diff --git a/biosimulator_processes/cobra_process.py b/biosimulator_processes/cobra_process.py index 1d5cac14c..b61d5a185 100644 --- a/biosimulator_processes/cobra_process.py +++ b/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 diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py index fbbc98452..7a51a6c52 100644 --- a/biosimulator_processes/copasi_process.py +++ b/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']) diff --git a/biosimulator_processes/smoldyn_process.py b/biosimulator_processes/smoldyn_process.py index 3ffaaf62f..a56b159fd 100644 --- a/biosimulator_processes/smoldyn_process.py +++ b/biosimulator_processes/smoldyn_process.py @@ -100,7 +100,7 @@ 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: @@ -108,10 +108,9 @@ def __init__(self, config: Dict[str, Any] = None): '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') diff --git a/biosimulator_processes/tellurium_process.py b/biosimulator_processes/tellurium_process.py index 02f1074ef..ccf484ef7 100644 --- a/biosimulator_processes/tellurium_process.py +++ b/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'):