python modules/packaging

[kzuberi]

Not doing it write rite right.

The python package in pipeline/builder isn't setup to be packaged/installed with setuptools or whatever. The snakemake files execute the scripts from within the modules directly, but the imports are setup in a sort of broken way.

I think the shortest step to fix things is to run the modules with python -m as suggested here and update the code to use relative imports. Can later consider setuptools.

I think.