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

plans/documentation-rendering-fixes/1-Sphinx-Build-Diagnostics-Warning-Audit.md

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+# Phase 1: Sphinx Build Diagnostics and Warning Audit
+
+## Phase Metadata
+- **Phase**: 1/6
+- **Estimated Duration**: 1.5 hours
+- **Dependencies**: None
+- **Status**: Not Started
+
+## 🎯 Phase Objective
+Perform comprehensive analysis of Sphinx build system to identify all warnings, errors, and HTML rendering failures. Establish baseline understanding of documentation infrastructure issues and create systematic remediation roadmap.
+
+## 🧠 Phase Context
+Before fixing documentation issues, we must understand the full scope of problems. This phase provides the diagnostic foundation for all subsequent fixes by cataloging every warning, error, and rendering failure in the Sphinx build system.
+
+## 📋 Implementation Tasks
+
+### Task Group 1: Build Environment Validation
+- [ ] **Validate Documentation Environment** (Est: 15 min) - Ensure solarwindpy-20250404 environment is active and Sphinx dependencies are available
+  - Commit: `<checksum>` 
+  - Status: Pending
+  - Notes: DocumentationMaintainer will verify environment setup
+- [ ] **Check Sphinx Configuration** (Est: 15 min) - Review docs/conf.py for basic configuration issues and version compatibility
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Identify any obvious configuration problems
+
+### Task Group 2: Build Execution and Warning Capture
+- [ ] **Execute Clean Documentation Build** (Est: 20 min) - Run `make clean && make html` and capture all warnings/errors
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Generate fresh build with complete warning log
+- [ ] **Categorize Sphinx Warnings** (Est: 30 min) - Systematically categorize all warnings by type (docstring, cross-reference, configuration, etc.)
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Create structured warning inventory
+
+### Task Group 3: HTML Rendering Analysis
+- [ ] **Audit Problem HTML Pages** (Est: 20 min) - Manually inspect solarwindpy.fitfunctions.html, solarwindpy.core.html, solarwindpy.instabilities.html, solarwindpy.solar_activity.html
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Document specific rendering failures and missing content
+- [ ] **Compare Working vs Broken Pages** (Est: 10 min) - Identify patterns between properly rendered pages and problematic ones
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Look for common patterns in rendering failures
+
+## ✅ Phase Acceptance Criteria
+- [ ] Complete Sphinx build warning inventory created and categorized
+- [ ] All problematic HTML pages identified with specific rendering issues documented
+- [ ] Baseline documentation build metrics established
+- [ ] Environment and configuration validated
+- [ ] Systematic remediation roadmap created based on diagnostic findings
+- [ ] Priority order established for fixing different types of issues
+
+## 🧪 Phase Testing Strategy
+- **Build Validation**: Ensure clean build environment and reproducible build process
+- **Warning Analysis**: Systematic categorization of all Sphinx warnings and errors
+- **HTML Inspection**: Manual verification of HTML output quality and completeness
+
+## 🔧 Phase Technical Requirements
+- **Environment**: solarwindpy-20250404 conda environment active
+- **Tools**: Sphinx, make, web browser for HTML inspection
+- **Documentation**: Access to docs/source/ and docs/build/ directories
+
+## 📂 Phase Affected Areas
+- `docs/build/` - Generated documentation for analysis
+- `docs/source/` - Source files for configuration review
+- Warning logs and diagnostic reports (temporary files)
+
+## 📊 Phase Progress Tracking
+
+### Current Status
+- **Tasks Completed**: 0/6
+- **Time Invested**: 0h of 1.5h
+- **Completion Percentage**: 0%
+- **Last Updated**: 2025-08-13
+
+### Blockers & Issues
+- None anticipated for diagnostic phase
+
+### Next Actions
+- Activate documentation environment
+- Execute clean Sphinx build with warning capture
+- Begin systematic warning categorization
+
+## 💬 Phase Implementation Notes
+
+### Implementation Decisions
+- Focus on comprehensive diagnosis before any fixes to ensure systematic approach
+- Use DocumentationMaintainer agent for technical analysis with coordination from planning agents
+
+### Lessons Learned
+[To be populated during implementation]
+
+### Phase Dependencies Resolution
+- No dependencies for this initial diagnostic phase
+- Provides foundation for all subsequent phases
+
+---
+*Phase 1 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.*

plans/documentation-rendering-fixes/2-Configuration-Infrastructure-Fixes.md

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+# Phase 2: Configuration and Infrastructure Fixes
+
+## Phase Metadata
+- **Phase**: 2/6
+- **Estimated Duration**: 2 hours
+- **Dependencies**: Phase 1 (diagnostic findings)
+- **Status**: Not Started
+
+## 🎯 Phase Objective
+Fix Sphinx configuration, build system, and documentation infrastructure issues identified in Phase 1. Establish robust foundation for reliable documentation builds and resolve configuration-related warnings.
+
+## 🧠 Phase Context
+Many Sphinx warnings and HTML rendering issues stem from configuration problems. This phase addresses the infrastructure foundation before tackling individual docstring issues, ensuring that fixes in later phases will be effective and sustainable.
+
+## 📋 Implementation Tasks
+
+### Task Group 1: Sphinx Configuration Optimization
+- [ ] **Update conf.py Settings** (Est: 30 min) - Fix Sphinx configuration based on Phase 1 findings (extensions, themes, paths)
+  - Commit: `<checksum>` 
+  - Status: Pending
+  - Notes: Address configuration warnings and compatibility issues
+- [ ] **Validate Extension Configuration** (Est: 20 min) - Ensure all Sphinx extensions are properly configured and compatible
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Fix extension-related warnings from diagnostic phase
+- [ ] **Optimize Theme and Template Settings** (Est: 15 min) - Configure documentation theme and templates for proper rendering
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Ensure consistent visual presentation across all pages
+
+### Task Group 2: Build System Infrastructure
+- [ ] **Fix Makefile and Build Scripts** (Est: 20 min) - Update documentation build system for reliable operation
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Address any build system issues found in Phase 1
+- [ ] **Configure Autodoc and API Generation** (Est: 25 min) - Ensure proper API documentation generation settings
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Fix autodoc warnings and API generation issues
+- [ ] **Implement Documentation Requirements** (Est: 10 min) - Ensure all required packages are available for documentation builds
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Verify documentation dependencies are properly specified
+
+### Task Group 3: Infrastructure Validation and Testing
+- [ ] **Execute Test Build** (Est: 15 min) - Run clean build to validate configuration fixes
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Verify configuration changes resolve infrastructure warnings
+- [ ] **Validate RST File Processing** (Est: 5 min) - Ensure all reStructuredText files process correctly with new configuration
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Check for any new warnings introduced by configuration changes
+
+## ✅ Phase Acceptance Criteria
+- [ ] Sphinx configuration optimized and warnings-free
+- [ ] Documentation build system operates reliably
+- [ ] All extensions and themes configured correctly
+- [ ] Infrastructure-related warnings eliminated
+- [ ] API documentation generation functioning properly
+- [ ] Clean test build validates configuration improvements
+- [ ] Foundation established for reliable docstring processing
+
+## 🧪 Phase Testing Strategy
+- **Configuration Testing**: Validate each configuration change with test builds
+- **Build System Validation**: Ensure make commands execute without infrastructure errors
+- **Extension Testing**: Verify all Sphinx extensions load and function correctly
+
+## 🔧 Phase Technical Requirements
+- **Configuration Files**: docs/conf.py, docs/Makefile, requirements files
+- **Sphinx Extensions**: autodoc, napoleon, viewcode, and theme extensions
+- **Environment**: Verified documentation build environment from Phase 1
+
+## 📂 Phase Affected Areas
+- `docs/conf.py` - Primary Sphinx configuration file
+- `docs/Makefile` - Documentation build system
+- `docs/requirements.txt` - Documentation build dependencies (if present)
+- `docs/source/_static/` - Static files and theme customizations (if applicable)
+
+## 📊 Phase Progress Tracking
+
+### Current Status
+- **Tasks Completed**: 0/8
+- **Time Invested**: 0h of 2h
+- **Completion Percentage**: 0%
+- **Last Updated**: 2025-08-13
