Release Version 3.2.1 · douymLab/PhyloSOLID

Highlights

Critical bug fixes for CV threshold search: Resolved two blocking issues that caused CV search failures in v3.2.0.
Duplicate mutation nodes eliminated: Fixed a typo in build_cluster_graph that caused the same mutation to be attached multiple times, leading to matrix dimension errors.
Logger standardization: Fixed NameError where logger was undefined in nested functions; all logging now uses consistent logger_obj parameter passing.
Improved robustness: Enhanced error handling in sub-grouping workflow, preventing silent failures during mutation placement.

Fixed NameError: name 'logger' is not defined: The get_mutation_clone_and_backbone_mut_as_keys_by_first_level_with_frequency function now correctly receives the logger instance via logger_obj parameter, resolving CV search failures at runtime.
Fixed ValueError: operands could not be broadcast together with shapes (1357,) (1357,2): Resolved the root cause where chr14_106276501_C_G (and similar low-support mutations) were being added to the scaffold tree multiple times due to a typo in build_cluster_graph (target_cluster → target_mut). This eliminates 2D array conflicts in m_current_cache.
Standardized logger parameter passing: Ensured all sub-functions across scaffold_builder.py, mutation_integrator.py, and full_tree_builder.py use logger_obj consistently, preventing future NameError issues.

Improved error handling in sub-grouping: Enhanced exception handling in perform_subgrouping_within_backbone_groups_and_build_initial_scaffold_tree, ensuring clean fallback behavior when community detection fails.
Better mutation filtering logic: Clarified the distinction between graph construction (which filters low-support mutations) and sub-grouping (which should retain all mutations for proper assignment).

This release is strongly recommended for all users running CV threshold search, as v3.2.0 contained critical bugs that could cause workflow failures.
No changes to input/output formats or command-line interfaces; fully backward compatible with v3.2.0 workflows.
For detailed usage, see the docs site: https://github.com/douymLab/PhyloSOLID/