# aliquot

## < a quantity that can be divided into another a whole number of time />

I just got a Macbook Air. Whaouh, it’s impressive! My preceding one was an 15” Macbook pro, but as I don’t have to do intensive computational work anymore, I thought going to a smaller computer would not be so bad. However, I ordered it from the App Store to customize it with the latest handy features (2.13 GHz core duo and 4 Go RAM). I won’t describe the specs of Airbook, but just summarize what I’ve installed so far.

## The bare essentials

I just grabbed the latest version of Aquamacs, TexLive, Git, and R (2.12). These are the very basic tools I used most of the day.

I updated the software shipped with the Mac. This took me a night. I finally add Dropbox (the Dev version).

## Some additional CLI and GUI tools

I then downloaded and installed GitX, Versions, asciidoc, latex2html, Papers, Graphviz, gnuplot with Aquaterm support, octave, Cyberduck, and Omnigraffle.

About computing stuff, I considered a lot of Lisp-related software (CMUCL, sbcl, CCL, clojure, mit-scheme) but also Incanter and weka. Also, I compiled sitecopy, wget, ncftp.

## Installing Python stuff

As I want to use the Python that is installed with the Mac (I know there are newer versions, but the 2.6.1 version is a decent one, and I don’t want to add too much software this time), I need to compile numpy and scipy. There are some dependencies to install first:

$sudo easy_install nose$ curl -O http://www.fftw.org/fftw-3.2.2.tar.gz
$tar xf fftw-3.2.2.tar.gz$ cd fftw-3.2.2
$./configure CC="gcc -arch i386 -arch x86_64" CXX="g++ -arch i386 -arch x86_64" \ CPP="gcc -E" CXXCPP="g++ -E"$ make
$sudo make install Actually, I didn’t install the UFMPACK (if it happens I need to do sparse algebra, I will reinstall scipy, but for the moment that’s fine). For numpy, I just ran: $ python setup.py build --fcompiler=gnu95
$sudo python setup.py install Everything went fine, except that now I have two versions of numpy, at two different places! The original one (very old) is in /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy, while the one I just compiled is in /Library/Python/2.6/site-packages/numpy. This would cause problem as scipy needs numpy >= 1.4 (as it happens to me, obviously). Again, I don’t want to modify the built-in distribution, so I just add the updated site-package to the PYTHONPATH, like this (in my .profile): export PYTHONPATH=/Library/Python/2.6/site-packages:${PYTHONPATH}

The problem is that it will only works for me, not as root. So I also need to add Defaults env_keep += "PYTHONPATH" to the sudoers file (sudo visudo at the bash prompt).

Then, I proceed with scipy the usual way:

$python setup.py build$ sudo python setup.py install

The compilation lasted about 15-20 min. And this is the first time I heard the Airbook. Ok, that seems to be ok now:

~ $python Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import numpy >>> import scipy >>> print numpy.__version__ 1.5.1 >>> print scipy.__version__ 0.8.0 Then , I need to install Matplotlib. I just correct a typo in make.osx, and finally: $ sudo make -f make.osx fetch deps mpl_build mpl_install

The above step download and install zlib (1.2.3), libpng (1.2.39), freetype2 (2.3.11), then pytz. Maybe I need to come back to this install if I want to use the Qt or Cairo backends. Just a little test to check that it works:

>>> import pylab as pl
>>> x = pl.randn(10000)
>>> pl.hist(x, 100)

Ok, that sounds good. Finally, to work more conveniently, I need ipython, and the installation did go like a charm (build and install from the setup.py file). So the preceding example can be reproduced with little effort, thanks to ipython -pylab.

That’s it!