PySB v1.6.0 Released

New Features

  • New reversible rule operator |; the previous <> operator is now pending deprecation (#309)
  • Saving and loading of SimulationResult objects with metadata in HDF5 format (#292)
  • PySB now supports Kappa 4, including custom rate laws with PySB Expressions. Kappa 3 support has been dropped (#334)
  • Rule pattern matching and new model test suite (#285)
  • Model components can now be accessed as attributes (#213)
  • Importing models from BioModels can now use either the EBI mirror (default) or the CalTech one (#325)
  • Cython support for ScipyOdeSimulator; this allows efficient simulation on Python 3, where weave is no longer an option (#320)

General Improvements

  • Native Python 3 compatibility for the whole PySB codebase (#312)
  • Internal species for tracking synthesis/degradation rules __source and __sink have been removed (#317)
  • Specifying a pattern with a dangling bond now causes an error (#328)
  • Simulator run() arguments are no longer persistent (#314)
  • State values in patterns are now verified (#322)
  • Frequently Asked Questions added to documentation (#331)
  • Loading CupSodaSimulator no longer initializes the GPU on import; instead it wait until instantiation (#332).
  • code updated for compatibility with matplotlib 2.1 (#303)
  • Improvements to ScipyOdeSimulator's weave interface, including better control of console output (#299) and ensuring C code is cacheable when unicode variable names are used (#301).
  • Graph objects in the Kappa interface (e.g. contact maps) are now returned as networkx graphs, not pygraphviz. pygraphviz support for reading .dot files in the Kappa interface has been replaced with pydot (#335).


  • Fix component rename when not using Self Exporter (#321)
  • ComplexPattern.__call__ now raises a DuplicateMonomerError when duplicate monomers are present (#323)
  • Fixes for ComplexPattern.is_concrete() (#307)
  • Reversible Rule.is_synth() and is_deg() now work for reversible patterns (#326)
  • Fix error when running Tyson model with CupSodaSimulator (#332)