Using this repository (tvb-framework) from github is now considered DEPRECATED. We advise you to use our main tvb-root repository instead

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-library>__ repo.

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-documentation/tree/master/demos