Thanks for the tip on fabricate, it appears to be just the tool I was looking for. A light weight dependency based "build" system in python that is not focused on distutils or making python packages. We shall see how well it works for data processing.
http://news.ycombinator.com/item?id=4190804
I use it on Windows too with an strace replacement I wrote which isn't online but if anyone's interested then just ask.