Logging for metaphlan4

Microbial community profiling MetaPhlAn
1

Given that the steps of metaphlan4 can take a while, it would be great to have logging.info() with progress updates.

For example:

import logging
logging.basicConfig(format='%(asctime)s - %(message)s', level=logging.DEBUG)

# later on
logging.info('Starting step 1...')
[...]
logging.info('Starting step N...')
2

Hi @nick-youngblut
We are currently working in a full refactoring of all the metaphlan 4 code (namely metaphlan 4.1) that will include a --verbose option for logging purposes. I will keep you posted

3

That’s great! Thanks @aitor.blancomiguez for the information. Good luck with the refactoring.