Adding logger in global level.

[RubelMozumder]

1. Module level logger.
2. Responsive for the nomad logger.
3. No error anymore from missing fields but a log warning for those fields, groups, and attributes.

PR #175 is closed and fixed here.

[coveralls]

Pull Request Test Coverage Report for Build 7277551900

• 33 of 37 (89.19%) changed or added relevant lines in 4 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.02%) to 44.55%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pynxtools/dataconverter/convert.py	5	9	55.56%

Totals
Change from base Build 7264459327:	0.02%
Covered Lines:	4864
Relevant Lines:	10918

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💛 - Coveralls

[domna]

Two points:

• I would rather not pass the logging to each function as parameter but use the central logger
• What is the rational behind removing the UNDOCUMENTED level? I think it's not too important to have this but generally I think it's nice to have them distinguishable.

[RubelMozumder]

Two points:

• I would rather not pass the logging to each function as parameter but use the central logger
• What is the rational behind removing the UNDOCUMENTED level? I think it's not too important to have this but generally I think it's nice to have them distinguishable.

I ran the XRD reader in nomad with and without passing nomad logger in convert, I got the following results:

1. As I said if we need to get log data in another process or platform, we must pass the corresponding logger from that process or platform.
2. Nomad logger does not support string format with % opt., but support `f-string, I think which is the modern way (especially after python-3.6) to write a variable passed string.

I would say we should use f-string as the logger message and we must pass the logger as a parameter in the function if we want users to get the pynxtools log data in nomad.

Here, I added two pics with and without passing the logger from nomad.

If you follow the last PR that was #175, I had the similar opinion.

[domna]

I ran the XRD reader in nomad with and without passing nomad logger in convert, I got the following results:

1. As I said if we need to get log data in another process or platform, we must pass the corresponding logger from that process or platform.

I had a look at how nomad is integrating this to see if we'd need to use some prefix to let the logs show up. I found, however, that the get_logger function wraps this to convert this to a structured log (with time, parser etc.). So you are right, we cannot just use logging and have to pass the logger.

2. Nomad logger does not support string format with % opt., but support `f-string, I think which is the modern way (especially after python-3.6) to write a variable passed string.

Yes, I think we talked about this already. We can just go to the f-string formatting. One note: For logging it's normally recommended due to the lazy evaluation with the % syntax (i.e., if the log is not displayed the code is not run). In reality this will however not really make I difference I guess.

[domna]

LGTM