Sunday, July 31, 2011

matplotlib on OS X Lion--revised

In the previous post, I repeated an installation of matplotlib (now for OS X Lion) following the same method that I've linked to a number of times on the blog. It worked this time as well, but lead me to consideration of other possible methods. I found one on the web here. So that's what this post is about.

BTW, whatever you do, do not follow the instructions that the matplotlib developers provide. You do not need another Python, including MacPython or the Endthought distribution or anything else..

To recap, matplotlib lists dependencies (in the make.osx file) of: libpng, libfreetype, and zlib. I read somewhere on the matplotlib site today (but can't find the link now) that zlib is not a required dependency. These days, the other two are actually provided by Apple:

> ls -al /usr/X11/lib/libpng*
-rwxr-xr-x 1 root wheel 296864 Jul 29 16:11 /usr/X11/lib/libpng.3.dylib
lrwxr-xr-x 1 root wheel 14 Jul 29 16:11 /usr/X11/lib/libpng.dylib -> libpng15.dylib
-rwxr-xr-x 1 root wheel 294160 Jul 29 16:11 /usr/X11/lib/libpng12.0.dylib
-rwxr-xr-x 1 root wheel 305008 Jul 29 16:11 /usr/X11/lib/libpng15.15.dylib
lrwxr-xr-x 1 root wheel 17 Jul 29 16:11 /usr/X11/lib/libpng15.dylib -> libpng15.15.dylib

> ls -al /usr/X11/lib/libfreetype*
-rwxr-xr-x 1 root wheel 1060416 Jul 29 16:11 /usr/X11/lib/libfreetype.6.dylib
lrwxr-xr-x 1 root wheel 19 Jul 29 16:11 /usr/X11/lib/libfreetype.dylib -> libfreetype.6.dylib

I'm not sure at the moment whether X11 came with Xcode (as it used to) or was present in the original Lion install.

In any case, I spent an hour or two trying to figure out how to use the build commands from the makefile that comes with matplotlib, but point at these libraries. In the process I found what appears to be a bug:

/usr/X11/include/png.h:666: error: forward declaration of ‘struct png_info_def’

(and see Prashant's answer here), but we're going to use a different approach so it doesn't matter. I'm not sure how our method solved this in the end. As mentioned, the approach is to use Homebrew, in particular, something called pkgconfig. I used a Ruby script that downloads and installs Homebrew, as described here. The install gave this warning:

Warning: The following *evil* dylibs exist in /usr/local/lib
They may break builds or worse. You should consider deleting them:

These are, of course, the libraries we just installed in order to get matplotlib to build.

That's what got me working on the other method more seriously. I don't think the danger is all that great, but clearly it is better to use libraries that are (i) still available from the maintainers and (ii) have been vetted at least to some extent by other folks including Apple. AFAIK there aren't any known security issues with the versions we installed previously. I ripped them out anyway (they seemed to confuse pkgconfig).

If we ask Homebrew for the libraries, it just points us to the ones we saw in /usr/X11:

> brew search libpng
Apple distributes libpng with OS X, you can find it in /usr/X11/lib.
However not all build scripts look here, so you may need to call ENV.x11
in your formula's install function.

> brew search freetype
Apple distributes freetype with OS X, you can find it in /usr/X11/lib.
However not all build scripts look here, so you may need to call ENV.x11
in your formula's install function.

Following the instructions in the blog post I first installed pkgconfig:

> sudo brew install pkgconfig
Cowardly refusing to `sudo brew'
> brew install pkgconfig


That's all the Homebrew we need. This is followed by:

cd ~/Desktop
git clone git://
cd matplotlib/
python build
sudo python install

And we can see that I really did overwrite the first matplotlib install, and that we're actually using the libraries from /usr/X11, by first doing


Then when we run a script that imports matplotlib.pyplot, the Terminal shows (among much else) this:

dyld: loaded: /usr/X11/lib/libfreetype.6.dylib
dyld: loaded: /usr/X11/lib/libpng15.15.dylib

So that's what I'd recommend and it seems to be working fine. This simple script works exactly as you'd expect.

import matplotlib.pyplot as plt
Y = [1,4,9,16]

So the next thing to do is to figure out pkgconfig and Homebrew work their magic!

P.S. You will still need to make and edit ~/.matplotlibas discussed last time.