Mountain Lion: Scientific Development Setup

发现这个工具似乎很好用Homebrew

 

Mountain Lion: Scientific Development Setup

Quick jot for memory on how to install octave + scientific python for Mountain Lion, since it's pretty new for now .. These steps are kind of a mess since I'm not really documenting them in sequence.

1. Install Xcode 4.5 + command line tools

2. Install homebrew
$ /usr/bin/ruby -e "$(/usr/bin/curl -fsSL https://raw.github.com/mxcl/homebrew/master/Library/Contributions/install_homebrew.rb)"

3. Test to make sure everything's okay
$ brew doctor
$ brew update

4. Get Mountain Lion and Homebrew to Be Happy

Visit http://xquartz.macosforge.org/trac/wiki and download and install 2.7.2+.

$ sudo xcode-select -switch /Applications/Xcode.app/Contents/Developer

$ ln -s /opt/X11 /usr/X11

5. Install python using homebrew (will take a long time)
$ brew install python

6. Make sure python is at /usr/local/bin/python
$ which python

7. Install pip for python
$ easy_install pip

8. Install gfortran using homebrew
$ brew install gfortran

If this gives the error message:

Currently the gfortran compiler provided by this brew is only supports
          the following versions of XCode
            - XCode 3.1.4 on OS X 10.5.x
            - XCode 3.2.2/3.2.3 -- 4.0 on OS X 10.6.x
            - XCode 4.1 or newer on OS X 10.7.x
etc.

then
$ brew edit gfortran

replace
    if MacOS.xcode_version >= '4.2' and MACOS_VERSION > 10.7
      ohai "Installing gfortran 4.2.4 for XCode 4.2 (build 5666)"
with
    if MacOS.xcode_version >= '4.2' and MACOS_VERSION >= 10.7
      ohai "Installing gfortran 4.2.4 for XCode 4.2 (build 5666) or higher"


(not necessary once the gfortran recipe is updated by homebrew)

9. Install scipy and numpy using pip
$ sudo pip install scipy
$ sudo pip install numpy

10. Install pkg-config using homebrew
$ brew install pkg-config

11. Install gcc using homebrew (not necessary?)
$ brew install gcc --use-llvm

12. Install matplotlib

From http://practicalcomputing.org/node/69:
$ sudo mkdir -p /usr/local/include
$ sudo ln -s /usr/X11/include/freetype2/freetype /usr/local/include/freetype
$ sudo ln -s /usr/X11/include/ft2build.h /usr/local/include/ft2build.h
$ sudo ln -s /usr/X11/include/png.h /usr/local/include/png.h
$ sudo ln -s /usr/X11/include/pngconf.h /usr/local/include/pngconf.h
$ sudo ln -s /usr/X11/include/pnglibconf.h /usr/local/include/pnglibconf.h
$ sudo mkdir -p /usr/local/lib
$ sudo ln -s /usr/X11/lib/libfreetype.dylib /usr/local/lib/libfreetype.dylib
$ sudo ln -s /usr/X11/lib/libpng.dylib /usr/local/lib/libpng.dylib

If you get the error:

 

unable to execute clang++: No such file or directory

 

then do

$ sudo ln -s /usr/bin/clang /usr/bin/clang++


Finally 
$ sudo pip install matplotlib-1.1.1.tar.gz

13. Install octave (will take a long time)

$ brew install fltk


If fltk cannot be installed with the following error
Error: Failed executing: make install (fltk.rb:24)
Then just install octave without fltk first (it's not crucial) .. until it's fixed 


$ brew install --with-magick-plus-plus GraphicsMagick

$ brew install octave --without-fltk
$ brew install gnuplot


If you get this error while compiling Octave:

sed: RE error: illegal byte sequence
...
Error: Failed executing: make all (octave.rb:84)

Then unset the LANG environmental variable first


$ unset LANG

see https://github.com/Homebrew/homebrew-dupes/pull/21

14. MacTeX, TeXShop and LyX
Finally, something that can be easily installed .. 
http://pages.uoregon.edu/koch/texshop/obtaining.html

http://www.lyx.org/Download/

Useful references:

1. http://penandpants.com/2012/02/24/install-python/
2. http://jholewinski.org/blog/installing-matplotlib-on-os-x-10-7-with-homebrew/
3. https://www.nesono.com/node/356