[pytim-develop] Failed CI run

[github-actions]

At least two repeated CI runs for pytim have failed.
Here is the last recorded status of the tests:

• installing python: passed
• installing the mdakit: passed
• installing mdanalysis: passed
• installing the test dependencies: passed
• running tests: fail
  Pinging maintainers: @Marcello-Sega

[Marcello-Sega]

All reported errors regard a missing attribute:

E   AttributeError: module 'MDAnalysis.topology' has no attribute 'guessers'

see, e.g., this log

This hints at a relatively recent major change in the topology module introduced by @aya9aladdin:

MDAnalysis/mdanalysis#3753

I'll try to fix it, but in the meantime if anyone has suggestions on how to do it (maybe @IAlibay?), it would be appreciated!

[IAlibay]

Thanks for looking at this @Marcello-Sega - it looks like we introduced a bit of a breaking change in the core library, we're tracking it here: MDAnalysis/mdanalysis#4748

We're still triaging things, but the plan is to fix things as much as possible in the core library for now.

[IAlibay]

@Marcello-Sega we reverted the API break, but please do be aware that the "old" guesser methods are now deprecated and will be removed in the 3.0 release of MDAnalysis (there will be at least two minor releases before this happens).

[Marcello-Sega]

Great, thanks a lot for keeping me posted @IAlibay!

Is there some example/docstring on how to use use the new implementation? I had a (very) cursory look at the code but coudln't find one.