Linux Package Manager

Here we describe how to install all the required Python packages using the Linux distribution package manager for Debian-based systems (such as Ubuntu). You must have root access to use this installation method.

System install with root

For a modern linux installation such as Ubuntu 13, the system Python version will be 2.7 or newer and all of the required core packages are available as package installs. The instructions below have been developed and tested with Ubuntu 13. Corresponding packages for recent Fedora are probably available but this has not been verified.

The benefit of using a root install via the system package manager is that it is simple and all dependencies are managed for you. The downside is that the package versions tend to be older and so you don’t keep up with the latest code development. In Ubuntu 13 the core packages (NumPy, Matplotlib) are a little out date, but unless you are really pushing for the latest features, the older stable versions will work perfectly well.

First install the core packages for analysis with the following:

sudo apt-get install python-dev
sudo apt-get install ipython
sudo apt-get install python-numpy
sudo apt-get install python-scipy
sudo apt-get install python-matplotlib
sudo apt-get install python-setuptools
sudo apt-get install python-pyfits
sudo apt-get install python-tables

Most of the remaining packages are not available in the package manager, so we install them using the Python package manager pip. To install pip:

sudo apt-get install python-pip

Then:

sudo pip install emcee
sudo pip install acor
sudo pip install pymc

Quick installation check

Open a new terminal window and type:

which ipython

You should see:

/usr/bin/ipython

Test your installation

To do a very basic test whether you meet the requirements and have a functioning core scientific Python installation, do the following to check version numbers. First on the command line check the version numbers of python and ipython:

python -V
ipython --version

Then run ipython from the command line with the --pylab flag:

ipython --pylab

and inside ipython run the following python commands:

import numpy
import scipy
import scipy.linalg
import pylab as plt
from enthought.mayavi import mlab

print numpy.__version__
print scipy.__version__
print matplotlib.__version__

x = numpy.linspace(0, 20, 100)
plt.plot(x, sin(x))
print scipy.linalg.eig([[1, 2], [3, 4]])

The commands above should succeed with no errors. The version numbers should meet the requirements, and finally you should see a plot of a sine wave.

To check the other required packages, do the following also from within ipython:

import emcee
import acor
import pymc

If all the above commands ran without errors, you’ve installed everything successfully!