solarwindpy 0.0.1.dev0__py3-none-any.whl → 0.1.1__py3-none-any.whl

plans/documentation-code-audit/0-Overview.md

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+# Documentation Code Audit - Overview
+
+## Plan Metadata
+- **Plan Name**: Documentation Code Audit
+- **Created**: 2025-08-21
+- **Branch**: plan/documentation-code-audit
+- **Implementation Branch**: feature/documentation-code-audit
+- **PlanManager**: UnifiedPlanCoordinator
+- **PlanImplementer**: UnifiedPlanCoordinator
+- **Structure**: Multi-Phase
+- **Total Phases**: 8
+- **Dependencies**: None
+- **Affects**: docs/source/*.rst, README.rst, all Python module docstrings, doctests, examples
+- **Estimated Duration**: 12-16 hours
+- **Status**: In Progress
+
+## Phase Overview
+- [x] **Phase 1: Discovery & Inventory** (Est: 2h) - Complete code example inventory across docs
+- [ ] **Phase 2: Execution Environment Setup** (Est: 1h) - Test environment and validation tools
+- [ ] **Phase 3: Systematic Validation** (Est: 3h) - Execute all examples and capture failures
+- [ ] **Phase 4: Code Example Remediation** (Est: 4h) - Fix broken imports, deprecated APIs, missing data
+- [ ] **Phase 5: Physics & MultiIndex Compliance** (Est: 2h) - Ensure examples follow physics rules and data patterns
+- [ ] **Phase 6: Doctest Integration** (Est: 2h) - Enable automated doctest validation
+- [ ] **Phase 7: Reporting & Documentation** (Est: 1h) - Create audit report and guidelines
+- [ ] **Phase 8: Closeout** (Est: 1h) - Final validation and plan completion
+
+## Phase Files
+1. [1-Discovery-Inventory.md](./1-Discovery-Inventory.md)
+2. [2-Execution-Environment-Setup.md](./2-Execution-Environment-Setup.md)
+3. [3-Systematic-Validation.md](./3-Systematic-Validation.md)
+4. [4-Code-Example-Remediation.md](./4-Code-Example-Remediation.md)
+5. [5-Physics-MultiIndex-Compliance.md](./5-Physics-MultiIndex-Compliance.md)
+6. [6-Doctest-Integration.md](./6-Doctest-Integration.md)
+7. [7-Reporting-Documentation.md](./7-Reporting-Documentation.md)
+8. [8-Closeout.md](./8-Closeout.md)
+
+## 🎯 Objective
+Audit, validate, and remediate all code examples across SolarWindPy documentation to ensure they are executable, scientifically accurate, and follow established physics rules and data patterns. Establish automated validation to prevent future regressions.
+
+## 🧠 Context
+Phase 1 discovery identified 47 code examples across 13 files with critical issues:
+- Deprecated Plasma constructor API (`Plasma(epoch=)`)
+- Non-existent methods (`add_ion_species`, `validate_physics`)
+- Missing imports and undefined variables in 80% of examples
+- Inconsistent import aliases (`sw` vs `swp`)
+- MultiIndex data structure examples without proper setup
+- Broken plotting and instability function references
+
+These issues undermine user confidence and create barriers to adoption. The audit will establish comprehensive validation and automated testing to maintain example quality.
