Releases: StochSS/GillesPy2
Releases · StochSS/GillesPy2
v.1.5.7
v1.5.7 CHANGELOG
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
v1.5.5
v1.5.5 CHANGELOG
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
v.1.5.3
v1.5.3 CHANGELOG
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
v1.5.2 CHANGELOG
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.1.5.0
1.5.0 CHANGELOG
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
1.4.2 CHANGELOG
CHANGES
- Auto solver selection process is now a callable function, get_best_solver() which returns a solver based on model configuration and user environment.
- Extended get_best_solver() to consider solver based on supported features and species mode
- added callable function to solvers get_solver_settings(), returns a tuple of relevant settings to model.run() for the solver
- Added badges for conda-forge and download statistics
FIXES
- Fixed issue where seeds were sometimes overlapped for VariableSSACSolver
- Fixed issue where timeout could cause an error for multiple trajectories
v1.4.1
1.4.1 CHANGELOG
CHANGES
- added initial value setter method for Species (myspecies.set_initial_value(val))
- BasicTauHybridSolver is now automatically selected with model.run() for models containing:
- Rate Rules, Assignment Rules, Events, Function Definitions
- axes scaling is now available with matplotlib and plotly plotting
FIXES
- Fixed issue where Tau selection occasionally caused an error
- Assignment rules now work correctly, again
- Rate Rules now work correctly, again
- Default matplotlib y scale now adjusts to simulation
- Events are now comparable
- Models containing Events are now comparable
- coverage badge in README is no longer static, now updates automatically