Fix up logging

Closes #106 (closed)

General clean up of the logger setup. This makes the logger be called by default (hence no need to call setup_logger() everytime) and ensures output is no duplicated.

• Checks if handlers already exist before adding them
• Add option to turn on/off printing of version information (off by default)
• Add call to setup_logger by default (with version information turned on by default)

mentioned in commit a9ce35f9

merged