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@spond spond released this 28 Apr 14:22
· 2 commits to master since this release
2.5.98
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Learn about vigilant mode.

HyPhy v2.5.98: Core Enhancements, Stability Fixes, and New Analysis Tools.

Core Engine and HBL:

  • Introduced dictionary path access via 'IDIV' operator (e.g., dict${{"key1","key2",..."keyN"}}) 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 ENV to allow fine-grained control over sparse matrix optimization heuristics.
  • Improved Simplex optimizer with forced checkpointing to detect and prevent numerical instability/caching errors; this fixes some obscure bugs

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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