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…ools.
Core Engine and HBL:
- Introduced dictionary path access via 'IDIV' operator (e.g., dict["key1"]["key2"]) for efficient nested lookups.
- Enhanced variable change tracking in 'LikelihoodFunction' to ensure consistent first-compute states and improve optimizer reliability.
- Added 'utility.truthy' to 'UtilityFunctions.bf' for robust boolean evaluation of HBL objects.
- Implemented 'DATA_STACK_SPARSE_THRESHOLD' to allow fine-grained control over sparse matrix optimization heuristics.
- Improved Simplex optimizer with forced checkpointing to detect and prevent numerical instability/caching errors.
Models and Analysis:
- Added 'CODON-ANTICODON' energy pairing properties to the 'MG_REV_PROPERTIES' model family.
- Introduced 'Clade-Support' helper tool to compute Effective Clade Breadth (ECB) for BUSTED-PH results, quantifying the independence of selection signals.
- Registered 'Clade-Support' in the standard analysis list ('files.lst').
- Updated 'MG_REV_PROPERTIES' to support new codon-level energy pairing properties.
Maintenance:
- Bumped version to 2.5.98 in 'global_things.cpp'.
- Code cleanup and documentation updates in 'associative_list.cpp', 'variable.h', and 'likefunc.cpp'.
- Fixed various compiler warnings and improved memory management for HBL object references.
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…ools.
Core Engine and HBL:
Models and Analysis:
Maintenance: