Safe Refactoring for Scientific Code

Overview

Change code structure without changing behavior. Zero tolerance for behavioral changes during refactoring.

Core principle: Establish baseline, refactor, verify exact match (within floating-point noise).

Announce at start: "I'm using the safe-refactoring skill to restructure this code."

When to Use This Skill

Use for:

• Improving code readability without changing logic
• Extracting reusable functions
• Renaming variables/functions for clarity
• Reorganizing code structure
• Performance optimization (without changing numerical behavior)

Don't use for:

• Changing behavior or algorithms (use scientific-tdd instead)
• Adding new features (use scientific-tdd instead)
• Fixing bugs (use scientific-tdd or fix directly with tests)

Process Checklist

Copy to TodoWrite:

Safe Refactoring Progress:
- [ ] Run full test suite (establish baseline)
- [ ] Run snapshot tests (establish baseline)
- [ ] Capture coverage report
- [ ] Perform refactoring
- [ ] Run full test suite (must match baseline exactly)
- [ ] Run snapshot tests (must match baseline exactly)
- [ ] Compare coverage (should stay same or improve)
- [ ] Run quality checks (ruff + black)
- [ ] Verify no numerical differences
- [ ] Commit refactoring

Strict Rules

ZERO tolerance for:

• Any test that passed before and fails after
• Any test that failed before and passes after (suggests test was broken)
• Any snapshot differences (not even floating-point noise)
• Decreased test coverage
• Any behavioral changes

If any of these occur: Revert and investigate why.

Detailed Steps

Step 1: Run Full Test Suite (Baseline)

/Users/edeno/miniconda3/envs/non_local_detector/bin/pytest -v 2>&1 | tee /tmp/baseline_tests.txt

Record:

• Total tests: grep "passed" /tmp/baseline_tests.txt
• Any failures (if refactoring existing code with known issues)
• Test execution time

Expected: All tests pass (or document any known failures)

Step 2: Run Snapshot Tests (Baseline)

/Users/edeno/miniconda3/envs/non_local_detector/bin/pytest -m snapshot -v 2>&1 | tee /tmp/baseline_snapshots.txt

CRITICAL: Snapshots must match exactly after refactoring.

Expected: All snapshot tests pass

Step 3: Capture Coverage Report

/Users/edeno/miniconda3/envs/non_local_detector/bin/pytest --cov=non_local_detector --cov-report=term --cov-report=json:coverage_baseline.json

Record: Coverage percentage for files being refactored

Why: Coverage should not decrease during refactoring (ideally improves)

Step 4: Perform Refactoring

Refactoring techniques:

1. Extract function:

   pythonCopy

   # Before
   def complex_function():
       # ... 50 lines of code
       result = x * 2 + y
       # ... more code
       return final_result
   
   # After
   def complex_function():
       # ... code
       result = _calculate_intermediate(x, y)
       # ... code
       return final_result
   
   def _calculate_intermediate(x, y):
       return x * 2 + y
   

2. Rename for clarity:

   pythonCopy

   # Before
   def f(x):
       return x * 2
   
   # After
   def calculate_doubled_value(value):
       return value * 2
   

3. Reorganize structure:

   pythonCopy

   # Before: All in one file
   
   # After: Separated into modules
   # - core_logic.py
   # - utilities.py
   # - validation.py
   

4. Optimize performance (numerically equivalent):

   pythonCopy

   # Before
   for i in range(n):
       result[i] = f(x[i])
   
   # After (JAX)
   result = jax.vmap(f)(x)
   

During refactoring:

• Make small, incremental changes
• Test after each change if possible
• Keep numerical operations identical
• Maintain exact same algorithms

Step 5: Run Full Test Suite (Verify Match)

/Users/edeno/miniconda3/envs/non_local_detector/bin/pytest -v 2>&1 | tee /tmp/refactored_tests.txt

Compare to baseline:

diff /tmp/baseline_tests.txt /tmp/refactored_tests.txt

MUST verify:

• Same number of tests run
• Same tests pass
• Same tests fail (if any)
• Similar execution time (within 20%)

If differences:

• Any new test failures: REVERT IMMEDIATELY
• Any new test passes: Investigate (test was broken?)
• Different test count: Investigate (tests missing or duplicated?)

Step 6: Run Snapshot Tests (Verify Match)

/Users/edeno/miniconda3/envs/non_local_detector/bin/pytest -m snapshot -v 2>&1 | tee /tmp/refactored_snapshots.txt

CRITICAL: Must match baseline EXACTLY.

