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ssys 0.6.1

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@wshlavacek wshlavacek released this 05 Jul 22:27

Patch release focused on SBML interpretation correctness and fail-closed parsing.

Fixed

  • SBML compartment volume, a species/model conversionFactor, and constant stoichiometryMath are now interpreted correctly. Previously these produced silently wrong ODEs; the fixes are verified against libRoadRunner and are no-ops for models that do not use the feature.

Changed

  • The SBML parser now fails closed with a structured unsupported_feature error on variable reaction stoichiometry and time-varying compartment volume, which are not power-law-recastable, instead of mis-integrating them.
  • The deprecated legacy Antimony parser (ssys.parse_antimony / --parser legacy) now fails closed on the same constructs it cannot correctly interpret (non-unit/multiple compartments, conversionFactor, variable stoichiometry) and emits a DeprecationWarning; the recast notebook no longer routes simulation through it.
  • Refreshed the BioModels benchmark: 848 transformations (86.7%) and 739 numerically validated models across 978 candidates.

Full changelog: https://github.com/lanl/ssys/blob/v0.6.1/CHANGELOG.md