Luna Morrow

Just leaving some comments here for whoever is assigned to check this PR: 1. I will be submitting a second PR to depreciate the API once I receive any feedback...

Update: That big block of code that I commented out was necessary. Turns out that its removal was causing 2 failures. I am adding it back in now, and attempting...

Thanks @yuxuanzhuang I am working through your comments now and will aim to push the updated branch shortly! Quick question about this comment: > You need to make sure acceptors_ag,...

> I also don't have experience handling depreciation before, so I might need help from @hmacdope :) Of course, all good! If you can just help me get this PR...

> Regarding depreciation, current provided code examples will break e.g. > > ```python > u = MDAnalysis.Universe(PSF, DCD) > > hbonds = HBA(universe=u) > hbonds.hydrogens_sel = hbonds.guess_hydrogens("protein") # this will...

@yuxuanzhuang I have made some changes, as I proposed above, which I will push shortly. I have pretty much eliminated the errors/failures bar these two. 1. `MDAnalysis.exceptions.NoDataError: This Universe does...

Thanks @yuxuanzhuang, and I completely understand. I appreciate you taking time out of your Easter weekend to give me a hand. Unfortunately I am really struggling with this and I...

Ok great, that is such a relief to hear @hmacdope. I have been panicking a bit! I'll focus on my written application and keep chugging away at this fix while...

> Side note while testing: slicing UpdatingAtomGroup will result in a static AtomGroup. -> need a workaround to return an `UpdatingAtomGroup` in e.g. `guess_donors` because `donors_ag` will be sliced by...

Hi @yuxuanzhuang @orbeckst @hmacdope. I'm jumping back on this PR as I have just finished off a bunch of university assessment. A couple weeks away from it was really beneficial...