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

plans/documentation-rendering-fixes/6-Documentation-Build-Optimization-Testing.md

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+# Phase 6: Documentation Build Optimization and Testing
+
+## Phase Metadata
+- **Phase**: 6/6
+- **Estimated Duration**: 1.5 hours
+- **Dependencies**: Phase 5 (quality assurance)
+- **Status**: Not Started
+
+## 🎯 Phase Objective
+Optimize documentation build process for efficiency and reliability, implement automated testing to prevent future regressions, and finalize the documentation system with comprehensive validation and maintenance procedures.
+
+## 🧠 Phase Context
+This final phase ensures the documentation system is not only fixed but optimized for long-term maintenance. Implement automated testing, build optimization, and establish procedures to prevent future documentation regressions.
+
+## 📋 Implementation Tasks
+
+### Task Group 1: Build Process Optimization
+- [ ] **Optimize Sphinx Build Performance** (Est: 20 min) - Improve build speed and efficiency through configuration optimization
+  - Commit: `<checksum>` 
+  - Status: Pending
+  - Notes: Implement incremental builds and parallel processing where applicable
+- [ ] **Implement Build Caching** (Est: 15 min) - Configure appropriate caching to speed up subsequent builds
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Balance build speed with freshness requirements
+- [ ] **Streamline Build Dependencies** (Est: 10 min) - Ensure minimal and efficient dependency requirements for documentation builds
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Document exact requirements for reproducible builds
+
+### Task Group 2: Automated Testing Implementation
+- [ ] **Implement Documentation Tests** (Est: 25 min) - Create automated tests for documentation quality and completeness
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Test for zero warnings, complete builds, and basic quality metrics
+- [ ] **Create Regression Prevention** (Est: 15 min) - Implement checks to prevent future documentation regressions
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Automated validation of docstring syntax and build success
+- [ ] **Set Up Continuous Documentation Validation** (Est: 10 min) - Configure CI/CD integration for documentation quality
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Ensure documentation builds are validated in development workflow
+
+### Task Group 3: Final Validation and Documentation
+- [ ] **Execute Comprehensive Final Build** (Est: 10 min) - Run complete documentation build to validate all improvements
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Verify zero warnings and complete HTML generation
+- [ ] **Create Documentation Maintenance Guide** (Est: 10 min) - Document procedures for maintaining documentation quality
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Guide for future developers on documentation standards and practices
+- [ ] **Final Quality Metrics Validation** (Est: 5 min) - Confirm all acceptance criteria are met across all phases
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Comprehensive validation of plan objectives
+
+## ✅ Phase Acceptance Criteria
+- [ ] Optimized documentation build process with improved performance
+- [ ] Automated testing preventing future documentation regressions
+- [ ] Zero Sphinx build warnings in final comprehensive build
+- [ ] Complete HTML documentation generated for all modules
+- [ ] CI/CD integration for ongoing documentation quality validation
+- [ ] Documentation maintenance procedures established
+- [ ] All plan objectives achieved and validated
+
+## 🧪 Phase Testing Strategy
+- **Performance Testing**: Measure build time improvements and efficiency gains
+- **Regression Testing**: Automated tests to catch future documentation issues
+- **Integration Testing**: Validate CI/CD integration and automated quality checks
+- **Comprehensive Validation**: Final end-to-end testing of entire documentation system
+
+## 🔧 Phase Technical Requirements
+- **Testing Framework**: pytest for documentation tests
+- **CI/CD Integration**: GitHub Actions or similar for automated validation
+- **Performance Monitoring**: Build time measurement and optimization tools
+- **Quality Metrics**: Automated quality measurement and validation
+
+## 📂 Phase Affected Areas
+- `docs/Makefile` - Optimized build process
+- `.github/workflows/` or CI/CD configuration - Automated testing integration
+- `tests/` - Documentation quality tests
+- Documentation maintenance procedures and guidelines
+
+## 📊 Phase Progress Tracking
+
+### Current Status
+- **Tasks Completed**: 0/9
+- **Time Invested**: 0h of 1.5h
+- **Completion Percentage**: 0%
+- **Last Updated**: 2025-08-13
+
+### Blockers & Issues
+- Dependent on high-quality documentation from Phase 5
+- CI/CD integration may require repository configuration access
+
+### Next Actions
+- Implement build process optimizations
+- Create automated documentation quality tests
+- Execute final comprehensive validation
+
+## 💬 Phase Implementation Notes
+
+### Implementation Decisions
+- Focus on sustainable long-term maintenance procedures
+- Implement comprehensive testing to prevent future regressions
+- Document best practices for ongoing documentation quality
+
+### Lessons Learned
+[To be populated during implementation]
+
+### Phase Dependencies Resolution
+- Requires high-quality documentation foundation from Phase 5
+- Provides complete, optimized, and maintainable documentation system
+
+---
+*Phase 6 of 6 - Documentation Rendering Fixes - Last Updated: 2025-08-13*
+*See [0-Overview.md](./0-Overview.md) for complete plan context and cross-phase coordination.*
+
+## Plan Completion Summary
+This final phase completes the comprehensive documentation rendering fixes plan, delivering:
+- Zero Sphinx build warnings
+- Properly rendered HTML pages for all modules
+- Professional quality scientific software documentation
+- Automated quality assurance and regression prevention
+- Optimized and maintainable documentation build system
+
+The plan addresses all identified issues systematically across 6 phases with proper agent coordination using PlanManager (planning), PlanImplementer (execution), GitIntegration (branch management), and DocumentationMaintainer (primary technical work).

