Scientific Python on Mac OS X 10.8 with homebrew

(newer version of this guide)

A step-by-step installation guide to setup a scientific python environment based on Mac OS X and homebrew.

Needless to say: Make a backup (Timemachine)

First install homebrew.
Follow their instructions, then come back here.

If you don’t have a clean install, some of the following steps might need minor additional attention (like changing permissions chmod, chown, chgrp or overwriting existing files in the linking step with brew link --overwrite package_that_failed. In this case i can only recommend a backup again).

In general: execute the following commands one line at a time and read the outputs! If you read some warnings about “keg-only” that’s fine, it just means that brew won’t “hide” your system’s stuff behind the stuff it installed itself so it doesn’t cause problems… brewed stuff will still use it.

# set up some taps and update brew
brew tap homebrew/science # a lot of cool formulae for scientific tools
brew tap homebrew/python # numpy, scipy
brew update && brew upgrade

# install a brewed python
brew install python

# install openblas (otherwise scipy's arpack tests will fail)
brew install openblas

# install PIL, imagemagick, graphviz and other
# image generating stuff (qt is nice for viewing)
brew install pillow imagemagick graphviz
brew install cairo --without-x
brew install py2cairo # this will ask you to download xquartz and install it
brew install qt pyqt

# install nose (unittests & doctests on steroids)
pip install virtualenv nose

# install numpy and scipy
brew install numpy --with-openblas # bug in Accelerate framework < Mac OS X 10.9
brew install scipy --with-openblas # bug in Accelerate framework < Mac OS X 10.9

# test the scipy install
brew test scipy

# some cool python libs (if you don't know them, look them up)
# time series stuff, natural language toolkit
# generate plots, symbolic maths in python, fancy debugging output
pip install pandas nltk matplotlib sympy q

# ipython and notebook support
brew install zmq
pip install ipython[zmq,qtconsole,notebook,test]

# html stuff (parsing)
pip install html5lib cssselect pyquery lxml BeautifulSoup

# webapps / apis (choose what you like)
pip install Flask Django

# semantic web stuff: rdf & sparql
pip install rdflib SPARQLWrapper

# picloud (easily run python scripts in the cloud)
pip install cloud

Have fun 😉

(As always: If you think something is missing leave a comment.)


update 2014-02-25: updated tap samualjohn/python to homebrew/python, new version linked

6 thoughts on “Scientific Python on Mac OS X 10.8 with homebrew

  1. Conal Sathi

    For some reason, the scipy test fails for me

    brew test scipy
    Testing scipy
    ==> python -c import scipy; scipy.test()
    Traceback (most recent call last):
    File “”, line 1, in
    ImportError: No module named scipy
    Error: scipy: failed

    Reply
    1. joern Post author

      hmm, this looks like it can’t find the scipy module in python. did you install brew python and use it?
      what’s your output for [cci_bash]which python[/cci_bash] (if it isn’t [cci_bash]/usr/local/bin/python[/cci_bash] then something is wrong)

      Reply
  2. Pingback: Scientific Python on Mac OS X 10.9 with homebrew | Jörn's Blog

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