bigraph-schema 0.0.65__tar.gz → 0.0.68__tar.gz

{bigraph-schema-0.0.65 → bigraph_schema-0.0.68}/.gitignore

@@ -15,3 +15,4 @@ bigraph_schema.egg-info/
 .devenv*
 .devenv/
 devenv.lock
+uv.lock

{bigraph-schema-0.0.65/bigraph_schema.egg-info → bigraph_schema-0.0.68}/PKG-INFO

@@ -1,24 +1,23 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: bigraph-schema
-Version: 0.0.65
+Version: 0.0.68
 Summary: A serializable type schema for compositional systems biology
-Home-page: https://github.com/vivarium-collective/bigraph-schema
 Author: Eran Agmon, Ryan Spangler
-Author-email: agmon.eran@gmail.com, ryan.spangler@gmail.com
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: AUTHORS.md
+Requires-Dist: fire
+Requires-Dist: numpy
+Requires-Dist: orjson
+Requires-Dist: parsimonious
+Requires-Dist: pint
+Requires-Dist: plum-dispatch
+Requires-Dist: pytest
+Requires-Dist: requests>=2.31.0
+Requires-Dist: setuptools
+Requires-Dist: twine>=4.0.2
+Dynamic: license-file
 
 # Bigraph-schema
 

{bigraph-schema-0.0.65 → bigraph_schema-0.0.68}/bigraph_schema/edge.py

@@ -46,11 +46,35 @@ class Edge:
         if config is None:
             config = {}
 
-        self.config = self.core.fill(self.config_schema, config)
-        self.initialize(self.config)
+        self._config = self.core.fill(self.config_schema, config)
+        self._composition = 'edge'
+        self._state = {}
 
-        # # Register port types
-        # self.register_interface()
+        self.initialize(self._config)
+
+    @property
+    def config(self):
+        return self._config
+
+    @config.setter
+    def config(self, config):
+        self._config = config
+
+    @property
+    def composition(self):
+        return self._composition
+
+    @composition.setter
+    def composition(self, composition):
+        self._composition = composition
+
+    @property
+    def state(self):
+        return self._state
+
+    @state.setter
+    def state(self, state):
+        self._state = state
 
     def initialize(self, config):
         """Optional hook for subclass-specific initialization."""

{bigraph-schema-0.0.65 → bigraph_schema-0.0.68}/bigraph_schema/tests.py

@@ -77,6 +77,8 @@ def register_cube(core):
 def test_basic_types(core):
     assert core.find('integer')
     assert core.find('cube')['depth']['_type'] == 'integer'
+    # inheritance
+    assert core.find('cube')['width']['_type'] == 'integer'
 
 
 def test_update_types(core):
@@ -85,6 +87,11 @@ def test_update_types(core):
     core.update_types({'A': {'_description':desc}})
     assert core.access('A') == {'_type': 'payload', '_description': desc}
 
+    core.update_types({'B': "alternate", 'C': "tertiary"})
+    assert core.access('A') == {'_type': 'payload', '_description': desc}
+    assert core.access('B') == {'_type': 'alternate'}
+    assert core.access('C') == {'_type': 'tertiary'}
+
 
 def test_reregister_type(core):
     """
@@ -92,15 +99,15 @@ def test_reregister_type(core):
 
     it replaces the schema if not strict
     """
-    core.register('A', {'_default': 'a'})
+    core.register('R_A', {'_default': 'a'})
     with pytest.raises(Exception) as e:
         core.register(
-            'A', {'_default': 'b'},
+            'R_A', {'_default': 'b'},
             strict=True)
 
-    core.register('A', {'_default': 'b'}, strict=False)
+    core.register('R_A', {'_default': 'b'}, strict=False)
 
-    assert core.access('A')['_default'] == 'b'
+    assert core.access('R_A')['_default'] == 'b'
 
 
 def test_merge_schemas(core):
@@ -161,37 +168,36 @@ def test_apply_update(core):
     assert new_state['depth'] == 39
 
 
-def print_schema_validation(core, library, should_pass):
+def check_validation(core, library, print_log=False):
     """
     validate_schema returns nothing for a valid schema declaration
 
     this helper function makes clearer reports out of the test
     failures
+    """
+    for key, declaration in library.items():
+        errors = core.validate_schema(declaration)
+        assert len(errors) == 0, {'key': key, 'declaration': declaration}
+        if print_log:
+            print(f'PASS: valid schema {key}')
+            pprint.pprint(declaration)
+
 
