Merge pull request #653 from StochSS/develop

Release 1.6.6
StochSS · Dec 2, 2021 · ad52917 · ad52917
2 parents eb1c4a2 + 9420bd1
commit ad52917
Show file tree

Hide file tree

Showing 12 changed files with 1,380 additions and 172 deletions.
diff --git a/examples/AdvancedFeatures/CLE_examples_convergence.ipynb b/examples/AdvancedFeatures/CLE_examples_convergence.ipynb
diff --git a/examples/ExtraModels/GeneticToggleSwitch.ipynb b/examples/ExtraModels/GeneticToggleSwitch.ipynb
diff --git a/gillespy2/__version__.py b/gillespy2/__version__.py
@@ -24,7 +24,7 @@
 # =============================================================================
 
 
-__version__      = '1.6.5'
+__version__      = '1.6.6'
 
 __title__        = 'GillesPy2'
 __description__  = 'Python interface for Gillespie-style biochemical simulations'

diff --git a/gillespy2/core/parameter.py b/gillespy2/core/parameter.py
@@ -58,6 +58,7 @@ def set_expression(self, expression):
         # strings will be caught below. It is perfectly fine to give a scalar
         # value as the expression. This can then be evaluated in an empty
         # namespace to the scalar value.
+        from gillespy2.core import log
 
         log.warning("'Parameter.set_expression' has been deprecated, future versions of GillesPy2 will not support"
                     " this function. To set expression within a parameter, use Parameter.expression = expression")

diff --git a/gillespy2/core/reaction.py b/gillespy2/core/reaction.py
@@ -304,8 +304,7 @@ def create_mass_action(self):
                 rname = r.name
             # Case 1: 2X -> Y
             if self.reactants[r] == 2:
-                propensity_function = (propensity_function +
-                                       "*" + rname + "*(" + rname + "-1)/vol")
+                propensity_function = "0.5 * {0} * {1} * ({1} - 1) / vol".format(propensity_function, rname)
                 ode_propensity_function += '*' + rname + '*' + rname
             else:
                 # Case 3: X1, X2 -> Y;

diff --git a/gillespy2/sbml/SBMLimport.py b/gillespy2/sbml/SBMLimport.py
@@ -125,7 +125,10 @@ def __get_parameters(sbml_model, gillespy_model):
     for i in range(sbml_model.getNumParameters()):
         parameter = sbml_model.getParameter(i)
         name = parameter.getId()
-        value = parameter.getValue()
+        if parameter.isSetValue():
+            value = parameter.getValue()
+        else:
+            value = 0
         init_state[name] = value
 
         # GillesPy2 represents non-constant parameters as species

diff --git a/gillespy2/solvers/cpp/c_solver.py b/gillespy2/solvers/cpp/c_solver.py
@@ -324,14 +324,14 @@ def _update_resume_data(self, resume: Results, simulation_data: "list[dict[str,
         resume_time = float(resume["time"][-1])
         increment = resume_time - float(resume["time"][-2])
         # Replace the simulation's timespan to continue where the Results object left off.
-        simulation_data[-1]["time"] = numpy.arange(start=(resume_time + increment),
+        simulation_data[-1]["time"] = numpy.arange(start=(resume_time),
                                                    stop=(resume_time + time_stopped + increment),
                                                    step=increment)
 
         for entry_name, entry_data in simulation_data[-1].items():
             # The results of the current simulation is treated as an "extension" of the resume data.
             # As such, the new simulation output is formed by joining the two end to end.
-            new_data = numpy.concatenate((resume[entry_name], entry_data), axis=None)
+            new_data = numpy.concatenate((resume[entry_name], entry_data[1:]), axis=None)
             simulation_data[-1][entry_name] = new_data
 
         return simulation_data