Metadata-Version: 2.1
Name: tvb-framework
Version: 2.1
Summary: A package for performing whole brain simulations
Home-page: http://www.thevirtualbrain.org
Author: Mihai Andrei, Lia Domide, Stuart Knock, Bogdan Neacsa, Paula Popa, Paula Sansz Leon, Marmaduke Woodman
Author-email: tvb.admin@thevirtualbrain.org
License: GPL-3.0-or-later
Download-URL: https://github.com/the-virtual-brain/tvb-framework
Description: TVB FRAMEWORK
        =============
        
        The Virtual Brain framework is a complete framework including:
        
        -  a plugable workflow manager;
        -  a data persistence layer (with a relational DB and File Storage);
        -  an HTML5 based user interface;
        -  visualizers for neuro-science related entities.
        
        The easiest way to make use of this code, is to obtain
        a Distribution of TVB with Python and all the necessary packages linked,
        and then clone this repo nearby. More details `in our
        documentation <http://docs.thevirtualbrain.org/manuals/ContributorsManual/ContributorsManual.html>`__.
        
        Alternatively, if you plan to develop long term with TVB, extensively
        modify code, add new dependencies, or you simply prefer to use your own
        Python installation, you may want to read this:
        `here <http://docs.thevirtualbrain.org/manuals/ContributorsManual/ContributorsManual.html#the-unaided-setup>`__.
        
        If you don't require the framework features listed above, the simulator
        and associated scientific modules can be used independently; please see
        the `tvb-library <https://github.com/the-virtual-brain/tvb-root/tree/master/scientific_library>`__
        folder.
        
        Framework structure
        -------------------
        
        ::
        
            tvb-gdist
                |
                |
            tvb-library     tvb-data
                  \          /
                    \       /
                    tvb.config
                        |
                        |
                    tvb.core
                        |
                        |
                    tvb.adapters
                        |
                        |
                    tvb.config.init
                        |
                        |
                    tvb.interfaces
        
        Usage
        -----
        
        To use TVB code, clone from GitHub (https://github.com/the-virtual-brain/tvb-framework), or get from Pypi::
        
            pip install tvb-framework
            python -m tvb.interfaces.web.run WEB_PROFILE tvb.config
        
        
        Your port **8080** should be free, as a CherryPy service will try to run there.
        Your default browser should automatically open http://localhost:8080/ which is the way to
        interact with TVB Web Interface.
        
        When using from sources (pypi or Github, not TVB_Distribution), if you want BCT adapters enabled, you should
        manually download BCT https://sites.google.com/site/bctnet/
        and set env variable **BCT_PATH** towards the directory where you unzip BCT, plus also have Octave or
        Matlab installed with command line API enabled.
        
        
        Testing
        =======
        
        For testing the package, the `Pytest  <https://docs.pytest.org/>`_
        framework is used. Pytest can be installed using pip.
        
        Pytest will run all files in the current directory and its subdirectories
        of the form test_*.py or \*_test.py.
        More generally, it follows `standard test discovery rules
        <https://docs.pytest.org/en/latest/getting-started.html>`_
        
        The command for running our tests has two forms.
        Recommendation when working with a git clone of tvb-framework::
        
            cd [folder_where_tvb_framework_is]
            pytest tvb/test/framework [--profile=TEST_POSTGRES_PROFILE] [--junitxml=path]
            # default profile value is TEST_SQLITE_PROFILE
        
        The second alternative form of running TVB tests, when installing TVB from Pypi, is::
        
            pip install -U tvb-framework
            pytest --pyargs tvb.tests.framework
        
        
        Coverage
        ========
        
        A coverage report can be generated with::
        
            pip install pytest-cov
            cd [folder_where_tvb_framework_is]
            py.test --cov=tvb tvb/tests/ --cov-branch --cov-report xml:[file_where_xml_will_be_generated]
        
        
        Further Resources
        =================
        
        -  For issue tracking we are using Jira: http://req.thevirtualbrain.org
        -  For API documentation and live demos, have a look here:
           http://docs.thevirtualbrain.org
        -  A public mailing list for users of The Virtual Brain can be joined
           and followed using: tvb-users@googlegroups.com
        -  Raw demo IPython Notebooks can be found under:
           https://github.com/the-virtual-brain/tvb-root/tree/master/tvb_documentation/demos
        
Keywords: tvb brain simulator neuroscience human animal neuronal dynamics models delay
Platform: UNKNOWN
Provides-Extra: postgres
Provides-Extra: hpc
Provides-Extra: test
