Implement a consistent logging for refinegems

[cb-Hades]

Due to the nature of refineGEMs (being a toolbox), it would be helpful to have a consistent logger that can be accessed and viewed from other tools that call functions from refinegems and not have everything being written to the root logger.

A good solution might be to write a logger with the Python logging module that can be imported from every module in refinegems, similar to COBRApy or Memote.

❕When implementing logging, keep in mind to handle exceptions correctly.

Modules

• gapfill (with note as logging option if something is between info and warning)
• db_access
• set_up -> e.g. file size in ..utility.set_up.download_url, out put of DIAMOND calls
• ...

Notes

• one logger for all modules or one for each submodule? Hierarchical? -> Important: correct propagation

• maybe add some decorator for special logging cases --> BUT: see above (how to log in hierachical logger?)

• Idea: do it similarly to COBRApy?

• Coloured text could be used for logging:

from colorama import init as colorama_init
from colorama import Fore

def coloured_example_text():
     colorama_init(autoreset=True)
     print(f'{Fore.RED}To use the KEGG comparison the specification of the organismid (KEGG organism code) is obligatory.\n' +
       'If there is no organism code available for your organism in KEGG but an entry for your organism exists in BioCyc, use the option \'BioCyc\'.\n' +
       'If no entry for your organism exists in KEGG and/or BioCyc, the gap analysis cannot be done.')

[cb-Hades]

I added a logger for all modules currently using logging and changed logging.xxx to logger.xxx.
The logger can now be propagated with the refinegems keyword.