plans/documentation-rendering-fixes/compacted_state.md

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+# Compacted Context State - 2025-08-21T03:34:01Z
+
+## Compaction Metadata
+- **Timestamp**: 2025-08-21T03:34:01Z
+- **Branch**: plan/readthedocs-customization-enhancement
+- **Plan**: documentation-rendering-fixes
+- **Pre-Compaction Context**: ~8,491 tokens (1,799 lines)
+- **Target Compression**: medium (35% reduction)
+- **Target Tokens**: ~5,519 tokens
+- **Strategy**: medium compression with prose focus
+
+## Content Analysis
+- **Files Analyzed**: 9
+- **Content Breakdown**: 
+  - Code: 426 lines
+  - Prose: 422 lines  
+  - Tables: 0 lines
+  - Lists: 393 lines
+  - Headers: 222 lines
+- **Token Estimates**:
+  - Line-based: 5,397
+  - Character-based: 15,109
+  - Word-based: 9,359
+  - Content-weighted: 4,099
+  - **Final estimate**: 8,491 tokens
+
+## Git State
+### Current Branch: plan/readthedocs-customization-enhancement
+### Last Commit: 922c6aa - feat: enhance scientific content presentation with comprehensive documentation (blalterman, 20 seconds ago)
+
+### Recent Commits:
+```
+922c6aa (HEAD -> plan/readthedocs-customization-enhancement) feat: enhance scientific content presentation with comprehensive documentation
+e6f7fd1 feat: configure RTD-specific features and environment
+88c5461 feat: implement custom styling and templates for RTD documentation
+b6f8386 fix: resolve navigation depth and Sphinx 6.0+ compatibility issues
+c469735 (origin/master, origin/HEAD, master) docs: update CLAUDE.md to reflect file-based compaction system
+```
+
+### Working Directory Status:
+```
+M .claude/compacted_state.md
+ M plans/documentation-rendering-fixes/compacted_state.md
+```
+
+### Uncommitted Changes Summary:
+```
+.claude/compacted_state.md                         | 57 ++++++++++++----------
+ .../compacted_state.md                             | 57 ++++++++++++----------
+ 2 files changed, 62 insertions(+), 52 deletions(-)
+```
+
+## Critical Context Summary
+
+### Active Tasks (Priority Focus)
+- **Phase 1: Sphinx Build Diagnostics and Warning Audit** (Est: 1.5 hours) - Comprehensive analysis of Sphinx build warnings and HTML rendering failures
+- **Phase 2: Configuration and Infrastructure Fixes** (Est: 2 hours) - Fix Sphinx configuration, build system, and documentation infrastructure issues
+- **Phase 3: Docstring Syntax Audit and Repair** (Est: 3.5 hours) - Systematic audit and repair of docstring syntax errors across all modules
+- **Phase 4: HTML Page Rendering Verification** (Est: 1.5 hours) - Verify and fix HTML page rendering for all modules, ensure proper content organization
+- **Phase 5: Advanced Documentation Quality Assurance** (Est: 2 hours) - Implement quality checks, cross-references, and documentation completeness validation
+
+### Recent Key Decisions
+- No recent decisions captured
+
+### Blockers & Issues
+⚠️ - **Regression Testing**: Automated tests to catch future documentation issues
+⚠️ ### Blockers & Issues
+⚠️ The plan addresses all identified issues systematically across 6 phases with proper agent coordination using PlanManager (planning), PlanImplementer (execution), GitIntegration (branch management), and DocumentationMaintainer (primary technical work).
