Gillespy2

Fix for conda-forge
Updated Authors

Changes:

Timeouts via signal handling
Privatized methods
Test scripts load Cython conditionally
Order Propensity Formulas / Sortable Elements
Fix: timesteps calculated by round now, instead of floor
Fix: matplotlib plot() is now resizeable
Fix: test runner wrappers python versioning
Fix: plot colors loopable beyond 10 species
Fix: uniform colors between plotplotly and plot
Opioid example model added
Plotly figures can be returned without plotting
SBML features:
Events [and all subentities of Events]
Assignment Rules
Initial Assignments
Initial Value Reassignments
Function Definitions
Species: Constant
Species: Boundary Condition
Non Constant Parameters
Local Parameters
Increased MathML support
Fix: Rate Rules nomenclature matches assignment rules and sbml
Fix: numpy float casting (response to user issue)
Added Pylint badge
Removed mxml and python_libsbml from requirements.txt
Updated Installation instructions
Reorganized example directory
Added auto-deployment to PyPi
Fix: multiple error / warning changes to provide more helpful information
Fix: tau selection fixed in response to hybrid dynamic error
Export to csv
Example UML Model added

-Updated requirements.txt to no longer require python_libsbml or lxml on installation

v.1.2.2
This release contains minor hotfixes for issues in release 1.2.1.

Changelist:
- Minor updates to README
- Hotfix for cython/numpy solvers resolving issue where timespan was sometimes getting a type error

- contains edits to README for PyPI displaying and compatibility

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]