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"description": "**Using this repository (tvb-library) from github is now considered DEPRECATED.\nWe advise you to use our main tvb-root repository instead**\n\nTHE VIRTUAL BRAIN SCIENTIFIC LIBRARY\n====================================\n\nThe Virtual Brain Project (TVB Project) has the purpose of offering some\nmodern tools to the Neurosciences community, for computing, simulating\nand analyzing functional and structural data of human brains.\n\n\"TVB Scientific Library\" is the most important scientific contribution\nof TVB Project, but only a part of our code. In order to use this TVB\nPython Library (modify/run/test), you are advised to follow the steps\ndescribed here:\nhttp://docs.thevirtualbrain.com/manuals/ContributorsManual/ContributorsManual.html#contributors-manual\n\nThe interaction with TVB source code is recommended for advanced users\nonly, for which the concepts proposed by TVB are known and understood,\nand which also have some programming knowledge.\n\n\"TVB Scientific Library\" comes in two major forms for code-contributors:\nas a light-weight Python library, or plugged into TVB framework\n(including Web interface and Persistence of data layers). Depending on\nyour needs and resources, you could use any of the two available options\nfor contributing and testing new code.\n\n\"TVB Scientific Library\" is a light-weight, stand-alone Python library\nthat contains all the needed packages in order to run simulations and\nanalysis on data without the need for the entire TVB Framework. This\nimplies that no storage will be provided so data from each session will\nbe lost on close. You need to either persist it yourself in some manner\nor use the full TVBFramework where HDF5 / database storage is provided\nas default.\n\nFor more details, check: http://www.thevirtualbrain.org/\n\n\"TVB Scientific Library\" contains the following packages: basic,\ndatatypes, simulator and analyzers. The dependencies between these\npackages can be seen in tvb-package-diagram.jpg . Following is a short\ndescription of each of these packages:\n\n- tvb.basic\n\nThis package is the base of TVB and holds sub-packages that are used by\nmost of the other packages like logging, global settings and the TVB\ntraits package. You should rarely (if at all) need to change code in\nthis package, and should know exactly what you are doing before\nattempting to change anything from here.\n\n- tvb.datatypes\n\nThe simulator and analyzers packages (as well as uploaders and\nvisualizers in TVB Framework) will need to have a common \"language\" in\norder to work with the same data. In TVB architecture, that \"common\nlanguage\" is represented by Data Types. TVB Data Types declarations are\nlocated in this package.\n\n- tvb.simulator\n\nThe Simulation Component is the most important component in The Virtual\nBrain solution, as it is the component responsible for all the\nscientific computation related to brain models and data.\n\nYou can find various demos of using the simulator here:\nhttp://docs.thevirtualbrain.org/demos/Demos.html .\n\n- tvb.analyzers\n\nHolds modules that can run various analysis of data resulted from the\nsimulator. TVB is not strong in\ndoing data analysis, we barely have a minimum set of analyzers for\nimmediate needs.\n\nNOTE:\n\nTo contribute to this repo, you are advised to first fork it under\nGitHub (through the web ui), and next clone that fork on your machine,\nand use it as you use any other git repository.\n\nTesting\n=======\n\nFor testing the package, the `Pytest `_\nframework is used. Pytest can be installed using pip.\n\nPytest will run all files in the current directory and its subdirectories\nof the form test_*.py or \\*_test.py.\nMore generally, it follows `standard test discovery rules\n`_\n\nThe command for running our tests has two forms.\nRecommendation when working with a git clone of tvb-library::\n\n cd [folder_where_tvb_library_is]\n pytest tvb/test [--junitxml=path]\n\nThe second alternative form of running TVB tests, when installing TVB from Pypi, is::\n\n pip install -U tvb-library\n pytest --pyargs tvb.tests.library\n\n\nCoverage\n--------\n\nA coverage report can be generated with::\n\n pip install pytest-cov\n cd [folder_where_tvb_library_is]\n py.test --cov-config .coveragerc --cov=tvb tvb/tests/ --cov-branch --cov-report xml:[file_where_xml_will_be_generated]\n\n\nFurther Resources\n=================\n\n- For issue tracking we are using Jira: http://req.thevirtualbrain.org\n- For API documentation and live demos, have a look here:\n http://docs.thevirtualbrain.org\n- A public mailing list for users of The Virtual Brain can be joined\n and followed using: tvb-users@googlegroups.com\n- Raw demo IPython Notebooks can be found under:\n https://github.com/the-virtual-brain/tvb-documentation/tree/master/demos\n\n\n",
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