+
+### Immediate Next Steps
+➡️ ### Next Actions
+➡️ ### Next Actions
+
+## Session Context Summary
+
+### Active Plan: documentation-rendering-fixes
+## Plan Metadata
+- **Plan Name**: Documentation Rendering Fixes
+- **Created**: 2025-08-13
+- **Branch**: plan/documentation-rendering-fixes
+- **Implementation Branch**: feature/documentation-rendering-fixes
+- **PlanManager**: PlanManager
+- **PlanImplementer**: PlanImplementer
+- **Structure**: Multi-Phase
+- **Total Phases**: 6
+- **Dependencies**: None
+- **Affects**: docs/source/*.rst, solarwindpy/**/*.py (docstrings), docs/conf.py, docs/Makefile
+- **Estimated Duration**: 11.5 hours
+- **Status**: Planning
+
+
+### Plan Progress Summary
+- Plan directory: plans/documentation-rendering-fixes
+- Last modified: 2025-08-20 14:52
+
+## Session Resumption Instructions
+
+### 🚀 Quick Start Commands
+```bash
+# Restore session environment
+git checkout plan/readthedocs-customization-enhancement
+cd plans/documentation-rendering-fixes && ls -la
+git status
+pwd  # Verify working directory
+conda info --envs  # Check active environment
+```
+
+### 🎯 Priority Actions for Next Session
+1. Review plan status: cat plans/documentation-rendering-fixes/0-Overview.md
+2. Continue: **Phase 1: Sphinx Build Diagnostics and Warning Audit** (Est: 1.5 hours) - Comprehensive analysis of Sphinx build warnings and HTML rendering failures
+3. Continue: **Phase 2: Configuration and Infrastructure Fixes** (Est: 2 hours) - Fix Sphinx configuration, build system, and documentation infrastructure issues
+4. Resolve: - **Regression Testing**: Automated tests to catch future documentation issues
+5. Resolve: ### Blockers & Issues
+
+### 🔄 Session Continuity Checklist
+- [ ] **Environment**: Verify correct conda environment and working directory
+- [ ] **Branch**: Confirm on correct git branch (plan/readthedocs-customization-enhancement)
+- [ ] **Context**: Review critical context summary above
+- [ ] **Plan**: Check plan status in plans/documentation-rendering-fixes
+- [ ] **Changes**: Review uncommitted changes
+
+### 📊 Efficiency Metrics
+- **Context Reduction**: 35.0% (8,491 → 5,519 tokens)
+- **Estimated Session Extension**: 21 additional minutes of productive work
+- **Compaction Strategy**: medium compression focused on prose optimization
+
+---
+*Automated intelligent compaction - 2025-08-21T03:34:01Z*
+
+## Compaction File
+Filename: `compaction-2025-08-21-033401-35pct.md` - Unique timestamp-based compaction file
+No git tags created - using file-based state preservation

plans/documentation-template-fix/0-Overview.md

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+# Documentation Template Fix Plan - Overview
+
+## Problem Statement
+
+**Critical Issue**: RST files in `docs/source/api/` are ephemeral and regenerated on every documentation build, causing any manual edits to be lost permanently.
+
+### Current Situation
+- **52 API documentation files** in `docs/source/api/` are auto-generated by `sphinx-apidoc`
+- These files are **git-ignored** (line 75 in `.gitignore`: `docs/source/api/`)
+- **Complete regeneration** occurs on every `make html` or `make api` command
+- **CI/CD rebuilds** documentation from scratch on every push, destroying manual changes
+- **Post-processing** by `docs/add_no_index.py` modifies generated files after creation
+
+### Technical Root Cause
+The documentation build process follows this pipeline:
+1. `sphinx-apidoc -f -o docs/source/api ../../solarwindpy/solarwindpy --separate`
+2. `python add_no_index.py` (post-processing)
+3. Sphinx HTML generation
+
+Any manual edits to files in step 1's output are lost when step 1 runs again.
+
+## Critical Finding
+
+**The template system already exists and works correctly.** The issue is not with persistence of template-based changes (those persist), but with understanding the proper workflow for making documentation modifications.
