Install Python / numpy / scipy / ipython / matplotlib / umfpack / pytables from source

install.sh

#!/bin/bash

# =================================================================
# Install a full scientific python stack from source, for Ubuntu, with
# python 2.7.3 (tested on a totally fresh Ubuntu12.04-amd64). Requires
# sudo for apt-getting dependencies like libatlas, Tk, etc
# =================================================================

# packages pulled from PyPI are currently
# scipy 0.10.1
# numpy 1.6.2
# ipython 0.13
# matplotlib 1.1.0 (Tk backend)
# numexpr 2.0.1
# cython 0.16
# pytables 2.4.0
# scikits.umfpack 5.1.0
# deap 0.8
# fastcluster 1.1.6

# will also install msmbuilder 2.5.1 if you have it in your home directory

# (and the boring ones are)
# setuptools 0.6c11
# pip 1.1
# nose 1.1.2
# virtualenv 1.7.2
# virtualenvwrapper 3.6

# we're going to install everything in $HOME/local
cd $HOME
mkdir -p local
cd local

# install libraries for python itself
sudo apt-get upgrade
sudo apt-get install -qq build-essential libz-dev libreadline-dev
sudo apt-get install -qq libncursesw5-dev libssl-dev libgdbm-dev
sudo apt-get install -qq libsqlite3-dev libbz2-dev zlib1g-dev

# install svn
sudo apt-get install -qq subversion

# install libraries for science
sudo apt-get install -qq gfortran swig liblapack-dev libzmq-dev
sudo apt-get install -qq libatlas-base-dev libjpeg-dev libhdf5-serial-dev
sudo apt-get install -qq liblzo2-dev libsuitesparse-dev

# install libraries for matplotlib
sudo apt-get install -qq libpng12-dev libfreetype6-dev tk-dev

# install python
if [ ! -d "$HOME/local/python" ]; then
    wget http://www.python.org/ftp/python/2.7.3/Python-2.7.3.tgz
    tar -xzvf Python-2.7.3.tgz
    cd Python-2.7.3
    ./configure --prefix=$HOME/local/python
    make
    make install
    cd ..
else
    echo "python already installed"
fi

# add python to path
export PATH=$HOME/local/python/bin:$PATH

#install python's setuptools
if [ ! -d "$HOME/local/setuptools-0.6c11" ]; then
    wget http://pypi.python.org/packages/source/s/setuptools/setuptools-0.6c11.tar.gz#md5=7df2a529a074f613b509fb44feefe74e
    tar -xzvf setuptools-0.6c11.tar.gz
    cd setuptools-0.6c11
    python setup.py install
    cd ..
else
    echo "setuptools already installed"
fi

# get the better python package manager, pip
easy_install pip
# install remaining python packages through pip
pip install numpy # core numerics library
pip install nose  # testing library
pip install numexpr # prereq for tables
pip install cython  # prereq for tables
pip install tables  # hdf5 support for python (savig big arrays on disk)
pip install scipy   # science stuff
pip install ipython # nice interactive prompt
pip install deap # mpi stuff
pip install pyzmq # socket lib for ipython.parallel
pip install fastcluster # fast hierarchical clustering library


# install matplotlib with the Tk backend, but not gtk
# if you want the gtk backend, there are a lot more dependencies
# since pip cannot install pygtk
pip install matplotlib


# install scikits.umfpack
if [ ! -d "$HOME/local/umfpack" ]; then
    svn checkout http://svn.scipy.org/svn/scikits/trunk/umfpack/
    cd umfpack
    python setup.py install
fi

pip install tornado

echo "Add $HOME/local/python/bin to your path (e.g. .bashrc)"
echo ""
echo 'echo "export PATH=\$HOME/local/python/bin:\$PATH" >> ~/.bashrc'

pip install virtualenv
pip install virtualenvwrapper