-    this is also why running the file outside pytest prints out
-    a huge wall of text
+def check_nonvalidation(core, library, print_log=False):
+    """
+    like check_validation but expects one or more errors
     """
     for key, declaration in library.items():
-        report = core.validate_schema(declaration)
-        if len(report) == 0:
-            message = f'valid schema: {key}'
-            if should_pass:
-                print(f'PASS: {message}')
-                pprint.pprint(declaration)
-            else:
-                raise Exception(f'FAIL: {message}\n{declaration}\n{report}')
-        else:
-            message = f'invalid schema: {key}'
-            if not should_pass:
-                print(f'PASS: {message}')
-                pprint.pprint(declaration)
-            else:
-                raise Exception(f'FAIL: {message}\n{declaration}\n{report}')
+        errors = core.validate_schema(declaration)
+        assert len(errors) != 0, {'key': key, 'declaration': declaration}
+        if print_log:
+            print(f'PASS: invalid schema {key}')
+            pprint.pprint(declaration)
 
 
 def test_validate_schema(core):
     # good schemas
-    print_schema_validation(core, base_types, True)
+    check_validation(core, base_types)
 
     good = {
         'not quite int': {
@@ -215,6 +221,7 @@ def test_validate_schema(core):
             }
         }
     }
+    check_validation(core, good)
 
     # bad schemas
     bad = {
@@ -225,11 +232,9 @@ def test_validate_schema(core):
             'right': {'_default': 1, '_apply': accumulate},
         },
     }
-
+    check_nonvalidation(core, bad)
     # test for ports and wires mismatch
 
-    print_schema_validation(core, good, True)
-    print_schema_validation(core, bad, False)
 
 
 def test_fill_integer(core):
@@ -344,14 +349,21 @@ def test_fill_from_parse(core):
                 'O': ['a']}}}
 
 
-# def test_fill_in_disconnected_port(core):
-#     test_schema = {
-#         'edge1': {
-#             '_type': 'edge',
-#             '_ports': {
-#                 '1': {'_type': 'float'}}}}
+def test_fill_in_disconnected_port(core):
+    test_schema = {
+        'edge1': {
+            '_type': 'edge',
+            '_ports': {
+                '1': {'_type': 'float'}}}}
 
-#     test_state = {}
+    test_state = {
+            # TODO - js - how do I represent non connection, rather
+            # than a connection with an empty value?
+            'edge1': {}}
+
+    filled = core.fill(
+            test_schema,
+            test_state)
 
 
 # def test_fill_type_mismatch(core):
@@ -366,6 +378,14 @@ def test_fill_from_parse(core):
 #                 '1': ['..', 'a'],
 #                 '2': ['a']},
 #             'a': 5}}
+#
+#     test_state = {
+#             'edge1': {},
+#             'a': 2}
+#
+#     filled = core.fill(
+#             test_schema,
+#             test_state)
 
 
 # def test_edge_type_mismatch(core):
@@ -749,7 +769,7 @@ def test_project(core):
         '2': 'a0>a0.1',
         '3': 'a0>a0.2>a0.2.0'}
 
-    # TODO: support separate schema/instance, and 
+    # TODO: support separate schema/instance, and
     #   instances with '_type' and type parameter keys
     # TODO: support overriding various type methods
     instance = {
@@ -2140,7 +2160,7 @@ def test_dataclass(core):
 
     complex_dict = asdict(complex_from)
 
-    # assert complex_dict == complex_state ? 
+    # assert complex_dict == complex_state ?
 
     assert complex_from.a['x']['oooo'] is None
     assert len(complex_from.c.d['A']['inputs']['GGG'])
@@ -2350,7 +2370,7 @@ def test_edge_cycle(core):
             assert key in result
 
 
-def test_merge(core):
+def test_merge2(core):
     schema = {
         'A': 'float',
         'B': 'enum[one,two,three]',
@@ -2422,6 +2442,7 @@ def test_update_removed(core):
         'c': 13.33333333}
 