+
+## 🔧 Technical Requirements
+- **Python Environment**: solarwindpy-20250403 conda environment
+- **Testing**: pytest with doctest integration
+- **Validation**: Physics constraint checking, MultiIndex structure verification
+- **Documentation**: Sphinx with code-block execution validation
+- **Tools**: Custom validation scripts for physics rules and data patterns
+- **Quality**: All examples must execute successfully and produce expected outputs
+
+## 📂 Affected Areas
+**RST Documentation Files:**
+- `docs/source/usage.rst` (7 broken examples)
+- `docs/source/tutorial/quickstart.rst` (2 examples)
+- `docs/source/installation.rst` (5 examples)
+- `README.rst` (6 examples)
+
+**Python Module Docstrings:**
+- `solarwindpy/core/plasma.py` (8 doctest examples)
+- `solarwindpy/core/ions.py` (1 doctest example)
+- `solarwindpy/fitfunctions/tex_info.py` (1 doctest example)
+- `solarwindpy/tools/__init__.py` (3 doctest examples)
+- `solarwindpy/core/spacecraft.py` (requires analysis)
+- `solarwindpy/instabilities/*.py` (multiple files require analysis)
+- `solarwindpy/plotting/tools.py` (requires analysis)
+
+## ✅ Acceptance Criteria
+- [ ] All 47+ identified code examples execute successfully
+- [ ] All doctests pass automated validation
+- [ ] Examples follow physics rules (SI units, thermal speed convention, NaN for missing data)
+- [ ] MultiIndex data structure examples include proper setup
+- [ ] Import aliases standardized to `swp` convention
+- [ ] Deprecated API usage eliminated
+- [ ] Automated validation integrated into CI/CD pipeline
+- [ ] Documentation guidelines updated with example standards
+- [ ] Test coverage maintained ≥ 95%
+- [ ] All phase deliverables completed and documented
+
+## 🧪 Testing Strategy
+**Multi-Layer Validation Approach:**
+1. **Syntax Validation**: Parse all code blocks for Python syntax errors
+2. **Import Resolution**: Verify all imports resolve correctly
+3. **Execution Testing**: Run examples in isolated environments
+4. **Physics Validation**: Check outputs against physics constraints
+5. **Doctest Integration**: Enable automated docstring example testing
+6. **Regression Prevention**: CI/CD hooks to validate new examples
+
+**Testing Tools:**
+- Custom script to extract and execute RST code blocks
+- Modified doctest runner with physics constraint checking
+- Physics validation hooks for thermal speed, units, and data patterns
+- MultiIndex structure validation utilities
+
+## 📊 Value Proposition Analysis
+
+### Scientific Software Development Value
+**Research Efficiency Improvements:**
+- **Eliminates user frustration**: 47 broken examples currently create adoption barriers
+- **Accelerates onboarding**: New users can follow working examples immediately
+- **Improves scientific reproducibility**: Validated examples ensure consistent results
+- **Enhances research velocity**: Researchers spend time on science, not debugging examples
+
+**Development Quality Enhancements:**
+- **Automated validation**: CI/CD integration prevents regression of example quality
+- **Physics compliance**: Examples follow established thermal speed and unit conventions
+- **Data structure consistency**: MultiIndex examples include proper setup patterns
+- **Documentation reliability**: Users can trust examples will work as shown
+
+### Developer Productivity Value
+**Planning Efficiency:**
+- **Systematic approach**: 8-phase structure ensures comprehensive coverage
+- **Automated discovery**: Inventory process scales to future documentation additions
+- **Standardized validation**: Reusable testing patterns for ongoing maintenance
+- **Quality gates**: Prevents accumulation of broken examples over time
+
+**Resource Optimization:**
+- **Reduced support burden**: Working examples decrease user support requests
+- **Faster issue resolution**: Automated validation identifies problems early
+- **Improved contributor experience**: Clear example standards for new contributors
+- **Enhanced package reputation**: Professional documentation quality
+
+## 💰 Resource & Cost Analysis
+
+### Development Investment
+**Implementation Time Breakdown:**
+- **Discovery & Setup**: 3 hours (completed inventory + environment)
+- **Validation & Remediation**: 7 hours (systematic testing + fixes)
+- **Integration & Documentation**: 4 hours (CI/CD + guidelines)
+- **Total Investment**: 14 hours
+
+**Maintenance Considerations:**
+- **Ongoing validation**: Automated via CI/CD hooks (minimal overhead)
+- **Example updates**: Clear patterns established for future additions
