bigraph-schema 0.0.49__tar.gz → 0.0.50__tar.gz

{bigraph-schema-0.0.49/bigraph_schema.egg-info → bigraph-schema-0.0.50}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.49
+Version: 0.0.50
 Summary: A serializable type schema for compositional systems biology
 Home-page: https://github.com/vivarium-collective/bigraph-schema
 Author: Eran Agmon, Ryan Spangler
@@ -27,12 +27,11 @@ License-File: AUTHORS.md
 [![PyPI version](https://img.shields.io/pypi/v/bigraph-schema.svg)](https://pypi.org/project/bigraph-schema/)
 [![Tutorial](https://img.shields.io/badge/GitHub%20Pages-Tutorial-brightgreen)](https://vivarium-collective.github.io/bigraph-schema/notebooks/demo.html)
 
-Welcome to `bigraph-schema` – a library providing a serializable type schema for compositional systems biology 
-simulations. This library is an integral component of the broader Process Bigraph project, which seeks to create an 
-innovative framework for representing, simulating, and analyzing complex biological systems.
+Welcome to `bigraph-schema` – a library providing a serializable type schema for composite systems simulations. 
+This library provides the core of the broader Vivarium 2.0 project.
 
-The goal of `bigraph-schema` is to support interoperability and extensibility across compositional modeling, 
-facilitating seamless integration with existing and future modeling platforms. This is achieved by establishing a 
+The goal of `bigraph-schema` is to support interoperability and extensibility across composite simulation formats, 
+facilitating integration with existing and future modeling platforms. This is achieved by establishing a 
 standardized and serializable schema for the complex, hierarchical, and multiscale nature of biological systems.
 
 ## Installation

{bigraph-schema-0.0.49 → bigraph-schema-0.0.50}/README.md

@@ -3,12 +3,11 @@
 [![PyPI version](https://img.shields.io/pypi/v/bigraph-schema.svg)](https://pypi.org/project/bigraph-schema/)
 [![Tutorial](https://img.shields.io/badge/GitHub%20Pages-Tutorial-brightgreen)](https://vivarium-collective.github.io/bigraph-schema/notebooks/demo.html)
 
-Welcome to `bigraph-schema` – a library providing a serializable type schema for compositional systems biology 
-simulations. This library is an integral component of the broader Process Bigraph project, which seeks to create an 
-innovative framework for representing, simulating, and analyzing complex biological systems.
+Welcome to `bigraph-schema` – a library providing a serializable type schema for composite systems simulations. 
+This library provides the core of the broader Vivarium 2.0 project.
 
-The goal of `bigraph-schema` is to support interoperability and extensibility across compositional modeling, 
-facilitating seamless integration with existing and future modeling platforms. This is achieved by establishing a 
+The goal of `bigraph-schema` is to support interoperability and extensibility across composite simulation formats, 
+facilitating integration with existing and future modeling platforms. This is achieved by establishing a 
 standardized and serializable schema for the complex, hierarchical, and multiscale nature of biological systems.
 
 ## Installation

{bigraph-schema-0.0.49 → bigraph-schema-0.0.50}/bigraph_schema/edge.py

@@ -23,6 +23,11 @@ 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-0.0.49 → bigraph-schema-0.0.50}/bigraph_schema/type_functions.py

@@ -1926,15 +1926,19 @@ def generate_map(core, schema, state, top_schema=None, top_state=None, path=None
         schema,
         'value')
 
-    # generated_schema = {}
-    # generated_state = {}
     # TODO: can we assume this was already sorted at the top level?
-
     generated_schema, generated_state = core.sort(
         schema,
         state)
 
-    all_keys = union_keys(schema, state)  # set(schema.keys()).union(state.keys())
+    try:
+        all_keys = union_keys(schema, state)  # set(schema.keys()).union(state.keys())
+    except Exception as e:
+        # provide the path at which the error occurred
+        raise Exception(
+            f"Error at path {path}:\n"
+            f"Expected schema: {core.representation(schema)}\n"
+            f"Provided state: {state}") from e
 
     for key in all_keys:
         if is_schema_key(key):

{bigraph-schema-0.0.49 → bigraph-schema-0.0.50}/bigraph_schema/type_system.py

@@ -130,6 +130,18 @@ class TypeSystem(Registry):
         return self
 
 
+    def update_types(self, type_updates):
+        for type_key, type_data in type_updates.items():
+            is_update = self.exists(type_key)
+
+            self.register(
+                type_key,
+                type_data,
+                update=is_update)
+
+        return self
+
+
     def lookup(self, type_key, attribute):
         return self.access(type_key).get(attribute)
 
@@ -164,7 +176,8 @@ class TypeSystem(Registry):
         return registry
 
 
-    def register(self, key, schema, alternate_keys=tuple(), force=False):
+    # TODO: explain this method
+    def register(self, key, schema, alternate_keys=tuple(), strict=True, update=False):
         """
         register the schema under the given key in the registry
         """
@@ -172,6 +185,13 @@ class TypeSystem(Registry):
         if isinstance(schema, str):
             schema = self.find(schema)
         schema = copy.deepcopy(schema)
+        if self.exists(key) and update:
+            if update:
+                found = self.find(key)
+                schema = deep_merge(
+                    found,
+                    schema)
+                strict = False
 
         if '_type' not in schema:
             schema['_type'] = key
@@ -187,18 +207,10 @@ class TypeSystem(Registry):
                 inherit_type = self.access(inherit)
                 new_schema = copy.deepcopy(inherit_type)
 
