Merge pull request #713 from StochSS/raise-err-objs

Fix for error handling

gillespy2/core/model.py

@@ -281,28 +281,28 @@ def sanitized_species_names(self):
 
     def problem_with_name(self, name):
         if name in Model.reserved_names:
-            return ModelError(
+            raise ModelError(
                 'Name "{}" is unavailable. It is reserved for internal GillesPy use. Reserved Names: ({}).'.format(name,
                                                                                                                    Model.reserved_names))
         if name in self.listOfSpecies:
-            return ModelError('Name "{}" is unavailable. A species with that name exists.'.format(name))
+            raise ModelError('Name "{}" is unavailable. A species with that name exists.'.format(name))
         if name in self.listOfParameters:
-            return ModelError('Name "{}" is unavailable. A parameter with that name exists.'.format(name))
+            raise ModelError('Name "{}" is unavailable. A parameter with that name exists.'.format(name))
         if name in self.listOfReactions:
-            return ModelError('Name "{}" is unavailable. A reaction with that name exists.'.format(name))
+            raise ModelError('Name "{}" is unavailable. A reaction with that name exists.'.format(name))
         if name in self.listOfEvents:
-            return ModelError('Name "{}" is unavailable. An event with that name exists.'.format(name))
+            raise ModelError('Name "{}" is unavailable. An event with that name exists.'.format(name))
         if name in self.listOfRateRules:
-            return ModelError('Name "{}" is unavailable. A rate rule with that name exists.'.format(name))
+            raise ModelError('Name "{}" is unavailable. A rate rule with that name exists.'.format(name))
         if name in self.listOfAssignmentRules:
-            return ModelError('Name "{}" is unavailable. An assignment rule with that name exists.'.format(name))
+            raise ModelError('Name "{}" is unavailable. An assignment rule with that name exists.'.format(name))
         if name in self.listOfFunctionDefinitions:
-            return ModelError('Name "{}" is unavailable. A function definition with that name exists.'.format(name))
+            raise ModelError('Name "{}" is unavailable. A function definition with that name exists.'.format(name))
         if name.isdigit():
-            return ModelError('Name "{}" is unavailable. Names must not be numeric strings.'.format(name))
+            raise ModelError('Name "{}" is unavailable. Names must not be numeric strings.'.format(name))
         for special_character in Model.special_characters:
             if special_character in name:
-                return ModelError(
+                raise ModelError(
                     'Name "{}" is unavailable. Names must not contain special characters: {}.'.format(name,
                                                                                                       Model.special_characters))
 
@@ -335,9 +335,7 @@ def add_species(self, obj):
                 self.add_species(S)
         else:
             try:
-                problem = self.problem_with_name(obj.name)
-                if problem is not None:
-                    raise problem
+                self.problem_with_name(obj.name)
                 self.listOfSpecies[obj.name] = obj
                 self._listOfSpecies[obj.name] = 'S{}'.format(len(self._listOfSpecies))
             except Exception as e:
@@ -418,9 +416,7 @@ def add_parameter(self, params):
                 self.add_parameter(p)
         else:
             if isinstance(params, Parameter) or type(params).__name__ == 'Parameter':
-                problem = self.problem_with_name(params.name)
-                if problem is not None:
-                    raise problem
+                self.problem_with_name(params.name)
                 self.update_namespace()
                 params._evaluate(self.namespace)
                 self.listOfParameters[params.name] = params
@@ -501,9 +497,7 @@ def add_reaction(self, reactions):
                 self.add_reaction(r)
         else:
             try:
-                problem = self.problem_with_name(reactions.name)
-                if problem is not None:
-                    raise problem
+                self.problem_with_name(reactions.name)
                 reactions.verify()
                 self.validate_reactants_and_products(reactions)
                 if reactions.name is None or reactions.name == '':
@@ -543,9 +537,7 @@ def add_rate_rule(self, rate_rules):
                 self.add_rate_rule(rr)
         else:
             try:
-                problem = self.problem_with_name(rate_rules.name)
-                if problem is not None:
-                    raise problem
+                self.problem_with_name(rate_rules.name)
                 if len(self.listOfAssignmentRules) != 0:
                     for i in self.listOfAssignmentRules.values():
                         if rate_rules.variable == i.variable:
@@ -588,9 +580,7 @@ def add_event(self, event):
                 self.add_event(e)
         else:
             try:
-                problem = self.problem_with_name(event.name)
-                if problem is not None:
-                    raise problem
+                self.problem_with_name(event.name)
                 if event.trigger is None or not hasattr(event.trigger, 'expression'):
                     raise ModelError(
                         'An Event must contain a valid trigger.')
@@ -615,9 +605,7 @@ def add_function_definition(self, function_definitions):
                 self.add_function_definition(fd)
         else:
             try:
-                problem = self.problem_with_name(function_definitions.name)
-                if problem is not None:
-                    raise problem
+                self.problem_with_name(function_definitions.name)
                 self.listOfFunctionDefinitions[function_definitions.name] = function_definitions
             except Exception as e:
                 raise ParameterError(
@@ -635,9 +623,7 @@ def add_assignment_rule(self, assignment_rules):
                 self.add_assignment_rule(ar)
         else:
             try:
-                problem = self.problem_with_name(assignment_rules.name)
-                if problem is not None:
-                    raise problem
+                self.problem_with_name(assignment_rules.name)
                 if len(self.listOfRateRules) != 0:
                     for i in self.listOfRateRules.values():
                         if assignment_rules.variable == i.variable:

