PySB v1.7.0 Released

New Features

  • Python 3.7 now officially supported (in addition to 3.6 and 2.7) (#368)
  • Filtering for ComponentSets (documentation) (#340)
  • SBML export now uses LibSBML and supports compartments and expressions (#367)
  • On demand observable trajectories without adding them to the model (documentation) (#337)

General Improvements

  • The <> operator for reversible rules in Python 2.7 has been formally deprecated. Use | instead (#344)
  • Products of synthesis rules are enforced to be concrete (#354)
  • Monomers' site and state names are validated upon definition (#352)
  • Expressions now must be created from sympy.Expr. Previously, unwrapped integers and floats were accepted (#350)
  • Capture BNG errors into PySB exception messages (#363)
  • Show line numbers in the debug log for BioNetGen language files to aid interpreting BNG error messages (#365)
  • Python model exporter now produces Python 3.x compatible code (#366)
  • Recover from non-functional Cython/weave compilers on Windows (#353)
  • Better tests for PySB exporters, and explicit ExpressionsNotSupported and CompartmentsNotSupported exceptions where applicable (#357)


  • Fix export to BNG of expressions containing log (#361)
  • Fix Kappa export when using parameters with overlapping (substring) names (#346)