+
+### Blockers & Issues
+- Dependent on Phase 1 diagnostic findings
+- May discover additional configuration issues during implementation
+
+### Next Actions
+- Review Phase 1 diagnostic findings
+- Begin Sphinx configuration optimization
+- Implement fixes based on warning categorization
+
+## 💬 Phase Implementation Notes
+
+### Implementation Decisions
+- Prioritize configuration fixes that resolve the most warnings
+- Ensure backwards compatibility while modernizing configuration
+- Use DocumentationMaintainer agent expertise for Sphinx best practices
+
+### Lessons Learned
+[To be populated during implementation]
+
+### Phase Dependencies Resolution
+- Uses diagnostic findings from Phase 1 to guide configuration fixes
+- Provides stable infrastructure foundation for Phase 3 docstring work
+
+---
+*Phase 2 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.*

plans/documentation-rendering-fixes/3-Docstring-Syntax-Audit-Repair.md

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+# Phase 3: Docstring Syntax Audit and Repair
+
+## Phase Metadata
+- **Phase**: 3/6
+- **Estimated Duration**: 3.5 hours
+- **Dependencies**: Phase 2 (infrastructure fixes)
+- **Status**: Not Started
+
+## 🎯 Phase Objective
+Systematically audit and repair docstring syntax errors across all SolarWindPy modules to eliminate Sphinx warnings and ensure proper API documentation generation. Focus on modules with known HTML rendering issues.
+
+## 🧠 Phase Context
+With infrastructure fixes from Phase 2, docstring syntax errors are now the primary barrier to proper HTML rendering. This phase systematically fixes docstring issues in all modules, with priority on problematic modules identified in Phase 1.
+
+## 📋 Implementation Tasks
+
+### Task Group 1: Core Module Docstring Repair
+- [ ] **Audit and Fix solarwindpy.core Module** (Est: 45 min) - Repair docstring syntax in core/*.py files (plasma.py, ions.py, base.py, etc.)
+  - Commit: `<checksum>` 
+  - Status: Pending
+  - Notes: Focus on modules causing solarwindpy.core.html rendering issues
+- [ ] **Audit and Fix solarwindpy.fitfunctions Module** (Est: 40 min) - Repair docstring syntax in fitfunctions/*.py files
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Priority module due to solarwindpy.fitfunctions.html rendering failures
+- [ ] **Audit and Fix solarwindpy.instabilities Module** (Est: 25 min) - Repair docstring syntax in instabilities/*.py files
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Address solarwindpy.instabilities.html rendering issues
+
+### Task Group 2: Solar Activity and Plotting Module Fixes
+- [ ] **Audit and Fix solarwindpy.solar_activity Module** (Est: 35 min) - Repair docstring syntax in solar_activity/ hierarchy
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Fix solarwindpy.solar_activity.html rendering and submodule documentation
+- [ ] **Audit and Fix solarwindpy.plotting Module** (Est: 30 min) - Repair docstring syntax in plotting/ hierarchy including labels/
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Ensure plotting documentation renders properly with visual elements
+- [ ] **Audit and Fix solarwindpy.tools Module** (Est: 15 min) - Repair docstring syntax in tools/*.py files
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Smaller module, fewer expected issues
+
+### Task Group 3: Docstring Quality and Standards
+- [ ] **Standardize Docstring Format** (Est: 20 min) - Ensure consistent NumPy/Google docstring format across all modules
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Apply consistent formatting standards for professional documentation
+- [ ] **Fix Cross-Reference Syntax** (Est: 15 min) - Repair Sphinx cross-reference syntax (:class:, :func:, :meth:, etc.)
