I suggest to switch to a very simple setup.py file and install in a virtual environment, if this is meant as a package. You can just copy the setup from pylogeny/tree, if you work with a flat file. For data, you add a folder where you store data (but you can even put your features into a Python script, and just use a long dictionary here, so even json, as I asked for in #2 is not needed (!)).
I suggest to switch to a very simple setup.py file and install in a virtual environment, if this is meant as a package. You can just copy the setup from pylogeny/tree, if you work with a flat file. For data, you add a folder where you store data (but you can even put your features into a Python script, and just use a long dictionary here, so even json, as I asked for in #2 is not needed (!)).