Logger config overrides client logger config

[uniqueg]

Problem

When importing genomepy before setting a host application's logger config, genomepy's logging configuration is used instead.

Similar issues in other packages:

• https://stackoverflow.com/questions/66747718/overriding-a-third-party-modules-logger
• functorch import messed up python logging module pytorch/pytorch#85952

To reproduce

Put the following in a script:

#!/usr/bin/env python3
import logging

import genomepy

logging.basicConfig(level=logging.INFO, format="%(message)s")

LOGGER = logging.getLogger("my_script")
LOGGER.info("Log message")

Running the script yields:

Log message

Rerunning the script after removing the import genomepy line (or moving it after the logging.basicConfig() call) yields:

INFO:my_script:Log message

Expected result

Importing a package should not affect the host application's logging configuration, even when it is imported before the host logger is configured.

Possible resolution

Instead of configuring the genomepy logger configuration in the library, consider configuring it in the CLI entry point (module genomepy.cli) instead. That way, host applications consuming genomepy can configure their logger any way they want, while your intended logging behavior is set for users of the genomepy console script.

Workaround

A workaround is to import genomepy after configuring the host application's logger.

System info

OS version: Ubuntu 20.04.5 LTS
Python version: 3.7.12
genomepy version: 0.15.0

[siebrenf]

Could you see if #241 fixes the issue? Unfortunately, I can't reproduce your issue! Here's what I tried:

scratch_12.py

#!/usr/bin/env python3
import logging
import genomepy

logging.basicConfig(level=logging.INFO, format="This is a logger message: %(message)s")

# promts a message
genomepy.manage_config("generate")

LOGGER = logging.getLogger("my_script")
LOGGER.info("Log message")

[uniqueg]

Strange...

With the exact same script I get the following output:

Created config file /home/uniqueg/.config/genomepy/genomepy.yaml
INFO:my_script:Log message

I'm at the airport, so no chance to try the PR right now, but will report back when I find the time. Thanks a lot.

[uniqueg]

Note that I installed genomepy via pip, not conda - maybe that makes a difference...

[uniqueg]

When installing dependencies via Mamba and then installing genomepy from the PR in #241 via pip install ., the genomepy logger does not hijack the manual logging config - neither in my test case nor in yours!

However, the situation is a little different, so I cannot say for sure whether it will fix the problem in the pip based installation...

[uniqueg]

In fact, when I check out the master branch and install via pip install ., I also cannot reproduce the issue I have reported. So either it's already fixed on the master branch OR it's really an issue that is specific to the installation from PyPI...

[siebrenf]

I'm hoping the new version magically fixes this 🤞