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@seanebum seanebum released this 10 Sep 15:41
a67eee8

1.2.1 Changelist:

  • contains edits to README for PyPI displaying and compatibility

1.2 Changelist:

New Features:

  • model.run now returns a Results object for single trajectories
  • model.run now returns an Ensemble object for multiple trajectories
  • Added built-in plotting (matplotlib and plotly) for Results and Ensemble Objects (use .plot, .plotplotly)
  • Added statistical plotting for Ensemble objects (use .plot_std_dev_error_bars
  • Overhauled Readme with better layout, logos, and examples
  • Added Code of Conduct
  • Added notebooks for the following models:
    • Vilar Oscillator
    • Brusselator
    • Oregonator

Fixes / Updates:

  • Made corrections to ssa_c_solver dependency graph to be non-symmetric. now runs vilar oscillator model [c_base/model.cpp]
  • Fixed error where Cython solver was incorrectly parsing species [cython_ssa_solver.pyx]
  • Fixed issue where propensities were being calculated incorrectly for bimolecular reactions of type 2X -> Y [gillespy2.py]
  • Included check for RateRules empty strings [gillespy2.py]
  • Included a check for RateRules valid associated species [gillespy2.py]
  • Modified RateRule instantiation to be positional or keyword [gillespy2.py]
  • Modified Tau Hybrid Switching Condition tests [basic_tau_hybrid_solver.py]
  • Cleaned/updated basic_tau_leaping comments [basic_tau_hybrid_solver.py]
  • Added loop break point for faster pure ode detection [basic_tau_hybrid_solver.py]