New features

StochKitSimulator, an interface to the stochastic simulator StochKit. See pysb.simulator.stochkit.StochKitSimulator.
InitialsSensitivity, a tool to perform pairwise sensitivity analysis of initial conditions. See pysb.tools.sensitivity_analysis.InitialSensitivity. EXPERIMENTAL.
Import models directly from BioModels from just their ID (BIOMDxxx... or MODELxxx...) with pysb.importers.sbml.model_from_biomodels().

General improvements

Faster simulation runs for models with many expressions (~60x speedup for a 200-expression model).
Improved accuracy and better error reporting when parsing SBML expressions in pysb.importers.sbml.
The Kappa interface has been upgraded to support Kappa version 4. This also means Kappa v3 is no longer supported.

CupSodaSimulator now works on Python 3.
Simulators now fully respect parameter value overrides for initial condition parameters (#252).
Simulators now allow overriding a non-zero initial condition to zero (#251).
Simulators no longer have problems with parameter names that are unicode objects (still only ASCII characters are allowed, though) (#278).
Model components with the same name as a top-level sympy object (anything you would see in from sympy import *) no longer cause errors when simulating (#259).
Applying a compartment condition to a MonomerPattern that already has one now correctly raises an exception (#258).
PysbFlatExporter now works with compartments using inline size declarations (#210).
ComplexPattern.is_equivalent_to now correctly handles certain combinations of compartments that were previously mishandled (#257).