Zhiyi Wu

@orbeckst Sorry for the delay. I have addressed the comments. I have removed most of the no cov. I have not changed the iloc as it is not so straightforward...

@orbeckst Sorry, I have pushed things to the wrong branch. I have removed the commit.

@orbeckst Thanks for the review. I think the major issue is with AutoMBAR and the case issue. To enforce uppercase, we could change the current AutoMBAR to AUTOMBAR. However, this...

@orbeckst Thanks for the review. I have - changed the change log - add the explanation to the convergence analysis - add tests to cover the extract dhdl and n_uk...

@wesselb Thank you. No it is not urgent.

Thanks.

@lohedges Thanks. When looking at the code, I see examples like `mol_edit.setProperty("test", Sire.Base.wrap(True))`, I wonder if this is the recommended practice or just `mol_edit.setProperty("test", True)` is enough?

@lohedges It seems that on my computer that `mol_edit.setProperty("test", True)` works. So your suggestion is that I should do `mol_edit.setProperty("test", Sire.Base.wrap(True))` to avoid any unexpected outcome.

@lohedges Thanks for the explanation. Another question, I wonder why do you copy the files, change something and then spawn the process manually in here https://github.com/michellab/BioSimSpace/blob/devel/python/BioSimSpace/FreeEnergy/_relative.py#L819-L865 Instead of just reuse...

@lohedges Thanks. The issue that I'm having is that I noticed that `init-lambda-state` was not set properly if I only config it in https://github.com/michellab/BioSimSpace/blob/devel/python/BioSimSpace/Process/_gromacs.py#L569 Then I noticed that it is...