🚀 SIMPLICITY v2.2.4: Heterogeneous Populations

This major release marks the integration of the long-shedders branch, evolving SIMPLICITY from an acute-infection model into a framework capable of handling population heterogeneity.

✨ Highlights & New Features

• Heterogeneous Population Modeling: Added full support for mixed populations containing both "Standard" and "Long-Shedder" host types. The model now features distinct infectiousness windows, detectability profiles, and lineage capacities for each sub-population.
• Evolutionary Calibration: This accounts for the compound evolutionary pressure generated by the continuous emergence of intra-host lineages ($k_v$) over time in distinct host types.
• Automated Calibration Pipeline

🧹 Housekeeping & Archiving (Important!)

To keep the root and scripts/ directories clean for version 2.0+, we performed a massive repository cleanup:

• Paper Archive: All specific figure-generating scripts and legacy experiments used for the original SIMPLICITY publication have been safely moved to scripts/00_SIMPLICITY_paper_archive/.
• Test Suite: Removed obsolete tests and added new, robust test files (e.g., tests/test_diag_mut_rates.py) to validate the new parameterization logic.