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Release notes for sbml2cellml 0.3.4

The simulations with CVODE are more robust. Of the 1060 manually curated models of BioModels which run, 908 simulate with libopencor like the roadrunner simulation of the original model (778 in 0.3.3), see the BioModels page.

Features

  • run_timecourse takes maximum_number_of_steps, the number of internal steps the solver may take between two time points of the output, 100000 by default. The 500 steps of libopencor ended the simulation of many models with mxstep steps taken before reaching tout, e.g., of 147 curated models of BioModels
  • the SBML test suite and BioModels checks repeat a simulation with relaxed tolerances (1e-8 relative and 1e-10 absolute, then 1e-7 and 1e-9) when CVODE gives up with the tight tolerances of the checks (1e-9 and 1e-12), for roadrunner and libopencor. Looser tolerances for every simulation are no alternative, results which pass would fail
  • tox r -e biomodels runs the local BioModels check in the locked environment

Changes

  • the full SBML test suite runs with python 3.14 only, in continuous integration and in the tox environment testsuite; the unit tests run with every supported python

Limitations

  • the unit check of the libcellml 0.7.1 analyser warns about consistent equations with units which have a multiplier and an exponent, e.g., per minute (cellml/libcellml#1463); the warnings do not make a model invalid
  • libsbml evaluates the rate rule of a variable as its value (sbmlteam/libsbml#491); the converter works around it since 0.3.3
  • events, the delay symbol and coupled algebraic rules are not converted
  • Windows is not supported, the Windows wheels of libcellml 0.7.1 contain ARM64 binaries
  • see the conversion issues in the documentation

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