Use python logging module instead of print statements

[sharkwouter]

At the moment we have a lot of print statements and we have a debug mode. This could be done better with the logging module. It could be a global logger. The logs should be written to a file.

[orende]

This has been done as part of #573 except for this line which I can't quite figure out if it's intentionally using a print statement or not.

[sharkwouter]

True, I'll go over our implementation one more time and see if we're at the point where it should be.