Cli cleanup

[jthorton]

This PR fixes some the CLI performance and cleans up some of the messages printed to screen but not all of them.

• Add tests for the CLI

[bieniekmateusz]

Thank you. I worry that the logger hides messages from less technical users. E.g. to get the messages you have to be able to configure the logger. What do you think of a "verbose" mode? Most users in this area would probably be interested in some feedback about what is happening.

[jthorton]

Sure for the CLI I can direct the logging to a log file and make the log messages show the identity of the molecule so it's clear which one they refer to as its not as clear when running with dask rather than one by one in a notebook.

[bieniekmateusz]

That's useful. I'll see later how to make sure that the users still get some kind of printing if they want to. Maybe just a function that sets logger. Go head and merge when you're ready.