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
andCompartmentsNotSupported
exceptions where applicable (#357)
Bugfixes
- Fix export to BNG of expressions containing
log
(#361) - Fix Kappa export when using parameters with overlapping (substring) names (#346)