Updating to Lion / Mountain Lion / Mavericks / Yosemite

Which computers should be updated?

At this time, I do not recommend updating Stimulus computers to Mac OS X Lion. It has not been tested thoroughly enough yet (though we do have one computer that seems to work okay, but not well tested).
Desktop and Master computers seem to be doing fine under Lion, Mavericks, and Yosemite.

After upgrading to Lion, I had to do the following to keep some functionality the way I liked it under Snow Leopard:

Install or re-install Bazaar
To use Python2.6 as the default (necessary for Bazaar) add this line to .bash_profile (or is it the .bashrc file? -- it is in Mountain Lion and Mavericks) file: export VERSIONER_PYTHON_VERSION=2.6
Re-install Google python libraries for both python 2.7 and python 2.6: (that is, run the installer calling python2.6 and python2.7)
Install Qt framework http://qt.nokia.com/downloads/qt-for-open-source-cpp-development-on-mac-os-x
Install Matlab, 2010a or later (2011 seems to have some funny behavior)
Install XQuartz: http://xquartz.macosforge.org/trac/wiki/X112.7.2 (this is an X11 replacement, seems to be way way faster than old X11). In Quartz, make sure you update your mouse preferences (I like emulating a 3 button mouse)
If you liked using Spaces in OS 10.6, install TotalSpaces (http://totalspaces.binaryage.com/) and possibly install Warp 1.3 (see thread)
Turn off some of the excessive eye candy: http://www.chriswrites.com/2012/01/turn-off-animations-eye-candy-effects-in-mac-os-x-lion/ (see here for Mountain Lion https://discussions.apple.com/thread/4189003?start=0&tstart=0)
Go to Classic Mode in Mail

Immediately update to 10.9.2 so that Apple Mail will work properly
Install or re-install Bazaar
To use Python2.6 as the default (necessary for Bazaar) add this line to the .bashrc file: export VERSIONER_PYTHON_VERSION=2.6
Re-install Google python libraries for both python 2.7 and python 2.6: (that is, run the installer calling python2.6 and python2.7) (note: I haven't actually tried this yet)
If you haven't already, Install XQuartz: http://xquartz.macosforge.org/trac/wiki/X112.7.5 (this is an X11 replacement, seems to be way way faster than old X11). In Quartz, make sure you update your mouse preferences (I like emulating a 3 button mouse)
If you liked using TotalSpaces, install TotalSpaces2 (http://totalspaces.binaryage.com/)
Install XCode, open a terminal and type xcode-select --install to install the command line tools (they decided to make the installation more obscure)
After your mail update has settled (and stopped updating itself and reworking its files), you can turn off the annoying animations: https://github.com/AndreasVerhoeven/NoMailAppAnimationsOnMavericks

WARNING: Psychtoolbox will probably not work for research purposes (testing okay). If you use Psychtoolbox, be sure to run UpdatePsychtoolbox in Matlab and then follow the instructions for the kernel extension help PsychtoolboxKernelDriver
If you haven't already, install XQuartz: http://xquartz.macosforge.org/landing/ (this is an X11 replacement, seems to be way way faster than old X11). In Quartz, make sure you update your mouse preferences (I like emulating a 3 button mouse)
Install XCode, open an XQuartz terminal and type xcode-select --install to install the command line tools (they decided to make the installation more obscure)
Install MacPorts at their website: https://www.macports.org/ . After you get it, open a terminal and run sudo port selfupdate.
Install or re-install bazaar with sudo port install bzr
If you use Google tools, re-install Google python libraries for both python 2.7 and python 2.6: (that is, run the installer calling python2.6 and python2.7) (note: I haven't actually tried this yet)
If you liked using TotalSpaces, install TotalSpaces2 (http://totalspaces.binaryage.com/)