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A package for performing whole brain simulations

Project 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.

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 repo.

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 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

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

Project details


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