Port in plotting/analysis functionality from alchemical-analysis and yank about alchemlyb HOT 7 OPEN

Cool, I'll try to keep posted on this. Automated bootstrap error (better that the internal error estimator in most cases).

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I already started point 4. in https://github.com/harlor/alchemlyb/tree/autocorrelation_analysis maybe I'll find time on the weekend to continue.

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Dear all.

Is this still being implemented? I am working on something which would benefit from the plotting included in achemical-analysis. I think a can help with the porting.

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Hi @luancarvalhomartins, welcome to alchemlyb!

I don't believe anyone is working on this at the moment; @harlor may want to share his thoughts. If you're interested in taking on the porting, I'd be happy to work with you in iterating on it.

There is interest beyond what is perhaps already listed here in the nascent FreeEnergyFramework that we will also want to build tooling to support, but I think starting with reproducing what is available from alchemical-analysis is the best place to begin. The patterns developed will certainly shape how we support plotting in other areas to come!

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Ok, I have good and bad news about that. Good news is that I ported and expanded parts of alchemical-analysis, specifically plotdFvsTime, plotdFvsLambda1, plotCFM and I am now writing something somewhat similar to Replica Mixing Convergence from YANK. Bad news is that I have done in a temporary way to be able to use on the I am working on. I will write a patch to alchemlyb adding a analysis module, but I think I will do that fully after I finish the task at hand.

@dotsdl , I am writting a separate email so we can coordinate on the port.

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In the spirit of rapid development, I would suggest just making a quick and dirty PR and then work from there with code reviews (instead of waiting for the "perfect" patch that's correct and 100% fits...). Experience shows that with new code coming into a reasonably established library such as alchemlyb there are many little things that need to be changed and adjusted anyway (and the only people who actually know these things are the developers/code reviewers), so no need to be even close to the final product on the first go round.

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Yes, I agree with the rest here. This is something we still want (and the lack of the functionality here means people occasionally ask me for help with alchemical-analysis and I have to decline) but it is not done yet.

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