feat: added justed process example to ntbk

biosimulator_processes/biosimulator_builder.py

@@ -186,14 +186,27 @@ def execute(self, num: int = None, duration: int = None, **run_params) -> None:
         self.start(num)
         return self.run(duration, **run_params)
 
+    def write_bigraph(self, fp: str, output_dir='out'):
+        """Use the builder instance attribute to write out the bigraph document to a fp."""
+        return self.builder_instance.write(filename=fp, outdir=output_dir)
+
     def wipe_builder(self):
         self.builder_instance = None
         print(f'Builder flushed! This is verified because builder is: {self.builder_instance}')
 
-    def flush(self, out_dir='out'):
+    def flush(self, out_dir='out', fp: str = None, write: bool = True) -> None:
+        """Optionally write the bigraph to document and wipe the current builder_instance instance.
+
+            Args:
+                out_dir:`str`: destination to which we save the document.
+                fp:`str`: path by which to save if write is true. Defaults to None.
+                write:`bool`: whether to write out the document before wiping. Defaults to `True`.
+        """
         from datetime import datetime
-        fp = f"BUILD_FLUSH_{str(datetime.now()).replace(' ', '__').replace(':', '_')}"
-        self.builder_instance.write(fp, out_dir)
+        if write:
+            if fp is None:
+                fp = f"BUILD_FLUSH_{str(datetime.now()).replace(' ', '__').replace(':', '_')}"
+            self.write_bigraph(fp, out_dir)
         return self.wipe_builder()
 
     def visualize_bigraph(self):

biosimulator_processes/data_model.py

@@ -214,16 +214,26 @@ def set_model_source_info(self, **kwargs):
 
 @dataclass
 class TimeCourseModel(SedModel):
+    """The data model declaration for process configuration schemas that support SED.
+
+        Attributes:
+            model_id: `str`
+            model_source: `Union[biosimulator_processes.data_model.ModelFilepath, biosimulator_processes.data_model.BiomodelId]`
+            model_language: `str`
+            model_name: `str`
+            model_changes: `biosimulator_processes.data_model.TimeCourseModelChanges`
+    """
     model_language: str = None,
     model_changes: TimeCourseModelChanges = None,
     model_units: ModelUnits = None
 
     def __init__(self,
                  model_source: Union[BiomodelID, ModelFilepath, str],
+                 model_changes=model_changes,
                  model_id=None,
                  model_name=None):
         """Class which inherits SedModel."""
-        super().__init__(model_source, model_id, model_name)
+        super().__init__(model_source, model_id, model_name, model_changes)
         # TODO: extract functionality for algorithms related to UTC sims
         self.model_id = self.set_id(model_id)
         self.model_name = self.set_name(model_name)