While working on another project, I noticed that neither distutils nor setuptools automatically install python packages within packages and this also applies to marmoset. So after installing marmoset with the setup.py, the marmoset package is installed but the packages within it are not, e.g.:
root@hpo:/tmp/marmoset# ls /usr/local/lib/python3.4/dist-packages/marmoset-0.5.0-py3.4.egg/marmoset/
app.py config.py __init__.py __pycache__ validation.py
The easiest way to solve this I found is to add the packages within marmoset explicitly to the liste of packages (e.g. ['marmoset', 'marmoset.cli'] etc.) but perhaps there is a more elegant way.