This version of PySB supports Python 3.6-3.9. Python 2.7 is no longer supported.

New features

Improvements

ScipyOdeSimulator speedup through refactoring, use of partial (#531, #483)
Use double precision for BNG and Kappa parameters (#490)
Allow constant expressions for compartment sizes (#525)
Faster SimulationResult loading: use slices (#491)
Implement BNG boolean treatment within expressions, e.g. evaluate (2 > 1) as True (#494)
Import ABC from collections.abc instead of collections for Python 3.9 compatibility (#485)
Implement the assumption that all symbolic variables in a model only take real values. The user can specify integer and non-negative enforced assumptions about parameter values. Changes are relevant for any simplifications of symbolic expressions in the model (#475)
Update tested Python versions on CI (#479)
Remove weave and theano support from ScipyOdeSimulator (#482)
Remove Python 2 support (#486, #487)
Update docs with Python version support (#492)
Update docs with stubs on calibration and PySB modules to tutorial (#509)
Update deprecated pandas call in CupSodaSimulator (#523)
Remove deprecated sympy.boolalg calls (#526)
Specify Python>=3.6 requirement in setup.py (#536)

Fix sympy 1.6 compatibility (#505)
Fix observable trajectories on HDF5 load (#502)
Fix reading of error messages from cupSODA (#510)
Fix SBML export with unset compartment size (#513)
Fix eqn_mode='python' for models with local functions (#495)
Fix typehints in core (#507, #520)
Fix BNG code generation for Eq and Ne (#528)
Fix StochKit export of certain PySB rate Expressions (#521)
Copy annotations when creating model from base (#493)
Fix SimulationResult loads when include_obs_exprs=True and model has no observables or expressions (#481)
Fix an error when using ScipyOdeSimulator with the num_processors option >1 (i.e. use multiprocessing) together with compiler='python' (#480)
Fix usage of super in multiple inheritance of sympy.Symbol (#474)
Fix readthedocs error with updated mock (#489)
Fix slice IndexError in tutorial (#529)
Fix tutorial typos (#511)
Fix DeprecationWarning leading to test failure with new versions of h5py (#537)