{
    "info": {
        "author": "The Mozaik team",
        "author_email": "antolikjan@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: Other/Proprietary License",
            "Natural Language :: English",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering"
        ],
        "description": "Installation intructions\n========================\n\nDependencies\n------------\n* python 2.7\n* scipy/numpy\n* nest (latest release, compiled with mpi)\n* mpi4py\n* pyNN (neo_output branch)\n* imagen\n* parameters\n* quantities \n* neo\n\nInstallation\n------------\n\nInstructions::\n\n  git clone https://github.com/antolikjan/mozaik.git\n  cd mozaik\n  python setup.py install\n  \nPlease see below:\n * the installation of the dependencies.\n * the installation on Ubuntu Linux\n * how to run the examples\n \n.. _ref-detailed:\n\nDetailed instructions\n---------------------\n\nMozaik requires currently some \"non-standard\" branches of software like the\npyNN which will be resolved in the future. Therefore more detailed installation\ninstructions follow.\n\n.. _ref-virtual-env:\n\nVirtual env\n___________\n\nWe recommend to install mozaik using the virtualenv python environment manager (http://pypi.python.org/pypi/virtualenv/) , to prevent potential\nconflicts with standard versions of required libraries. Users can follow for example http://simononsoftware.com/virtualenv-tutorial tutorial or just do the following steps:\n \n * Install virtualenv\n * Create (for example in your home directory) a directory where all virtual environments will be created home/virt_env\n * Create the virtual environment for mozaik:: \n    \n    virtualenv virt_env/virt_env_mozaik/ --verbose --no-site-packages\n\n * Load the virtual environment for mozaik by::\n \n    source virt_env/virt_env_mozaik/bin/activate\n\nYour shell should look now something like::\n\n(virt_env_mozaik)Username@Machinename:~$\n\nYou can use pip to view the installed packages::\n\n  pip freeze\n\nDependencies \n____________\n\nNote that if the installation is done in your virtualenv environment, it doesn't require any root privilege.\n\n * scipy\n * numpy\n * mpi4py\n * matplotlib (1.1 and higher)\n * quantities\n * PyNN::\n     \n       git clone https://github.com/NeuralEnsemble/PyNN.git\n     \n   * Then, in your virtual environment:: \n   \n       python setup.py install\n * Neo::\n \n    git clone https://github.com/apdavison/python-neo python-neo\n    cd python-neo\n    python setup.py install\n    \n * imagen::        \n \n      pip install --user imagen\n * parameters::\n \n     git clone https://github.com/apdavison/parameters.git parameters\n     cd parameters\n     python setup.py install\n * NeuroTools::\n \n     svn co https://neuralensemble.org/svn/NeuroTools/trunk NeuroTools\n     python setup.py install\n \nFor mozaik itself, you need to clone with the help of git::\n\n  git clone https://github.com/antolikjan/mozaik.git\n  python setup.py install\n\n\nVIRTUALENV NOTE: You might already have some of the above packages\nif you've used the option --system-site-packages when creating the virtual environment for mozaik.\nYou can list the packages you have e.g. with the help of yolk):\nIf you've set up the virt_env with the option --system-site-packages and\nyou're using scipy, numpy, matplotlib anyway you don't have to install those in your virt_env.\n\n.. _ref-ubuntu:\n\nUbuntu\n------\n\nFollowing these instruction should give you a working copy of mozaik on a \nfresh installation of Ubuntu (at the time of the writing the version was 12.04)\n\nFirst the list of ubuntu package dependencies::\n\n  sudo apt-get install python2.7 python-dev python-pip python-nose subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5 libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin\n\n\nVirtual env\n____________\n\nThen python virtualenv and virtualenvwrapper (an handy way to manage python virtual environments)::\n\n$ sudo pip install virtualenv\n$ sudo pip install virtualenvwrapper\n\nTo setup `virtualenvwrapper <http://virtualenvwrapper.readthedocs.org/en/latest//>`_ add the following lines at the top of ~/.bash_profile (create it if you don't have one)::\n\n    # virtualenvwrapper\n    export WORKON_HOME=~/.virtualenvs\n    source /usr/local/bin/virtualenvwrapper.sh\n    export PIP_VIRTUALENV_BASE=$WORKON_HOME\n    