Python on Mac OS X has traditionally been a bit of a struggle, dealing with paths etc. to make sure the built-in Python (out of date) doesn’t conflict with the Python I want to use (e.g. from Homebrew). Further complicating this, I had at various points installed Enthought EPD and Enthought Canopy. I’d like the state of Python on my computer to be less haphazard. To make that happen, I need to uninstall all Enthought products, and get everything cleaned out with respect to Homebrew, Xcode, and Virtualenv.

Cleaning / Updates

In the case of Homewbrew and Xcode, I just need to upgrade the packages and make sure everything is installed correctly. My Macbook Air has limited hard drive space, so I install the Xcode command line tools only. In the case of homebrew brew upgrade mostly worked, but something I’d done had left the libpng and freetype2 packages with problems:

Error: You must `brew link libpng' before qt can be installed
Warning: Could not link qt. Unlinking...
Error: You must `brew link libpng' before pyqt can be installed
Warning: Could not link pyqt. Unlinking...
Error: You must `brew link libpng' before shiboken can be installed
Warning: Could not link shiboken. Unlinking...
Error: You must `brew link libpng' before pyside can be installed
Warning: Could not link pyside. Unlinking...
Error: You must `brew link freetype' before fontconfig can be installed
Error: You must `brew link freetype' before pango can be installed

The problem was that the links already existed, but were owned by root, and even with the brew link --overwrite libpng syntax, it wouldn’t work. The next guess is to use sudo, but homebrew doesn’t like using sudo. Ultimately, I used brew link --overwrite --dry-run libpng to identify the files that needed to be overwritten, chown-ed them, performed the linking, and then chown-ed them back to root. I doubt this was the best solution, but it worked.

To clean up, I removed all my old virtual environments and uninstalled homebrew’s python, and I cleaned up the /usr/local/share/python folder, which had some out-of-date scripts in there. Then I reinstalled homebrew’s python, and created a new virtual environment.


Aside from installing one of the pre-built python packages like Anaconda, Enthought Canopy, etc., one of the best ways to install the scientific computing libraries for Python (numpy, scipy, etc.) on Mac OS X is using Chris Fonnesbeck’s excellent ScipySuperpack.

Fortunately, it works well with a virtualenv, and all I had to do was:

mkvirtualenv pydev
curl -o

This installed most of what I need, and then I installed Sympy and IPython as well:

pip install sympy
pip install ipython[zmq,qtconsole,notebook,test]


Statsmodels has a git repository, so I first cloned that into my own Git account, and got a local copy:

git clone [email protected]:ChadFulton/statsmodels.git

ScipySuperpack comes with statsmodels=0.5.0, so I need to remove that and start using my local copy, which I can do via python develop

pip uninstall statsmodels
cd statsmodels
python develop

Now, pip freeze shows the local development copy of statsmodels:

-e [email protected]:ChadFulton/statsmodels.git@661c4dc86b2c4c9fc4ce7c63efcded94b90ed0de#egg=statsmodels-dev

Code Standards

Finally, there are two packages not installed above that will be helpful for developing: pep8 and pylint. pep8 checks code for adherence to the pep8 python style guide, and pylint is a static code checker.

Installing these is as easy as

pip install pep8 pylint