Installation

Conda

Make sure you have the conda-forge channel active, because some of our dependencies are not available in the default channels.

Use our brainiak channel to install:

conda install -c brainiak brainiak

Note that SSSRM currently uses Theano, which requires the Xcode Command Line Tools on MacOS.

Source

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

Note that if your MacOS does not have gcc (a prerequisite of mpich), it will take a long time (perhaps over an hour) to install gcc from source for you.

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.

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.