The only change in this release is that Python version requirements are now specified in setup.py metadata (Python 2.7, or >=3.5). This is anticipated to be the final PySB release to support Python 2.7.
read moreThis version of PySB supports Python 3.6-3.9. Python 2.7 is no longer supported.
SimulationResult.save() now use JSON, rather than pickleValueError if a rule defined with reverse rate, but expression is not reversible (#471)Local functions allow PySB expressions to accept a tagged MonomerPattern or ComplexPattern as an argument. For example, in the following snippet, A synthesizes C with rate dependent on bound B:
Observable('AB_motif', A(b=1) % B(a=1))
Tag('x')
Expression('f_synth …PySB will support Python 2.7 until January 1, 2020. After that date, PySB's major version number will be incremented (PySB 2.x). From PySB 2.x onward, our policy will be to support the three most recent minor versions of Python (most likely Python 3.6, 3.7, and …
read moreMultiState capability, which enables a single Monomer site to be specified with multiple states (documentation) (#410)ScipyOdeSimulator multiprocessing capability, using n_processors argument (documentation) (#395)CupSodaSimulator (#409)__init__ are now validated by ScipyOdeSimulator (#381), StochKitSimulator (#382), and CupSodaSimulator (#383)And, Or, Floor, Ceiling, Min, Max, Abs, and the constants …<> operator for …|; the previous <> operator is now pending deprecation (#309)SimulationResult objects with metadata in HDF5 format (#292)Expressions. Kappa 3 support has been dropped (#334)BngSimulator, an interface to all simulators provided by BioNetGen: ODE, partitioned-leaping, SSA (stochastic) and NFsim (network-free stochastic). See pysb.simulator.bng.BngSimulator (#272).
ScipyOdeSimulator is faster in "pure Python" mode (i.e. without weave and a …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.pysb.importers.sbml.model …pysb.simulator.CupSodaSimulator for more.*Brand new Simulator classes and SimulationResult classes in the
pysb.simulator package. The old pysb.integrate API is unchanged but has been
reimplemented using the Simulator class.
* Model import from other types of models in the pysb.importers package.
Currently supports BNGL and SBML model import.
Release to fix one minor bug with the PyPI upload.
PySB has officially adopted semantic versioning. This means v1.1.0 includes new features as compared to v1.0.x, but is still backwards compatible so you won't have to change any of your models to upgrade to it.
PySB v1.0.1 has been released
read morePySB v1.0.0 has been released
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