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Release notes for sbml2cellml 0.3.1

Documentation release with a graphical overview of the SBML test suite results, together with the conversions added since 0.3.0. Of the 1535 runnable cases of the SBML test suite, 1462 convert to valid CellML (1420 in 0.3.0) and 1010 simulate with libopencor like the expected results (857 in 0.3.0), see the SBML test suite page.

Features

  • bar diagram of the SBML test suite results, i.e., the cases which pass, fail and skip every stage of the roundtrip, in the README and on the SBML test suite page; sbml2cellml-testsuite run and report write it for light and dark backgrounds (sbml2cellml.testsuite.figure)
  • the tables of the SBML test suite report list the total number of cases, the failure reasons of a stage start with its number of failed cases
  • algebraic rules are converted in both directions: an SBML algebraic rule becomes an implicit CellML equation, an implicit CellML equation an SBML algebraic rule
  • the rateOf symbol is replaced by the right-hand side of the differential equation of its variable
  • the conversion factors of species and the model are applied to the reaction terms
  • plus, times, and, or and xor with less than two arguments are replaced by their value

Fixes

  • a rule or kinetic law without math no longer fails the conversion, it is ignored
  • documentation: the headings of the conversion page were missing in the page navigation (the page had two top level headings), and pages outside of a section looked like members of the section above them; every page is part of a section now
  • documentation: the PyPI badges use the current shields.io routes

Changes

  • documentation: the roadmap became the conversion issues page, which only lists the remaining issues
  • documentation: the simulation page covers the simulation of SBML with roadrunner and of CellML with libopencor with the setup of both optional simulators

Limitations

  • events, the delay symbol and coupled algebraic rules are not converted
  • units are not converted, every variable is dimensionless; numbers with the units of an SBML unit definition are not supported
  • Windows is not supported, the Windows wheels of libcellml 0.7.1 contain ARM64 binaries
  • see the conversion issues in the documentation

Your sbml2cellml team