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PySCeS release 1.1.1
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@jmrohwer jmrohwer released this 25 Jul 18:11
· 102 commits to main since this release
1.1.1
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We are pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (https://pysces.github.io/) version 1.1.1. This is the first release in the 1.1 series and contains some new features and various bug fixes.

New features

  • When used in a notebook environment, the ipympl backend for matplotlib is now enabled if installed. This allows use in JupyterLab (as opposed to classic notebook). If ipympl is not installed, fallback is to the standard nbAgg, which is part of matplotlib.
  • Simulation results (mod.sim object) can now be returned as a pandas DataFrame if pandas is installed, otherwise a numpy recarray is returned as before. This option is configurable with custom_datatype = pandas in the user and system configuration files (see https://pyscesdocs.readthedocs.io/en/latest/userguide_doc.html#configuration), and can be enabled or disabled per session or per model: 
    pysces.enablePandas()
pysces.enablePandas(False)
mod.enableDataPandas()
mod.enableDataPandas(False)

Bug fixes

  • Fixed a bug in simulations with RateRules using Assimulo, where a wrong solver variable was being assigned internally.
  • Fixed SBML export when assignment rules were evaluating reaction rates.
  • Enabled assignment rules (forcing functions) to track parameter changes when using CVODE. This is needed in case events change parameters during the course of the simulation.

README: https://github.com/PySCeS/pysces/blob/master/README.md

DOCUMENTATION: https://pyscesdocs.readthedocs.io/en/latest/

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