Install Scientific Python on Mac OS X

These instructions detail how I install the scientific Python stack on my Mac. You can always check the Install Python page for other installation options.

I’m running the latest OS X Mountain Lion (10.8) but I think these instructions should work back to Snow Leopard (10.6). These instructions differ from my previous set primarily in that I now use Homebrew to install NumPy, SciPy, and matplotlib. I do this because Homebrew makes it easier to compile these with non-standard options that work around an issue with SciPy on OS X.

I’ll show how I install Python and the basic scientific Python stack:

If you need other libraries they can most likely be installed via pip and any dependencies can probably be installed via Homebrew.

Command Line Tools

The first order of business is to install the Apple command line tools. These include important things like development headers, gcc, and git. Head over to developer.apple.com/downloads, register for a free account, and download (then install) the latest “Command Line Tools for Xcode” for your version of OS X.

If you’ve already installed Xcode on Lion or Mountain Lion then you can install the command line tools from the preferences. If you’ve installed Xcode on Snow Leopard then you already have the command line tools.

Homebrew

Homebrew is my favorite package manager for OS X. It builds packages from source, intelligently re-uses libraries that are already part of OS X, and encourages best practices like installing Python packages with pip.

To install Homebrew paste the following in a terminal:

ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"

The brew command and any executables it installs will go in the directory /usr/bin/local so you want to make sure that goes at the front of your system’s PATH. As long as you’re at it, you can also add the directory where Python scripts get installed. Add the following line to your .profile, .bash_profile, or .bashrc file:

export PATH=/usr/local/bin:/usr/local/share/python:$PATH

At this point you should close your terminal and open a new one so that this PATH setting is in effect for the rest of the installation.

Python

Now you can use brew to install Python:

brew install python

Afterwards you should be able to run the commands

which python
which pip

and see

/usr/local/bin/python
/usr/local/bin/pip

for each, respectively. (It’s also possible to install Python 3 using Homebrew: brew install python3.)

NumPy

It is possible to use pip to install NumPy, but I use a Homebrew recipe so I avoid some problems with SciPy. The recipe isn’t included in stock Homebrew though, it requires “tapping” two other sources of Homebrew formula:

brew tap homebrew/science
brew tap samueljohn/python

You can learn more about these at their respective repositories:

With those repos tapped you can almost install NumPy, but first you’ll have
to use pip to install nose:

pip install nose

I compile NumPy against OpenBLAS to avoid a SciPy issue. Compiling OpenBLAS requires gfortran, which you can get via Homebrew:

brew install gfortran
brew install numpy --with-openblas

SciPy

And then you’re ready for SciPy:

brew install scipy --with-openblas

matplotlib

matplotlib generally installs just fine via pip but the custom Homebrew formula takes care of installing optional dependencies too:

brew install matplotlib

IPython

You’ll want Notebook support with IPython and that requires some extra dependencies, including ZeroMQ via brew:

brew install zeromq
pip install jinja2
pip install tornado
pip install pyzmq
pip install ipython

pandas

Pandas should install via pip:

pip install pandas

Testing It Out

The most basic test you can do to make sure everything worked is open up an IPython session and type in the following:

import numpy
import scipy
import matplotlib
import pandas

If there are no errors then you’re ready to get started! Congratulations and enjoy!

Install Scientific Python on Mac OS X