Verbosity level

[PierreSnell]

Describe the problem you encountered PyOpenMS is logging too much text for a production library and there is no way to reduce the verbosity.

To Reproduce Steps to reproduce the behavior:

1. Load an experiment
2. Run mass trace detection or elution peakdetection or similar algorithms
3. See :

   Progress of 'mass trace detection':
   -- done [took 0.03 s (CPU), 0.02 s (Wall)] -- 
   Progress of 'elution peak detection':
   -- done [took 0.08 s (CPU), 0.02 s (Wall)] -- 
   Progress of 'assembling mass traces to features':
   -- done [took 0.04 s (CPU), 0.02 s (Wall)] -- 

I'm converting thousands of files and I got all of the output from pyopenms where my logging get drown in the rest.

What should be happening Having a handle on the logger so we can do something like :

import logging
logging.getLogger("PyopenmsLoggerName").setLevel(ERROR)

or something similar like from pyopenms import setDebugLevel; setDebugLevel(ERROR)

System information:

• OS: Linux
• OS Version: 6.2.6
• Python version: 3.9 or 3.10
• pyopenms version: latest (pypi latest build)
• How did you install pyopenms? Please cross a box with an X.
  • [x] nightly wheel from pyopenms private pypi repo

[jpfeuffer]

Can be done with pyopenms.LogConfigHandler().setLogLevel("INFO") or any other level now.

Note there are still some limitations: https://github.com/OpenMS/OpenMS/issues/6827