Metadata-Version: 2.1
Name: py4cytoscape
Version: 0.0.3
Summary: Cytoscape Automation API
Home-page: https://github.com/bdemchak/py4cytoscape
Author: Barry Demchak
Author-email: bdemchak@ucsd.edu
Maintainer: Barry Demchak
Maintainer-email: bdemchak@ucsd.edu
License: MIT License
Description: # py4cytoscape
        
        This project recreates the [R-based ``RCy3`` Cytoscape Automation library](https://github.com/cytoscape/RCy3) as a Python package. The idea is to allow a Cytoscape workflow to be written in one language (R or Python) and translated to another language (Python or R) without having to learn different Cytoscape interfaces. The previous Cytoscape Python interface ([Py2Cytoscape](https://github.com/cytoscape/py2cytoscape)) has different features than the Cytoscape R library, and is therefore deprecated.
        
        Additionally, this project attempts to maintain the same function signatures, return values, function implementation and module structure as the RCy3, thereby enabling smooth maintenance and evolution of both ``RCy3`` and ``py4cytoscape``.
        
        This project uses PyCharm because of its excellent code management and debugging features.
        
        Over time, py4cytoscape functionality should match RCy3 functionality. Once that occurs, novel Py2Cytoscape functions will be added to both as appropriate.
        
        An overall scorecard comparing Py2Cytoscape, ``RCy3`` and ``py4cytoscape`` can be found [here](https://docs.google.com/spreadsheets/d/1uhBTbOMI4QMKUpLaOTuf6BP5wgqU6-pOzkj6BNmC4CY/edit?usp=sharing). Pay close attention to columns E and F, which show how much of RCy3 is reflected in py4cytoscape.
        
        # Documentation
        
        To understand the API structure and see calling examples, see the ``py4cytoscape`` [documentation](https://py4cytoscape.readthedocs.io/en/latest/).
         
        ## How to install and test
        
        For an explanation of ``py4cytoscape`` installation and testing, see the [INSTALL.rst](INSTALL.rst) file.
        
        ## How run a simple workflow
        
        For a quick tutorial on how to build a workflow in Python and using ``py4cytoscape``, see
        https://py4cytoscape.readthedocs.io/en/latest/tutorials/index.html.
        You can try ``py4cytoscape`` with a web browser only, without installing anything in your local environment.
        
        ## How to configure logging
        
        ``py4cytoscape`` logging is based on the Python ``logging`` package, which is based on the Java ``logging`` framework. 
        
        For an explanation of log configuration and use, see the [LOGGING.rst](LOGGING.rst) file.
        
        ## License
        
        ``py4cytoscape`` is released under the MIT License (see [LICENSE.rst](LICENSE.rst) file):
        
        ```
            Copyright (c) 2018-2020 The Cytoscape Consortium
            Barry Demchak <bdemchak@ucsd.edu>
        ```
        
Keywords: data visualization,visualization,cytoscape,bioinformatics,graph,network
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.6
Description-Content-Type: text/markdown
