TODO: write about the idea, the roadmap, the existing files, make README .rst

This is a Python 2 project meant to be run on Unix platforms. If you run windows, install Linux on a VM. Virtualbox works and is free.

Non-python dependencies:
- NEST (NEST Neural Simulator) + PyNEST
  OR
- Brian (http://www.briansimulator.org)

- VTK (The Visualization Toolkit) + Python 2 bindings

Python pip-installable dependencies:
- coverage
- PyNN
- SimPy
- mock
- nose
- numpy
((( - ctype, a dep of python-magic, needs to be installed like that (pypa/pip#317):
pip install --no-install ctypes
cd <yourvirtualenv>/build/ctypes/source/libffi)
chmod +x configure
pip install ctypes
)))
- python-magic
- PIL

if using Brian:
- scipy which requires:
 - a fortran compiler if you pip install it (On Arch, use gcc-fortran)
 - the basic linear algebra subprograms library (blas on Arch)
 - the Linear Algebra PACKage (lapack)
- sympy, note that a bug in package numbering semantics may prevent you from pip installing it, in which case you should request for the exact latest version: pip install sympy==0.7.1
- matplotlib

For now, switching between simulators is done manually. For instance, switching from PyNN to Brian: grep -ilr 'pyNN.nest' *.py */*.py */*/*.py | xargs sed -i 's/pyNN.nest/pyNN.brian/g'

The project should be installed locally as a non-priviledged user except if you know what you are doing.

Install NEST under your home directory, e.g. ~/local-install/

Modify your environment setup script:
NEST_INSTALL_DIR=$HOME/local-install
NEST_SUBFOLDER_PATH=$HOME/nest
NESTRCFILENAME=$NEST_SUBFOLDER_PATH/config/nestrc
NEST_DATA_PATH=$NEST_SUBFOLDER_PATH/nest_data
NEST_DATA_PREFIX="out_"
export NEST_INSTALL_DIR NESTRCFILENAME NEST_DATA_PATH NEST_DATA_PREFIX
export LD_LIBRARY_PATH=$NEST_INSTALL_DIR/lib/nest:$LD_LIBRARY_PATH

source it and mkdir -p $NEST_DATA_PATH $NEST_DATA_PATH/../config

edit your /etc/ld.so.conf, add there /home/<<yourself>>/local-install/lib/nest and run ldconfig

Install VTK using your OS's package manager, e.g.
apt-get install vtk, pacman -S vtk, emerge vtk

Do the following modifications to your environment:
Add $HOME/local-install/usr/bin:$HOME/local-install/usr/local/bin:$HOME/local-install/bin to your PATH
Add .:$HOME/local-install/lib/python2.7/site-packages to your PYTHONPATH, additionally to the place of your system-wide python library (soemthing like /usr/lib/python2.7/site-packages)

Anstall virtualenv and virtualenvwrapper (with pip or your distro)

Modify your environment setup script again:
export WORKON_HOME=your_python_virtualenv/directory, for instance $HOME/virtualenvs. Remember to mkdir $HOME/virtualenvs
export VIRTUALENVWRAPPER_PYTHON=`which python2`, or `which python2.7` or whatever your python 2 binary is called

Add source /usr/local/bin/virtualenvwrapper.sh to your .bash_profile
Add alias ipython='python2 -c "from IPython import embed; embed()" 2>/dev/null || python2 -c "import IPython; IPython.Shell.IPShell().mainloop()"' to your .bashrc

Have bash_profile source bashrc.

mkvirtualenv cogneuro
mkdir -p dev/cogneuro/ && cd dev/cogneuro
pip install PyNN mock nose
git clone git://github.com/agravier/pycogmo.git
cd pycogmo/src/attention_net/
python attention_net.py


Detailed instructions to install NEST 2.0.0-rc4

sudo apt-get install build-essential autoconf automake libtool libltdl-dev libreadline5-dev libncurses5-dev libgsl0-dev python-numpy python-scipy python-matplotlib ipython
cd nest-2.0.0rc4
./configure --prefix=$HOME/local-install PYTHON_EXEC='/usr/bin/python2.7' --with-python='/usr/bin/python2.7' && make && make install && make installcheck


to create an environment: mkvirtualenv <name>
to activate an environment: . ~/venvs/<name>/bin/activate
e.g. . ~/virtualenvs/cogneuro/bin/activate
to deactivate it: deactivate                                                                                         to install something in the virtual env: pip install <python package>

useful:
pip install yolk
yolk -l