 
+# TODO fix this test
 def fix_test_slice_edge(core):
     initial_schema = {
         'edge': {
@@ -2460,6 +2481,7 @@ def fix_test_slice_edge(core):
     assert inner_state == 55555
 
 
+# TODO fix this test
 def fix_test_complex_wiring(core):
     initial_schema = {
         'edge': {
@@ -2545,6 +2567,7 @@ if __name__ == '__main__':
     core = register_test_types(core)
 
     test_basic_types(core)
+    test_update_types(core)
     test_reregister_type(core)
     test_generate_default(core)
     test_apply_update(core)
@@ -2554,6 +2577,7 @@ if __name__ == '__main__':
     test_establish_path(core)
     test_overwrite_existing(core)
     test_fill_in_missing_nodes(core)
+    test_fill_in_disconnected_port(core)
     test_fill_from_parse(core)
     test_fill_ports(core)
     test_expected_schema(core)
@@ -2561,12 +2585,12 @@ if __name__ == '__main__':
     test_serialize_deserialize(core)
     test_project(core)
     test_inherits_from(core)
+    test_check(core)
     test_apply_schema(core)
     test_resolve_schemas(core)
     test_add_reaction(core)
     test_remove_reaction(core)
     test_replace_reaction(core)
-    test_unit_conversion(core)
     test_map_type(core)
     test_tree_type(core)
     test_maybe_type(core)
@@ -2581,8 +2605,10 @@ if __name__ == '__main__':
     test_foursquare(core)
     test_divide(core)
     test_merge(core)
+    test_merge2(core)
     test_bind(core)
     test_slice(core)
+    test_star_path(core)
     test_set_slice(core)
     test_dataclass(core)
     test_enum_type(core)
@@ -2590,7 +2616,6 @@ if __name__ == '__main__':
     test_representation(core)
     test_generate(core)
     test_edge_cycle(core)
-    test_merge(core)
     test_remove_omitted(core)
     test_union_key_error(core)
     test_tree_equivalence(core)
@@ -2598,5 +2623,9 @@ if __name__ == '__main__':
     test_update_removed(core)
     test_merge_schemas(core)
 
+    # test_reaction(core)
+    # test_link_place(core)
+    # test_unit_conversion(core)
     # test_slice_edge(core)
     # test_complex_wiring(core)
+    # test_fill_type_mismatch(core)

{bigraph-schema-0.0.65 → bigraph_schema-0.0.68}/bigraph_schema/type_system.py

@@ -478,11 +478,11 @@ class TypeSystem(Registry):
 
 
     def _parameters_for(self, initial_schema):
-        '''
+        """
         find any type parameters for this schema if they are present
 
         helper for type_functions
-        '''
+        """
 
         if '_type_parameters' in initial_schema:
             schema = initial_schema
@@ -507,9 +507,9 @@ class TypeSystem(Registry):
 
 
     def default(self, schema):
-        '''
+        """
         produce the default value for the provided schema
-        '''
+        """
 
         default = None
         found = self.retrieve(schema)
@@ -565,10 +565,10 @@ class TypeSystem(Registry):
 
 
     def choose_method(self, schema, state, method_name):
-        '''
+        """
         find in the provided state, or schema if not there,
         a method for the given method_name
-        '''
+        """
 
         method_key = f'_{method_name}'
         found = None
@@ -601,10 +601,10 @@ class TypeSystem(Registry):
 
 
     def slice(self, schema, state, path):
-        '''
+        """
         find the subschema and substate at a node in the place graph
         given by the provided path
-        '''
+        """
 
         if not isinstance(path, (list, tuple)):
             path = [path]
@@ -1077,10 +1077,10 @@ class TypeSystem(Registry):
 
 
     def set_slice(self, schema, state, path, target_schema, target_state, defer=False):
-        '''
+        """
         Makes a local modification to the schema/state at the path, and
         returns the top_schema and top_state
-        '''
+        """
 
         path = resolve_path(path)
 
@@ -1633,11 +1633,11 @@ class TypeSystem(Registry):
                 return method
 
     def representation(self, schema, path=None, parents=None):
-        '''
+        """
         produce a string representation of the schema
 
         * intended to be the inverse of parse_expression()
-        '''
+        """
 
         path = path or []
         parents = parents or []