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Fix broken internal links and references
+- [ ] **Validate Mathematical Notation** (Est: 10 min) - Ensure LaTeX math expressions render properly in docstrings
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Critical for scientific software documentation
+
+### Task Group 4: Validation and Testing
+- [ ] **Execute Post-Fix Build** (Est: 15 min) - Run clean Sphinx build to validate docstring fixes
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Verify docstring repairs eliminate warnings
+- [ ] **Spot Check API Documentation** (Est: 10 min) - Review generated API documentation for completeness and accuracy
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Ensure docstring fixes result in proper API documentation
+
+## ✅ Phase Acceptance Criteria
+- [ ] All docstring syntax errors eliminated across target modules
+- [ ] Consistent docstring format applied throughout codebase
+- [ ] Cross-references and internal links functioning correctly
+- [ ] Mathematical notation rendering properly in documentation
+- [ ] Sphinx build produces significantly fewer warnings
+- [ ] API documentation generated correctly for all public functions/classes
+- [ ] HTML pages show proper content organization with descriptions
+
+## 🧪 Phase Testing Strategy
+- **Module-by-Module Validation**: Test each module after docstring fixes
+- **Syntax Verification**: Use Sphinx's strict mode to catch remaining syntax issues
+- **Cross-Reference Testing**: Validate all internal documentation links
+- **API Coverage**: Ensure all public APIs have proper documentation
+
+## 🔧 Phase Technical Requirements
+- **Docstring Standards**: NumPy/Google docstring format
+- **Sphinx Syntax**: Proper reStructuredText and Sphinx directive usage
+- **Mathematical Notation**: LaTeX math expressions for scientific content
+- **Cross-References**: Sphinx intersphinx and autodoc linking
+
+## 📂 Phase Affected Areas
+- `solarwindpy/core/*.py` - All core module docstrings
+- `solarwindpy/fitfunctions/*.py` - All fitfunctions module docstrings
+- `solarwindpy/instabilities/*.py` - All instabilities module docstrings
+- `solarwindpy/solar_activity/**/*.py` - All solar activity module docstrings
+- `solarwindpy/plotting/**/*.py` - All plotting module docstrings
+- `solarwindpy/tools/*.py` - All tools module docstrings
+
+## 📊 Phase Progress Tracking
+
+### Current Status
+- **Tasks Completed**: 0/11
+- **Time Invested**: 0h of 3.5h
+- **Completion Percentage**: 0%
+- **Last Updated**: 2025-08-13
+
+### Blockers & Issues
+- Dependent on stable Sphinx configuration from Phase 2
+- May discover complex docstring issues requiring additional time
+
+### Next Actions
+- Begin with core module docstring audit
+- Prioritize modules with known HTML rendering failures
+- Apply systematic docstring syntax fixes
+
+## 💬 Phase Implementation Notes
+
+### Implementation Decisions
+- Focus on modules with known HTML rendering issues first
+- Apply consistent docstring standards across all modules
+- Use DocumentationMaintainer agent for docstring syntax expertise
+
+### Lessons Learned
+[To be populated during implementation]
+
+### Phase Dependencies Resolution
+- Requires stable Sphinx infrastructure from Phase 2
+- Provides clean docstrings for HTML rendering validation in Phase 4
+
+---
+*Phase 3 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.*

plans/documentation-rendering-fixes/4-HTML-Page-Rendering-Verification.md

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+# Phase 4: HTML Page Rendering Verification
+
+## Phase Metadata
+- **Phase**: 4/6
+- **Estimated Duration**: 1.5 hours
+- **Dependencies**: Phase 3 (docstring fixes)
+- **Status**: Not Started
+
+## 🎯 Phase Objective
+Verify and fix HTML page rendering for all modules, ensuring proper content organization, complete API documentation display, and elimination of rendering failures identified in Phase 1.
+
+## 🧠 Phase Context
+With infrastructure and docstring fixes complete, this phase validates that all HTML pages render correctly. Focus on previously problematic pages (solarwindpy.fitfunctions.html, solarwindpy.core.html, etc.) while ensuring comprehensive coverage across all modules.
