Version 3.0.0

Highlights

• Smarter Conflict Resolution: Evaluates all candidate positions and selects optimal based on penalty scores (lowest penalty first) instead of breaking on conflict.
• Sequential Mutation Reattachment: Changed from batch to one-by-one reattachment for more robust tree building.
• Accelerated Leiden Clustering: Significantly improved speed of Leiden graph-based cell grouping.
• Structured Outputs: All critical outputs organized into dedicated directories.
• Performance Optimizations: Major speed improvements across Steps 1, 4, 6, and 6.6.

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What's New

Core Algorithm

• Conflict Resolution: Rollback mechanism now evaluates all candidates and selects optimal position.
• Mutation Reattachment: Sequential one-by-one reattachment for conservative and robust tree building.
• Leiden Clustering: Significantly accelerated.

Performance Optimizations

• Step 1: Block-based multi-threaded parsing; added --load_workers and --export_workers.
• Step 4: Extensive caching (fin_cache); numpy-vectorized penalty scoring replacing pandas loops.
• Step 6: Optimized Bayesian scoring; reduced deep-copy overhead.
• Step 6.6: Numpy-vectorized FP/FN recomputation across trees.

Code Quality

• Code refactoring with cleaner organization and improved annotations.
• Structured outputs in dedicated directories.

New Files

• src/bootstrap_support.py: Bootstrap analysis utilities.
• src/utils.py: Shared utility functions.

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Notes

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