v1.8.2

Changes

• [#938]
  • Added argument to Tau-Hybrid solves that allows the tau step size to be set to a constant value (constant_tau_step_size).
  • Optimized Tau-Hybrid solvers to only use ODE integrator when necessary.
• [#943] Clarified usage of integrator argument in Model.run method.
• [#944] Updates to CSV.

Bug Fixes

• [#937, #941] SBML import fixes (python reserved words and dependent parameters).
• [#942] Fixed time span export when exporting to StochSS Live! model.

Full Changelog: v1.8.1...v1.8.2

v1.8.1

Changes

• [#922] Updated copyright dates.
• [#929] Removed StochKit solvers

Bug Fixes

• [#924] Fixed dependency warnings.
• [#928] Fixed reaction dependency graphs for C++ Solvers.

Full Changelog: v1.8.0...v1.8.1

v1.8.0

Changes

• [#879] Converted make structure with S-Construct structure.
• [#913] Updates to tau hybrid solvers.

Bug Fixes

• [#914] Fixed compiler warnings.
• [#916] Fixed notebook plotting using plotly.
• [#918] Fixes for the SSA C solver.

Full Changelog: v1.7.2...v1.8.0

v1.7.2

Changes

• [#893] Added Github action for pylint.

Bug Fixes

• [#878] Fixed stochastic propensities for homo-dimer bimolecular reactions.
• [#881] Fixed conflicting error message.
• [#885] Fixed SBML event assignments.
• [#892] Fixed issue with raising errors of incorrect type.
• [#900] Fixed rounding in event assignments with discrete/continuous species.
• [#903] Fixed tau step selection in the NumPy TauHybrid solver.

closes #696
closes #709
closes #771
closes #790
closes #851
closes #874
closes #876
closes #880
closes #884
closes #886
closes #887
closes #895
closes #896
closes #898
closes #902

Full Changelog: v1.7.1...v1.7.2

v1.7.1

Changes

• [#867] Improvements to the Tau Hybrid C Solver.
• [#868] Updated authors and acknowledgments.

Bug Fixes

• [#862] Fixed the get_solver_settings function for all solvers.
• [#864] Bug fixes to Tau Hybrid C Solver.
• [#866] Fixed results objects generated by the ODE C Solver.
• [#870] Fixed homo-dimer bimolecular propensity function for mass-action reactions.
• [#872] Fixed anonymize function for models with events.

Full Changelog: v1.7.0...v1.7.1

v1.7.0

Changes

• [#756] Added system support for folder with spaces in installation path on Linux and MacOS.
• [#770] Reaction now accept an ODE propensity function in addition to the stochastic propensity function.
• [#773] Added an example to demonstrate the correct method of using timespans with negative values.
• [#786] ODECSolver and TauHybridCSolver now accept integrator options.
• [#797] Updates to examples.
• [#817] Updated documentation.
• [#829] Improved tau hybrid step selection.

Bug Fixes

• [#787] TimeSpan.arange and TimeSpan.linspace now accept floats for t
• [#799] Fixed issue with SBML compartments missing the size attribute being set to nan.
• [#820] Fixed time plotting when using Results.plot_mean_stdev.
• [#832] Fixed error reporting when importing SBML models.
• [#841] Fixed multi-firing events in the tau hybrid c solver.
• [#850] CLE Solver now uses model's timespan if t and increment are not provided.
• [#853] Fixed Stochastic/Deterministic switching in the tau hybrid solvers.

Full Changelog: v1.6.9...v1.7.0

v1.6.9

GillesPy2 Release v1.6.9

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: v1.6.8...v1.6.9

v1.6.8

GillesPy2 Release v1.6.8

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: v1.6.7...v1.6.8

v1.6.7

GillesPy2 Release v1.6.7

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

v1.6.6

GillesPy2 Release v1.6.6

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