+
+## 📋 Implementation Tasks
+
+### Task Group 1: Critical Page Rendering Verification
+- [ ] **Verify solarwindpy.core.html Rendering** (Est: 20 min) - Validate complete rendering of core module documentation
+  - Commit: `<checksum>` 
+  - Status: Pending
+  - Notes: Ensure all classes and functions display with proper descriptions
+- [ ] **Verify solarwindpy.fitfunctions.html Rendering** (Est: 20 min) - Validate fitfunctions module HTML page completeness
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Check mathematical expressions and class hierarchies render correctly
+- [ ] **Verify solarwindpy.instabilities.html Rendering** (Est: 15 min) - Validate instabilities module documentation display
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Ensure scientific content and equations render properly
+- [ ] **Verify solarwindpy.solar_activity.html Rendering** (Est: 15 min) - Validate solar activity module and submodule documentation
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Check hierarchical submodule documentation structure
+
+### Task Group 2: Comprehensive Page Audit
+- [ ] **Audit All Module HTML Pages** (Est: 20 min) - Systematic check of all generated HTML pages for completeness
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Verify plotting, tools, and all other module pages render correctly
+- [ ] **Verify API Documentation Completeness** (Est: 15 min) - Ensure all public APIs appear in generated documentation
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Check for missing classes, functions, or incomplete descriptions
+
+### Task Group 3: Content Organization and Navigation
+- [ ] **Fix Content Organization Issues** (Est: 10 min) - Address any remaining content placement or organization problems
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Ensure definitions appear in correct locations with proper descriptions
+- [ ] **Validate Cross-Page Navigation** (Est: 5 min) - Test navigation between documentation pages and internal links
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Verify table of contents and cross-references work correctly
+
+## ✅ Phase Acceptance Criteria
+- [ ] All previously problematic HTML pages render completely and correctly
+- [ ] No missing content or misplaced definitions in any module documentation
+- [ ] All public APIs display with proper descriptions and signatures
+- [ ] Mathematical expressions and scientific content render properly
+- [ ] Navigation and cross-references function correctly
+- [ ] HTML page quality matches professional scientific software standards
+- [ ] Zero HTML rendering errors or incomplete pages
+
+## 🧪 Phase Testing Strategy
+- **Visual Inspection**: Manual review of all HTML pages for completeness and quality
+- **Content Verification**: Systematic check that all expected content appears correctly
+- **Navigation Testing**: Verify internal links and cross-references work properly
+- **Comparative Analysis**: Compare fixed pages against original broken versions
+
+## 🔧 Phase Technical Requirements
+- **Web Browser**: For manual HTML page inspection
+- **Sphinx Build Output**: Fresh documentation build from Phase 3 fixes
+- **Documentation Standards**: Scientific software documentation quality benchmarks
+
+## 📂 Phase Affected Areas
+- `docs/build/html/` - All generated HTML documentation pages
+- `docs/build/html/solarwindpy.*.html` - Specific module documentation pages
+- Navigation and cross-reference validation across all pages
+
+## 📊 Phase Progress Tracking
+
+### Current Status
+- **Tasks Completed**: 0/8
+- **Time Invested**: 0h of 1.5h
+- **Completion Percentage**: 0%
+- **Last Updated**: 2025-08-13
+
+### Blockers & Issues
+- Dependent on successful docstring fixes from Phase 3
+- May identify residual rendering issues requiring additional fixes
+
+### Next Actions
+- Execute fresh documentation build with Phase 3 fixes
+- Begin systematic HTML page verification
+- Address any remaining rendering issues
+
+## 💬 Phase Implementation Notes
+
+### Implementation Decisions
+- Focus on previously problematic pages first to validate fix effectiveness
+- Use systematic approach to ensure no pages are missed
+- Document any remaining issues for final resolution
+
+### Lessons Learned
+[To be populated during implementation]
+
+### Phase Dependencies Resolution
+- Requires clean docstrings from Phase 3
+- Provides validated HTML output for quality assurance in Phase 5
+
+---
+*Phase 4 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.*

plans/documentation-rendering-fixes/5-Advanced-Documentation-Quality-Assurance.md

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+# Phase 5: Advanced Documentation Quality Assurance
+
+## Phase Metadata
+- **Phase**: 5/6
+- **Estimated Duration**: 2 hours
+- **Dependencies**: Phase 4 (HTML rendering verification)
+- **Status**: Not Started
+
+## 🎯 Phase Objective
+Implement comprehensive documentation quality assurance including cross-references, link validation, documentation completeness checks, and professional quality standards for scientific software documentation.
+
+## 🧠 Phase Context
+With basic rendering fixed, this phase elevates documentation quality to professional scientific software standards. Focus on comprehensive quality checks, user experience improvements, and establishing quality metrics for ongoing maintenance.
