Jonathan Barnoud

As you wrote in your summary email, it is time to focus on the tests. Before even writing new tests, most of the existing tests should pass. At this point,...

Looking at the CI error report, another issue seems that you try guessing the masses before guessing the types: ``` 2022-08-01T04:37:58.3102637Z ___________ ERROR at setup of TestFHIAIMSWriter.test_write_selection ___________ 2022-08-01T04:37:58.3102880Z [gw0]...

About https://github.com/MDAnalysis/mdanalysis/pull/3753#issuecomment-1200827768 > I have seen many changes recently, but none seemed to touch the line I mentioned above. Just to clarify, I expect that the issue with Universe.empty can...

By the way, thank you for the pep8 fixes. I know it must have been annoying to do but it makes a big difference in the long run.

> That's why I'm trying to check that guessing happens when a topology came from a parser that already used to call guessers, not any other source that doesn't need...

From your table, the rule looks rather simple : if it is read do not guess, even if it is in the list of things to guess. In any case...

> We are removing documentation about things which are currently guessed by default By default, masses and types are guessed if they cannot be read. This was the overall behaviour,...

We are almost there functionally. Do you keep track of what still needs to be done?

With #3779 merged, you should merge the develop branch into this one. Be careful that there is at least one merge conflict to solve.

Do not forget to spend some time on the documentation. There, you have 3 distinct audiences: * regular users of MDAnalysis who will use the guesser * advanced users who...