[REF] Move logger management to new functions

[tsalo]

Closes #719.

Changes proposed in this pull request:

• Add new functions to set up and tear down loggers, to be called at beginning and end of workflows, respectively.
• Do not propagate REPORT and REFERENCES messages to the stream. This reduces clutter in the terminal.
• Replace file-specific loggers with a general one (GENERAL).

The changes to the loggers doesn't show up in the CI, because pytest's logging is different from the logging set up in the workflows... but it looks good when run locally! Here's a snippet of my Terminal output from a local run:

INFO     tedana:tedana_workflow:463 Computing EPI mask from first echo
INFO     tedana:tedana_workflow:475 Computing T2* map
INFO     combine:make_optcom:225 Optimally combining data with voxel-wise T2* estimates
INFO     gscontrol:gscontrol_raw:50 Applying amplitude-based T1 equilibration correction

[codecov]

Codecov Report

Merging #750 (bebeb13) into main (d449925) will increase coverage by 0.08%.
The diff coverage is 96.55%.

@@            Coverage Diff             @@
##             main     #750      +/-   ##
==========================================
+ Coverage   92.61%   92.69%   +0.08%     
==========================================
  Files          27       27              
  Lines        2125     2121       -4     
==========================================
- Hits         1968     1966       -2     
+ Misses        157      155       -2     

Impacted Files	Coverage Δ
tedana/decomposition/_utils.py	0.00% <0.00%> (ø)
tedana/workflows/parser_utils.py	94.73% <ø> (-1.27%)	⬇️
tedana/utils.py	97.38% <97.05%> (-0.12%)	⬇️
tedana/combine.py	91.42% <100.00%> (ø)
tedana/decay.py	97.24% <100.00%> (ø)
tedana/decomposition/ica.py	82.75% <100.00%> (ø)
tedana/decomposition/pca.py	86.66% <100.00%> (ø)
tedana/gscontrol.py	100.00% <100.00%> (ø)
tedana/io.py	93.04% <100.00%> (ø)
tedana/metrics/_utils.py	67.34% <100.00%> (ø)
... and 9 more

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[emdupre]

The output logs look reasonable in the latest artifacts ! Just confirming that when running locally:

INFO     GENERAL:tedana.py:367 Using output directory: /tmp/data/five-echo/TED.five-echo

updates to

INFO     tedana:tedana_workflow:367 Using output directory: /tmp/data/five-echo/TED.five-echo

is that right ?

Assuming so, is there anything specific you'd like feedback on here ?

[tsalo]

@emdupre yeah, that looks right! There's nothing in particular that I'm worried about, so any review of any part of it would be appreciated.

[eurunuela]

LGTM!

[jbteves]

LGTM, this cleans up quite a bit!