+- **Documentation reviews**: Integrated into existing PR workflow
+- **User support reduction**: Working examples decrease support load
+
+### Token Usage Economics
+**Current vs Enhanced Token Usage:**
+- **Manual debugging sessions**: 500-1000 tokens per broken example issue
+- **User support responses**: 200-400 tokens per documentation question
+- **Automated validation**: 50-100 tokens for CI/CD integration
+- **Net savings**: 75-85% reduction in documentation-related support tokens
+
+**Break-Even Analysis:**
+- **Investment**: ~3500 tokens for comprehensive plan execution
+- **Savings per issue**: 400-800 tokens (debugging + support)
+- **Break-even**: 5-10 prevented issues (achieved within first month)
+- **Annual benefit**: 15,000-25,000 tokens saved from reduced support burden
+
+## ⚠️ Risk Assessment & Mitigation
+
+### Technical Implementation Risks
+**Risk Matrix:**
+
+| Risk | Probability | Impact | Mitigation Strategy |
+|------|-------------|--------|-----------------|
+| API breaking changes during fixes | Medium | High | Use deprecation warnings, maintain backward compatibility |
+| Physics validation false positives | Low | Medium | Comprehensive test suite with known-good examples |
+| Documentation build failures | Low | High | Isolated testing environment, rollback procedures |
+| Performance impact from validation | Low | Low | Optimize validation scripts, run in CI only |
+
+**Technical Mitigation Strategies:**
+- **Incremental deployment**: Fix examples in phases to isolate issues
+- **Rollback procedures**: Git branch structure enables quick reversion
+- **Comprehensive testing**: Validate fixes against full test suite
+- **Physics expert review**: Ensure scientific accuracy of corrected examples
+
+### Project Management Risks
+**Timeline and Resource Risks:**
+- **Scope creep**: Additional examples discovered during validation (20% buffer included)
+- **Dependency delays**: External package updates affecting examples (version pinning)
+- **Review bottlenecks**: Physics validation requiring expert input (parallel review process)
+- **Integration complexity**: CI/CD hook integration (phased rollout approach)
+
+### Scientific Workflow Risks
+**Research Impact Assessment:**
+- **User confusion**: Temporary inconsistency during remediation (clear communication plan)
+- **Research disruption**: Changes to example patterns (maintain backward compatibility)
+- **Adoption barriers**: Stricter validation requirements (comprehensive documentation)
+- **Scientific accuracy**: Risk of introducing physics errors (expert validation process)
+
+## 🔒 Security Proposition
+
+### Code-Level Security Assessment
+**Dependency Vulnerability Analysis:**
+- **Documentation dependencies**: Sphinx, docutils, and related packages
+- **Testing dependencies**: pytest, doctest integration tools
+- **No new external dependencies**: Remediation uses existing SolarWindPy stack
+- **Validation scripts**: Custom Python code with standard library usage
+
+**Authentication and Access Control Impacts:**
+- **No authentication changes**: Documentation remains publicly accessible
+- **CI/CD integration**: Uses existing GitHub Actions security model
+- **Development workflow**: Maintains current branch protection and review requirements
+- **No sensitive data exposure**: Examples use synthetic or public scientific data
+
+**Attack Surface Assessment:**
+- **Documentation endpoints**: No changes to web service attack surface
+- **Code execution**: Validation scripts run in isolated CI environment
+- **Input validation**: Examples use controlled, validated scientific data
+- **No external integrations**: Self-contained validation within existing infrastructure
+
+### Scientific Computing Environment Security
+**Development Workflow Security:**
+- **Automated validation**: Reduces human error in example verification
+- **Code review process**: Physics validation requires expert review
+- **Version control**: All changes tracked through established git workflow
+- **Isolation**: Testing occurs in dedicated conda environments
+
+**CI/CD Pipeline Considerations:**
+- **Validation hooks**: Integrate with existing pre-commit and GitHub Actions
+- **No secret management**: Examples use synthetic data, no credentials required
+- **Environment isolation**: Each validation runs in clean environment
+- **Audit trail**: All validation results logged and tracked
+
+**Note**: This security assessment covers code-level security only. FAIR data compliance is explicitly excluded and not implemented in this system.
+
+## 💾 Token Usage Optimization
+
+### Current Token Usage Patterns
+**Manual Documentation Debugging:**
+- **Issue identification**: 200-400 tokens per broken example discovery
+- **Root cause analysis**: 300-600 tokens for complex API mismatches
+- **Fix implementation**: 400-800 tokens per remediation session
+- **Validation testing**: 200-400 tokens per example verification
+- **Total per issue**: 1100-2200 tokens for complete resolution
+
+**Inefficiency Sources:**
+- **Repetitive debugging**: Similar issues across multiple examples
+- **Context rebuilding**: Starting from scratch for each documentation issue
+- **Manual validation**: Human-driven testing of example correctness
+- **Support overhead**: User questions about broken examples
+
+### Optimized Token Usage Strategy
+**Hook-Based Generation and Validation:**
+- **Automated discovery**: Systematic inventory with minimal token overhead
+- **Batch processing**: Fix similar issues across multiple examples simultaneously
+- **Pattern recognition**: Reuse solutions for common problems (import fixes, API updates)
+- **Continuous validation**: Prevent future issues through automated testing
+
+**Context Preservation Benefits:**
+- **Persistent state**: Maintain context across validation phases
+- **Knowledge transfer**: Document patterns for future maintenance
+- **Automated reporting**: Generate summaries without manual analysis
+- **Scaling efficiency**: Handle large documentation sets with consistent approach
+
+**Token Savings Metrics:**
+- **Per-issue reduction**: 70-80% fewer tokens through systematic approach
+- **Prevention value**: Eliminate recurring support and debugging sessions
+- **Maintenance efficiency**: Future documentation updates require minimal validation overhead
+
+## ⏱️ Time Investment Analysis
+
+### Implementation Time Breakdown
+**Phase-by-Phase Estimates (with confidence intervals):**
+
+| Phase | Estimated Time | Confidence | Key Activities |
+|-------|----------------|------------|----------------|
+| 1. Discovery & Inventory | 2h (completed) | 95% | Systematic code example discovery |
+| 2. Environment Setup | 1h ± 0.5h | 90% | Testing infrastructure preparation |
+| 3. Systematic Validation | 3h ± 1h | 80% | Execute all examples, capture failures |
+| 4. Code Remediation | 4h ± 1.5h | 75% | Fix imports, APIs, data setup |
+| 5. Physics Compliance | 2h ± 0.5h | 85% | Validate scientific accuracy |
+| 6. Doctest Integration | 2h ± 1h | 80% | Automated testing setup |
+| 7. Reporting | 1h ± 0.25h | 95% | Documentation and guidelines |
+| 8. Closeout | 1h ± 0.25h | 90% | Final validation and completion |
+
+**Total Estimated Duration**: 16h ± 3h (13-19 hour range)
+
+### Time Savings Analysis
+**Per-Plan Time Savings:**
+- **Immediate user support reduction**: 5-8 hours/month
+- **Faster new user onboarding**: 2-3 hours saved per new contributor
+- **Reduced debugging overhead**: 10-15 hours/year for development team
+- **Documentation maintenance efficiency**: 3-5 hours/quarter
+
+**Long-Term Efficiency Gains:**
+- **Prevented regression time**: 20-30 hours/year through automated validation
+- **Improved contributor efficiency**: 5-10% faster documentation updates
+- **Enhanced user adoption**: Reduced friction leads to faster community growth
+- **Scientific productivity**: Researchers spend more time on science, less on setup
+
+### Break-Even Calculation
+**Investment vs Returns Analysis:**
+- **Initial investment**: 16 hours development time
+- **Monthly savings**: 5-8 hours in reduced support and debugging
+- **Break-even timeline**: 2-3 months
+- **Annual ROI**: 300-400% (48-60 hours saved vs 16 hour investment)
+
+**Payback Timeline:**
+- **Month 1**: 20-30% payback through immediate user support reduction
+- **Month 3**: Full payback achieved
+- **Year 1**: 3-4x return on investment
+- **Ongoing**: Compound benefits through improved documentation quality
+
+## 🎯 Usage & Adoption Metrics
+
+### Target Use Cases
+**Primary Applications:**
+- **New user onboarding**: Working examples reduce adoption barriers
+- **Scientific research**: Reliable examples accelerate research workflows
+- **Educational materials**: Teachers and students can trust documentation
+- **Developer contributions**: Clear example standards guide new contributors
+
+**Secondary Applications:**
+- **Package documentation standards**: Template for other scientific Python packages
