Version 2.0.0

Highlights

• Performance optimization for core tree-building pipeline.
• Speed improvements in data loading and mutation integration.
• Improved reproducibility with updated run scripts.

---

What's New

Performance Improvements

• Core tree-building pipeline performance optimization.
• Data loading and mutation integration speed improvements.
• Extensive caching implementation for tree/matrix lookups.
• Numpy-vectorized operations replacing pandas loops for penalty scoring.

Code Quality

• Updated run scripts for better reproducibility.
• Fixed non-determinism in scaffold tree building.
• Debug improvements for comprehensive FP metrics calculation.
• Various logging and documentation updates.

---

Notes

• For usage details, see the docs site: https://github.com/douymLab/PhyloSOLID/