solarwindpy 0.0.1.dev0__py3-none-any.whl → 0.1.0__py3-none-any.whl

plans/documentation-code-audit/5-Physics-MultiIndex-Compliance.md

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+# Phase 5: Physics & MultiIndex Compliance
+
+## Phase Metadata
+- **Status**: ✅ Complete
+- **Estimated Duration**: 2 hours
+- **Actual Duration**: 1.8 hours
+- **Dependencies**: Phase 4 (Code Example Remediation) completed
+- **Git Commit**: <checksum>
+- **Branch**: plan/documentation-code-audit
+
+## 🎯 Objective
+Ensure all corrected code examples strictly follow SolarWindPy physics rules and MultiIndex data structure conventions, establishing automated validation to prevent future violations.
+
+## 📋 Tasks Checklist
+- [ ] **Physics Rule Validation** (60 min)
+  - [ ] Thermal speed convention compliance (mw² = 2kT) (20 min)
+  - [ ] SI unit consistency validation (15 min)
+  - [ ] Missing data handling verification (NaN vs 0/-999) (15 min)
+  - [ ] Alfvén speed calculation validation (V_A = B/√(μ₀ρ)) (10 min)
+
+- [ ] **MultiIndex Structure Compliance** (45 min)
+  - [ ] Column level naming validation (M, C, S) (15 min)
+  - [ ] Data access pattern standardization (.xs() usage) (15 min)
+  - [ ] DataFrame index requirements (Epoch naming) (10 min)
+  - [ ] Species and component consistency (5 min)
+
+- [ ] **Automated Validation Integration** (15 min)
+  - [ ] Create physics compliance checker script (10 min)
+  - [ ] Integrate with example validation framework (5 min)
+
+## 📁 Deliverables
+- [ ] **physics_compliance_validator.py**: Automated physics rule checking
+- [ ] **multiindex_structure_validator.py**: MultiIndex pattern validation
+- [ ] **compliance_report.json**: Complete compliance assessment results
+- [ ] **physics_examples_guide.md**: Best practices documentation
+- [ ] **automated_validation_hooks.py**: CI/CD integration preparation
+
+## 🔬 Physics Rules Validation
+
+### Thermal Speed Convention (mw² = 2kT)
+```python
+class ThermalSpeedValidator:
+    def validate_convention(self, thermal_speed, temperature, mass):
+        """
+        Validate thermal speed follows mw² = 2kT convention
+        
+        Parameters:
+        - thermal_speed: calculated thermal speed [km/s]
+        - temperature: temperature [K]
+        - mass: particle mass [kg]
+        """
+        k_B = 1.380649e-23  # Boltzmann constant [J/K]
+        
+        # Expected thermal speed: w = sqrt(2kT/m)
+        expected_w = np.sqrt(2 * k_B * temperature / mass) / 1000  # Convert to km/s
+        
+        relative_error = abs(thermal_speed - expected_w) / expected_w
+        
+        if relative_error > 0.01:  # 1% tolerance
+            raise PhysicsViolation(
+                f"Thermal speed convention violation: {relative_error:.3%} error\n"
+                f"Expected: {expected_w:.2f} km/s, Got: {thermal_speed:.2f} km/s"
+            )
+        
+        return True
+
+    def validate_examples_with_thermal_speed(self, examples):
+        """Check all examples that calculate thermal speed"""
+        violations = []
+        
+        for example in examples:
+            if self.contains_thermal_speed_calculation(example.code):
+                try:
+                    result = execute_example(example.code)
+                    if 'thermal_speed' in result.outputs and 'temperature' in result.outputs:
+                        self.validate_convention(
+                            result.outputs['thermal_speed'],
+                            result.outputs['temperature'],
+                            result.outputs.get('mass', 1.67262192e-27)  # Default proton mass
+                        )
+                except PhysicsViolation as e:
+                    violations.append({
+                        'example_id': example.id,
+                        'violation': str(e),
+                        'file': example.file_path
+                    })
+        
+        return violations
+```
+
+### SI Units Consistency
+```python
+class SIUnitsValidator:
+    def __init__(self):
+        self.expected_units = {
+            'density': 'cm^-3',      # Number density (display unit)
+            'velocity': 'km/s',      # Velocity (display unit)
+            'temperature': 'K',       # Temperature
+            'magnetic_field': 'nT',   # Magnetic field (display unit)
+            'thermal_speed': 'km/s',  # Thermal speed (display unit)
+            'pressure': 'Pa',         # Pressure (SI base)
+            'energy': 'J',           # Energy (SI base)
+        }
+    
+    def validate_units_in_example(self, example_code):
+        """Ensure examples use correct units for display vs calculation"""
+        # Internal calculations should use SI
+        # Display/user interface should use conventional units
+        violations = []
+        
+        if self.uses_non_si_in_calculation(example_code):
+            violations.append("Non-SI units used in internal calculations")
+        
+        if self.missing_unit_conversions(example_code):
+            violations.append("Missing unit conversions for display")
+        
+        return violations
+    
+    def uses_non_si_in_calculation(self, code):
+        """Check if code uses non-SI units in calculations"""
+        # Look for calculations with non-SI units
+        non_si_patterns = [
+            r'\* 1e6',  # Converting to cm^-3 in calculation
+            r'/ 1000',  # Converting to km/s in calculation
+            r'\* 1e9',  # Converting to nT in calculation
+        ]
+        
+        for pattern in non_si_patterns:
+            if re.search(pattern, code):
+                return True
+        return False
+```
+
+### Missing Data Handling
+```python
+class MissingDataValidator:
+    def validate_nan_usage(self, example_code, example_outputs):
+        """Ensure NaN used for missing data, not 0 or -999"""
+        violations = []
+        
+        # Check for problematic missing data indicators
+        if '-999' in example_code or '0' in example_code:
+            if self.uses_zero_for_missing_data(example_code):
+                violations.append("Uses 0 for missing data instead of NaN")
+            
+            if self.uses_fill_values(example_code):
+                violations.append("Uses -999 fill values instead of NaN")
+        
+        # Check outputs for proper NaN handling
+        if example_outputs:
+            for var_name, data in example_outputs.items():
+                if hasattr(data, 'isnull'):
+                    if not self.proper_missing_data_handling(data):
+                        violations.append(f"Variable {var_name} has improper missing data handling")
+        
+        return violations
+    
+    def proper_missing_data_handling(self, data):
+        """Check if data uses NaN for missing values"""
+        if hasattr(data, 'values'):
+            # Check pandas Series/DataFrame
+            return not np.any((data.values == 0) | (data.values == -999))
+        elif isinstance(data, np.ndarray):
+            # Check numpy arrays
+            return not np.any((data == 0) | (data == -999))
+        return True
+```
+
+## 📊 MultiIndex Structure Validation
+
+### Column Level Naming (M, C, S)
+```python
+class MultiIndexValidator:
+    def __init__(self):
+        self.required_levels = ['M', 'C', 'S']
+        self.valid_measurements = ['n', 'v', 'w', 'b', 'T', 'P']
+        self.valid_components = ['x', 'y', 'z', '']
+        self.valid_species = ['p1', 'p2', 'a', 'he', '']
+    
+    def validate_column_structure(self, dataframe):
+        """Validate MultiIndex column structure"""
+        violations = []
+        
+        if not isinstance(dataframe.columns, pd.MultiIndex):
+            violations.append("Columns must be MultiIndex with (M, C, S) levels")
+            return violations
+        
+        # Check level names
+        if list(dataframe.columns.names) != self.required_levels:
+            violations.append(
+                f"Column level names must be {self.required_levels}, "
+                f"got {list(dataframe.columns.names)}"
+            )
+        
+        # Validate measurement types (M level)
+        measurements = dataframe.columns.get_level_values('M').unique()
+        invalid_measurements = set(measurements) - set(self.valid_measurements)
+        if invalid_measurements:
+            violations.append(f"Invalid measurements: {invalid_measurements}")
+        
+        # Validate components (C level)
+        components = dataframe.columns.get_level_values('C').unique()
+        invalid_components = set(components) - set(self.valid_components)
+        if invalid_components:
+            violations.append(f"Invalid components: {invalid_components}")
+        
+        # Validate species (S level)
+        species = dataframe.columns.get_level_values('S').unique()
+        invalid_species = set(species) - set(self.valid_species)
+        if invalid_species:
+            violations.append(f"Invalid species: {invalid_species}")
+        
+        return violations
+```
+
+### Data Access Pattern Validation
+```python
+class DataAccessValidator:
+    def validate_xs_usage(self, example_code):
+        """Ensure examples use .xs() for views, not copies"""
+        violations = []
+        
+        # Check for inefficient data access patterns
+        inefficient_patterns = [
+            r'\.loc\[.*level.*\]',  # Should use .xs() instead
+            r'\.iloc\[.*\]',        # Positional access is fragile
+            r'\[\(.*,.*,.*\)\]',     # Direct tuple indexing
+        ]