{bigraph-schema-0.0.65 → bigraph_schema-0.0.68/bigraph_schema.egg-info}/PKG-INFO

@@ -1,24 +1,23 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: bigraph-schema
-Version: 0.0.65
+Version: 0.0.68
 Summary: A serializable type schema for compositional systems biology
-Home-page: https://github.com/vivarium-collective/bigraph-schema
 Author: Eran Agmon, Ryan Spangler
-Author-email: agmon.eran@gmail.com, ryan.spangler@gmail.com
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: AUTHORS.md
+Requires-Dist: fire
+Requires-Dist: numpy
+Requires-Dist: orjson
+Requires-Dist: parsimonious
+Requires-Dist: pint
+Requires-Dist: plum-dispatch
+Requires-Dist: pytest
+Requires-Dist: requests>=2.31.0
+Requires-Dist: setuptools
+Requires-Dist: twine>=4.0.2
+Dynamic: license-file
 
 # Bigraph-schema
 

{bigraph-schema-0.0.65 → bigraph_schema-0.0.68}/bigraph_schema.egg-info/requires.txt

@@ -5,3 +5,6 @@ parsimonious
 pint
 plum-dispatch
 pytest
+requests>=2.31.0
+setuptools
+twine>=4.0.2

{bigraph-schema-0.0.65 → bigraph_schema-0.0.68}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "bigraph-schema"
-version = "0.0.65"
+version = "0.0.68"
 description = "A serializable type schema for compositional systems biology"
 readme = "README.md"
 requires-python = ">=3.7"
@@ -16,6 +16,9 @@ dependencies = [
     "pint",
     "plum-dispatch",
     "pytest",
+    "requests>=2.31.0",
+    "setuptools",
+    "twine>=4.0.2",
 ]
 
 [tool.setuptools]

bigraph_schema-0.0.68/setup.py

@@ -0,0 +1,42 @@
+from setuptools import setup, find_packages
+
+
+VERSION = '0.0.68'
+
+
+with open("README.md", "r") as readme:
+    description = readme.read()
+
+
+setup(
+    name="bigraph-schema",
+    version=VERSION,
+    author="Eran Agmon, Ryan Spangler",
+    # author_email="agmon.eran@gmail.com, ryan.spangler@gmail.com",
+    # description="A serializable type schema for compositional systems biology",
+    # long_description=description,
+    # long_description_content_type="text/markdown",
+    # url="https://github.com/vivarium-collective/bigraph-schema",
+    # packages=find_packages(),
+    # classifiers=[
+    #     "Development Status :: 3 - Alpha",
+    #     "Intended Audience :: Developers",
+    #     "License :: OSI Approved :: MIT License",
+    #     "Operating System :: OS Independent",
+    #     "Programming Language :: Python",
+    #     "Programming Language :: Python :: 3.7",
+    #     "Programming Language :: Python :: 3.8",
+    #     "Programming Language :: Python :: 3.9",
+    #     "Programming Language :: Python :: 3.10",
+    #     "Programming Language :: Python :: 3.11",
+    # ],
+    # python_requires=">=3.7",
+    # install_requires=[
+    #     # List your package dependencies here
+    #     "numpy",
+    #     "parsimonious",
+    #     "fire",
+    #     "pytest",
+    #     "pint",
+    # ],
+)

bigraph-schema-0.0.65/setup.py

@@ -1,42 +0,0 @@
-from setuptools import setup, find_packages
-
-
-VERSION = '0.0.65'
-
-
-with open("README.md", "r") as readme:
-    description = readme.read()
-
-
-setup(
-    name="bigraph-schema",
-    version=VERSION,
-    author="Eran Agmon, Ryan Spangler",
-    author_email="agmon.eran@gmail.com, ryan.spangler@gmail.com",
-    description="A serializable type schema for compositional systems biology",
-    long_description=description,
-    long_description_content_type="text/markdown",
-    url="https://github.com/vivarium-collective/bigraph-schema",
-    packages=find_packages(),
-    classifiers=[
-        "Development Status :: 3 - Alpha",
-        "Intended Audience :: Developers",
-        "License :: OSI Approved :: MIT License",
-        "Operating System :: OS Independent",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-    ],
-    python_requires=">=3.7",
-    install_requires=[
-        # List your package dependencies here
-        "numpy",
-        "parsimonious",
-        "fire",
-        "pytest",
-        "pint",
-    ],
-)