New SciPy Superpack

Before I go any further, I should stress that the “new” in the title of the post means “new for me,” not “new to the rest of the world.” Because I’m still running Lion1 I need to use a version of the Superpack that’s a little behind the times. But it’s more up-to-date than the one I installed back in June.

The Superpack I’m talking about is Chris Fonnesbeck’s SciPy Superpack, a set of Python modules and a shell script that ties everything together and does the installation. The modules you get in the Superpack are:

It also installs gFortran because some parts of these modules need to be compiled.

When I first installed the Superpack in June, everything worked fine, but there was one small annoyance. Every time I imported something from the scipy.stats library, I’d get this warning:

RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility

I soon learned that this was not a warning I needed to worry about, but I still didn’t like seeing it. My hope was that more recent versions of these packages would suppress the warning. Luckily, that turned out to be true, and now I have the modules I want with no extraneous warnings when my scripts run.

The newer versions of the modules are installed as .egg files alongside the older versions in /Library/Python/2.7/site-packages. I assume I can just delete the older versions with no ill effect, but I haven’t bothered and probably won’t. Based on my experience in upgrading from Snow Leopard to Lion, I fully expect all of my site-packages libraries to get wiped out. There’s no sense in doing any maintenance on a directory that’s likely to need a complete rebuild in a month or so.

If you’re running Mountain Lion (and I suspect most of you are), you should get the fully up-to-date Superpack for 10.8. It has more recent versions of almost all of the packages.

  1. My old iMac at work isn’t eligible for Mountain Lion, and I want my two computers to be as close in capabilities as possible. I’ll upgrade my MacBook Air when I get a new iMac in (I hope) December