Merge pull request #620 from StochSS/fix-live-output-final-graph

HOTFIX: Live output graph final step

gillespy2/core/liveGraphing.py

@@ -247,5 +247,3 @@ def display(self, curr_state, curr_time, trajectory_base, finished=False):
 
         if self.file_path is not None and self.display_type != "graph":
             file_obj.close()
-        if finished:
-            time.sleep(3)

gillespy2/core/results.py

@@ -242,13 +242,19 @@ def to_array(self):
         return results
 
     @classmethod
-    def build_from_solver_results(cls, solver):
+    def build_from_solver_results(cls, solver, live_output_options):
         """
         Build a gillespy2.Results object using the provided solver results.
 
         :param solver: The solver used to run the simulation.
         :type solver: gillespy2.GillesPySolver
+
+        :param live_output_options: dictionary contains options for live_output. By default {"interval":1}.
+            "interval" specifies seconds between displaying.
+            "clear_output" specifies if display should be refreshed with each display
+        :type live_output_options: dict
         """
+        print(live_output_options)
         if solver.rc == 33:
             from gillespy2.core import log
             log.warning('GillesPy2 simulation exceeded timeout.')
@@ -260,7 +266,10 @@ def build_from_solver_results(cls, solver):
                 temp = Trajectory(data=solver.result[i], model=solver.model, solver_name=solver.name, rc=solver.rc)
                 results_list.append(temp)
 
-            return Results(results_list)
+            results = Results(results_list)
+            if "type" in live_output_options.keys() and live_output_options['type'] == "graph":
+                results.plot()
+            return results
         else:
             raise ValueError("number_of_trajectories must be non-negative and non-zero")
 

gillespy2/solvers/cpp/ode_c_solver.py

@@ -111,4 +111,4 @@ def run(self=None, model: Model = None, t: int = 20, number_of_trajectories: int
         self.result = simulation_data
         self.rc = int(sim_status)
 
-        return Results.build_from_solver_results(self)
+        return Results.build_from_solver_results(self, live_output_options)

gillespy2/solvers/cpp/ssa_c_solver.py

@@ -113,4 +113,4 @@ def run(self=None, model: Model = None, t: int = 20, number_of_trajectories: int
         self.result = simulation_data
         self.rc = int(sim_status)
 
-        return Results.build_from_solver_results(self)
+        return Results.build_from_solver_results(self, live_output_options)

gillespy2/solvers/cpp/tau_hybrid_c_solver.py

@@ -141,4 +141,4 @@ def run(self=None, model: Model = None, t: int = 20, number_of_trajectories: int
         self.result = simulation_data
         self.rc = int(sim_status)
 
-        return Results.build_from_solver_results(self)
+        return Results.build_from_solver_results(self, live_output_options)

gillespy2/solvers/cpp/tau_leaping_c_solver.py

@@ -111,4 +111,4 @@ def run(self=None, model: Model = None, t: int = 20, number_of_trajectories: int
         self.result = simulation_data
         self.rc = int(sim_status)
 
-        return Results.build_from_solver_results(self)
+        return Results.build_from_solver_results(self, live_output_options)

gillespy2/solvers/numpy/ode_solver.py

@@ -200,7 +200,7 @@ def run(self, model=None, t=20, number_of_trajectories=1, increment=None, show_l
         if hasattr(self, 'has_raised_exception'):
             raise self.has_raised_exception
 
-        return Results.build_from_solver_results(self)
+        return Results.build_from_solver_results(self, live_output_options)
 
     def ___run(self, model, curr_state, curr_time, timeline, trajectory_base, tmpSpecies, live_grapher, t=20,
                number_of_trajectories=1, increment=0.05, timeout=None, show_labels=True, integrator='lsoda',

gillespy2/solvers/numpy/ssa_solver.py

@@ -163,7 +163,7 @@ def run(self, model=None, t=20, number_of_trajectories=1, increment=None, seed=N
         if hasattr(self, 'has_raised_exception'):
             raise self.has_raised_exception
 
-        return Results.build_from_solver_results(self)
+        return Results.build_from_solver_results(self, live_output_options)
 
     def ___run(self, model, curr_state, total_time, timeline, trajectory_base, live_grapher, t=20,
                number_of_trajectories=1, increment=0.05, seed=None, debug=False, show_labels=True, resume=None,

gillespy2/solvers/numpy/tau_hybrid_solver.py

@@ -932,7 +932,7 @@ def run(self, model=None, t=20, number_of_trajectories=1, increment=None, seed=N
         if hasattr(self, 'has_raised_exception'):
             raise self.has_raised_exception
 
-        return Results.build_from_solver_results(self)
+        return Results.build_from_solver_results(self, live_output_options)
 
     def ___run(self, model, curr_state, curr_time, timeline, trajectory_base, initial_state, live_grapher, t=20,
                number_of_trajectories=1, increment=0.05, seed=None,

gillespy2/solvers/numpy/tau_leaping_solver.py

@@ -232,7 +232,7 @@ def run(self, model=None, t=20, number_of_trajectories=1, increment=None, seed=N
             if hasattr(self, 'has_raised_exception'):
                 raise self.has_raised_exception
 
-            return Results.build_from_solver_results(self)
+            return Results.build_from_solver_results(self, live_output_options)
 
     def ___run(self, model, curr_state,total_time, timeline, trajectory_base, tmpSpecies, live_grapher, t=20,
                number_of_trajectories=1, increment=0.05, seed=None, debug=False, profile=False, show_labels=True,