Gillespy2

Changes
- [737] Restructured our examples
- [744] Updated warning messages and removed the warning package
- [745] Removed deprecated basic solvers
- [746] CLESolver now added to `get_best_solver_algo` function and can be selected with `algorithm="CLE"`
- [754] Deprecated `model` argument in `solver.run()`
- [764] Added `Model.add()` function to allow multiple different components to be added at once
- [775] Added a Dimerization notebook to examples

Fixes
- [734] Improvements to error handling
- [742] Fixed model validation
- [747] Fixed issue with model timespan not being used in `solver.run()`
- [750] Fixed issue causing `Model.delete_event` to fail
- [755] Fixed live graphing errors when using the ODECSolver
- [763] Added a JSON encoder for `export_StochSS`
- [769] Fixed issue with double logging

**Full Changelog**: https://github.com/StochSS/GillesPy2/compare/v1.6.8...v1.6.9

Changes

- Added `cleanup_tempfiles()` function for clearing out gillespy2 temp files
- [726]
- [706]
- TauHybridCSolver now added to `get_best_solver()` and `get_best_algo()` methods and will be appropriately selected based on model SBML feature set
- [697]


Fixes

- Fixed initialization errors in integrator for TauHybridCSolver
- [719]
- Fixed Event Trigger evaluation in TauHybridCSolver
- [717]
- [683]
- Fixed the issue where numerical errors were introduced with continuous values when being evaluated for stochastic reactions in TauHybridCSolver
- [711]
- Fixed multi-trajectory bug in TauHybridCSolver
- [703]
- C-based solver interrupts and timeouts are now appropriately handled
- [701]
- [684]
- Multiple updates to error handling
- [713]
- [693]
- [699]
- [680]


**Full Changelog**: https://github.com/StochSS/GillesPy2/compare/v1.6.7...v1.6.8

Changes

- [594] Added support for Events in TauHybridCSolver
- [658] Added example for live output using C solver

Fixes

- [668] Fixed issue where bimolecular reactions were not appropriately incorporating stoichiometry > 1 in ODECSolver
- [675] Fixed issue where missing 'vol' attribute caused exception in NumPy ODESolver
- [667] Fixes for issues in example notebooks

Changes
- [639] Added CLE Solver
- [647] Now handles SBML parameters without declared values

Fixes
- [652] Fixed bug in deprecation warning
- [649] Fixed issue with SSA propensities for 2A->B style reactions
- [643] Fixed pause/resume issue in C-based solvers
- [648] Fixed Python tau hybrid repeating events

Changes

- [630] Parameters can now reference other parameters correctly when creating a model. Additionaly, when creating a parameter, setting "value=" has been removed (use "expression=" instead).
- [627] Removed debug print for live_output that was always printing
- [625] Fixed issue where Parameters with float value expressions caused an error in the __str__ method.
- [620] Fixed issue where current state was being plotted as final timestep in live_output.

Changes
- [609] Solver.run() now returns a Result Object
- [616] Live graphing added for C based solvers
- [603] Added live output to file option
- [445] Model.run() now allows kwarg "increment" as an alternative for creating timespans
- [583, 615] Updates to Hybrid C solver (beta)

Fixes
- [610] Fixed issue where ODE C Solver sometimes plotted one too many steps
- [607] Fixed timeouts for Tau Hybrid Solver
- [590] Fixed wrong values in model for Vilar Oscillator example notebook