v1.2.1
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]