bigraph-schema 0.0.51__tar.gz → 0.0.52__tar.gz

{bigraph-schema-0.0.51/bigraph_schema.egg-info → bigraph-schema-0.0.52}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.51
+Version: 0.0.52
 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-0.0.51 → bigraph-schema-0.0.52}/bigraph_schema/__init__.py

@@ -3,4 +3,4 @@ from bigraph_schema.registry import (
     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
+from bigraph_schema.type_system import TypeSystem, type_schema_keys, resolve_path

{bigraph-schema-0.0.51 → bigraph-schema-0.0.52}/bigraph_schema/edge.py

@@ -23,11 +23,6 @@ class Edge:
             self.config_schema,
             config)
 
-        # TODO: make generate work here
-        # _, self.config = self.core.generate(
-        #     self.config_schema,
-        #     config)
-
         self.initialize(self.config)
 
 

{bigraph-schema-0.0.51 → bigraph-schema-0.0.52}/bigraph_schema/registry.py

@@ -32,6 +32,9 @@ def deep_merge(dct, merge_dct):
         dct = {}
     if merge_dct is None:
         merge_dct = {}
+    if not isinstance(merge_dct, dict):
+        return merge_dct
+
     for k, v in merge_dct.items():
         if (k in dct and isinstance(dct[k], dict)
                 and isinstance(merge_dct[k], collections.abc.Mapping)):

{bigraph-schema-0.0.51 → bigraph-schema-0.0.52}/bigraph_schema/type_functions.py

@@ -1915,6 +1915,18 @@ def generate_any(core, schema, state, top_schema=None, top_state=None, path=None
 def generate_quote(core, schema, state, top_schema=None, top_state=None, path=None):
     return schema, state, top_schema, top_state
 
+
+def default_quote(schema, core):
+    if '_default' in schema:
+        return copy.deepcopy(schema['_default'])
+    else:
+        return None
+
+
+def deserialize_quote(schema, state, core):
+    return state
+
+
 def generate_map(core, schema, state, top_schema=None, top_state=None, path=None):
     schema = schema or {}
     state = state or core.default(schema)
@@ -2516,6 +2528,8 @@ registry_types = {
 
     'quote': {
         '_type': 'quote',
+        '_deserialize': deserialize_quote,
+        '_default': default_quote,
         '_generate': generate_quote,
         '_sort': sort_quote,
         '_description': 'protect a schema from generation, ie in the config for a nested composite which has type information we only want to evaluate inside of the composite'},

{bigraph-schema-0.0.51 → bigraph-schema-0.0.52}/bigraph_schema/type_system.py

@@ -609,7 +609,6 @@ class TypeSystem(Registry):
         * intended to be the inverse of parse_expression()
         '''
 
-
         path = path or []
         parents = parents or []
         schema_id = id(schema)
@@ -1095,6 +1094,8 @@ class TypeSystem(Registry):
 
 
     def apply_update(self, schema, state, update):
+        schema = self.access(schema)
+
         if isinstance(update, dict) and '_react' in update:
             new_state = self.react(
                 schema,
@@ -1143,7 +1144,7 @@ class TypeSystem(Registry):
             for key, branch in update.items():
                 if key not in schema:
                     raise Exception(
-                        f'trying to update a key that is not in the schema'
+                        f'trying to update a key that is not in the schema '
                         f'for state: {key}\n{state}\nwith schema:\n{schema}')
                 else:
                     subupdate = self.apply_update(
@@ -1312,6 +1313,8 @@ class TypeSystem(Registry):
         returns the top_schema and top_state
         '''
 
+        path = resolve_path(path)
+
         if len(path) == 0:
             # deal with paths of length 0
             # this should never happen?
@@ -1356,8 +1359,6 @@ class TypeSystem(Registry):
                 result_state)
 
         else:
-            path = resolve_path(path)
-
             head = path[0]
             tail = path[1:]
 

{bigraph-schema-0.0.51 → bigraph-schema-0.0.52/bigraph_schema.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.51
+Version: 0.0.52
 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-0.0.51 → bigraph-schema-0.0.52}/setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup, find_packages
 
 
-VERSION = '0.0.51'
+VERSION = '0.0.52'
 
 
 with open("README.md", "r") as readme: