v1.6.5

GillesPy2 Release v1.6.5

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.

v1.6.4

GillesPy2 Release v1.6.4

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

v1.6.3

GillesPy2 Release v1.6.3

Changes

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

Technical Changes

• PR #557: Initial implementation of the C++ Tau Hybrid solver.
• PR #575: ODE C++ solvers can now accept non-integer initial populations.
• PR #576: Simplified dependency lists and standardized target names in the c_base Makefile.
• PR #579: Updated gillespy2.solvers.numpy.base_ solver documentation with deprecated-on notice.
• PR #575: Fixed a C++ solver build failure in certain environments that was caused by compiler type narrowing errors.

v1.6.2

GillesPy2 Release v1.6.2

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

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

v1.6.0

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

v1.5.9 CHANGELOG

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

v1.5.8 CHANGELOG

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