Use logmuse for logging setup

[stolarczyk]

alright, I brought it back to how it was set up before, so it isn't a blocking issue.

We will need to try to use logmuse for that in the future.

Originally posted by @stolarczyk in https://github.com/pepkit/looper/issues/328#issuecomment-856918904

[ayobi]

I believe logmuse is now set up and you can now use the verbs --verbosity, --silent, and --logdev. In __init__.py I commented out: https://github.com/pepkit/looper/blob/7ce633327929c44829286a3204da93fb5456d398/looper/__init__.py#L42-L50 and https://github.com/pepkit/looper/blob/7ce633327929c44829286a3204da93fb5456d398/looper/__init__.py#L110-L115 for now since they use the same verbage as logmuse's verbosity. I added: https://github.com/pepkit/looper/blob/7ce633327929c44829286a3204da93fb5456d398/looper/__init__.py#L135 and in looper.py I added: https://github.com/pepkit/looper/blob/7ce633327929c44829286a3204da93fb5456d398/looper/looper.py#L1040 and commented out some other code that was referencing the verbosity phrase.

Commit is here: fea166c

[nsheff]

Great!

Instead of commenting out, feel free to just remove any of the redundant code... I'd rather not have huge commented out code blocks of deprecated code in there; this is the benefit of version control, we can always go back to a previous commit to see old code if we need to.

[nsheff]

Hmm, it looks like you still have some logmuse-related commands in there separately in the parser, like --logging-level and --dbg. aren't these added by logmuse? So I think this is not complete yet.

[ayobi]

Yeah, I thought so about removing the code rather than commenting it out, but I was kinda doing a practice run to see how it would be. I'll clean that up tomorrow.

Looking at the tutorial, Part 2: Add CLI Args, it only mentions those three that I listed. Looking briefly in the code I see that it focuses on those 3 as well.

https://github.com/databio/logmuse/blob/1b1b712c800a71dcc8a5986b142158dd634ba208/logmuse/est.py#L45-L79

I'll take a deeper look tomorrow.