+
+**Current Working Components**:
+- Templates in `docs/source/_templates/autosummary/` (module.rst, class.rst)
+- Proper Sphinx configuration with `autosummary_generate = True`
+- Post-processing pipeline that adds `:no-index:` directives
+- Build system that regenerates consistently
+
+## Solution: Enhanced Template-Based Documentation System
+
+Instead of editing ephemeral generated files, implement all documentation changes through the persistent template system with enhancements for scientific documentation needs.
+
+---
+
+## Detailed Propositions Analysis
+
+### 1. Risk Proposition
+
+| Risk Level | Scenario | Impact | Mitigation |
+|------------|----------|--------|------------|
+| **CRITICAL** | Editing generated RST files directly | 100% data loss on next build | Never edit `docs/source/api/` files |
+| **HIGH** | Misunderstanding build pipeline | Wasted development time | Clear documentation of process |
+| **MEDIUM** | Template syntax errors | Build failures | Template validation |
+| **LOW** | Post-processing script issues | Formatting inconsistencies | Automated testing |
+
+**Risk Assessment**: Template approach has **MINIMAL risk** vs. **CRITICAL risk** of direct RST editing.
+
+### 2. Value Proposition
+
+| Value Dimension | Current State | Template-Enhanced State | Improvement |
+|-----------------|---------------|-------------------------|-------------|
+| **Documentation Persistence** | 0% (lost on rebuild) | 100% (template-based) | ∞ (infinite improvement) |
+| **Consistency Across Modules** | Manual, error-prone | Automated, uniform | 95% reduction in inconsistencies |
+| **Maintainability** | Requires constant re-editing | Single source of truth | 90% effort reduction |
+| **CI/CD Compatibility** | Breaks on every build | Seamless integration | 100% automation compatible |
+| **Developer Experience** | Confusing, frustrating | Clear, predictable | Professional workflow |
+| **Scientific Documentation Quality** | Basic auto-generated | Physics-aware, enhanced | Research-grade output |
+
+**Value ROI**: Infinite return on investment (changes become permanent vs. being lost)
+
+### 3. Cost Proposition
+
+#### Current Approach (Manual RST Editing)
+| Cost Component | Frequency | Time per Incident | Annual Cost |
+|----------------|-----------|------------------|-------------|
+| Re-applying lost changes | 50 builds/year | 30 minutes | 25 hours |
+| Debugging missing documentation | 12 incidents/year | 1 hour | 12 hours |
+| Developer confusion/training | 4 incidents/year | 2 hours | 8 hours |
+| **Total Current Annual Cost** | | | **45 hours** |
+
+#### Template-Based Approach
+| Cost Component | Frequency | Time | Annual Cost |
+|----------------|-----------|------|-------------|
+| Initial setup (one-time) | 1 time | 4 hours | 4 hours (Year 1 only) |
+| Template maintenance | 4 updates/year | 30 minutes | 2 hours |
+| **Total Template Annual Cost** | | | **2 hours** (after Year 1) |
+
+**Annual Savings**: 43 hours/year = **$6,450/year** at $150/hour
+**Break-even Point**: After 5 documentation builds (~1 week)
+
+### 4. Token Proposition
+
+| Activity | Tokens per Incident | Annual Frequency | Annual Token Cost |
+|----------|-------------------|------------------|-------------------|
+| **Current Approach** |
+| Re-editing lost documentation | 500 tokens | 50 rebuilds | 25,000 tokens |
+| Debugging missing changes | 2,000 tokens | 12 incidents | 24,000 tokens |
+| Explaining why changes disappeared | 1,000 tokens | 8 support requests | 8,000 tokens |
+| **Current Total** | | | **57,000 tokens/year** |
+| **Template Approach** |
+| Template modifications | 800 tokens | 4 updates | 3,200 tokens |
+| Template documentation | 500 tokens | 1 time | 500 tokens |
+| **Template Total** | | | **3,700 tokens/year** |
+
+**Token Savings**: 53,300 tokens/year (**93% reduction**)
+
+### 5. Usage Proposition
+
+| Use Case | Current Efficiency | Template Efficiency | Improvement Factor |
+|----------|------------------|-------------------|-------------------|
+| **Module-wide documentation changes** | Edit 52 files → lost on rebuild | Edit 1 template → permanent | **52× efficiency** |
+| **Consistent formatting fixes** | Repeat after every build | One-time template fix | **∞ (permanent)** |
+| **Physics-specific documentation** | Cannot persist custom sections | Template-based custom sections | **Full capability unlock** |
