Some things I did that made it easier:
• I used a clean install of OS X. I did this to make sure cruft (links, alternative versions of libraries from old installs) does not interfere. Also, this way I can be sure that things work for the reasons I have written about here.
To do the install I just made a second partition on my hard drive and installed OS X on it from a USB installer. If you've never done this before, good instructions for the USB part are here.
It's quite straightforward. Use the App store to update when the install is complete. I now have OS X 10.8.4.
Although it's not necessarily good practice, I used the same username and password for my accounts on OS X on both partitions, this allows me to read and write files in both accounts easily using the Finder.
• I used the System Python. This doesn't appear to be a very popular choice, but it avoids the headache of having multiple Pythons and various $PATH issues, etc. If you do install a second Python, make sure it's a framework version, since even saving a plot as a png using matplotlib will fail otherwise. I may do some more experiments later, but I think this is the right choice
My Python is
$ which python /usr/bin/python |
(well, it's not really the whole of Python on OS X, but that is a whole 'nother story).
$ python Python 2.7.2 (default, Oct 11 2012, 20:14:37) |
A bonus is that we already have numpy
>>> import numpy >>> numpy.__version__ '1.6.1' |
• I used Homebrew to get the most important matplotlib prerequisites, libpng and freetype. zlib is also a prerequisite but comes with OS X.
The instructions for Homebrew are here. Weirdly, I got a prompt for an admin password, which happened because the directory where Homebrew puts stuff, /usr/local, did not exist yet. So I bailed from the process and first did:
sudo mkdir /usr/local |
Now, look for issues revealed by brew doctor and fix them if needed. Finally:
$ brew doctor Your system is ready to brew. $ brew update Already up-to-date. $ brew install pkgconfig libpng freetype .. $ brew list freetype libpng pkg-config |
the "Bottles" mentioned in the output I cut means these are pre-built.
I got pkgconfig because it helped with building/linking problems previously, but should not really be necessary when the libraries are in /usr/local. Not sure why it is some times pkg-config and other times pkgconfig, but OK:
$ ls /usr/local/bin/pkg-config /usr/local/bin/pkg-config $ ls /usr/local/lib/pkgconfig/ freetype2.pc libpng.pc libpng15.pc |
(If you use e.g. the XQuartz versions of these two libraries, you can set the PKG_CONFIG_PATH environment variable to point to the correct directory, and pkg-config will do the rest).
Now we're ready for matplotlib.
$ git clone git://github.com/matplotlib/matplotlib.git .. $ cd matplotlib $ python setup.py build $ sudo python setup.py install |
And test it:
cd ..
python
>>> import matplotlib.pyplot as plt
>>> Y = [1,4,9,16]
>>> plt.scatter(range(len(Y)),Y,s=250,color='r')
<matplotlib.collections.PathCollection object at 0x103963110>
>>> plt.savefig('example.png') |
Works!
>>> import matplotlib >>> matplotlib.test() ..KK.KK.....KK.KK..KK.KK.KK.KK.KK etc. |
I didn't test extensively but there don't seem to be massive failures. And matplotlib has lots of optional prerequisites I didn't install that would explain some failures.
It's worth pointing out that the matplotlib install process grabs several additional packages:
$ ls /Library/Python/2.7/site-packages README distribute-0.6.28-py2.7.egg easy-install.pth matplotlib-1.4.x-py2.7-macosx-10.8-intel.egg nose-1.3.0-py2.7.egg pyparsing-1.5.7-py2.7.egg setuptools.pth tornado-3.1-py2.7.egg $ |
Let's get a few more things while we're at it:
$ sudo easy_install pip Password: **** Searching for pip Reading http://pypi.python.org/simple/pip/ Best match: pip 1.3.1 .. Installing pip script to /usr/local/bin Installing pip-2.7 script to /usr/local/bin .. |
Come to think of it, SciPy would be a great addition. For that we need gfortran (Fortran compiler) and Cython:
$ brew install gfortran (takes a while, several dependencies).. |
Homebrew doesn't have Cython so:
$ sudo pip install cython |
And now for SciPy:
$ git clone git://github.com/scipy/scipy.git scipy $ cd scipy $ python setup.py build $ sudo python setup.py install $ cd .. $ python .. >>> from scipy.stats import norm >>> norm.cdf(2) 0.97724986805182079 |
Finally, get PyCogent too..
$ git clone git://github.com/pycogent/pycogent.git $ cd pycogent $ python setup.py build $ sudo python setup.py install |
That was pretty easy!
