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!

Upgrading to Mountain Lion

I just upgraded to Mountain Lion and here are some of my notes related to scientific Python installs.

If you’ve already got a working installation it will likely continue to work after upgrading. Regardless of whether you plan to keep using an existing install or make a new one you’ll probably want to do the following two things:

Xcode

You’ll need a Mountain Lion compatible set of command line tools and development libraries so reinstall Xcode or the Command Line Tools for Xcode. I personally prefer the later now that I use Sublime Text 2 for code editing. If you install Xcode make sure to install the command line tools from the preferences.

X11

ML doesn’t come with X11 installed so install XQuartz from http://xquartz.macosforge.org/ if you anticipate needing X11.

Python Libraries

  • NumPy compiles without issue.
  • SciPy is waiting on a small change before it will compile on Mountain Lion. I expect that to go in soon and they may release SciPy 0.10.2 to make it Mountain Lion compatible. Even if they don’t you’ll be able to install from the GitHub repository once the change is made.
  • matplotlib must be installed from the GitHub repository at this time.

Install Python, NumPy, SciPy, and matplotlib on Mac OS X – Double Click

Update: These instructions are over a year old, though they may still work for you. See the “Install Python” page for the most up-to-date instructions.

I’ve already written a post about installing Python, NumPy, SciPy, and matplotlib on Lion, but it involves a lot of working at the command line, modifying your .bash_profile and dealing with compiler problems. That’s what I’ll call the compile-it-yourself (CIY) method. What I’ll describe below I’ll call the “double click” method.

I personally use the CIY method because it allows me to very easily control what’s installed. With Homebrew and pip I can uninstall and upgrade different things at will, or choose to install bleeding-edge versions. But it’s more hassle than everyone wants and there’s now an easier way using double-click installers.

Until recently the CIY was the only way to get everything working on Lion but now the developers of NumPy, SciPy, and matplotlib have all caught up and it’s possible to just download and double-click on a few DMG files to get a basic scientific Python installation working. Once you get to know Python, though, you will undoubtedly want to install some other packages and when that time comes I suggest you use pip.

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Install Python, NumPy, SciPy, and matplotlib on Mac OS X

Update: These instructions are over a year old, though they may still work for you. See the “Install Python” page for the most recent instructions.

A bit ago a friend and I both had fresh Mac OS X Lion installs so I helped him set up his computers with a scientific Python setup and did mine at the same time.

These instructions are for Lion but should work on Snow Leopard or Mountain Lion without much trouble. On Snow Leopard you won’t install Xcode via the App Store, you’ll have to download it from Apple.

After I’d helped my friend I found this blog post describing a procedure pretty much the same as below.

Update: If doing all the stuff below doesn’t seem like your cup of tea, it’s also possible to install Python, NumPy, SciPy, and matplotlib using double-click binary installers (resulting in a much less flexible installation), see this post to learn how.

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