Metadata-Version: 2.1
Name: bigraph-viz
Version: 0.0.17
Summary: A graphviz-based plotting tool for compositional bigraph schema
Home-page: https://github.com/vivarium-collective/bigraph-viz
Author: Eran Agmon
Author-email: agmon.eran@gmail.com
License: UNKNOWN
Description: # Bigraph-viz
        
        [![PyPI](https://img.shields.io/pypi/v/bigraph-viz.svg)](https://pypi.org/project/bigraph-viz/)
        [![GitHub Pages](https://img.shields.io/badge/GitHub%20Pages-Tutorial-brightgreen)](https://vivarium-collective.github.io/bigraph-viz/notebooks/basics.html)
        
        **Bigraph-viz** is an easy-to-use plotting tool for compositional bigraph schema, built on top of Graphviz. 
        
        <p align="center">
            <img src="https://github.com/vivarium-collective/bigraph-viz/blob/main/doc/_static/nested_composite.png?raw=true" width="600" alt="Bigraph-viz example">
        </p>
        
        ## Compositional Schemas and Milner Bigraphs
        
        Compositional Bigraph Schemas (CIP) are based on a mathematical formalism introduced by 
        <a href="https://www.google.com/search?q=the+space+and+motion+of+communicating+agents+by+robin+milner" target="_blank">Robin Milner in 2009</a>
        , and used in Vivarium. 
        Bigraphs consist of networks with embeddable nodes that can be placed *within* other nodes and dynamically restructured.
        CIP reimagines the bigraph concept. Variables are contained within Stores (the circles in the figure), which can be embedded
        in a hierarchy, as shown by the dark edges. Instead of Milner's hyperedges, CIP employs Processes (the rectangles) which 
        connect via wires (dashed edges) to shared variables within the Stores. Processes and Stores form a type of bipartite graph, 
        as illustrated by the dashed edges.
        
        In Vivarium, the CIP is used to structure a modular multiscale simulation. Bigraph-viz is part of an effort to
        standardize this structure, so that it can be used as an exchange format for multiscale simulations.
        
        ## Getting Started
        
        
        ### Dependencies
        
        Before installing `bigraph-viz`, make sure you have [Graphviz](https://pypi.org/project/graphviz/).
        
        #### Ubuntu/Debian
        
        ```console
        sudo apt-get install -y graphviz
        ```
        #### macOS
        
        ```console
        brew install graphviz
        ```
        
        #### Windows
        Download and install the Graphviz installer from the [official website](https://graphviz.org/download/). 
        Make sure to add the Graphviz bin directory to your system's PATH.
        
        ### Installation
        
        Once Graphviz is installed, you can install `bigraph-viz` using pip:
        
        ```console
        pip install bigraph-viz
        ```
        
        ## Tutorial
        
        To get started with Bigraph-viz, explore the [Bigraph Schema Basics](https://vivarium-collective.github.io/bigraph-viz/notebooks/basics.html) tutorial.
        
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
Requires-Python: >=3.6
Description-Content-Type: text/markdown
