Release v1.6.7 #660
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Release v1.6.7 #660
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- Added `Event` class - Added basic macros for event parameters and their associated static methods
In order to accommodate for SBML features, parameters must be vectorized instead of global variables. - Added `get_parameters` and `get_constants` template functions - Heap-allocates data for each type of variable - Replaced all references in C++ solver to parameters with vectorized equivalents - Replaced call to `sanitized_parameter_names` with manual sanitization in Python model - Instead of `P0, P1, etc` parameters are `P[0], P[1], etc` for variables and `C[0], C[1], etc` for constants - Modified rate rules to accept vectorized parameters - Removed `IPropensityFunction` and replaced with static `propensity` method - Static member of the `Reaction` class
- Added `execute` member methods to assign variables to state vecs - Added `use_state` member method to save the current state for later execution - Implemented rule of 5 for `Event` class - Implemented template injection functions - Added new implementation of `use_events`, no longer uses lambdas - Added new `assign` static method to dispatch event assignments
- Added `species_id` and `param_id` dicts to `SanitizedModel` class - Maps un-sanitized species/parameter names to their IDs - Modified `TauHybridCSolver` options to provide definitions - Defs for: events, # of events, assignments, # of event assignments
- Modified `TauHybridCSolver` template option generation to use a globally unique assignment ID - Added a (currently useless) call to `use_events` just to test
- Updated template to determine `use_trigger_state` and `persistent` flags - Updated event eval functions (`trigger`, `delay`, `priority`) to support expressions - Added `EventExecution` object to represent execution state of event - Call `Even#get_execution` to use, saves state automatically - Added `execution_time` property to execution state - Moved persistent state from `Event` to `EventExecution` - Removed `Event` as "unsupported SBML feature" in Python solver
Still missing trigger state memory (currently executes constantly) - Added events vector to solver function signature - Added priority queues to Hybrid solver iteration - Added comparison operators to `EventExecution` object - Moved `priority` method from `Event` to `EventExecution` - Added copy of assignments list on copy/move constructors - Fixed sizing issue for event template - Fixed off-by-1 error when generating assignment IDs in Python
- Added `is_persistent()` method to `Event` class - Added `volatile_queue` list for events that need to be re-checked continuously
- Added methods to `Integrator` class to enable root-finding - Modified trigger pipeline to fire detected events without using trigger calls directly
All triggers are evaluated at the end of every iteration. No root-finding is performed. - Removed calls to `use_events()` in integrator.cpp - Added `trigger_state` to track transition state of each trigger
Goal is to use new layout where root-finder can search for both events and reactions. - Added `Integrator#use_events` and `Integrator#use_reactions` - Updated `Integrator#integrate` to use new layout
- Added "trigger pool" data set to track event trigger state - Added "roots found" return parameters to `integrate()` method
Parameter bug was caused by parameters never been templated as variable (always constants). - Fixed bug where parameter assignments are ignored - Added `variable` member to `SanitizedModel` - Removed `variable` param from `SanitizedModel#get_template`, instead pulls from `self` - Updated docstrings in new integrator methods - Updated root-finder return to apply direct reactions - Fixed parameter overrides not applying - Added array to track which parameters have overrides
- Added comprehensive test cases for event features - Fixed non-persistent triggers by reordering volatile trigger checks - Fixed delay time checks - Fixed calls to `memcpy` in `EventExecution`'s copy constructor
- Added `initial_value` handling to template gen - Added initial value as macro parameter for `EVENT`
Comp - Moved event execution code to separate `EventList` class - Contains exact same code, just abstracted away - Added check to trigger state at beginning of trajectory - Moved first trajectory value to be after events have been processed
Live output example for C solvers
- Bug occurred when stochastic event fired - Root-finder list was never cleared - Errant `continue` skipped over state update code - Bug occurred when array is not zero-initialized - Caused compiler-specific bug where stochastic events were impossible to find
…ESolver.run. Switcch all refs to 'model' in ODESolver to 'self.model'.
…ef to 'model' to 'self.model'.
…unc call to CLE_solver.run. Switched all refs to 'model' in CLE_solver to 'self.model'.
…er func call to NumPySSASolver.run. Switched all refs to 'model' in NumPySSASolver to 'self.model'.
…ter func call to TauHybridSolver.run. Switched all refs to 'model' in TauHybridSolver to 'self.model'.
…eter func call to TauLeapingSolver.run. Switched all refs to 'model' in TauLeapingSolver to 'self.model'.
…unc call to ODECSolver.run. Switched all refs to 'model' in ODECSolver to 'self.model'.
…unc call to SSACSolver.run. Switched all refs to 'model' in SSACSolver to 'self.model'.
…unc call to SSACSolver.run. Switched all refs to 'model' in SSACSolver to 'self.model'.
…meter func call to TauLeapingCSolver.run. Switched all refs to 'model' in TauLeapingCSolver to 'self.model'.
…ts, and Function Definitions.
…ature/cpp-hybrid-events
C++ Hybrid Solver: Events
Fixing hybrid continuous notebook
HOTFIX: Resolve parameters at run
Removed events from the unsupported sbml features.
Fixing #668 ODECsolver not handling bimolecular reactions correctly
Ode solver vol issue
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GillesPy2 Release v1.6.7
Changes
Fixes
closes #628
closes #657
closes #661
closes #665
closes #668
closes #675