FIX: Live graphing in ODECSolver using wrong decoder

gillespy2/solvers/cpp/c_base/ode_cpp_solver/ODESolver.cpp

@@ -118,18 +118,13 @@ namespace Gillespy
 		realtype end_time = simulation->end_time;
 		realtype step_length = increment;
 
-		// The time reached by the solver for output.
-		realtype tret = 0;
-
-		int current_time = 0;
 		for (tout = step_length; !interrupted && tout < end_time || cmpf(tout, end_time); tout += step_length)
 		{
 			// CV_NORMAL causes the solver to take internal steps until it has reached or just passed the `tout`
 			// parameter. The solver interpolates in order to return an approximate value of `y(tout)`.
 			// CVode() returns a vector `y0` (or `y(tout)`), and corresponding variable value `t` = `tret` (return time).
 			// With CV_NORMAL `tret` is equal to `tout` and `y0` = `y(tout)`.
-			flag = CVode(cvode_mem, tout, y0, &tret, CV_NORMAL);
-			current_time++;
+			flag = CVode(cvode_mem, tout, y0, &simulation->current_time, CV_NORMAL);
 
 			for (sunindextype species = 0; species < N; species++)
 			{

gillespy2/solvers/cpp/ode_c_solver.py

@@ -17,7 +17,7 @@
 """
 import numpy as np
 
-from gillespy2.solvers.cpp.c_decoder import BasicSimDecoder
+from gillespy2.solvers.cpp.c_decoder import IterativeSimDecoder
 from gillespy2.solvers.utilities import solverutils as cutils
 from gillespy2.core import GillesPySolver, Model
 from gillespy2.core.gillespyError import *
@@ -117,7 +117,7 @@ def run(self=None, model: Model = None, t: int = None, number_of_trajectories: i
             display_args = None
 
         args = self._make_args(args)
-        decoder = BasicSimDecoder.create_default(number_of_trajectories, number_timesteps, len(self.model.listOfSpecies))
+        decoder = IterativeSimDecoder.create_default(number_of_trajectories, number_timesteps, len(self.model.listOfSpecies))
 
         sim_exec = self._build(self.model, self.target, self.variable, False)
         sim_status = self._run(sim_exec, args, decoder, timeout, display_args)

gillespy2/solvers/cpp/tau_hybrid_c_solver.py

@@ -1,3 +1,4 @@
+import numpy as np
 import gillespy2
 from gillespy2.solvers.cpp.c_decoder import IterativeSimDecoder
 from gillespy2.solvers.utilities import solverutils as cutils