Implement advanced (e.g. expanded ensemble) parsers for GROMACS/provide sample data

[davidlmobley]

As per #11 , we need some more advanced parsers for expanded ensemble and other more sophisticated free energy calculations for the GROMACS side of things. @mrshirts and @trje3733 will help with this, though the likely timescale is a couple of months.

Progress could perhaps be made sooner if sample XVG files could be provided. @mrshirts , are you currently doing these calculations or do you know anyone who is, so we could get some samples?

[mrshirts]

I have a set of xvg files that cover a lot of these cases. What's the best way to get them to you?

[davidlmobley]

If they're small, @mrshirts , you can upload a zip here. Otherwise, you should put in Google Drive or Dropbox or something similar (someplace that gives you a shareable URL) and put the URL here.

[mrshirts]

Working on it. Trying to figure out why alchemical-analysis is having issues parsing these files now.

[davidlmobley]

@mrshirts - that's part of why I want things to come in through alchemlyb. I'm fairly convinced alchemical-analysis needs a complete rewrite/rearchitecting to be really maintainable, and I'd like it to rely on alchemlyb to get data IN and to drive analysis. Then it would just add bells and whistles on top of alchemlyb.

[mrshirts]

test_alchemical.zip

OK, here we go. Some test files, plus the output from alchemical_analysis.py. I'm happy to explain anything that doesn't make sense, or how alchemical_analysis.py is doing the parsing.

[orbeckst]

Once @trje3733 is eligible as an assignee, add him to the issue.

[orbeckst]

@trje3733 do you have any questions on how to proceed? Would it help to discuss next Monday at the scheduled conference call?

[orbeckst]

@trje3733 I only just realized that you opened alchemistry/alchemtest#16... looking at it now. (see also alchemistry/alchemtest#16 (comment) to get quicker reactions)