Hybrid Rate Rules #583
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Hybrid Rate Rules #583
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- Restructure call order in constructor - Add `use_*` methods for reactions to separate concerns
When calling `BuildEngine#prepare`, the `model` argument can be either a `Model` or `SanitizedModel`. - Converts `Model` to `SanitizedModel` - Hybrid solver overrides `_build` to pre-convert and add options - Removed `__init__` call in hybrid solver, replaced with `_build`
- No classes accept `custom_definitions` as constructor arguments - No functions accept `custom_definitions` as arguments - Replaced `custom_definitions` with `SanitizedModel#get_options`
- Added template handling for rate rules in C++ templates - Updated `DifferentialEquation` class to operate on rate rules - Replaced `std::vector` usage with raw pointers - Allows passing integrator state from Sundials to rate rule object
- Pulls `name` property from `Species` object - Converts from string to `Species` if necessary - Moved reserved names to a separate dict
- Add new template header, `template_params.h` - Provides `extern` declarations to Gillespy params - Remove `static` keyword from `template.cpp` params
Branch `feature/expression-validation` implements these already
Was preventing new options from being populated if no prior options existed - Changed call to use auxiliary method to generate options dict - Explicit check added to the result of this method
- Added `boundary_conditions` property to C++ `HybridSpecies` class - Added template parameter `boundary_mode` to `GPY_HYBRID_SPECIES_MODES` - Added `boundary_conditions` check before state update
- Added `#include` for math operations in partial template header - Added `std` namespace strip to be compatible with C operations - Added `factorial()` definition
- Created `test_tau_hybrid_c_solver.py` test file with test cases for `TauHybridCSolver` - Added test cases for models using rate rules and boundary conditions - Fixed issue in RHS function not initializing boundary condition values
seanebum
approved these changes
Sep 14, 2021
… feature/cpp-hybrid-rate-rules
BryanRumsey
requested changes
Sep 21, 2021
… feature/cpp-hybrid-rate-rules
… parameter as a variable.
BryanRumsey
approved these changes
Sep 21, 2021
briandrawert
approved these changes
Sep 21, 2021
Merged
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NOTE: This implementation of rate rules is dependent on the
Expressionutility class implemented in PR #582. Please merge that one in first!Implementation of SBML rate rules (represented with
RateRuleclass) for theTauHybridCSolverclass. Includes full support for math operations, as well as access to the point-in-time valuet. Expressions are contextual to differential equations and make use of integrator state in the RHS function of the integrator.Changes
TauHybridCSolverclass for SBML rate rules.template_params.hheader file to allow solver-specific template objects to access model parameters.cmathinclude to provide access to math functions in propensity functions and rate rules