Phase 2: Create Compatibility Layer and Transition Structure

[Sinitca-Aleksandr]

This issue tracks the second phase of our C/C++ code migration plan. The goal is to create a compatibility layer that maintains backward compatibility while introducing the new module structure.

Objectives:

1. Create compatibility shim in StatTools/init.py
2. Establish dual import paths (old and new)
3. Set up transition directory structure
4. Implement deprecation warnings for old imports
5. Ensure seamless migration experience

Implementation Plan:

1. Update StatTools/init.py to include compatibility layer:

   # Maintain backward compatibility during transition
   from fluctuation_analysis_tools import *
   
   # Legacy imports
   from fluctuation_analysis_tools.legacy import StatTools as legacy_StatTools

2. Create _cpp_extensions directory structure:
   • _cpp_extensions/init.py (bindings entry point)
   • _cpp_extensions/core.so (compiled extension)
3. Update setup.py to build extensions in correct location
4. Add migration documentation showing equivalent imports
5. Implement deprecation warnings for old import paths

Acceptance Criteria:

• Both old and new import paths work identically
• Deprecation warnings appear for old imports (not errors)
• All functionality accessible through both paths
• Migration guide documented with examples
• Tests verify compatibility layer works correctly