Metadata-Version: 1.2
Name: brainiak
Version: 0.6
Summary: Brain Imaging Analysis Kit
Home-page: http://brainiak.org
Author: Princeton Neuroscience Institute and Intel Corporation
Author-email: mihai.capota@intel.com
License: Apache 2
Description-Content-Type: UNKNOWN
Description: Brain Imaging Analysis Kit
        ==========================
        
        .. image:: https://travis-ci.org/brainiak/brainiak.svg?branch=master
            :target: https://travis-ci.org/brainiak/brainiak
        
        .. image:: https://badges.gitter.im/brainiak/brainiak.svg
           :alt: Join the chat at https://gitter.im/brainiak/brainiak
           :target: https://gitter.im/brainiak/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 16.04 is used in these instructions)::
        
            apt install build-essential libgomp1 libmpich-dev mpich python3-dev \
                python3-pip python3-venv
        
        Install updated version of the following Python packages::
        
            python3 -m pip install --user -U pip
        
        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 "\
            "-Wl,-rpath,/usr/local/opt/llvm/lib $LDFLAGS"
            export CPPFLAGS="-I/usr/local/opt/llvm/include $CPPFLAGS"
        
        Install updated versions of the following Python packages::
        
            python3 -m pip install -U pip
        
        
        Installing and upgrading
        ========================
        
        The Brain Imaging Analysis Kit is available on PyPI. You can install it (or
        upgrade to the latest version) using the following command::
        
            python3 -m pip 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/brainiak/brainiak/issues/61
        
        Until we reach version 1.0, we will only support the latest released version.
        Therefore, if you have a problem with an older version, please upgrade to the
        latest version before creating an issue on GitHub.
        
        
        Docker
        ======
        
        You can also test BrainIAK without installing it using Docker::
        
            docker pull brainiak/brainiak
            docker run -it -p 8888:8888 -v brainiak:/mnt --name demo brainiak/brainiak
        
        To run Jupyter notebooks in the running container, try::
        
            python3 -m notebook --allow-root --no-browser --ip=0.0.0.0
        
        Then visit http://localhost:8888 in your browser and enter the token. Protip:
        run ``screen`` before running the notebook command.
        
        Note that we do not support MPI execution using Docker containers and that performance will not be optimal.
        
        
        Support
        =======
        
        If you have a question or feedback, chat with us on `Gitter
        <https://gitter.im/brainiak/brainiak>`_ or email our list at
        brainiak@googlegroups.com. If you find a problem with BrainIAK, you can also
        `open an issue on GitHub <https://github.com/brainiak/brainiak/issues>`_.
        
        
        Examples
        ========
        
        We include BrainIAK usage examples in the examples directory of the code
        repository, e.g., `funcalign/srm_image_prediction_example.ipynb
        <https://github.com/brainiak/brainiak/blob/master/examples/funcalign/srm_image_prediction_example.ipynb>`_.
        
        To run the examples, download an archive of the `latest BrainIAK release from
        GitHub <https://github.com/brainiak/brainiak/releases>`_. Note that we only
        support the latest release at this moment, so make sure to upgrade your
        BrainIAK installation.
        
        
        Documentation
        =============
        
        The documentation is available at `pythonhosted.org/brainiak`_.
        
        .. _pythonhosted.org/brainiak:
            https://pythonhosted.org/brainiak
        
        
        Contributing
        ============
        
        We welcome contributions. Have a look at the issues labeled "`easy`_" for
        starting contribution ideas. Please read the guide in `CONTRIBUTING.rst`_
        first.
        
        .. _easy:
           https://github.com/brainiak/brainiak/issues?q=is%3Aissue+is%3Aopen+label%3Aeasy
        .. _CONTRIBUTING.rst:
           https://github.com/brainiak/brainiak/blob/master/CONTRIBUTING.rst
        
        
        Citing
        ======
        
        Please cite BrainIAK in your publications as: "Brain Imaging Analysis Kit,
        http://brainiak.org." Additionally, if you use `RRIDs
        <https://scicrunch.org/resolver>`_ to identify resources, please mention
        BrainIAK as "Brain Imaging Analysis Kit, RRID:SCR_014824". Finally, please cite
        the publications referenced in the documentation of the BrainIAK modules you
        use, e.g., `SRM <http://pythonhosted.org/brainiak/brainiak.funcalign.html>`_.
        
Keywords: neuroscience,algorithm,fMRI,distributed,scalable
Platform: UNKNOWN
Requires-Python: >=3.4
