bigraph-schema 0.0.29__tar.gz → 0.0.31__tar.gz

{bigraph-schema-0.0.29/bigraph_schema.egg-info → bigraph-schema-0.0.31}/PKG-INFO

@@ -1,25 +1,21 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.29
+Version: 0.0.31
 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
-License: UNKNOWN
-Platform: UNKNOWN
 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
-Classifier: Programming Language :: Python :: 3.6
 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: >=3.6
+Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: AUTHORS.md
@@ -49,12 +45,10 @@ pip install bigraph-schema
 
 To get started with bigraph-schema, check out our resources:
 
-* [Demo notebook](https://vivarium-collective.github.io/bigraph-schema/notebooks/demo.html): An interactive Jupyter notebook providing a hands-on demonstration of the functionality of bigraph-schema.
-* [Bigraph Schema Basics Tutorial](https://vivarium-collective.github.io/bigraph-viz/notebooks/basics.html): A comprehensive tutorial covering the essential aspects of the bigraph-schema library. 
+* [Type System Overview](https://vivarium-collective.github.io/bigraph-schema/notebooks/core.html): A tutorial demonstrating the functionality of bigraph-schema's type system, "core".
+* [Bigraph Schema Basics Tutorial](https://vivarium-collective.github.io/bigraph-viz/notebooks/basics.html): A  tutorial covering the essential aspects of the bigraph-schema library. 
 This resource will guide you through the core concepts and methods, helping you to master the basic operations.
 
 ## License
 
 Bigraph-schema is open-source software released under the [Apache 2 License](https://github.com/vivarium-collective/bigraph-schema/blob/main/LICENSE).
-
-

{bigraph-schema-0.0.29 → bigraph-schema-0.0.31}/README.md

@@ -23,8 +23,8 @@ pip install bigraph-schema
 
 To get started with bigraph-schema, check out our resources:
 
-* [Demo notebook](https://vivarium-collective.github.io/bigraph-schema/notebooks/demo.html): An interactive Jupyter notebook providing a hands-on demonstration of the functionality of bigraph-schema.
-* [Bigraph Schema Basics Tutorial](https://vivarium-collective.github.io/bigraph-viz/notebooks/basics.html): A comprehensive tutorial covering the essential aspects of the bigraph-schema library. 
+* [Type System Overview](https://vivarium-collective.github.io/bigraph-schema/notebooks/core.html): A tutorial demonstrating the functionality of bigraph-schema's type system, "core".
+* [Bigraph Schema Basics Tutorial](https://vivarium-collective.github.io/bigraph-viz/notebooks/basics.html): A  tutorial covering the essential aspects of the bigraph-schema library. 
 This resource will guide you through the core concepts and methods, helping you to master the basic operations.
 
 ## License

{bigraph-schema-0.0.29 → bigraph-schema-0.0.31}/bigraph_schema/__init__.py

@@ -1,2 +1,2 @@
 from bigraph_schema.type_system import TypeSystem, Edge
-from bigraph_schema.registry import get_path, establish_path, set_path, deep_merge
+from bigraph_schema.registry import get_path, establish_path, set_path, transform_path, deep_merge, validate_merge

{bigraph-schema-0.0.29 → bigraph-schema-0.0.31}/bigraph_schema/protocols.py

@@ -1,7 +1,9 @@
 """
-===============================================
-Protocols for retrieving processes from address
-===============================================
+=========
+Protocols
+=========
+
+This module contains the protocols for retrieving processes from address.
 """
 
 import sys
@@ -10,6 +12,9 @@ import importlib
 
 
 def function_module(function):
+    """
+    Retrieves the fully qualified name of a given function.
+    """
     module = inspect.getmodule(function)
 
     return f'{module.__name__}.{function.__name__}'

bigraph-schema-0.0.31/bigraph_schema/react.py

@@ -0,0 +1,50 @@
+"""
+=====
+React
+=====
+"""
+
+
+def react_divide_counts(config):
+    """
+    Divides counts among daughters based on their ratios in a reaction configuration.
+
+    This function constructs a reaction configuration to divide counts among daughter entities based on specified
+    ratios. If no ratio is specified for a daughter, the counts are divided evenly. The configuration includes the
+    setup for input ('redex'), output ('reactum'), and the division operation ('calls').
+
+    Args:
+    - config (dict): Configuration dict with keys 'id' (string), 'state_key' (string), 'daughters' (list of dicts).
+        Each daughter dict may include 'id' (string) and optionally 'ratio' (float).
+
+    Returns:
+    - dict: A dictionary with keys 'redex', 'reactum', and 'calls', detailing the reaction setup.
+    """
+
+    redex = {
+        config['id']: {
+            config['state_key']: '@counts'}}
+
+    bindings = [
+        f'{daughter["id"]}_counts'
+        for daughter in config['daughters']]
+
+    reactum = {
+        daughter['id']: {
+            config['state_key']: binding}
+        for binding, daughter in zip(bindings, config['daughters'])}
+
+    even = 1.0 / len(config['daughters'])
+    ratios = [
+        daughter.get('ratio', even)
+        for daughter in config['daughters']]
+
+    calls = [{
+        'function': 'divide_counts',
+        'arguments': ['@counts', ratios],
+        'bindings': bindings}]
+
+    return {
+        'redex': redex,
+        'reactum': reactum,
+        'calls': calls}