+        
+        for pattern in inefficient_patterns:
+            if re.search(pattern, example_code):
+                violations.append(f"Use .xs() for MultiIndex access instead of {pattern}")
+        
+        # Check for proper .xs() usage
+        xs_patterns = [
+            r"\.xs\('\w+', level='M'\)",  # Measurement access
+            r"\.xs\('\w+', level='S'\)",  # Species access  
+            r"\.xs\('\w+', level='C'\)",  # Component access
+        ]
+        
+        has_proper_xs = any(re.search(pattern, example_code) for pattern in xs_patterns)
+        if '.xs(' in example_code and not has_proper_xs:
+            violations.append("Improper .xs() usage - specify level parameter")
+        
+        return violations
+    
+    def validate_index_naming(self, dataframe):
+        """Ensure DataFrame index is named 'Epoch' for time series"""
+        violations = []
+        
+        if hasattr(dataframe, 'index'):
+            if dataframe.index.name != 'Epoch' and len(dataframe) > 1:
+                violations.append("Time series DataFrame index should be named 'Epoch'")
+        
+        return violations
+```
+
+## 🔧 Automated Validation Framework
+
+### Integrated Compliance Checker
+```python
+class ComplianceValidator:
+    def __init__(self):
+        self.thermal_speed_validator = ThermalSpeedValidator()
+        self.si_units_validator = SIUnitsValidator()
+        self.missing_data_validator = MissingDataValidator()
+        self.multiindex_validator = MultiIndexValidator()
+        self.data_access_validator = DataAccessValidator()
+    
+    def validate_example_compliance(self, example):
+        """Comprehensive compliance check for single example"""
+        violations = {
+            'physics': [],
+            'multiindex': [],
+            'data_access': [],
+            'units': [],
+            'missing_data': []
+        }
+        
+        # Execute example to get outputs
+        try:
+            result = execute_example(example.code)
+            
+            # Physics validation
+            violations['physics'].extend(
+                self.thermal_speed_validator.validate_examples_with_thermal_speed([example])
+            )
+            
+            # Units validation
+            violations['units'].extend(
+                self.si_units_validator.validate_units_in_example(example.code)
+            )
+            
+            # Missing data validation
+            violations['missing_data'].extend(
+                self.missing_data_validator.validate_nan_usage(example.code, result.outputs)
+            )
+            
+            # MultiIndex validation
+            for output_name, output_data in result.outputs.items():
+                if hasattr(output_data, 'columns') and isinstance(output_data.columns, pd.MultiIndex):
+                    violations['multiindex'].extend(
+                        self.multiindex_validator.validate_column_structure(output_data)
+                    )
+                    violations['multiindex'].extend(
+                        self.data_access_validator.validate_index_naming(output_data)
+                    )
+            
+            # Data access pattern validation
+            violations['data_access'].extend(
+                self.data_access_validator.validate_xs_usage(example.code)
+            )
+            
+        except Exception as e:
+            violations['physics'].append(f"Example execution failed: {str(e)}")
+        
+        return violations
+    
+    def generate_compliance_report(self, examples):
+        """Generate comprehensive compliance report"""
+        report = {
+            'timestamp': datetime.now().isoformat(),
+            'total_examples': len(examples),
+            'compliance_summary': {
+                'physics_compliant': 0,
+                'multiindex_compliant': 0,
+                'fully_compliant': 0
+            },
+            'violations_by_category': {
+                'physics': [],
+                'multiindex': [],
+                'data_access': [],
+                'units': [],
+                'missing_data': []
+            },
+            'example_details': []
+        }
+        
+        for example in examples:
+            violations = self.validate_example_compliance(example)
+            
+            is_physics_compliant = len(violations['physics']) == 0
+            is_multiindex_compliant = (
+                len(violations['multiindex']) == 0 and 
+                len(violations['data_access']) == 0
+            )
+            is_fully_compliant = all(len(v) == 0 for v in violations.values())
+            
+            # Update summary counts
+            if is_physics_compliant:
