py4cytoscape 0.0.5

Cytoscape Automation API

py4cytoscape

This project recreates the R-based RCy3 Cytoscape Automation library 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) 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. The official Automation API definition met by both RCy3 and py4cytoscape is here. The API is versioned, and you can see which API version RCy3 or py4cytoscape implements by executing the cytoscape_version_info() or cytoscapeVersionInfo() function.

An overall scorecard comparing Py2Cytoscape, RCy3 and py4cytoscape can be found here. 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.

How to install and test

For an explanation of py4cytoscape installation and testing, see the 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 file.

License

py4cytoscape is released under the MIT License (see LICENSE.rst file):

    Copyright (c) 2018-2020 The Cytoscape Consortium
    Barry Demchak <[e-mail]>