+- **Community building**: Professional documentation enhances package reputation
+- **Research reproducibility**: Validated examples ensure consistent scientific results
+- **Support infrastructure**: Reduced burden through self-service documentation
+
+### Adoption Strategy
+**Phased Rollout Approach:**
+1. **Phase 1**: Core usage examples (highest impact, immediate user benefit)
+2. **Phase 2**: Advanced scientific features (research community value)
+3. **Phase 3**: Developer and contributor documentation (community growth)
+4. **Phase 4**: Automated validation integration (long-term sustainability)
+
+**Success Factors:**
+- **User feedback integration**: Responsive to community needs and issues
+- **Scientific accuracy**: Physics expert validation ensures credibility
+- **Maintenance sustainability**: Automated validation prevents regression
+- **Clear documentation**: Guidelines enable community contributions
+
+### Success Metrics
+**Quantitative Indicators:**
+- **Example execution rate**: Target 100% successful execution
+- **User support reduction**: 60-80% decrease in documentation-related issues
+- **Documentation build time**: <5% increase despite enhanced validation
+- **Community contributions**: 25-40% increase in documentation-related PRs
+- **New user retention**: 15-25% improvement in first-month engagement
+
+**Qualitative Indicators:**
+- **User satisfaction**: Positive feedback on documentation reliability
+- **Scientific community adoption**: Citations and academic usage
+- **Developer experience**: Contributor feedback on documentation standards
+- **Package reputation**: Recognition as high-quality scientific software
+- **Educational impact**: Adoption in academic courses and tutorials
+
+**Measurement Timeline:**
+- **Immediate (1 month)**: Example execution success rate
+- **Short-term (3 months)**: User support ticket reduction
+- **Medium-term (6 months)**: Community contribution metrics
+- **Long-term (12 months)**: User retention and satisfaction scores
+
+## 📊 Progress Tracking
+
+### Overall Status
+- **Phases Completed**: 1/8
+- **Tasks Completed**: 8/45 (estimated)
+- **Time Invested**: 2h of 16h
+- **Last Updated**: 2025-08-21
+
+### Implementation Notes
+**Phase 1 Completion (Discovery & Inventory):**
+- Comprehensive inventory completed: 47 examples across 13 files
+- Critical issues identified: deprecated APIs, broken imports, missing data setup
+- Inventory JSON created with detailed issue categorization
+- Next phase priorities established
+
+**Current Status:**
+- Branch: plan/documentation-code-audit (active)
+- Inventory file: docs_audit_inventory.json (comprehensive)
+- Ready to proceed with Phase 2: Execution Environment Setup
+
+## 🔗 Related Plans
+- **readthedocs-customization-enhancement**: Complementary documentation improvements
+- **api-documentation-overhaul**: Future plan for comprehensive API docs
+- **testing-infrastructure-enhancement**: Related automated testing improvements
+
+## 💬 Notes & Considerations
+**Key Insights from Phase 1:**
+- 80% of examples lack proper setup/imports - systemic issue requiring standardized patterns
+- Deprecated Plasma constructor appears in multiple critical examples
+- MultiIndex examples assume complex data structure without initialization
+- Physics validation requirements not currently enforced in examples
+- Inconsistent import alias usage creates user confusion
+
+**Strategic Considerations:**
+- Prioritize high-impact usage.rst fixes for immediate user benefit
+- Establish example standards to prevent future regressions
+- Integrate physics validation into example testing workflow
+- Consider automated example generation for complex data structures
+
+---
+*This multi-phase plan uses the plan-per-branch architecture where implementation occurs on feature/documentation-code-audit branch with progress tracked via commit checksums across phase files.*

plans/documentation-code-audit/1-Discovery-Inventory.md

@@ -0,0 +1,183 @@
+# Phase 1: Discovery & Inventory
+
+## Phase Metadata
+- **Status**: ✅ Completed
+- **Estimated Duration**: 2 hours
+- **Actual Duration**: 2 hours
+- **Completion Date**: 2025-08-21
+- **Git Commit**: <checksum>
+- **Branch**: plan/documentation-code-audit
+
+## 🎯 Objective
+Conduct comprehensive discovery and inventory of all code examples across SolarWindPy documentation to identify broken examples, deprecated APIs, missing imports, and compliance issues.
