Creates AnalysisBase function PropkaTraj

[IAlibay]

Supersedes #25
Fixes #23, #19, and temporarily addresses #24

This ended up a relaxing enough weekend thing to do...

Changes made:

• Created a new AnalysisBase class named PropkaTraj which essentially has the same functionality as get_propka.
• Major differences from get_propka include;
  • temporarily files are now written to the current directory (in the future we should consider moving this to an actual temporary directory).
  • if a bad frame is identified but skip_failure is True, then a warning is thrown, but the statistics about the number of bad frames still users the logger (can go either way here, I just thought you'd definitely want to warn users they lost a frame, but statistics is more of a log thing).
• get_propka has now been deprecated.
• Both get_propka and PropkaTraj now warn users if they don't pass purely protein residues as a selection. This can be removed once the MDAnalysis writer is fixed (should be easy enough to do, but I can't seem to find a good reference for the full list of "standard residues" ).
• Adds test to cover trajectories with bad frames and various warnings (coverage is now 100%).
• Updated the notebook, README, and INSTALL instructions to reflect the new class.

Questions:

• I've set the next version as 1.0.3 and the deprecation to occur in 2.0.0. My thought here is that if the next version is propka 3.2 compatible, you might want to bump up the version number by a major number. That can be changed though.

[IAlibay]

Does the copyright notice need to be changed? I know in the past you've added authors to it, but I thought it be better to ask.

[orbeckst]

add yourself & change the year, please

[IAlibay]

Do you have a preferred ordering? It's not alphabetical, the closest I could find was that it was ordered by number of commits, but I guess it's more "first author" "corresponding author"?

Also should Shujie Fan be added too?

[orbeckst]

You're thorough :-) – and thanks for remembering Shujie.

Let's do David, Irfan, Ricky, Armin, Shujie, Oliver.

[codecov]

Codecov Report

Merging #26 into master will increase coverage by 22.91%.
The diff coverage is 100.00%.

@@             Coverage Diff              @@
##           master       #26       +/-   ##
============================================
+ Coverage   77.08%   100.00%   +22.91%     
============================================
  Files           2         2               
  Lines          48       103       +55     
============================================
+ Hits           37       103       +66     
+ Misses         11         0       -11     

Impacted Files	Coverage Δ
propkatraj/__init__.py	100.00% <100.00%> (ø)
propkatraj/propkatraj.py	100.00% <100.00%> (+23.40%)	⬆️

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[orbeckst]

Awesome!

Minor things in comments – mainly that the next release will be 1.1.0 instead of 1.0.3.

[IAlibay]

Thanks for the review @orbeckst, that should be everything addressed.

[orbeckst]

Cheers!