pass core in to the processes

biosimulator_processes/cobra_process.py

@@ -41,8 +41,8 @@ class CobraProcess(Process):
         'model_file': 'sbml',
     }
 
-    def __init__(self, config=None):
-        super().__init__(config)
+    def __init__(self, config=None, core=None):
+        super().__init__(config, core)
         self.model = read_sbml_model(self.config['model_file'])
         self.reactions = self.model.reactions
         self.metabolites = self.model.metabolites

biosimulator_processes/copasi_process.py

@@ -19,8 +19,8 @@
 class CopasiProcess(Process):
     config_schema = {'model_file': 'string'}
 
-    def __init__(self, config=None):
-        super().__init__(config)
+    def __init__(self, config=None, core=None):
+        super().__init__(config, core)
 
         # Load the single cell model into Basico
         self.copasi_model_object = load_model(self.config['model_file'])

biosimulator_processes/smoldyn_process.py

@@ -100,18 +100,17 @@ class SmoldynProcess(Process):
         'animate': 'bool',
     }
 
-    def __init__(self, config: Dict[str, Any] = None):
+    def __init__(self, config: Dict[str, Any] = None, core=None):
         """A new instance of `SmoldynProcess` based on the `config` that is passed. The schema for the config to be passed in
             this object's constructor is as follows:
 
             config_schema = {
                 'model_filepath': 'string',  <-- analogous to python `str`
                 'animate': 'bool'  <-- of type `bigraph_schema.base_types.bool`
 
-
             # TODO: It would be nice to have classes associated with this.
         """
-        super().__init__(config)
+        super().__init__(config, core)
 
         # specify the model fp for clarity
         self.model_filepath = self.config.get('model_filepath')

biosimulator_processes/tellurium_process.py

@@ -16,8 +16,8 @@ class TelluriumStep(Step):
         'antimony_string': 'string',
     }
 
-    def __init__(self, config=None):
-        super().__init__(config)
+    def __init__(self, config=None, core=None):
+        super().__init__(config, core)
 
         # initialize a tellurium(roadrunner) simulation object. Load the model in using either sbml(default) or antimony
         if self.config.get('antimony_string') and not self.config.get('sbml_model_path'):