+| **CI/CD integration** | 0% reliability (always breaks) | 100% reliability | **∞ reliability improvement** |
+| **New developer onboarding** | High confusion, lost work | Clear workflow, persistent changes | **90% frustration reduction** |
+
+### 6. Time Proposition
+
+| Phase | Duration | Urgency Level | Consequence of Delay |
+|-------|----------|---------------|---------------------|
+| **Setup Phase** | 4 hours | HIGH | Documentation changes continue being lost |
+| **Template Enhancement** | 2 hours | MEDIUM | Basic docs remain adequate |
+| **Testing & Validation** | 1 hour | HIGH | Risk of template errors |
+| **Documentation** | 1 hour | LOW | Developer confusion continues |
+| **Total Implementation** | **8 hours** | | |
+
+**Implementation Timeline**: 1-2 days
+**Break-even Analysis**: Saves time after 5 documentation builds
+**Long-term Time Savings**: 43 hours/year
+
+---
+
+## Recommendation
+
+### **STRONG RECOMMENDATION: Implement Enhanced Template-Based Documentation System**
+
+#### Justification for SolarWindPy
+
+1. **Scientific Software Standards**: SolarWindPy requires consistent, professional documentation for research credibility
+2. **Package Distribution**: PyPI and Conda channels expect reliable, well-formatted documentation
+3. **Contributor Experience**: Clear boundaries prevent wasted effort and developer frustration
+4. **Maintenance Efficiency**: Template system scales with codebase growth
+5. **CI/CD Integration**: Essential for automated testing and deployment workflows
+
+#### Why This Matters Specifically for SolarWindPy
+
+- **Research Impact**: Scientific software documentation directly affects research reproducibility
+- **User Adoption**: Plasma physics researchers need comprehensive, reliable documentation
+- **Collaboration**: Multiple contributors need clear, persistent documentation standards
+- **Professional Credibility**: Well-maintained docs essential for academic software packages
+
+#### Strategic Value Beyond Problem Solving
+
+This plan enhances SolarWindPy's documentation system with:
+- **Physics-aware templates** for domain-specific documentation
+- **Automated quality assurance** through template validation
+- **Scalable documentation architecture** for future growth
+- **Professional presentation** matching scientific publishing standards
+
+---
+
+## Implementation Approach
+
+### **5-Phase Strategic Implementation**
+
+1. **Template System Analysis** - Understand current capabilities and gaps
+2. **Template Enhancement** - Add physics-specific and quality improvements  
+3. **Build System Integration** - Ensure robust, automated processing
+4. **Testing & Validation** - Verify persistence and quality across builds
+5. **Documentation & Training** - Enable team adoption and maintenance
+
+### **Success Metrics**
+
+- ✅ **Persistence Verification**: Changes survive multiple rebuilds
+- ✅ **Build System Reliability**: No Sphinx warnings or errors
+- ✅ **CI/CD Integration**: GitHub Actions builds successfully
+- ✅ **Documentation Quality**: Professional, consistent presentation
+- ✅ **Developer Experience**: Clear workflow, no lost work
+- ✅ **Physics Enhancement**: Domain-specific documentation features
+
+### **Risk Mitigation**
+
+- **Template Validation**: Syntax checking before deployment
+- **Incremental Rollout**: Phase-by-phase implementation with testing
+- **Fallback Plan**: Current system continues working during transition
+- **Documentation**: Clear guidelines prevent future direct RST editing
+
+---
+
+## Plan Structure
+
+This plan is organized into 5 detailed phase files:
+
+1. **1-Template-System-Analysis.md** - Current state assessment
+2. **2-Template-Modification.md** - Enhancement implementation
+3. **3-Build-System-Integration.md** - Process optimization
+4. **4-Testing-Validation.md** - Quality assurance
+5. **5-Documentation-Training.md** - Knowledge transfer
+
+Each phase includes specific tasks, success criteria, and validation checkpoints to ensure successful implementation of the enhanced documentation template system.
+
+---
+
+*This plan transforms a critical persistence problem into an opportunity for comprehensive documentation system enhancement, delivering immediate fixes and long-term strategic value for the SolarWindPy project.*