fix: property name standardization and comprehensive test fixes

[ryanmccann1024]

Description:
This PR implements comprehensive property name standardization across the FUSION codebase and resolves numerous test failures. The changes include applying coding standards to core modules (interfaces, IO, reporting), standardizing property names throughout the system, fixing parameter mismatches, and updating method signatures for consistency. Additionally, extensive test fixes were implemented to ensure all tests pass with the new standardized naming conventions.

🔧 Type of Change

Primary Change Type:

• 🐛 Bug Fix - Non-breaking change that fixes an issue
• ✨ New Feature - Non-breaking change that adds functionality
• 💥 Breaking Change - Change that would cause existing functionality to break
• 🔄 Refactor - Code change that neither fixes a bug nor adds a feature
• 📚 Documentation - Documentation only changes
• 🧪 Tests - Adding missing tests or correcting existing tests
• 🏗️ Build/CI - Changes to build process or CI configuration
• 🎨 Style - Code style changes (formatting, missing semicolons, etc.)
• ⚡ Performance - Performance improvements
• 🔒 Security - Security vulnerability fixes

Component(s) Affected:

• CLI Interface (fusion/cli/)
• Configuration System (fusion/configs/)
• Simulation Core (fusion/core/)
• ML/RL Modules (fusion/modules/rl/, fusion/modules/ml/)
• Routing Algorithms (fusion/modules/routing/)
• Spectrum Assignment (fusion/modules/spectrum/)
• SNR Calculations (fusion/modules/snr/)
• Visualization (fusion/visualization/)
• GUI Interface (fusion/gui/)
• Unity/HPC Integration (fusion/unity/)
• Testing Framework (tests/)
• Documentation
• GitHub Workflows (.github/)
• Build/Dependencies

🧪 Testing

Test Coverage:

• Unit tests added/updated
• Integration tests added/updated
• Manual testing performed
• Existing tests still pass
• Performance impact assessed

Test Details:
Comprehensive test suite fixes were implemented to address failures caused by:

• Property name standardization changes
• Method signature updates
• Module reorganization and import path changes
• Parameter name mismatches (e.g., spectrum assignment parameter corrections)
• Missing required fields in function calls

Test Configuration Used:

# Standard test configurations updated for new property names
[general_settings]
# Updated to use standardized property naming conventions

Commands to Reproduce Testing:

# Run the full test suite
python -m pytest tests/
# Run specific test modules that were updated
python -m pytest tests/test_spectrum_assignment.py
python -m pytest tests/test_snr_measurements.py  
python -m pytest tests/test_routing.py

Test Results:

• Operating System: Cross-platform compatible
• Python Version: 3.11+
• Test Environment: Local development environment

📊 Impact Analysis

Performance Impact:

• No performance impact
• Performance improved
• Minor performance decrease (acceptable)
• Significant performance impact (needs discussion)

Memory Usage:

• No change in memory usage
• Memory usage optimized
• Minor increase in memory usage
• Significant memory impact

Backward Compatibility:

• Fully backward compatible
• Minor breaking changes with migration path
• Major breaking changes (requires version bump)

Dependencies:

• No new dependencies
• New dependencies added (list in Additional Notes)
• Dependencies removed/updated

🔄 Migration Guide

Breaking Changes (if any):

• Property names standardized across modules (some internal APIs may have changed)
• Method signatures updated for spectrum dynamic slicing and related functions
• Configuration parameter names updated to follow consistent naming conventions
• Some test utility function signatures updated

Migration Steps:

1. Update any custom code that references internal module properties to use new standardized names
2. Review configuration files for any parameter name changes
3. Update test fixtures if using internal testing utilities
4. Run comprehensive tests to verify compatibility

Before/After Examples:

# Before (inconsistent property naming)
# Various naming conventions across modules

# After (standardized property naming)  
# Consistent naming conventions throughout all modules

✅ Code Quality Checklist

Architecture & Design:

• Follows established architecture patterns
• Code is modular and follows separation of concerns
• Interfaces are well-defined and documented
• Error handling is comprehensive
• Logging is appropriate and informative

Code Standards:

• Code follows project style guidelines
• Variable and function names are descriptive
• Code is properly commented
• Complex logic is documented
• No dead code or unused imports

Configuration & CLI:

• CLI arguments follow established patterns
• Configuration validation updated (if needed)
• Schema updated for new config options
• Backward compatibility maintained for configs

Security:

• No sensitive information hardcoded
• Input validation performed where needed
• No security vulnerabilities introduced
• Dependencies scanned for vulnerabilities

📚 Documentation

Documentation Updates:

• Code comments added/updated
• API documentation updated
• User guide/tutorial updated
• Configuration reference updated
• CHANGELOG.md updated
• README updated (if needed)

Examples Added:

• Usage examples in docstrings
• Configuration examples
• CLI usage examples
• Integration examples

🚀 Deployment

Deployment Considerations:

• Safe to deploy to all environments
• Requires environment-specific configuration
• Needs database migration (if applicable)
• Requires manual steps (document below)

Manual Steps Required:
None - changes are primarily internal standardization and test fixes.

🔍 Review Guidelines

For Reviewers:

• PR description is clear and complete
• Code changes align with described functionality
• Tests are comprehensive and pass
• Documentation is adequate
• No obvious security issues
• Performance impact is acceptable

Review Focus Areas:

• Property name consistency across all affected modules
• Test coverage and fixes for standardized naming
• Method signature updates and parameter corrections
• Import path and module organization changes

📝 Additional Notes

Major Changes Implemented:

1. Property Name Standardization: Applied consistent naming conventions across:

   • Core simulation modules
   • Interfaces module
   • IO and reporting modules
   • Spectrum assignment and SNR modules

2. Coding Standards Application: Updated modules to follow project coding standards:

   • interfaces module
   • IO module
   • reporting module

3. Test Infrastructure Fixes: Comprehensive test suite updates including:

   • Fixed all test failures caused by property name changes
   • Updated import statements for reorganized modules
   • Corrected parameter mismatches in function calls
   • Added missing required fields (seeds, stop_flag, etc.)

4. Method Signature Updates:

   • Updated spectrum dynamic slicing method signatures
   • Corrected parameter names in spectrum assignment
   • Fixed Windows encoding errors

5. Documentation Cleanup:

   • Removed outdated architecture plan documents
   • Updated coding standards documentation
   • Enhanced configuration templates

Commit Summary:

• 139+ commits consolidating refactoring efforts
• Builds on previous PRs refactor(cli): reorganize parameters module and eliminate code duplication #115, refactor: apply coding standards to interfaces, io, and reporting modules #119 and related work
• Resolves all pylint code quality issues
• Implements centralized TODO tracking system
• Adds comprehensive configuration system documentation

Testing Notes:
All tests now pass with the standardized property names and updated module structure. The changes maintain functionality while improving code consistency and maintainability.

Future Work:

• Monitor for any remaining edge cases in property usage
• Continue standardization efforts in remaining modules as needed

Related PRs:

• Merges work from refactor: apply coding standards to interfaces, io, and reporting modules #119 (interfaces/IO/reporting coding standards)
• Builds on refactor(cli): reorganize parameters module and eliminate code duplication #115 (CLI organization)
• Consolidates multiple refactoring branches

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🏁 Final Checklist

Before submitting this PR, confirm:

• I have followed the contributing guidelines
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published