bigraph-schema 0.0.46__tar.gz → 0.0.48__tar.gz

{bigraph-schema-0.0.46/bigraph_schema.egg-info → bigraph-schema-0.0.48}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.46
+Version: 0.0.48
 Summary: A serializable type schema for compositional systems biology
 Home-page: https://github.com/vivarium-collective/bigraph-schema
 Author: Eran Agmon, Ryan Spangler

bigraph-schema-0.0.48/bigraph_schema/__init__.py

@@ -0,0 +1,6 @@
+from bigraph_schema.registry import (
+    deep_merge, validate_merge, default, Registry, hierarchy_depth, is_schema_key, establish_path,
+    strip_schema_keys, type_parameter_key, non_schema_keys, set_path, transform_path)
+from bigraph_schema.utilities import get_path, visit_method
+from bigraph_schema.edge import Edge
+from bigraph_schema.type_system import TypeSystem, type_schema_keys

bigraph-schema-0.0.48/bigraph_schema/edge.py

@@ -0,0 +1,49 @@
+"""
+====
+Edge
+====
+
+Base class for all edges in the bigraph schema.
+"""
+
+class Edge:
+    config_schema = {}
+
+
+    def __init__(self, config=None, core=None):
+        if core is None:
+            raise Exception('must provide a core')
+
+        self.core = core
+
+        if config is None:
+            config = {}
+
+        self.config = self.core.fill(
+            self.config_schema,
+            config)
+
+        self.initialize(self.config)
+
+
+    def initialize(self):
+        pass
+
+
+    def initial_state(self):
+        return {}
+
+
+    def inputs(self):
+        return {}
+
+
+    def outputs(self):
+        return {}
+
+
+    def interface(self):
+        """Returns the schema for this type"""
+        return {
+            'inputs': self.inputs(),
+            'outputs': self.outputs()}

{bigraph-schema-0.0.46 → bigraph-schema-0.0.48}/bigraph_schema/registry.py

@@ -17,31 +17,6 @@ from pprint import pformat as pf
 from bigraph_schema.protocols import local_lookup_module, function_module
 
 
-NONE_SYMBOL = '!nil'
-
-
-required_schema_keys = set([
-    '_default',
-    '_apply',
-    '_check',
-    '_serialize',
-    '_deserialize',
-    '_fold',
-])
-
-
-optional_schema_keys = set([
-    '_type',
-    '_value',
-    '_description',
-    '_type_parameters',
-    '_inherit',
-    '_divide',
-])
-
-
-type_schema_keys = required_schema_keys | optional_schema_keys
-
 
 def deep_merge_copy(dct, merge_dct):
     return deep_merge(copy.deepcopy(dct), merge_dct)
@@ -371,19 +346,3 @@ class Registry(object):
 
     def validate(self, item):
         return True
-
-
-def test_remove_omitted():
-    result = remove_omitted(
-        {'a': {}, 'b': {'c': {}, 'd': {}}},
-        {'b': {'c': {}}},
-        {'a': {'X': 1111}, 'b': {'c': {'Y': 4444}, 'd': {'Z': 99999}}})
-
-    assert 'a' not in result
-    assert result['b']['c']['Y'] == 4444
-    assert 'd' not in result['b']
-
-
-if __name__ == '__main__':
-    test_reregister_type()
-    test_remove_omitted()