Factored out transition building
Got rid of a special case in the transition matrix computations
Replaced for loops and explicit sums with a linear algebra expression

It might be less clear to read, but there are fewer local variables and loops in the code now and that is good. Plus, with scipy I think this code should also be a lot faster.
Moved the general transition code to its own module and added a class for parsing information to it.
Renamed state sets
Merge branch 'feature/cleaner_transition_computations' into develop
Moved some computations outside a loop
Removed duplicated code
Fixed header bug in log output
Put all the isolation model code in the same module.
Basic setuptools script
Added numpy and scipy as dependencies
A bit more documentation
Merge branch 'release/distutils_setup'