matplotlib followup for Python 3 on OS X 10.8

In my last post, I reported success in installing matplotlib on OS X. I realize now that this is not anything new to report, since the currently recommended install process (which I read belatedly today) in the README is to use Homebrew (or MacPorts), which is what I did. I'm just happy to know that it works.

I thought I'd say a word about Python 3 here.

I did

$ brew install python3 --framework

which first installed readline and sqlite (linked into /usr/local/opt), as well as gdbm and xz, and also Distribute and pip.

So now we have:

$ ls /usr/local/lib/python3.3/site-packages/ __pycache__ setuptools-0.6c11-py3.3.egg-info distribute-0.6.45-py3.3.egg setuptools.pth easy-install.pth site.py pip-1.3.1-py3.3.egg sitecustomize.py

$ python3 Python 3.3.2 (default, Jun 19 2013, 15:41:32) [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from test import autotest == CPython 3.3.2 (default, Jun 19 2013, 15:41:32) [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] == Darwin-12.4.0-x86_64-i386-64bit little-endian == /usr/local/bin Testing with flags: sys.flags(debug=0, inspect=0, interactive=0, optimize=0, dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0, verbose=0, bytes_warning=0, quiet=0, hash_randomization=1) [ 1/372] test_grammar [ 2/372] test_opcodes [ 3/372] test_dict [ 4/372] test_builtin

The tests hang at this point, and I haven't figured out why yet. They do fine with my system Python. Then I did:

$ pip3 install numpy $ pip3 install nose

since we need numpy for matplotlib (and don't get it for free as with System Python).

Following this advice, I did:

$ python3 .. >>> import numpy >>> numpy.test('full') Ran 4808 tests in 64.611s OK (KNOWNFAIL=6, SKIP=6) <nose.result.TextTestResult run=4808 errors=0 failures=0>

Now to matplotlib

$ git clone git://github.com/matplotlib/matplotlib.git $ cd matplotlib $ python3 setup.py build $ sudo python3 setup.py install

(Grabs pyparsing, dateutil, tornado).

$ cd.. $ python3 .. >>> 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 0x1094e4650> >>> plt.savefig('example.png')

works!

$ pip3 install cython

had a permissions problem, so I did

$ sudo chmod -R 755 /usr/local/lib/python3.3/site-packages/ $ pip3 install cython

Now, for scipy

$ git clone git://github.com/scipy/scipy.git scipy $ cd scipy $ python3 setup.py build $ sudo python3 setup.py install

$ cd .. $ python3 .. >>> from scipy.stats import norm >>> norm.cdf(2) 0.97724986805182079

>>> import scipy >>> scipy.test('full') .. Ran 7486 tests in 725.812s FAILED (KNOWNFAIL=42, SKIP=296, failures=82)

Some failures, but all in all it looks good, and a very easy install.

Matplotlib (and SciPy) on OS X Mountain Lion

Yesterday I installed matplotlib on my MacBook---for about the 10th time. This can be a complex undertaking, but a basic installation is relatively easy, so I thought I would outline it here.

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

If you check for the libraries loaded (I used export DYLD_PRINT_LIBRARIES=1), you'll see we're using Accelerate.

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!