-                # schema = self.resolve(
-                #     new_schema,
-                #     schema)
-
                 schema = self.merge_schemas(
                     new_schema,
                     schema)
 
-                # schema = type_merge(
-                #     new_schema,
-                #     schema)
-
                 self.inherits[key].append(
                     inherit_type)
 
@@ -233,7 +245,7 @@ class TypeSystem(Registry):
             key,
             schema,
             alternate_keys,
-            force)
+            strict=strict)
 
 
     def resolve_parameters(self, type_parameters, schema):
@@ -717,6 +729,9 @@ class TypeSystem(Registry):
         method_function = registry.access(
             found)
 
+        if method_function is None:
+            raise Exception(f'no method "{method_name}" found for state {state} and schema {schema}')
+
         return method_function
 
 
@@ -1371,11 +1386,13 @@ class TypeSystem(Registry):
             state,
             'deserialize')
 
-        return deserialize_function(
+        deserialized = deserialize_function(
             schema,
             state,
             self)
 
+        return deserialized
+
 
     def fill_ports(self, interface, wires=None, state=None, top_schema=None, top_state=None, path=None):
         # deal with wires

{bigraph-schema-0.0.49 → bigraph-schema-0.0.50}/bigraph_schema/type_system_tests.py

@@ -74,7 +74,7 @@ def test_reregister_type(core):
             'A', {'_default': 'b'},
             strict=True)
 
-    core.register('A', {'_default': 'b'})
+    core.register('A', {'_default': 'b'}, strict=False)
 
     assert core.access('A')['_default'] == 'b'
 
@@ -2262,7 +2262,7 @@ def test_merge(core):
     assert 'D' in top_state
     assert top_schema['D']['_type'] == 'float'
 
-def test_remove_omitted():
+def test_remove_omitted(core=None):
     result = remove_omitted(
         {'a': {}, 'b': {'c': {}, 'd': {}}},
         {'b': {'c': {}}},
@@ -2273,6 +2273,22 @@ def test_remove_omitted():
     assert 'd' not in result['b']
 
 
+def test_union_key_error(core):
+    schema = core.access('map[map[float]]')
+    state = {
+        'a': {'b': 1.1},
+        'c': {'d': 2.2},
+        'e': 3.3  # this should be an error
+    }
+    generate_method = core.choose_method(schema, state, 'generate')
+
+    # assert that the Exception is raised
+    with pytest.raises(Exception):
+        result = generate_method(core, schema, state)
+
+
+
+
 if __name__ == '__main__':
     core = TypeSystem()
     core = register_test_types(core)
@@ -2322,4 +2338,5 @@ if __name__ == '__main__':
     test_generate(core)
     test_edge_cycle(core)
     test_merge(core)
-    test_remove_omitted()
+    test_remove_omitted(core)
+    test_union_key_error(core)

{bigraph-schema-0.0.49 → bigraph-schema-0.0.50/bigraph_schema.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.49
+Version: 0.0.50
 Summary: A serializable type schema for compositional systems biology
 Home-page: https://github.com/vivarium-collective/bigraph-schema
 Author: Eran Agmon, Ryan Spangler
@@ -27,12 +27,11 @@ License-File: AUTHORS.md
 [![PyPI version](https://img.shields.io/pypi/v/bigraph-schema.svg)](https://pypi.org/project/bigraph-schema/)
 [![Tutorial](https://img.shields.io/badge/GitHub%20Pages-Tutorial-brightgreen)](https://vivarium-collective.github.io/bigraph-schema/notebooks/demo.html)
 
-Welcome to `bigraph-schema` – a library providing a serializable type schema for compositional systems biology 
-simulations. This library is an integral component of the broader Process Bigraph project, which seeks to create an 
-innovative framework for representing, simulating, and analyzing complex biological systems.
+Welcome to `bigraph-schema` – a library providing a serializable type schema for composite systems simulations. 
+This library provides the core of the broader Vivarium 2.0 project.
 
-The goal of `bigraph-schema` is to support interoperability and extensibility across compositional modeling, 
-facilitating seamless integration with existing and future modeling platforms. This is achieved by establishing a 
+The goal of `bigraph-schema` is to support interoperability and extensibility across composite simulation formats, 
+facilitating integration with existing and future modeling platforms. This is achieved by establishing a 
 standardized and serializable schema for the complex, hierarchical, and multiscale nature of biological systems.
 
 ## Installation

{bigraph-schema-0.0.49 → bigraph-schema-0.0.50}/setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup, find_packages
 
 
-VERSION = '0.0.49'
+VERSION = '0.0.50'
 
 
 with open("README.md", "r") as readme: