Metadata-Version: 1.1
Name: cdapsutil
Version: 0.2.0
Summary: Python utilities for CDAPS
Home-page: https://github.com/idekerlab/cdapsutil
Author: Christopher Churas
Author-email: churas.camera@gmail.com
License: BSD license
Description: ===============================
        CDAPS Python Utilities
        ===============================
        
        .. image:: https://img.shields.io/pypi/v/cdapsutil.svg
                :target: https://pypi.python.org/pypi/cdapsutil
        
        .. image:: https://travis-ci.com/idekerlab/cdapsutil.svg?branch=master
            :target: https://travis-ci.com/idekerlab/cdapsutil
        
        .. image:: https://coveralls.io/repos/github/idekerlab/cdapsutil/badge.svg?branch=master
            :target: https://coveralls.io/github/idekerlab/cdapsutil?branch=master
        
        .. image:: https://readthedocs.org/projects/cdapsutil/badge/?version=latest
                :target: https://cdapsutil.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        
        Library that enables invocation of `Community Detection APplication and Service <https://cdaps.readthedocs.io/>`_
        algorithms via Python
        
        
        .. warning::
        
            cdapsutil is experimental and may contain errors and interfaces may change
        
        Dependencies
        -------------
        
        * `ndex2 <https://pypi.org/project/ndex2>`_
        * `requests <https://pypi.org/project/requests>`_
        * `tqdm <https://pypi.org/project/tqdm>`_
        
        Compatibility
        ---------------
        
        * Python 3.4+
        
        Installation
        ---------------
        
        .. code-block:: console
        
            pip install cdapsutil
        
        or directly via:
        
        .. code-block::
        
            git clone https://github.com/idekerlab/cdapsutil
            cd cdapsutil
            python setup.py install
        
        Usage
        -------
        
        Run Community Detection
        
        .. code-block::
        
            import json
            import cdapsutil
            import ndex2
        
        
            # Download BioGRID: Protein-Protein Interactions (SARS-CoV) from NDEx
            client = ndex2.client.Ndex2()
            client_resp = client.get_network_as_cx_stream('669f30a3-cee6-11ea-aaef-0ac135e8bacf')
            net_cx = ndex2.create_nice_cx_from_raw_cx(json.loads(client_resp.content))
        
            # Create CommunityDetection object
            cd = cdapsutil.CommunityDetection()
        
            # Run HiDeF on CDAPS REST service
            hier_net = cd.run_community_detection(net_cx, algorithm='hidef')
        
        
        Run Functional Enrichment
        
        Coming soon...
        
        Cite CDAPS
        -----------
        
        If you find this utility and service useful, please cite:
        
        Singhal A, Cao S, Churas C, Pratt D, Fortunato S, Zheng F, et al. (2020) Multiscale community detection in Cytoscape. PLoS Comput Biol 16(10): e1008239. https://doi.org/10.1371/journal.pcbi.1008239
        
        
        Credits
        ---------
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        
        
        =======
        History
        =======
        
        0.2.0 (2022-10-04)
        ----------------------
        
        * Fixed bug where not setting a name on a network
          would cause ``CommunityDetection.run_community_detection()``
          to raise a ``TypeError``. When encountered code now sets network
          name to **unknown** `Issue #1 <https://github.com/idekerlab/cdapsutil/issues/1>`__
        
        0.2.0a1 (2021-03-30)
        ----------------------
        
        * First release on PyPI.
        
Keywords: cdapsutil
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
