refactor(modules): apply comprehensive coding standards to all modules

[ryanmccann1024]

Description:
This PR completes a major refactoring effort to bring all FUSION modules up to the newly established coding standards. This includes reorganizing the entire codebase structure, implementing a modular architecture, standardizing interfaces, and improving code quality across all components.

🔧 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:
All existing tests have been updated to work with the new modular structure. Tests now import from the new fusion package structure and have been refactored to follow the same coding standards as the main codebase.

Test Configuration Used:

[general_settings]
# Standard test configuration maintained

Commands to Reproduce Testing:

# Run all tests
python -m pytest tests/

# Run specific module tests
python -m pytest tests/test_routing.py
python -m pytest tests/test_spectrum_assignment.py

Test Results:

• Operating System: macOS 15.0.0
• Python Version: 3.12
• Test Environment: local

📊 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):

• Complete restructure from flat module layout to hierarchical fusion package
• All imports must be updated from src.module to fusion.core.module
• Configuration system completely rewritten with new validation
• CLI arguments reorganized with new parameter registry system

Migration Steps:

1. Update all imports to use new fusion package structure
2. Update configuration files to use new standardized format
3. Update CLI commands to use new entry points (fusion.cli.run_sim, etc.)
4. Review and update any custom scripts that depend on the old structure

Before/After Examples:

# Before (old usage)
from src.engine import Engine
from src.routing import RoutingAlgorithm
from run_sim import main

# After (new usage)  
from fusion.core.simulation import SimulationEngine
from fusion.modules.routing import RoutingRegistry
from fusion.sim.run_simulation import run_simulation

✅ 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:

1. Update all deployment scripts to use new package structure
2. Update environment variables if using old module paths
3. Ensure all configuration files are updated to new format

🔍 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:

• New fusion package structure and module organization
• Interface definitions in fusion/interfaces/
• Configuration system in fusion/configs/
• Registry patterns used throughout (CLI, routing, spectrum, etc.)
• Coding standards compliance (see CODING_STANDARDS.md)

📝 Additional Notes

Key Refactoring Achievements:

1. Modular Architecture: Migrated from flat structure to hierarchical fusion package
2. Standardized Interfaces: Created abstract base classes for all major components
3. Registry Pattern: Implemented registry pattern for routing, spectrum, SNR, and CLI parameters
4. Configuration Management: New robust configuration system with validation and schemas
5. Enhanced CLI: Modular CLI with parameter registry and better organization
6. Improved Testing: All tests updated and reorganized to match new structure
7. Documentation: Added comprehensive docstrings and type hints throughout
8. Error Handling: Standardized error handling with custom exceptions
9. Code Quality: Applied pylint standards and resolved all major issues

New Key Files Added:

• CODING_STANDARDS.md - Comprehensive coding guidelines
• fusion/interfaces/ - Abstract interfaces for all major components
• fusion/configs/ - New configuration management system
• fusion/cli/parameters/ - Modular CLI parameter definitions
• Makefile - Development automation
• Enhanced GitHub templates for issues and PRs

Open Questions:

• Should we maintain backward compatibility shims for the old import paths?
• Are there any specific performance benchmarks we should run?

Future Work:

• Complete documentation updates for all new modules
• Add integration tests for new interfaces
• Performance optimization pass
• Add more comprehensive examples

Related PRs:

• This completes the refactoring effort started in previous PRs

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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