Gillespy2

Changes
- Initial implementation of the Tau Hybrid C++ solver.
- ODE C++ solvers can now accept non-integer initial populations.

Technical Changes
- [PR 557](https://github.com/StochSS/GillesPy2/pull/557): Initial implementation of the C++ Tau Hybrid solver.
- [PR 575](https://github.com/StochSS/GillesPy2/pull/575): ODE C++ solvers can now accept non-integer initial populations.
- [PR 576](https://github.com/StochSS/GillesPy2/pull/576): Simplified dependency lists and standardized target names in the `c_base` Makefile.
- [PR 579](https://github.com/StochSS/GillesPy2/pull/579): Updated `gillespy2.solvers.numpy.base_` solver documentation with deprecated-on notice.
- [PR 575](https://github.com/StochSS/GillesPy2/pull/575): Fixed a C++ solver build failure in certain environments that was caused by compiler type narrowing errors.

Minor fixes relating to the v1.6.1 release. For a complete change log please refer to v1.6.1.

GillesPy2 Release v1.6.1 Changelog

Changes
- Updated the `StartHere.ipynb` notebook in the `examples/` directory to reference up-to-date documentation and better reflect modern use cases of GillesPy2.
- Added checks to ensure that SBML models with features not supported by GillesPy2 cannot be loaded.
- Updated documentation at [stochss.github.io/GillesPy2](https://stochss.github.io/GillesPy2) -- check it out!

Fixes
- Fixed crash caused by the GillesPy2 Model referencing functions deprecated in release v1.6.0
- Fixed invalid behavior where higher-order reactions would use the incorrect propensity functions.
- Fixed broken links in README.md to reference up-to-date documentation.

Technical Changes

- [PR 549](https://github.com/StochSS/GillesPy2/pull/549): Fixed a crash in `Model#get_best_solver_algo` caused by the usage of a deprecated function.
- [PR 550](https://github.com/StochSS/GillesPy2/pull/549): Fixed an issue where higher-order reactions use the incorrect propensity function.
- [PR 561](https://github.com/StochSS/GillesPy2/pull/561): Updated broken links in the README.md
- [PR 562](https://github.com/StochSS/GillesPy2/pull/562): Fixed invalid Sphinx documentation generation in source files with invalid reST-format docstrings.
- [PR 553](https://github.com/StochSS/GillesPy2/pull/555): Added ability to set reaction rate to a string.
- [PR 554](https://github.com/StochSS/GillesPy2/pull/555): Added Model to test suite which tests all the possible features of a GillesPy2 `Model`.
- [PR 555](https://github.com/StochSS/GillesPy2/pull/555): Added additional check to `SBMLImport#__get_kinetic_law` to ensure SBML Reactions without propensity functions cannot be loaded.
- [PR 556](https://github.com/StochSS/GillesPy2/pull/556): Updated and refactored the `StartHere.ipynb` example notebook.
- [GH 558](https://github.com/StochSS/GillesPy2/issues/558): Updated docsite to use `gh-pages` branch, updated documentation to v1.6.1
- [PR 559](https://github.com/StochSS/GillesPy2/pull/559): Tweaked generated documentation to be more readable.
- [PR 568](https://github.com/StochSS/GillesPy2/pull/568): Added license header to source files.

GillesPy2 Release v1.6.0 Changelog

Changes
- Models can now be converted to and from JSON.
- Improved model and simulation generation for C++ solvers.
- Models can now be converted to and from the StochSS format.
- Added example model to illustrate the polymerization of styrene.

Fixes
- Fixed a bug where the C++ Tau Leaping solver would repeatedly re-instantiate its RNG.
- Fixed a bug where the C++ Tau Leaping solver would not seed its RNG with a user-passed value.
- Fixed a bug where large species and parameter counts would cause the NumPy SSA and C++ solvers to output unexpected results.

v.1.5.11
CHANGELOG

FIXES
- Fixed attribute error raised by StochMLDocument.to_model()
- Fixed rules error caused by rules name collisions
- Update C TauLeaping solver to accept tau_tol argument
- Updated plotly function to stop getting deprecation warning

v.1.5.10
CHANGELOG

FIXES
- Fixed issue where the manifest did not include the correct cpp template files

v.1.5.9

CHANGES

- Added C++ implementations of ODE and Tau-Leaping solvers
- Refactored Tau Hybrid Python solver to use scipy.integrate.LSODA instead of scipy.integrate.solve_ivp
- Now building biosimulator image on release
- Simulations now require unique names for all namespace elements (reactions, rate rules, events, parameters, species)
- Added argument 'algorithm=' to model.run()

FIXES

- Fixed issue where some event triggers were not being reached in tau hybrid solver
- Fixed issue where systems containing rate rules which intersected with fully deterministic reactions would lose initial rate rule values
- Fixed issue where non-unique names would cause simulation issues in tau hybrid solver
- Fixed issue where identical trajectories were being returned with results.to_array()
- Fixed SSACSolver and VariableSSACSolver timeout events
- Fixed SBML function definitions - 'args' is now correctly retained as an attribute of function definitions

v.1.5.8

CHANGES

- Added C++ implementations of ODE and Tau-Leaping solvers
- Refactored Tau Hybrid Python solver to use scipy.integrate.LSODA instead of scipy.integrate.solve_ivp
- Now building biosimulator image on release
- Simulations now require unique names for all namespace elements (reactions, rate rules, events, parameters, species)
- Added argument 'algorithm=' to model.run()

FIXES

- Fixed issue where some event triggers were not being reached in tau hybrid solver
- Fixed issue where systems containing rate rules which intersected with fully deterministic reactions would lose initial rate rule values
- Fixed issue where non-unique names would cause simulation issues in tau hybrid solver
- Fixed issue where identical trajectories were being returned with results.to_array()
- Fixed SSACSolver and VariableSSACSolver timeout events
- Fixed SBML function definitions - 'args' is now correctly retained as an attribute of function definitions