Remove logging abstraction to facilitate debugging and reduce bloat.

[sobolevnrm]

Also performed minor delinting.

Fixes #108

[codecov]

Codecov Report

Merging #109 (e081bd5) into master (f3bbd80) will increase coverage by 0.03%.
The diff coverage is 60.10%.

@@            Coverage Diff             @@
##           master     #109      +/-   ##
==========================================
+ Coverage   73.27%   73.31%   +0.03%     
==========================================
  Files          24       24              
  Lines        3982     3987       +5     
==========================================
+ Hits         2918     2923       +5     
  Misses       1064     1064              

Impacted Files	Coverage Δ
propka/parameters.py	62.80% <21.73%> (+0.15%)	⬆️
propka/ligand_pka_values.py	26.08% <25.00%> (+3.55%)	⬆️
propka/coupled_groups.py	76.10% <28.57%> (+0.15%)	⬆️
propka/bonds.py	60.95% <30.00%> (+0.15%)	⬆️
propka/run.py	63.88% <33.33%> (-7.08%)	⬇️
propka/lib.py	65.71% <50.00%> (-2.50%)	⬇️
propka/version.py	63.70% <57.14%> (+0.27%)	⬆️
propka/group.py	77.26% <64.70%> (+0.03%)	⬆️
propka/hydrogens.py	15.76% <66.66%> (+0.46%)	⬆️
propka/molecular_container.py	92.59% <75.00%> (ø)
... and 6 more

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[orbeckst]

Overall this looks good.

There's one message that was originally tagged "info" but is clearly "error" – see comment.

It's not clear to me if the default for logging is to show messages and at which level. There should be some user documentation for how to enable different levels. Similarly, is there a commandline option to change the logging level?

[orbeckst]

This looks like latex, meant to be copied and pasted. Is this used by anyone? If so, perhaps make it easier to grep it from the logs by prefixing every line with some marker such as "LATEX>" or somesuch??

It might not be worth any effort, though. Up to you.

[sobolevnrm]

You and @speleo3 know that I love to delete code... and I don't think anyone is using this. I would happily delete if you both agree.

[orbeckst]

It's the same to me – I am pretty sure I never looked at it.