Install Homebrew on OS earlier than 10.9
ruby -e "$(curl -fsSkL raw.github.com/mistydemeo/tigerbrew/go/install)" (in .bash_profile) export PATH=/usr/local/sbin:/usr/local/bin:$PATH
Install pymvpa (adapted from Moffet's Crash Log)
1) Install Homebrew: ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install" 2) mkdir /Users/Shared/PyMVPA; cd /Users/Shared/ 3) sudo easy_install pip 4) pip install virtualenv 5) virtualenv PyMVPA 6) cd PyMVPA 7) . bin/activate 8) pip install numpy 9) pip install scipy 10) pip install nibabel 11) pip install ipython'[all]' 12) pip install scikit-learn 13) pip install matplotlib 14) brew install swig 15) Grab the PyMVPA source (and place into your virtualenv folder): git clone git://github.com/PyMVPA/PyMVPA.git 16)Install libsvm: brew install gnuplot brew install qt4 brew install libsvm 17)Install PyMVPA: make 3rd python setup.py build_ext –with-libsvm python setup.py install –with-libsvm 18) Download tutorial data at: http://data.pymvpa.org/datasets/haxby2001/ 19) Unzip and Place data in /Users/Shared/PyMVPA/Tutorial_Data
And remember that you should cd to another directory when calling the test command:
from mvpa2.tutorial_suite import *
Otherwise you will see the following complaint:
WARNING: Failed to load fast implementation of SMLR. May be you forgotten to build it. We will use much slower pure-Python version. Original exception was dlopen(mvpa2/clfs/libsmlrc/smlrc.so, 6): image not found * Please note: warnings are printed only once, but underlying problem might occur many times * WARNING: SMLR: C implementation is not available. Using pure Python one
This is because when you import mvpa2 under the pymvpa source code directory (where you make it), python takes the mvpa-subdirectory as the place from where is imports the mvpa-package. This won't work, at least for SVM / SMLR, that use C-code bindings that have to be compiled (source).
Use python effectively in OSX
After Homebrew installation is done, we can install Python. We’re going to start by installing Python 2.7:
$brew install python
Now, we need to tell the system to use our freshly new Python interpreter instead of the default one.
$ which python /usr/bin/python
The default Python interpreter is under /usr/bin, and the Homebrew’s one is under /usr/local/bin so we’re going to edit /etc/paths so the /usr/local/bin binaries will be prioritised over /usr/bin.
$ sudo nano /etc/paths
If you open /etc/paths, you should see this:
/usr/bin /bin /usr/sbin /sbin /usr/local/bin
Move /usr/local/bin at the beginning of the file so Homebrew binaries take on system binaries;
/usr/local/bin /usr/bin /bin /usr/sbin /sbin
Finally, check everything is ok: typing python should launch the Homebrew version
$ source /etc/paths $ which python /usr/local/bin/python $ python Python 2.7.8 (default, Jul 2 2014, 10:14:46) [GCC 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.40)] on darwin Type "help", "copyright", "credits" or "license" for more information.