tests are passing

process_bigraph/composite.py

@@ -161,15 +161,15 @@ def deserialize_process(schema, encoded, core):
 
 
 def deserialize_step(schema, encoded, core):
-    deserialized = encoded.copy()
-    if not encoded['address']:
-        return encoded
+    if not encoded:
+        deserialized = core.default(schema)
+    else:
+        deserialized = encoded.copy()
 
-    protocol = encoded['address'].split(':', 1)
-    if len(protocol) == 1:
-        return encoded
+    if not deserialized['address']:
+        return deserialized
 
-    protocol, address = encoded['address'].split(':', 1)
+    protocol, address = deserialized['address'].split(':', 1)
 
     if 'instance' in deserialized:
         instantiate = type(deserialized['instance'])
@@ -184,7 +184,7 @@ def deserialize_step(schema, encoded, core):
 
     config = core.deserialize(
         instantiate.config_schema,
-        encoded.get('config', {}))
+        deserialized.get('config', {}))
 
     if not 'instance' in deserialized:
         process = instantiate(config, core=core)
@@ -222,7 +222,7 @@ def deserialize_step(schema, encoded, core):
         '_description': '',
         # TODO: support reference to type parameters from other states
         'address': 'protocol',
-        'config': 'tree[any]'},
+        'config': 'quote'},
 
     # TODO: slice process to allow for navigating through a port
     'process': {
@@ -238,7 +238,7 @@ def deserialize_step(schema, encoded, core):
         # TODO: support reference to type parameters from other states
         'interval': 'interval',
         'address': 'protocol',
-        'config': 'tree[any]'}}
+        'config': 'quote'}}
 
 
 BASE_PROTOCOLS = {
@@ -397,10 +397,10 @@ def __init__(self, config=None, core=None):
         if config is None:
             config = {}
 
-        # check that all keywords in config are in config_schema
-        for key in config.keys():
-            if key not in self.config_schema:
-                raise Exception(f'config key {key} not in config_schema for {self.__class__.__name__}')
+        # # check that all keywords in config are in config_schema
+        # for key in config.keys():
+        #     if key not in self.config_schema:
+        #         raise Exception(f'config key {key} not in config_schema for {self.__class__.__name__}')
 
         # fill in defaults for config
         self.config = self.core.fill(

process_bigraph/experiments/growth_division.py

@@ -92,6 +92,7 @@ def generate_bridge(schema, state, interval=1.0):
         for port in ['inputs', 'outputs']}
 
     config = {
+        '_type': 'quote',
         'state': state,
         'bridge': bridge}
 

process_bigraph/processes/parameter_scan.py

@@ -169,6 +169,7 @@ def update(self, inputs):
         # TODO: instead of the composite being a reference it is instead read through
         #   some port and lives in the state of the simulation (??)
         self.composite.merge(
+            self.inputs(),
             inputs)
 
         self.composite.run(
@@ -325,7 +326,7 @@ def update(self, inputs):
 
             for observable in self.config['observables']:
                 subschema = self.results_schema[key]
-                value_schema, value = core.slice(
+                value_schema, value = self.core.slice(
                     subschema,
                     values,
                     observable)

process_bigraph/tests.py

@@ -433,7 +433,7 @@ def test_emitter(core):
     # TODO: support omit as well as emit
 
 
-def test_run_process():
+def test_run_process(core):
     timestep = 0.1
     runtime = 10.0
     initial_A = 11.11
@@ -470,7 +470,7 @@ def test_run_process():
     assert results[0]['results']['species'][0]['A'] == initial_A
 
 
-def test_nested_wires():
+def test_nested_wires(core):
     timestep = 0.1
     runtime = 10.0
     initial_A = 11.11
@@ -507,7 +507,7 @@ def test_nested_wires():
     assert results[0]['results']['species']['A'][0] == initial_A
 
 
-def test_parameter_scan():
+def test_parameter_scan(core):
     # TODO: make a parameter scan with a biosimulator process,
     #   ie - Copasi
 
@@ -547,7 +547,7 @@ def test_parameter_scan():
     result = scan.update({}, 0.0)
 
 
-def test_composite_workflow():
+def test_composite_workflow(core):
     # TODO: Make a workflow with a composite inside
     pass
 
@@ -566,8 +566,6 @@ def test_grow_divide(core):
                 'mass': initial_mass,
                 'grow_divide': grow_divide}}}
 
-    import ipdb; ipdb.set_trace()
-
     composite = Composite({
         'state': environment},
         core=core)