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Mac OS Python Installation for Scientific Computing

This gist describes how to install the basic tools you'll need to do scientific computing with Python on Mac OS X. These have been tested with Mac OS X 10.6 and 10.7.

Your Mac comes with Python installed by in /usr/bin/; however, you probably don't want to use that Python because it is rarely updated and, it's not a good idea to mess with that which OS X has installed.

Install Homebrew

So, most Python developers on Macs install a copy of Python with homebrew, a 3rd party package manager (that you're probably already using). I'll show you how to do that here.

If you don't have homebrew installed, install it as such

ruby <(curl -fsSkL

To use software installed by Homebrew, you'll want to alter your path, usually in your .baschrc or something similar

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

Get the OSX command line tools

At this point, we need to ensure that you have the appropriate compilers on your syste: Apple's "command line tools". (If you've been using homebrew for a while, you've probably already done this step). Your Mac does not include the command line tools by default; instead, they are part of Xcode. There are two ways to get the tools. The first is to install Xcode from the AppStore, then install the "command line tools" using the Components tab of the Downloads preferences panel in Xcode. The second way to install the command line tools is to download them from the Apple developer center. That can be a much faster way. Neither way is better for our purposes. But, if you plan on doing OSX/iOS development, go ahead and get the full XCode.

Install Python via homebrew

Now, install Python, building it as a "Framework" for OS X

brew install python --framework --universal

After that, if you plan to use this Python as the default in your path, you'll need to update your "Framework Python" symlink. That should be something like

cd /System/Library/Frameworks/Python.framework/Versions
sudo rm Current
ln -s /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/Current

I say "something like", becase your version, e.g. "2.7.3", may be different.

Install common dependencies

Many scientific computing libraries in Python are actually written in C under the hood, and even Fortran. So, you'll need to install some binary dependencies. We'll do that with homebrew.

brew install gfortran  # for scipy
brew install pkg-config  # for matplotlib
brew install zmq  # for ipython

Install pip and virtualenv

Now let's make sure pip is installed. Do which python. If it says /usr/local/bin/python, your PATH is set up correctly. If not, make sure you fix it (see above).

Now, install pip, which is a tool for installing Python packages.

easy_install pip

From now on, we'll use pip instead of easy_install. Then, install virtualenv so that we can create different Python environments for each project we work on, similar to rvm in Ruby.

pip install virtualenv

Create your first project

OK - now you're ready to install some fun packages for scientific meyhem in Python. This typically goes something like as follows. First, create a directory

mkdir myproject
cd myproject

Then create a new virtual environment called myvenv

virtualenv --distribute myvenv

Now "activate" that virtual env by sourcing the appropriate file. Assuming you're in the same directory

. ./myvenv/bin/activate

Now, when you type which python you should see something that includes myvenv, which means you're using the virtual environment and that you're free to install all sorts of Python packages willy-nilly because they won't effect your other projects.

Here's how you install some basic packages you may want

pip install numpy
pip install scipy
pip install ipython
pip install pandas
pip install scikit-learn

There it is. Now you've got the basic set of tools that most people use to write machine learning code in Python. You should be able to start up an Ipython notebook like this

ipython notebook --pylab inline

Enjoy! If you're part of, don't hesitate to contact me with questions.

Now you're ready to start a Python project!

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