gillespy2/solvers/numpy/CLE_solver.py

@@ -250,7 +250,9 @@ def run(self, model=None, t=20, number_of_trajectories=1, increment=None, seed=N
             while self.result is None:
                 pass
         if hasattr(self, 'has_raised_exception'):
-            raise self.has_raised_exception
+            raise SimulationError(
+                f"Error encountered while running simulation:\nReturn code: {int(self.rc)}.\n"
+            ) from self.has_raised_exception
 
         return Results.build_from_solver_results(self, live_output_options)
 

gillespy2/solvers/numpy/ode_solver.py

@@ -205,7 +205,9 @@ def run(self, model=None, t=20, number_of_trajectories=1, increment=None, show_l
             while self.result is None:
                 pass
         if hasattr(self, 'has_raised_exception'):
-            raise self.has_raised_exception
+            raise SimulationError(
+                f"Error encountered while running simulation:\nReturn code: {int(self.rc)}.\n"
+            ) from self.has_raised_exception
 
         return Results.build_from_solver_results(self, live_output_options)
 

gillespy2/solvers/numpy/ssa_solver.py

@@ -169,7 +169,9 @@ def run(self, model=None, t=20, number_of_trajectories=1, increment=None, seed=N
             while self.result is None:
                 pass
         if hasattr(self, 'has_raised_exception'):
-            raise self.has_raised_exception
+            raise SimulationError(
+                f"Error encountered while running simulation:\nReturn code: {int(self.rc)}.\n"
+            ) from self.has_raised_exception
 
         return Results.build_from_solver_results(self, live_output_options)
 

gillespy2/solvers/numpy/tau_hybrid_solver.py

@@ -938,7 +938,9 @@ def run(self, model=None, t=20, number_of_trajectories=1, increment=None, seed=N
         except:
             pass
         if hasattr(self, 'has_raised_exception'):
-            raise self.has_raised_exception
+            raise SimulationError(
+                f"Error encountered while running simulation:\nReturn code: {int(self.rc)}.\n"
+            ) from self.has_raised_exception
 
         return Results.build_from_solver_results(self, live_output_options)
 

gillespy2/solvers/numpy/tau_leaping_solver.py

@@ -237,7 +237,9 @@ def run(self, model=None, t=20, number_of_trajectories=1, increment=None, seed=N
             while self.result is None:
                 pass
         if hasattr(self, 'has_raised_exception'):
-            raise self.has_raised_exception
+            raise SimulationError(
+                f"Error encountered while running simulation:\nReturn code: {int(self.rc)}.\n"
+            ) from self.has_raised_exception
 
         return Results.build_from_solver_results(self, live_output_options)