Expected: All snapshot tests pass, no differences

If snapshot differences:

1. DO NOT UPDATE SNAPSHOTS
2. Investigate why behavior changed
3. This is NOT a refactoring if behavior changed
4. Revert and reconsider approach

Step 7: Compare Coverage

/Users/edeno/miniconda3/envs/non_local_detector/bin/pytest --cov=non_local_detector --cov-report=term --cov-report=json:coverage_refactored.json

Compare:

# If you have jq installed
jq '.totals.percent_covered' coverage_baseline.json
jq '.totals.percent_covered' coverage_refactored.json

Expected:

• Coverage stays same or improves
• Never decreases

If coverage decreased:

• Some code paths no longer tested
• Investigate and fix or revert

Step 8: Run Quality Checks

/Users/edeno/miniconda3/envs/spectral_connectivity/bin/ruff check src/
/Users/edeno/miniconda3/envs/spectral_connectivity/bin/ruff format src/
/Users/edeno/miniconda3/envs/non_local_detector/bin/black src/

Expected: All checks pass

Fix any issues: Refactoring is good opportunity to improve code quality

Step 9: Verify No Numerical Differences

For mathematical code, verify numerical equivalence:

# Run golden regression
/Users/edeno/miniconda3/envs/non_local_detector/bin/pytest \
  src/non_local_detector/tests/test_golden_regression.py -v

Expected: Exact match (or differences < 1e-14)

If differences > 1e-14:

• This is NOT a pure refactoring
• Behavior has changed
• Use numerical-validation skill instead

Step 10: Commit Refactoring

Only commit if ALL checks pass:

git add <refactored_files> <test_files>
git commit -m "refactor: improve <component> code structure

- Extract <function> for reusability
- Rename <variable> for clarity
- Reorganize <module> structure

No behavioral changes:
- All tests pass (N tests)
- Snapshots unchanged
- Coverage: X% → Y%

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

Co-Authored-By: Claude <noreply@anthropic.com>"

Performance Optimization Refactoring

When optimizing for performance:

1. Capture performance baseline:

   bashCopy

   pytest --durations=10 > /tmp/baseline_durations.txt
   

2. Make optimization

3. Verify numerical equivalence (use numerical-validation skill)

4. Measure performance improvement:

   bashCopy

   pytest --durations=10 > /tmp/optimized_durations.txt
   

5. Document improvement:

   Copy

   Optimization: Use JAX vmap instead of for loop
   Speedup: 3.2x (450ms → 140ms)
   Numerical difference: < 1e-14 (verified)
   

Integration with Other Skills

• Before refactoring: Consider if change actually needs new behavior (use scientific-tdd instead)
• With numerical-validation: If refactoring mathematical code, use numerical-validation to verify equivalence
• With jax skill: When optimizing JAX code, use jax skill for best practices

Example Workflow

Task: Extract position decoding logic into reusable function

1. Baseline:
   - Run pytest: 427 passed, 0 failed
   - Run snapshots: 15 passed, 0 failed
   - Coverage: 69%

2. Refactor:
   - Extract _decode_position_from_posterior() function
   - Update 3 call sites to use new function
   - No logic changes, just extraction

3. Verify:
   - Run pytest: 427 passed, 0 failed ✓
   - Run snapshots: 15 passed, 0 failed ✓
   - Coverage: 69% (unchanged) ✓

4. Quality:
   - Ruff: All checks pass ✓
   - Black: Formatted ✓

5. Commit:
   "refactor: extract position decoding into reusable function"

Red Flags

STOP and revert if:

• Any test changes status (pass → fail or fail → pass)
• Any snapshot differences appear
• Coverage decreases
• Numerical differences > 1e-14
• You're tempted to update snapshots
• You're adding new logic (use scientific-tdd instead)

Safe to proceed if:

• All tests match baseline exactly
• No snapshot changes
• Coverage same or better
• Code quality improves
• No new functionality added

Common Mistakes

"It's just a small behavioral change"

• No such thing in refactoring
• Any behavioral change = not refactoring
• Use scientific-tdd for behavioral changes

"I'll update the snapshots since the new output is better"

• That's not refactoring, it's changing behavior
• Refactoring = zero snapshot changes
• Use scientific-tdd if output should change

"Tests are slow, I'll skip them"

• Never skip tests during refactoring
• Tests are your safety net
• Without tests, you can't verify it's a refactoring

"Coverage went down but the code is better"

• Better code shouldn't lose coverage
• Investigate why coverage decreased
• Fix or revert