process-bigraph 0.0.33__tar.gz → 0.0.35__tar.gz

{process-bigraph-0.0.33/process_bigraph.egg-info → process-bigraph-0.0.35}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: process-bigraph
-Version: 0.0.33
+Version: 0.0.35
 Home-page: https://github.com/vivarium-collective/process-bigraph
 Author: Ryan Spangler, Eran Agmon
 Author-email: ryan.spangler@gmail.com, agmon.eran@gmail.com

{process-bigraph-0.0.33 → process-bigraph-0.0.35}/process_bigraph/composite.py

@@ -401,6 +401,8 @@ class Composite(Process):
     def load(cls, path, core=None):
         with open(path) as data:
             document = json.load(data)
+            composition = document['composition']
+            document['composition'] = core.deserialize('schema', composition)
 
             composite = cls(
                 document,
@@ -456,10 +458,6 @@ class Composite(Process):
             self.composition,
             edge_state)
 
-        # self.state = deep_merge(
-        #     self.state,
-        #     edge_state)
-
         # TODO: call validate on this composite, not just check
         # assert self.core.validate(
         #     self.composition,
@@ -511,6 +509,9 @@ class Composite(Process):
             self.composition,
             self.state)
 
+    def serialize_schema(self):
+        return self.core.serialize('schema', self.composition)
+
     def save(self,
              filename='composite.json',
              outdir='out',
@@ -531,8 +532,7 @@ class Composite(Process):
             document['state'] = serialized_state
 
         if schema:
-            serialized_schema = self.core.representation(
-                self.composition)
+            serialized_schema = self.serialize_schema()
             document['composition'] = serialized_schema
 
         # save the dictionary to a JSON file

{process-bigraph-0.0.33 → process-bigraph-0.0.35}/process_bigraph/emitter.py

@@ -234,19 +234,25 @@ class RAMEmitter(Emitter):
 
         return {}
 
-    def query(self, query=None):
+    def query(self, query=None, schema=None):
         """
         Query the history of the emitter.
         :param query: a list of paths to query from the history. If None, the entire history is returned.
         :return: results of the query in a list
         """
+        schema = schema or self.inputs()
         if isinstance(query, list):
             results = []
             for t in self.history:
                 result = {}
                 for path in query:
-                    element = get_path(t, path)
-                    result = set_path(result, path, element)
+                    _, state = self.core.slice(
+                        schema=schema,
+                        state=t,
+                        path=path)
+                
+                    # element = get_path(t, path)
+                    result = set_path(result, path, state)
                 results.append(result)
                 # element = get_path(self.history, path)
                 # result = set_path(result, path, element)

{process-bigraph-0.0.33 → process-bigraph-0.0.35}/process_bigraph/tests.py

@@ -610,6 +610,19 @@ def test_grow_divide(core):
     assert '0_0_0_0_1' in composite.state['environment']
     assert composite.state['environment']['0_0_0_0_1']['mass'] == composite.state['environment']['0_0_0_0_1']['grow_divide']['instance'].state['mass']
 
+    # check recursive schema reference
+    assert (id(composite.composition['environment']['_value']['grow_divide']) ==
+            id(composite.composition['environment']['_value']['grow_divide']['_outputs']['environment']['_value']['grow_divide']))
+
+    composite.save('test_grow_divide_saved.json')
+
+    c2 = Composite.load(
+        'out/test_grow_divide_saved.json',
+        core=core)
+    
+    assert (id(composite.composition['environment']['_value']['grow_divide']) ==
+            id(composite.composition['environment']['_value']['grow_divide']['_outputs']['environment']['_value']['grow_divide']))
+
 
 def test_gillespie_composite(core):
     composite_schema = {

{process-bigraph-0.0.33 → process-bigraph-0.0.35/process_bigraph.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: process-bigraph
-Version: 0.0.33
+Version: 0.0.35
 Home-page: https://github.com/vivarium-collective/process-bigraph
 Author: Ryan Spangler, Eran Agmon
 Author-email: ryan.spangler@gmail.com, agmon.eran@gmail.com

{process-bigraph-0.0.33 → process-bigraph-0.0.35}/setup.py

@@ -2,7 +2,7 @@ import re
 from setuptools import setup, find_packages
 
 
-VERSION = '0.0.33'
+VERSION = '0.0.35'
 
 
 with open("README.md", "r") as readme: