Release Version 3.3.1 · douymLab/PhyloSOLID

Deterministic parallel CV search: Fixed critical issue where the same CV threshold produced different results when run in parallel search mode versus single-run mode.
Random seed isolation: Worker processes now have properly isolated RNG states, ensuring consistent results across all runs.
Improved reproducibility: Set iteration order is now deterministic across parallel workers, eliminating non-deterministic behavior in tree construction.

What's New

Fixed parallel vs single-run inconsistency: Worker processes in multiprocessing.Pool now re-initialize random seeds at entry point based on cv_value, ensuring each CV threshold has deterministic and independent RNG state.
Fixed set iteration non-determinism: find_all_path_nodes_scaffold, get_all_path_nodes_with_group_filter, and find_all_path_nodes now return sorted lists, eliminating iteration order variability across parallel workers.
Fixed Leiden algorithm RNG state: leiden_mutation_groups now explicitly resets random.seed() and np.random.seed() before running community detection, ensuring deterministic clustering results.
Enhanced reproducibility module: set_seed() now includes additional random module reset for forked processes, ensuring complete RNG isolation.

Improved deterministic behavior in parallel execution: All path-finding functions now guarantee consistent iteration order regardless of execution environment.
Enhanced random seed management: Worker processes now properly isolate RNG states, preventing cross-contamination between CV thresholds.

This release is strongly recommended for all users running CV threshold search, as previous versions could produce inconsistent results across runs.
No changes to input/output formats or command-line interfaces; fully backward compatible with v3.3.0 workflows.
For detailed usage, see the docs site: https://github.com/douyinlab/PhyloSOLID/