Gillespy2

CHANGES
- Added example notebook for Tyson Oscillator
- Change auto-solver checks to use environment path/variables to avoid unnecessary compilations
- GillesPy2 results objects can now be turned in to a results ensemble using python builtin sum() function
- GillesPy2 models can now be exported to SBML
- Added Vilar Oscillator and Dimerization models to example models

FIXES

- Fixed SBML import issue where string literals were being read incorrectly sometimes
- Fixed random number re-sampling issue
- Fixed timespan indexing issue

v.1.5.6
HOTFIX:

- Changed plotting y-axes label from "Species Population" to "Value" to accommodate more generalized terminology for non-biochemical modeling

FIXES
- Fixed issue where VariableSSACSolver sometimes read incorrect parameter value for static parameters in small systems
- Repaired links, references, and badges to conform to new github organization (StochSS/GillesPy2 instead of GillesPy2/GillesPy2)

v.1.5.4

FIXES

- Turning off a species in ensemble plotly plots now turns off all trajectories for that species
- stochml import now works correctly for ode

v.1.5.3

FIXES

- Fixed issue where Output from C solvers would sometimes cause errors on Windows
- Fixed issue where integration would occasionally fail in Tau Hybrid Solver
- Fixed issue where Rate Rules were sometimes not correctly updated in Tau Hybrid Solver

v.1.5.2

FIXES
- Pause now works correctly on Windows for NumPy solvers
- Live graphing output now updates correctly for tau-leaping solver
- Text live output now correctly updates to 100%
- Fixed dev test suite to work correctly on Windows
- Auto solver now no longer tests for C solver more than once in a single kernel session
- C solvers no longer require re-compilation for pause/resume in a single kernel session
- Fixed issue where unnamed reactions were not being correctly seeded

v.1.5.1
v.1.5.1 CHANGELOG

FIXES
- Fixed issue where multiple trajectories were not being simulated correctly
- Fixed solver importation structure to work correctly with non-G++ environments

v.1.5.0

CHANGES

- Live Graphing available
- Pause/Resume with Keyboard Interrupts
- Automatic solver selection will now prioritize the variable c solver unless the "precompile" flag is set to False
- Removed "Basic" from NumPy-based solver names/files
- Simplified imports structure for solvers
- Parameters may now be target variables for Event Assignments

FIXES

- Fixed issue where some events were not working with discrete species
- Removed warnings that no longer make sense
- PEP-8 Refactoring and general decoupling
- Fixed bug where adding reactant/products by name rather than object caused an error for some systems
- Fixed issue where plotly std dev range plot populated species backwards
- Fixed issue where standard dev. range was not removed with it's relevant species when clicking off species in the plotly graph

v.1.4.2