+
+## 📋 Tasks Checklist
+- [x] **Scan RST documentation files** (45 min)
+  - [x] `docs/source/usage.rst` - 7 code blocks identified
+  - [x] `docs/source/tutorial/quickstart.rst` - 2 code blocks identified  
+  - [x] `docs/source/installation.rst` - 5 code blocks identified
+  - [x] `README.rst` - 6 code blocks identified
+
+- [x] **Analyze Python module docstrings** (60 min)
+  - [x] `solarwindpy/core/plasma.py` - 8 doctest examples
+  - [x] `solarwindpy/core/ions.py` - 1 doctest example
+  - [x] `solarwindpy/fitfunctions/tex_info.py` - 1 doctest example  
+  - [x] `solarwindpy/tools/__init__.py` - 3 doctest examples
+  - [x] Additional modules requiring detailed analysis identified
+
+- [x] **Categorize issues by severity** (10 min)
+  - [x] Critical: Deprecated API usage (Plasma constructor)
+  - [x] Critical: Non-existent methods (add_ion_species, validate_physics)
+  - [x] High: Missing imports and undefined variables (80% of examples)
+  - [x] Medium: Inconsistent import aliases (sw vs swp)
+  - [x] Medium: Missing MultiIndex data structure setup
+
+- [x] **Create comprehensive inventory document** (5 min)
+  - [x] JSON format with detailed issue categorization
+  - [x] Line-by-line tracking of all code examples
+  - [x] Dependencies and issue classification
+  - [x] Priority recommendations for remediation
+
+## 📁 Deliverables
+- ✅ **docs_audit_inventory.json**: Comprehensive inventory of 47 examples across 13 files
+- ✅ **Issue categorization**: Critical, High, Medium, Low severity classifications
+- ✅ **Pattern analysis**: Common import patterns, data access patterns, operations
+- ✅ **Next phase priorities**: Actionable priority list for systematic remediation
+
+## 🔍 Key Findings
+
+### Critical Issues Discovered
+1. **Deprecated Plasma Constructor**: `Plasma(epoch=)` usage in usage.rst
+2. **Non-existent Methods**: `add_ion_species()`, `validate_physics()` referenced but don't exist
+3. **Broken Import References**: `solarwindpy.plotting.time_series`, `solarwindpy.instabilities.beta_ani_inst`
+
+### High-Impact Issues
+4. **Missing Data Setup**: 80% of examples assume complex MultiIndex data without initialization
+5. **Undefined Variables**: `data`, `df`, `temperature_data` variables used without definition
+6. **Incomplete Examples**: Ellipsis (`...`) in DataFrame construction examples
+
+### Consistency Issues
+7. **Import Alias Inconsistency**: Mixed usage of `import solarwindpy as sw` vs `import solarwindpy as swp`
+8. **Missing Dependencies**: Examples reference modules without proper imports
+
+### Statistics Summary
+- **Total Examples Found**: 47
+- **Files with Examples**: 13
+- **Examples with Issues**: 42 (89%)
+- **Critical Issues**: 8
+- **High-Impact Issues**: 15
+- **Medium Issues**: 19
+
+## 🔄 Impact Analysis
+
+### User Experience Impact
+- **New User Friction**: Broken examples create immediate adoption barriers
+- **Documentation Credibility**: 89% failure rate undermines package reliability
+- **Support Burden**: Broken examples generate user support requests
+- **Research Productivity**: Scientists waste time debugging instead of doing research
+
+### Development Impact
+- **Maintenance Overhead**: Manual validation required for all documentation changes
+- **Quality Assurance**: No automated validation of example correctness
+- **Contributor Confusion**: Inconsistent patterns make contribution difficult
+- **Technical Debt**: Accumulated broken examples require systematic remediation
+
+## 📊 Remediation Priority Matrix
+
+### Phase 2 Immediate Priorities
+1. **Environment Setup**: Create testing infrastructure for example validation
+2. **Critical API Fixes**: Address deprecated Plasma constructor immediately
+3. **Import Standardization**: Establish consistent `swp` alias usage
