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ssys 0.6.1

ssys 0.6.1 Latest
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@wshlavacek wshlavacek released this 05 Jul 22:27
v0.6.1
d7a7eca

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

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ssys 0.6.0

ssys 0.6.0

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@wshlavacek wshlavacek released this 05 Jul 10:21
v0.6.0
a956b10

ssys recasts a system of ODEs into canonical form and
verifies the result symbolically and numerically.

This is the first public release of ssys on PyPI.

Install

pip install ssys

Recast a batch of models from the command line:

ssys-recast --manifest models.manifest --outdir out --mode simplified

Supported platforms

  • Python 3.10, 3.11, and 3.12
  • Linux, macOS, and Windows — all tested in CI

Highlights in 0.6.0

  • ODE → S-system (or GMA) recasting with automatic lifting of rational and
    composite functions, plus symbolic + numerical validation of every recast.
  • Named validation profiles: strict, structural, symbolic, numerical,
    and trajectory.
  • Relicensed to the MIT License for LANL open-source release (LANL O5066).
  • Supported Python range pinned to 3.10–3.12 while ssys depends on NumPy 1.x and
    RoadRunner 2.7.x.
  • Packaged validation-report JSON Schema (v1.0), reachable via
    ssys.load_validation_report_schema().

Scope and maturity

  • Alpha. APIs and validation thresholds may still change.
  • Input trust boundary: ssys treats Antimony and SBML inputs as trusted
    local scientific model files.

See CHANGELOG.md for the
full history.

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