Metadata-Version: 1.0
Name: brainiak
Version: 0.3.2
Summary: Brain Imaging Analysis Kit
Home-page: https://github.com/IntelPNI/brainiak
Author: Princeton Neuroscience Institute and Intel Corporation
Author-email: bryn.keller@intel.com
License: Apache 2
Description: Brain Imaging Analysis Kit
        ==========================
        
        .. image:: https://travis-ci.org/IntelPNI/brainiak.svg?branch=master
            :target: https://travis-ci.org/IntelPNI/brainiak
        
        .. image:: https://badges.gitter.im/IntelPNI/brainiak.svg
           :alt: Join the chat at https://gitter.im/IntelPNI/brainiak
           :target: https://gitter.im/IntelPNI/brainiak?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
        
        The Brain Imaging Analysis Kit is a package of Python modules useful for
        neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI)
        analysis.
        
        The package was originally created by a collaboration between Intel and the
        Princeton Neuroscience Institute (PNI).
        
        To reduce verbosity, we may refer to the Brain Imaging Analysis Kit using the
        ``BrainIAK`` abbreviation. Whenever lowercase spelling is used (e.g., Python
        package name), we use ``brainiak``.
        
        
        Requirements
        ============
        
        We support Linux and MacOS with Python version 3.4 or higher. Most of the
        dependencies will be installed automatically. However, a few need to be
        installed manually.
        
        
        Linux
        -----
        
        Install the following packages (Ubuntu 14.04 is used in these instructions)::
        
            apt install build-essential cmake libgomp1 mpich python3-dev python3-pip
        
        Install updated version of the following Python packages::
        
            pip3 install --user -U pip virtualenv
        
        Note the ``--user`` flag, which instructs Pip to not overwrite system
        files. You must add ``$HOME/.local/bin`` to your ``$PATH`` to be able to run
        the updated Pip, e.g., by adding the following line to ``$HOME/.profile``
        and launching a new login shell (e.g., logout or execute ``bash -l``)::
        
            PATH="$HOME/.local/bin:$PATH"
        
        
        MacOS
        -----
        
        Install the Xcode Command Line Tools::
        
            xcode-select --install
        
        Install ``brew`` from https://brew.sh. If you already have ``brew``, examine
        the output of the following command to make sure it is working::
        
            brew doctor
        
        Then install the following::
        
            brew install llvm cmake mpich python3
        
        You must instruct programs to use this ``clang`` version at ``/usr/local/opt/llvm/bin``.
        One way to do this, which
        works for most programs, is setting the ``CC`` environment variable. You can
        add the following lines to ``$HOME/.profile`` (or ``$HOME/.bash_profile``, if
        you have one). For them to take effect, you must logout or launch a new login
        shell, e.g., ``bash -l``::
        
            export CC=/usr/local/opt/llvm/bin/clang
            export CXX=/usr/local/opt/llvm/bin/clang++
        
        In addition, you also need to specify the directories that the newly installed `clang`
        will seek for compiling and linking::
        
            export LDFLAGS="-L/usr/local/opt/llvm/lib $LDFLAGS"
            export CPPFLAGS="-I/usr/local/opt/llvm/include $CPPFLAGS"
        
        Install updated versions of the following Python packages::
        
            pip3 install -U pip virtualenv
        
        
        Installing
        ==========
        
        The Brain Imaging Analysis Kit is available on PyPI::
        
            pip3 install -U brainiak
        
        Note that you may see a ``Failed building wheel for brainiak`` message (`issue
        #61`_). Installation will proceed despite this failure. You can safely ignore it
        as long as you see ``Successfully installed`` at the end.
        
        .. _issue #61:
           https://github.com/IntelPNI/brainiak/issues/61
        
        Documentation
        =============
        
        The documentation is available at `pythonhosted.org/brainiak`_.
        
        .. _pythonhosted.org/brainiak:
            https://pythonhosted.org/brainiak
        
        
        Contributing
        ============
        
        We welcome contributions. Please read the guide in `CONTRIBUTING.rst`_.
        
        .. _CONTRIBUTING.rst:
           https://github.com/IntelPNI/brainiak/blob/master/CONTRIBUTING.rst
        
Keywords: neuroscience,algorithm,fMRI,distributed,scalable
Platform: UNKNOWN
