where appropriate
• Follow existing conventions for shapes and broadcasting

Step 5: Run Test - Confirm GREEN

/​Users/​edeno/​miniconda3/​envs/​non_local_detector/​bin/​pytest src/​non_local_detector/​tests/<test_file>.py::test_name -v

Expected output: Test passes

If test fails: Debug until it passes, then verify you're testing the right thing.

Step 6: Run Full Test Suite

Check for regressions:

/​Users/​edeno/​miniconda3/​envs/​non_local_detector/​bin/​pytest -v

Expected: All tests pass (same count as before)

If new failures: Your change broke something - fix before proceeding.

Step 7: Numerical Validation (if applicable)

If you modified mathematical/​algorithmic code:

Use numerical-validation skill:

@numerical-validation

This verifies:

• Mathematical invariants still hold
• Property-based tests pass
• Golden regression tests pass
• No unexpected numerical differences

Step 8: Refactor (optional)

If code can be improved while keeping tests green:

• Improve readability
• Extract reusable functions
• Optimize performance (but verify numerics don't change)

After each refactor:

/​Users/​edeno/​miniconda3/​envs/​non_local_detector/​bin/​pytest -v

Step 9: Commit

git add <test_file> <implementation_file>
git commit -m "feat: add <feature description>

- Add test for <specific behavior>
- Implement <what you implemented>
- All tests passing (<N> tests)

🤖 Generated with [Claude Code](https://claude.com/​claude-code)

Co-Authored-By: Claude <[email protected]>"

Example Workflow

Task: Add new random walk transition with custom variance

1. Read: src/​non_local_detector/​continuous_state_transitions.py
2. Read: src/​non_local_detector/​tests/​transitions/​test_continuous_transitions.py
3. Write test: test_random_walk_custom_variance()
4. Run test: FAIL - "NotImplementedError: custom variance not supported"
5. Implement: Add variance parameter to RandomWalk class
6. Run test: PASS
7. Run full suite: 427 tests passed
8. Run numerical validation: All invariants hold
9. Commit: "feat: add custom variance support to RandomWalk"

Integration with Other Skills

• Before using this skill: Often preceded by brainstorming or design discussion
• Use with numerical-validation: For mathematical code changes
• After this skill: May use safe-refactoring for cleanup
• Alternative to this skill: Use safe-refactoring if changing structure, not behavior

Red Flags

Don't:

• Write implementation before test (except for documented bug fixes)
• Skip running test to see it fail
• Add untested code "for future use"
• Skip full test suite after implementation
• Commit failing tests
• Skip numerical validation for mathematical code

Do:

• Write descriptive test names
• Test one behavior per test
• Use appropriate numerical tolerances (1e-10 for probabilities)
• Run tests frequently
• Commit small, working increments
• Ask if unsure whether to use TDD for a specific change