documentation

process_bigraph/composite.py

@@ -835,7 +835,7 @@ def save(self,
              schema=False,
              state=False):
 
-        # add upcoming deprecation warning
+        # upcoming deprecation warning
         print("Warning: save() is deprecated and will be removed in a future version. "
               "Use use Vivarium for managing simulations instead of Composite.")
 
@@ -902,6 +902,11 @@ def outputs(self):
 
 
     def read_emitter_config(self, emitter_config):
+
+        # upcoming deprecation warning
+        print("Warning: read_emitter_config() is deprecated and will be removed in a future version. "
+              "Use use Vivarium for managing simulations and emitters instead of Composite.")
+
         address = emitter_config.get('address', 'local:ram-emitter')
         config = emitter_config.get('config', {})
         mode = emitter_config.get('mode', 'none')

process_bigraph/vivarium.py

@@ -11,6 +11,17 @@
 
 
 class Vivarium:
+    """
+    Vivarium is a controlled virtual environment for composite process-bigraph simulations.
+
+    It manages packages and sets up the conditions for running simulations, and collects results through emitters.
+
+    Attributes:
+        document (dict): The configuration document for the simulation.
+        core (ProcessTypes): The core process types manager.
+        composite (Composite): The composite object managing the simulation.
+        require (list): List of required packages for the simulation.
+    """
     def __init__(self,
                  document=None,
                  processes=None,