composite type initialization

process_bigraph/__init__.py

@@ -12,3 +12,4 @@
 # TODO
 process_registry.register('console-emitter', ConsoleEmitter)
 process_registry.register('ram-emitter', RAMEmitter)
+

process_bigraph/composite.py

@@ -335,7 +335,7 @@ def build_step_network(steps):
 
             if ancestors[step_key]['output_paths'] is None:
                 ancestors[step_key]['output_paths'] = find_leaves(
-                    wires['outputs'])
+                    wires.get('outputs', {}))
             output_paths = ancestors[step_key]['output_paths']
 
             for input in input_paths:
@@ -414,17 +414,19 @@ def determine_steps(steps, remaining, fulfilled):
 
 
 class Composite(Process):
-    """Composite parent class.
-
     """
+    Composite parent class.
+    """
+
+
     config_schema = {
         # TODO: add schema type
         'composition': 'tree[any]',
         'state': 'tree[any]',
         'schema': 'tree[any]',
         'bridge': 'wires',
-        'global_time_precision': 'maybe[float]',
-    }
+        'global_time_precision': 'maybe[float]'}
+
 
     # TODO: if processes are serialized, deserialize them first
     def __init__(self, config=None, local_types=None):
@@ -669,8 +671,6 @@ def apply_updates(self, updates):
                 series = [series]
 
             for update in series:
-                # print(update)
-
                 paths = hierarchy_depth(update)
                 update_paths.extend(paths.keys())
 
@@ -778,8 +778,6 @@ def determine_steps(self):
 
 
     def run_steps(self, step_paths):
-        print(f'running steps: {step_paths}')
-
         if len(step_paths) > 0:
             updates = []
             for step_path in step_paths:

process_bigraph/registry.py

@@ -24,3 +24,4 @@
 
 #: Maps process names to :term:`protocol methods`
 protocol_registry = Registry()
+

process_bigraph/tests.py

@@ -27,36 +27,6 @@ def update(self, state, interval):
             'level': state['level'] * self.config['rate']}
 
 
-def test_serialized_composite():
-    # This should specify the same thing as above
-    composite_schema = {
-        '_type': 'process[exchange:float]',
-        'address': 'local:!process_bigraph.composite.Composite',
-        'config': {
-            'state': {
-                'increase': {
-                    '_type': 'process[level:float]',
-                    'address': 'local:!process_bigraph.tests.IncreaseProcess',
-                    'config': {'rate': '0.3'},
-                    'wires': {'level': ['value']}
-                },
-                'value': '11.11',
-            },
-            'schema': {
-                'increase': 'process[level:float]',
-                # 'increase': 'process[{"level":"float","down":{"a":"int"}}]',
-                'value': 'float',
-            },
-            'bridge': {
-                'exchange': 'value'
-            },
-        }
-    }
-
-    composite_instance = types.deserialize(composite_schema, {})
-    composite_instance.update()
-
-
 def test_default_config():
     process = IncreaseProcess()
     assert process.config['rate'] == 0.1
@@ -259,6 +229,11 @@ def test_dependencies():
     assert composite.state['h'] == -17396.469884
 
 
+def test_dependency_cycle():
+    # test a step network with cycles in a few ways
+    pass
+
+
 class SimpleCompartment(Process):
     config_schema = {
         'id': 'string'}
@@ -329,13 +304,6 @@ def update(self, state, interval):
 
 
 # TODO: create reaction registry, register this under "divide"
-def divide_reaction(config):
-    return {
-        'redex': {
-            config['id']: {}},
-        'reactum': {
-            daughter_config['id']: daughter_config['state']
-            for daughter_config in config['daughters']}}
 
 
 def engulf_reaction(config):
@@ -375,8 +343,6 @@ def test_reaction():
                             'inner': ['inner']}}}}}}
 
 
-
-
 if __name__ == '__main__':
     test_default_config()
     test_merge_collections()

process_bigraph/type_system.py

@@ -278,7 +278,7 @@ def infer_schema(self, schema, state, top_state=None, path=None):
             else:
                 for key, value in state.items():
                     inner_path = path + (key,)
-                    if get_path(schema, inner_path) is None or get_path(state, inner_path) is None:
+                    if get_path(schema, inner_path) is None or get_path(state, inner_path) is None or (isinstance(value, dict) and '_type' in value):
                         schema, top_state = self.infer_schema(
                             schema,
                             value,

pytest.ini

@@ -1,6 +1,6 @@
 [pytest]
 python_files = *.py
 addopts = --doctest-modules --strict-markers
-testpaths = vivarium
+testpaths = process_bigraph
 markers =
     slow: indicates slow tests (deselect with '-m "not slow"')