export PIP_RESPECT_VIRTUALENV=true\n\nFor the first time, run bash_profile (the next times it will be loaded by your terminal)::      \n\n$ source .bash_profile\n\nTo create a new managed virtualenv you just need to::\n\n    $ mkvirtualenv --no-site-packages mozaik\n    $ workon mozaik\n    (mozaik)$>\n \nTo produce a requirement file (it will list all the installed package in the virtual environment, so that pip can reinstall the same set of packages)::\n\n(mozaik)$> pip freeze > requirements.txt\n \nThen you can use it to replicate installation::\n\n(mozaik)$> pip install -r requirements.txt\n \nTo exit the environment::\n\n(mozaik)$> deactivate\n\n\nDependencies \n____________\n\n \nNow you can install in this protected environment all other dependencies::\n\n  pip install --upgrade distribute\n  pip install numpy mpi4py \n  pip install scipy matplotlib quantities lazyarray\n  pip install imagen interval PIL\n\nNow we can install *Nest* (always in the virtual environment):\n\n    - download the latest version from their `website <http://www.nest-initiative.org/index.php/Software:Download>`_\n    - untar and cd into it::\n\n        tar xvfz nest-2.2.2.tar.gz\n        cd nest-2.2.2\n    - then configure, choose if you want mpi. And, if you decide to have nest installed somewhere else from normal places add it with a prefix, then you also need to specify the pynest prefix. So if 'mozaik' is your virtual environment, and if the directory of all the virtual environments is virt_env, then the configure line should look like::\n    \n       (mozaik)$ ./configure --with-mpi --prefix=$HOME/opt/nest --with-pynest-prefix=$HOME/virt_env/mozaik\n    - finally, by launching make and install, it installs PyNest in ::\n\n        (mozaik)$ make\n        (mozaik)$ make install\n    - in the ./~nestrc, uncomment the lines regarding mpirun, and check that the mpirun executables are installed. Then::\n\n        make installcheck\n    - nest will reside in $HOME/virt_env/mozaik/lib/python2.7/site-packages. Check that the package is seen by python using::\n     \n        python -c 'import nest'\n\nInstall PyNN::\n\n    git clone https://github.com/NeuralEnsemble/PyNN.git\n    cd PyNN/\n    python setup.py install\n\nthat will reside in $HOME/virt_env/mozaik/lib/python2.7/site-packages/PyNN-0.8dev-py2.7.egg-info. Check::\n\n    python -c 'import pyNN'\n\nInstall NEO::\n\n    git clone https://github.com/apdavison/python-neo python-neo\n    cd python-neo/\n    python setup.py install\n\nInstall Parameters package::\n\n    git clone https://github.com/apdavison/parameters.git parameters\n    cd parameters/\n    python setup.py install\n\nInstall NeuroTools::\n\n    svn co https://neuralensemble.org/svn/NeuroTools/trunk NeuroTools\n    cd NeuroTools/\n    python setup.py install\n\nInstall TableIO (not always necessary). Download it from http://kochanski.org/gpk/misc/TableIO.html::\n\n    tar xvzf TableIO-1.2.tgz\n    python setup.py install\n    \nAnd, finally, Mozaik::\n    \n    git clone https://github.com/antolikjan/mozaik.git\n    cd mozaik/\n    python setup.py install\n    \n.. _ref-run:\n\nRunning examples\n----------------\n\nIf you use mpi and mpirun, you should install first the mpi executables if not already done::\n\n  sudo apt-get install openmpi-bin\n  \nThen, you go to the examples directory in the mozaik loaded from github (see above) and launch the model VogelsAbbott2005::\n\n  cd examples\n  cd VogelsAbbott2005\n  mpirun python run.py nest 2 param/defaults 'test'\n  \nThis will launch the example with the nest simulator, on 2 nodes, using the parameter param/defaults. Last, 'test' is the name of this run.\n\n:copyright: Copyright 2011-2013 by the *mozaik* team, see AUTHORS.\n:license: `CECILL <http://www.cecill.info/>`_, see LICENSE for details.",
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        "home_page": "http://neuralensemble.org/mozaik",
        "keywords": "computational neuroscience simulation large-scale model spiking",
        "license": "CeCILL http://www.cecill.info",
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        "name": "mozaik",
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        "summary": "Python package mozaik is an integrated workflow framework for large scale neural simulations.",
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