So it turned out that while you could use the Neptune executable (e.g., "neptune file.rb"), you couldn't do a "require neptune" from your own code and call Neptune jobs from there. Thus after a quick fix, Neptune 0.0.3 is out to fix this problem!
However, I still think it looks a bit weird to have code that says:
job "mpi" do @something = baz end
When in reality this may be cleaner:
neptune "mpi" do :something => baz end
An upcoming release may fix this, so stay tuned!