+
+### Phase 3-4 Core Remediation
+4. **Data Structure Examples**: Create reusable MultiIndex setup patterns
+5. **Method Validation**: Verify all referenced methods exist and work correctly
+6. **Missing Imports**: Systematic addition of required imports to all examples
+
+### Phase 5-6 Quality Assurance
+7. **Physics Compliance**: Ensure examples follow thermal speed and unit conventions
+8. **Automated Testing**: Integrate doctest and example validation into CI/CD
+
+## 🔗 Dependencies for Next Phase
+- **Testing Environment**: Conda environment with full SolarWindPy installation
+- **Validation Scripts**: Tools to extract and execute RST code blocks
+- **Physics Validation**: Integration with existing physics constraint checking
+- **CI/CD Integration**: Hooks for automated example testing
+
+## 📝 Implementation Notes
+
+### Discovery Process
+1. **Systematic File Scanning**: Used grep and manual analysis to identify all code blocks
+2. **Issue Classification**: Categorized issues by type and severity for prioritization
+3. **Pattern Recognition**: Identified common problems for batch remediation strategies
+4. **Dependency Mapping**: Tracked import requirements and missing dependencies
+
+### Documentation Structure Analysis
+- **RST Files**: Mix of `code-block:: python` and `code-block:: bash` directives
+- **Docstring Examples**: Standard Python doctest format with `>>>` prompts
+- **Complexity Range**: From simple imports to complex MultiIndex data manipulation
+- **Scientific Domain**: Physics calculations, data analysis, visualization examples
+
+### Key Patterns Identified
+```python
+# Common import patterns found:
+import solarwindpy as swp        # Preferred standard
+import solarwindpy as sw         # Inconsistent usage
+import solarwindpy.plotting as swpp
+from solarwindpy.fitfunctions import Gaussian
+from solarwindpy.instabilities import beta_ani_inst  # Broken
+
+# Common data access patterns:
+plasma.data.xs('n', level='M')   # Number density
+plasma.data.xs('v', level='M')   # Velocity
+plasma.p1.n                      # Proton density shorthand
+plasma.get_ion('p1')             # Ion access method
+```
+
+## ✅ Completion Criteria Met
+- ✅ All documentation files systematically analyzed
+- ✅ Complete inventory with line-by-line tracking
+- ✅ Issues categorized by severity and type
+- ✅ Remediation priorities established
+- ✅ Next phase dependencies identified
+- ✅ Comprehensive JSON inventory document created
+
+## 🔄 Transition to Phase 2
+**Ready for Phase 2: Execution Environment Setup**
+- Inventory complete with 47 examples catalogued
+- Critical issues identified and prioritized
+- Testing infrastructure requirements defined
+- Validation strategy framework established
+
+**Next Actions:**
+1. Set up isolated testing environment
+2. Create example extraction and execution tools
+3. Establish validation criteria and success metrics
+4. Begin systematic validation of highest-priority examples
+
+---
+
+**📝 User Action Required**: After reviewing this completed phase, run:
+```bash
+git add plans/documentation-code-audit/1-Discovery-Inventory.md docs_audit_inventory.json
+git commit -m "docs: complete Phase 1 discovery and inventory for documentation code audit
+
+- Comprehensive inventory of 47 examples across 13 files
+- Identified critical issues: deprecated APIs, broken imports, missing data
+- Categorized issues by severity with remediation priorities
+- Created docs_audit_inventory.json with detailed findings
+- Ready for Phase 2: Execution Environment Setup
+
+🤖 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 1 completion - comprehensive discovery and inventory complete" \
+  --context "47 examples catalogued, ready for Phase 2 environment setup"
+```
+
+**Phase 1 Complete** ✅