+
+## 📋 Implementation Tasks
+
+### Task Group 1: Cross-Reference and Link Validation
+- [ ] **Validate All Internal Cross-References** (Est: 25 min) - Test all Sphinx cross-references (:class:, :func:, :meth:, etc.) for accuracy
+  - Commit: `<checksum>` 
+  - Status: Pending
+  - Notes: Ensure all internal links resolve correctly
+- [ ] **Run Sphinx Linkcheck** (Est: 20 min) - Execute sphinx-build linkcheck to identify and fix broken external links
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Validate external references and citations
+- [ ] **Fix Cross-Reference Inconsistencies** (Est: 15 min) - Repair any broken or inconsistent internal documentation links
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Ensure consistent reference formatting throughout
+
+### Task Group 2: Documentation Completeness and Coverage
+- [ ] **Audit API Documentation Coverage** (Est: 30 min) - Ensure all public APIs have complete documentation
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Identify and document any missing API documentation
+- [ ] **Validate Scientific Content Accuracy** (Est: 20 min) - Review scientific content for accuracy and completeness
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Ensure physics formulas and references are correct
+- [ ] **Check Documentation Examples** (Est: 10 min) - Verify code examples in docstrings are functional and accurate
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Test example code snippets where applicable
+
+### Task Group 3: Professional Quality Standards
+- [ ] **Implement Documentation Style Guide** (Est: 15 min) - Ensure consistent documentation style across all modules
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Apply scientific software documentation best practices
+- [ ] **Optimize Search and Navigation** (Est: 10 min) - Improve documentation searchability and user navigation experience
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Enhance table of contents and index organization
+- [ ] **Validate Accessibility Standards** (Est: 5 min) - Ensure documentation meets basic web accessibility standards
+  - Commit: `<checksum>`
+  - Status: Pending
+  - Notes: Check for proper heading hierarchy and alt text
+
+## ✅ Phase Acceptance Criteria
+- [ ] All internal cross-references validated and functioning
+- [ ] Zero broken external links in documentation
+- [ ] Complete API documentation coverage for all public interfaces
+- [ ] Scientific content accuracy validated
+- [ ] Consistent documentation style applied throughout
+- [ ] Professional quality matching leading scientific software projects
+- [ ] Enhanced user navigation and search functionality
+- [ ] Documentation accessibility standards met
+
+## 🧪 Phase Testing Strategy
+- **Link Validation**: Automated testing of all internal and external links
+- **Coverage Analysis**: Systematic review of API documentation completeness
+- **Quality Metrics**: Establish measurable documentation quality standards
+- **User Experience Testing**: Navigation and search functionality validation
+
+## 🔧 Phase Technical Requirements
+- **Sphinx Tools**: linkcheck, search indexing, accessibility validation
+- **Quality Standards**: Scientific software documentation best practices
+- **Coverage Analysis**: Tools for measuring documentation completeness
+
+## 📂 Phase Affected Areas
+- All documentation pages for cross-reference validation
+- `docs/source/` - Source files for style and completeness improvements
+- Search indexes and navigation structures
+- External link references and citations
+
+## 📊 Phase Progress Tracking
+
+### Current Status
+- **Tasks Completed**: 0/9
+- **Time Invested**: 0h of 2h
+- **Completion Percentage**: 0%
+- **Last Updated**: 2025-08-13
+
+### Blockers & Issues
+- Dependent on properly rendered HTML from Phase 4
+- May identify additional quality issues requiring fixes
+
+### Next Actions
+- Begin comprehensive cross-reference validation
+- Execute linkcheck for external link validation
+- Implement systematic quality improvements
+
+## 💬 Phase Implementation Notes
+
+### Implementation Decisions
+- Focus on professional quality standards appropriate for scientific software
+- Implement systematic quality checks for ongoing maintenance
+- Use DocumentationMaintainer agent expertise for quality standards
+
+### Lessons Learned
+[To be populated during implementation]
+
+### Phase Dependencies Resolution
+- Requires properly rendered HTML pages from Phase 4
+- Provides high-quality documentation foundation for optimization in Phase 6
+
+---
+*Phase 5 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.*