+                report['compliance_summary']['physics_compliant'] += 1
+            if is_multiindex_compliant:
+                report['compliance_summary']['multiindex_compliant'] += 1
+            if is_fully_compliant:
+                report['compliance_summary']['fully_compliant'] += 1
+            
+            # Collect violations by category
+            for category, violation_list in violations.items():
+                report['violations_by_category'][category].extend(violation_list)
+            
+            # Add example details
+            report['example_details'].append({
+                'example_id': example.id,
+                'file_path': example.file_path,
+                'violations': violations,
+                'physics_compliant': is_physics_compliant,
+                'multiindex_compliant': is_multiindex_compliant,
+                'fully_compliant': is_fully_compliant
+            })
+        
+        return report
+```
+
+## 📊 Success Metrics
+
+### Physics Compliance Targets
+- **Thermal Speed Convention**: 100% compliance with mw² = 2kT
+- **SI Units**: 100% internal calculations use SI units
+- **Missing Data**: 100% use NaN for missing data (no 0 or -999)
+- **Scientific Accuracy**: All physics calculations within 1% theoretical values
+
+### MultiIndex Compliance Targets
+- **Column Structure**: 100% use (M, C, S) naming convention
+- **Data Access**: 90% use .xs() for MultiIndex access (some .loc acceptable)
+- **Index Naming**: 100% time series use 'Epoch' index name
+- **Consistency**: 100% species and component codes follow standards
+
+### Automation Integration Targets
+- **Validation Speed**: <10 seconds for all 47 examples
+- **Error Detection**: 95% accuracy in identifying violations
+- **CI/CD Ready**: Validation hooks prepared for automated testing
+- **Documentation**: Clear guidelines for future example creation
+
+## ⚡ Execution Strategy
+
+### Phase 5 Implementation Order
+1. **Physics Rule Validation** (60 min)
+   - Focus on thermal speed and unit conventions first
+   - Validate against existing examples with known physics
+   - Create automated checking for future examples
+
+2. **MultiIndex Structure Validation** (45 min)
+   - Ensure all data structures follow established patterns
+   - Validate access patterns and naming conventions
+   - Document best practices for consistency
+
+3. **Automation Integration** (15 min)
+   - Create validation scripts for CI/CD integration
+   - Prepare hooks for automated checking
+   - Test validation speed and accuracy
+
+### Risk Mitigation
+- **Physics Expertise**: Validate rules with domain experts
+- **Performance**: Optimize validation scripts for speed
+- **False Positives**: Tune validation thresholds to avoid over-strictness
+- **Backward Compatibility**: Ensure validation doesn't break existing patterns
+
+## ✅ Completion Criteria
+- [ ] All examples validated against physics rules
+- [ ] MultiIndex structure compliance verified
+- [ ] Automated validation framework operational
+- [ ] Compliance report showing >95% rule adherence
+- [ ] CI/CD integration hooks prepared
+- [ ] Best practices documentation created
+
+## 🔄 Transition to Phase 6
+**Preparation for Phase 6: Doctest Integration**
+- Physics and MultiIndex compliance established
+- Automated validation framework operational
+- Examples following consistent patterns
+- Ready for doctest automation integration
+
+**Next Phase Prerequisites:**
+- Compliant examples as baseline for doctest integration
+- Validation framework ready for CI/CD integration
+- Clear patterns documented for automated testing
+- Physics rules encoded in validation scripts
+
+---
+
+**📝 User Action Required**: After completing this phase, run:
+```bash
+git add plans/documentation-code-audit/5-Physics-MultiIndex-Compliance.md \
+        physics_compliance_validator.py multiindex_structure_validator.py \
+        compliance_report.json physics_examples_guide.md automated_validation_hooks.py
+git commit -m "docs: complete Phase 5 physics and MultiIndex compliance validation
+
+- Established comprehensive physics rule validation (thermal speed, units, missing data)
+- Validated MultiIndex structure compliance across all examples
+- Created automated validation framework for CI/CD integration
+- Achieved >95% compliance with established physics and data conventions
+- Documented best practices for consistent future example creation
+
+🤖 Generated with [Claude Code](https://claude.ai/code)
+
+Co-Authored-By: Claude <noreply@anthropic.com>"
+```
+
+**Then create compacted state for session continuity:**
+```bash
+python .claude/hooks/create-compaction.py \
+  --trigger "Phase 5 completion - physics and MultiIndex compliance validated" \
+  --context "Ready for doctest integration in Phase 6"
+```