merge with latest main

process_bigraph/__init__.py

@@ -1,6 +1,5 @@
 import pprint
 
-from process_bigraph.protocols import local_lookup
 from process_bigraph.composite import Process, Step, Composite, ProcessTypes
 
 

process_bigraph/composite.py

@@ -10,14 +10,15 @@
 import collections
 from typing import Dict
 
+
 from bigraph_schema import Edge, TypeSystem, get_path, validate_merge, establish_path, set_path, deep_merge
 from bigraph_schema.registry import Registry
 
 from process_bigraph.protocols import local_lookup, local_lookup_module
 
 
 # TODO: implement these
-def apply_process(current, update, schema, core):
+def apply_process(schema, current, update, core):
     process_schema = schema.copy()
     process_schema.pop('_apply')
     return core.apply(
@@ -26,17 +27,17 @@ def apply_process(current, update, schema, core):
         update)
 
 
-def check_process(state, schema, core):
+def check_process(schema, state, core):
     return 'instance' in state and isinstance(
         state['instance'],
         Edge)
 
 
-def divide_process(value, schema, core):
+def divide_process(schema, value, core):
     return value
 
 
-def serialize_process(value, schema, core):
+def serialize_process(schema, value, core):
     """Serialize a process to a JSON-safe representation."""
     # TODO -- need to get back the protocol: address and the config
     process = value.copy()
@@ -57,7 +58,7 @@ def assert_interface(interface):
     'float': 'float'}
 
 
-def deserialize_process(encoded, schema, core):
+def deserialize_process(schema, encoded, core):
     """Deserialize a process from a serialized state.
 
     This function is used by the type system to deserialize a process.
@@ -91,7 +92,7 @@ def deserialize_process(encoded, schema, core):
         encoded.get('interval'))
 
     if not 'instance' in deserialized:
-        process = instantiate(config, core)
+        process = instantiate(config, core=core)
         deserialized['instance'] = process
 
     deserialized['config'] = config
@@ -100,7 +101,7 @@ def deserialize_process(encoded, schema, core):
     return deserialized
 
 
-def deserialize_step(encoded, schema, core):
+def deserialize_step(schema, encoded, core):
     deserialized = encoded.copy()
     protocol, address = encoded['address'].split(':', 1)
 
@@ -120,7 +121,7 @@ def deserialize_step(encoded, schema, core):
         encoded.get('config', {}))
 
     if not 'instance' in deserialized:
-        process = instantiate(config, core)
+        process = instantiate(config, core=core)
         deserialized['instance'] = process
 
     deserialized['config'] = config
@@ -346,7 +347,6 @@ def lookup_address(self, address):
         if protocol == 'local':
             self.lookup_local(config)
 
-
 def hierarchy_depth(hierarchy, path=()):
     """
     Create a mapping of every path in the hierarchy to the node living at
@@ -383,7 +383,7 @@ class Step(Edge):
 
 
     def __init__(self, config=None, core=None):
-        self.core = core
+        self.core = core or ProcessTypes()
 
         if config is None:
             config = {}
@@ -427,7 +427,8 @@ class can provide a ``defaults`` class variable to specify the
     config_schema = {}
 
     def __init__(self, config=None, core=None):
-        self.core = core
+        self.core = core or ProcessTypes()
+
         if config is None:
             config = {}
 

process_bigraph/experiments/minimal_gillespie.py

@@ -14,15 +14,16 @@
 from process_bigraph import Step, Process, Composite, ProcessTypes
 
 
-@pytest.fixture
-def core():
-    return ProcessTypes()
-
-
 # 'map[float](default:1.0|apply:set)'
 # 'float(default:1.0)'
 
 
+EXPORT = {
+    'default 1': {
+        '_inherit': 'float',
+        '_default': 1.0}}
+
+
 class GillespieInterval(Step):
     config_schema = {
         'ktsc': {
@@ -165,13 +166,14 @@ def update(self, state, interval):
         return update
 
 
-def test_gillespie_composite(core):
-    core.register(
-        'default 1', {
-            '_inherit': 'float',
-            '_default': 1.0})
-
+@pytest.fixture
+def core():
+    core = ProcessTypes()
+    core.import_types(EXPORT)
+    return core
+    
 
+def test_gillespie_composite(core):
     composite_schema = {
         # This all gets inferred -------------
         # ==================================
@@ -280,7 +282,9 @@ def test_gillespie_composite(core):
             # 'mRNA': {
             #     'C': '21.0'}}}
 
-    gillespie = Composite(composite_schema, core)
+    gillespie = Composite(
+        composite_schema,
+        core=core)
 
     updates = gillespie.update({
         'DNA': {
@@ -311,6 +315,7 @@ def test_stochastic_deterministic_composite(core):
 
 if __name__ == '__main__':
     core = ProcessTypes()
+    core.import_types(EXPORT)
 
     test_gillespie_composite(core)
     test_union_tree(core)

process_bigraph/tests.py

@@ -43,7 +43,8 @@ def update(self, state, interval):
 
 
 def test_default_config(core):
-    process = IncreaseProcess({}, core)
+    process = IncreaseProcess(core=core)
+
     assert process.config['rate'] == 0.1
 
 
@@ -56,14 +57,22 @@ def test_merge_collections(core):
     assert c[('what',)] == [1, 2, 3, 4, 5, 11]
 
 
+@pytest.fixture
+def core():
+    return ProcessTypes()
+
+
 def test_process(core):
-    process = IncreaseProcess({'rate': 0.2}, core)
+    process = IncreaseProcess({'rate': 0.2}, core=core)
     interface = process.interface()
     state = core.fill(interface['inputs'])
     state = core.fill(interface['outputs'])
     update = process.update({'level': 5.5}, 1.0)
 
-    new_state = core.apply(interface['outputs'], state, update)
+    new_state = core.apply(
+        interface['outputs'],
+        state,
+        update)
 
     assert new_state['level'] == 1.1
 
@@ -96,7 +105,7 @@ def test_composite(core):
                 'interval': 1.0,
                 'inputs': {'level': ['value']},
                 'outputs': {'level': ['value']}},
-            'value': '11.11'}}, core)
+            'value': '11.11'}}, core=core)
 
     initial_state = {'exchange': 3.33}
 
@@ -120,7 +129,7 @@ def test_infer(core):
                 'config': {'rate': '0.3'},
                 'inputs': {'level': ['value']},
                 'outputs': {'level': ['value']}},
-            'value': '11.11'}}, core)
+            'value': '11.11'}}, core=core)
 
     assert composite.composition['value']['_type'] == 'float'
     assert composite.state['value'] == 11.11
@@ -184,8 +193,7 @@ def test_step_initialization(core):
                     'a': ['B'],
                     'b': ['C']},
                 'outputs': {
-                    'c': ['D']}}}}, core)
-
+                    'c': ['D']}}}}, core=core)
 
     assert composite.state['D'] == (13 + 21) * 21
 
@@ -247,7 +255,9 @@ def test_dependencies(core):
             'outputs': {
                 'c': ['i']}}}
 
-    composite = Composite({'state': operation}, core)
+    composite = Composite(
+        {'state': operation},
+        core=core)
 
     assert composite.state['h'] == -17396.469884