New guesser interface broke behaviour downstream

[IAlibay]

Several mdakits' CI broke overnight with the following error: ValueError: there is no reference attributes in this universeto guess types froma

This means that the new guessers interface did a breaking change that we aren't aware of.

This will need to be fixed before the 2.8 release.

[lilyminium]

I'm just out but can look at this in an hour or so!

[IAlibay]

Prolif also fails because we removed the guessers interface: ModuleNotFoundError: No module named 'MDAnalysis.topology.guessers'

[IAlibay]

Similarly pytim fails because it attempts to call guess_types but it no longer exists: https://github.com/MDAnalysis/MDAKits/actions/runs/11422930196/job/31781508635#step:10:33

[IAlibay]

cc @Marcello-Sega - this is where we're tracking the breaking changes from the guessers update: https://github.com/MDAnalysis/MDAKits/issues/217

[IAlibay]

I have raised #4749, #4750, and #4751 as issues that need fixing before the release.

[orbeckst]

@lilyminium and @IAlibay I put both your names on this omnibus issue as the two people with best insight into what needs to be done.

You also already created PRs addressing all the sub-issues (thank you!) so I assigned the issues to the PR authors so that it's clear that we are actively working on the problems.

Please ask for help where needed.

[orbeckst]

I created the post https://github.com/MDAnalysis/mdanalysis/discussions/4758 as an official note.

[IAlibay]

This is now done as far as I know.