tvb-framework 2.9

A package for performing whole brain simulations

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.

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.

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 folder.

Framework structure

tvb-gdist
    |
    |
tvb-library     tvb-data
      \          /
        \       /
        tvb.config
            |
            |
        tvb.core
            |
            |
        tvb.adapters
            |
            |
        tvb.config.init
            |
            |
        tvb.interfaces

tvb-data should be installed from Zenodo: https://zenodo.org/record/10128131. After download, unzip and execute python setup.py develop in the correct env.

Usage

To use TVB code, clone from GitHub (https://github.com/the-virtual-brain/tvb-root), 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.

Testing

For testing the package, the Pytest framework is used. Pytest can be installed using pip.

In addition to tvb-framework needed just for launching the web, tests require few extra dependencies just for test (e.g. pytest-benchmark), which need to be installed manually. The entire list of these dependencies for testing is found in tvb_framework/setup.py under extras_require.

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

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: [e-mail]

• Raw demo IPython Notebooks can be found under: https://github.com/the-virtual-brain/tvb-root/tree/master/tvb_documentation/demos

Acknowledgments

This project has received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement Nos. 785907 (Human Brain Project SGA2), 945539 (Human Brain Project SGA3) and VirtualBrainCloud 826421.