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        "author": "Vladimir Rynkov",
        "author_email": "vrynkov@yahoo.edu",
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            "Development Status :: 2 - Pre-Alpha",
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            "License :: OSI Approved :: BSD License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3.6",
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        "description": "===========================\nNDEx BioGRID Content Loader\n===========================\n\n\n.. image:: https://img.shields.io/pypi/v/ndexbiogridloader.svg\n        :target: https://pypi.python.org/pypi/ndexbiogridloader\n\n.. image:: https://img.shields.io/travis/ndexcontent/ndexbiogridloader.svg\n        :target: https://travis-ci.org/ndexcontent/ndexbiogridloader\n\n.. image:: https://coveralls.io/repos/github/ndexcontent/ndexbiogridloader/badge.svg?branch=master\n        :target: https://coveralls.io/github/ndexcontent/ndexbiogridloader?branch=master\n\n.. image:: https://readthedocs.org/projects/ndexbiogridloader/badge/?version=latest\n        :target: https://ndexbiogridloader.readthedocs.io/en/latest/?badge=latest\n        :alt: Documentation Status\n\n\nPython application for loading BioGRID data into `NDEx <http://ndexbio.org>`_.\n\nThis tool downloads and unpacks the `BioGRID <https://thebiogrid.org/>`_ files below\n\n    `BIOGRID-ORGANISM-4.2.191.tab2.zip <https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.187/BIOGRID-ORGANISM-3.5.87.tab2.zip>`_\n\n    `BIOGRID-CHEMICALS-4.2.191.chemtab.zip <https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.187/BIOGRID-CHEMICALS-3.5.187.chemtab.zip>`_\n\n**NOTE:** ``ndexloadbiogrid.py`` script ``--biogridversion`` parameter dictates version (``4.2.191`` above)\n\n\n\n\n\nDependencies\n------------\n\n* `ndex2 <https://pypi.org/project/ndex2>`_\n* `ndexutil <https://pypi.org/project/ndexutil>`_\n* `requests <https://pypi.org/project/requests>`_\n* `pandas <https://pypi.org/project/pandas>`_\n* `networkx <https://pypi.org/project/networkx>`_\n* `scipy <https://pypi.org/project/scipy>`_\n* `tqdm <https://pypi.org/project/tqdm>`_\n* `py4cytoscape <https://pypi.org/project/py4cytoscape>`_\n\nCompatibility\n-------------\n\n* Python 3.6+\n\nInstallation\n------------\n\nFrom PyPi:\n\n.. code-block::\n\n   pip install ndexbiogridloader\n\nBuild from source:\n\n.. code-block::\n\n   git clone https://github.com/ndexcontent/ndexbiogridloader\n   cd ndexbiogridloader\n   make dist\n   pip install dist/ndexloadbiogrid*whl\n\n\nRun **make** command with no arguments to see other build/deploy options including creation of Docker image\n\n.. code-block::\n\n   make\n\nOutput:\n\n.. code-block::\n\n   clean                remove all build, test, coverage and Python artifacts\n   clean-build          remove build artifacts\n   clean-pyc            remove Python file artifacts\n   clean-test           remove test and coverage artifacts\n   lint                 check style with flake8\n   test                 run tests quickly with the default Python\n   test-all             run tests on every Python version with tox\n   coverage             check code coverage quickly with the default Python\n   docs                 generate Sphinx HTML documentation, including API docs\n   servedocs            compile the docs watching for changes\n   testrelease          package and upload a TEST release\n   release              package and upload a release\n   dist                 builds source and wheel package\n   install              install the package to the active Python's site-packages\n   dockerbuild          build docker image and store in local repository\n   dockerpush           push image to dockerhub\n\n\nConfiguration\n-------------\n\nThe **ndexloadbiogrid.py** requires a configuration file in the following format be created.\nThe default path for this configuration is :code:`~/.ndexutils.conf` but can be overridden with\n:code:`--conf` flag.\n\n**Format of configuration file:**\n\n.. code-block::\n\n    [<value in --profile (default ndexbiogridloader)>]\n\n    user = <NDEx username>\n    password = <NDEx password>\n    server = <NDEx server(omit http) ie public.ndexbio.org>\n\n**Example of default configuration file:**\n\n.. code-block::\n\n    [ndexbiogridloader]\n    user = joe123\n    password = somepassword123\n    server = dev.ndexbio.org\n\n\n\nUsage\n-----\n\nFor information invoke :code:`ndexloadbiogrid.py -h`\n\nThe command shown below will download the default version of BioGRID files (4.2.191) to the working\ndirectory :code:`biogrid_data`, will generate CX networks in this directory, and then upload these networks\nto default account specified in :code:`[ndexbiogridloader]` section of default configuration file:\n\n.. code-block::\n\n   ndexloadbiogrid.py biogrid_data\n\n\n.. note::\n\n   By default Cytoscape must be running to generate the layout for each network. See ``--layout`` flag\n   options to generate networks without Cytoscape.\n\n\nCredits\n-------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n\n\n\n=======\nHistory\n=======\n\n1.0.0 (11-09-2020)\n------------------\n\n* New default behavior: **force-directed-cl** layout is now applied on\n  networks via py4cytoscape library and a running instance of Cytoscape.\n  Alternate Cytoscape layouts and the networkx \"spring\" layout can be\n  run by setting appropriate value via the new **--layout** flag\n\n0.3.0 (10-27-2020)\n------------------\n\n* Updated default ``--biogridversion`` version to ``4.2.191``\n\n* All generated networks get networkx spring layout added by default\n\n* Added tqdm progress bar support. Set ``--noprogressbar`` flag to disable\n\n* Added --skipupload flag to skip the upload to NDEx step\n\n* Added logic to retry failed upload of network to NDEx.\n  ``--maxretries`` and ``--retry_sleep`` allow caller to control\n  behavior\n\n* Added ``--organismfile`` and ``--chemicalsfile`` to let caller override\n  defaults\n\n0.2.0 (2020-07-27)\n------------------\n\n* Updated default ``--biogridversion`` version to ``3.5.187``\n\n* Modified organism_list file to include 3 strains of\n  coronavirus (SARS-1, SARS-2 and MERS)\n\n* Modified organism_style file to add an orange border\n  to all viral protein nodes. 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