Python for Bioinformatics: matplotlib on OS X Lion--old

Sunday, July 31, 2011

matplotlib on OS X Lion--old

[ UPDATE: I'm going to leave this post up, for the record, but I found a better way, and that's in the following post. ]

Just a note to say that I got matplotlib installed with only a few issues to solve. As before, I relied on Gavin Huttley's instructions (here). Although the matplotlib instructions say you should install a different Python, I've found that just leads to confusion down the road, and I want to try to use the system version only if I can get away with it. YMMV.

The sticking points for the install always have to do with the basic dependencies, which are listed at the top of the file make.osx in the matplotlib source (from here). The source is the last link at the bottom.


ZLIBVERSION=1.2.3
PNGVERSION=1.2.39
FREETYPEVERSION=2.3.11

As silly as it seems, although OS X provides excellent functionality for dealing with compression, png images and fonts, we need to install these libraries for matplotlib to use. Unfortunately, I'm not expert enough to alter matplotlib to get rid of these dependencies, so we're stuck with it.

libpng

I got libpng-1.2.39 from here. I used this version b/c that's what matplotlib asks for, despite the fact that the current release is 1.5.4 (here). Standard magic incantations:

./configure
make
sudo make install

freetype

curl -O http://ftp.twaren.net/Unix/NonGNU/freetype/freetype-2.3.7.tar.bz2

According to Gavin's notes, we need these compiler flags for the other two (but they interfere with the libpng build):

export MACOSX_DEPLOYMENT_TARGET=10.7
export CFLAGS="-arch i386 -arch x86_64"
export FFLAGS="-arch i386 -arch x86_64"

./configure
make
sudo make install

zlib

zlib is a compression library. The current version is 1.2.5. I tried this:

curl -O http://www.zlib.net/zlib-1.2.3.tar.gz

but as I've seen before, although you get a (small) file back that has the right icon, it is really a 404 Page Not Found, which doesn't do me any good. It seems the older versions have been disappeared off the web and I couldn't find them poking around on the site. What I should've done at this point is try the version they do offer, but instead I went to my other machine and grabbed 1.2.3. I guess that since I'd used it before to build zlib, I found I needed to clean it first:

make clean
make
sudo make install

matplotlib

Finally, I got the matplotlib source. I altered the file make.osx:

PREFIX=/usr/local
PYVERSION=2.7
PYTHON=python${PYVERSION}
ZLIBVERSION=1.2.3
PNGVERSION=1.2.39
FREETYPEVERSION=2.3.7
MACOSX_DEPLOYMENT_TARGET=10.7
OSX_SDK_VER=10.7
ARCH_FLAGS="-arch i386-arch x86_64"

make -f make.osx mpl_build
sudo python setup.py install

mkdir ~/.matplotlib
cp matplotlibrc.template ~/.matplotlib/matplotlibrc

Edit the above file to have:

backend      : MacOSX

> python
Python 2.7.1 (r271:86832, Jun 16 2011, 16:59:05) 
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from matplotlib import *
>>>

Yes!

[ UPDATE: I see I used freetype 2.3.7 rather than 2.3.11, by mistake.

And if you don't like my approach, you could use Homebrew and follow this post. I don't have any experience with this yet. ]