Jonathan Barnoud

> ```python > >>> context = Context.from_files('martini.itp', 'martini_aa.itp', > 'martini_ions.itp', name='my_martini') > >>> u = mda.Universe('martini.gro') > >>> u.guess_TopologyAttr('masses', from_attrs=['names', 'resnames'], > context='my_martini') > ``` I really like that. I...

> MARTINI all have either 72 (which is the case for non-polarizable version) or 36 and 72 for (polarizable version). The particle which has a mass of 36 can be...

Do not forget to stop ignoring the module in thee mypy config file.

``` package/MDAnalysis/analysis/polymer.py:78: error: "AtomGroup" has no attribute "__iter__" (not iterable) package/MDAnalysis/analysis/polymer.py:87: error: "AtomGroup" has no attribute "__iter__" (not iterable) ``` There are a bunch of errors like this one. We...

@ALescoulie these 2 mypy errors are about one of your recent changes. Maybe you are interested in having a look? ``` package/MDAnalysis/analysis/nucleicacids.py:134: error: Incompatible types in assignment (expression has type...

> Random guesses but does using > > '''python def **iter**(): pass ''' > > or the forward declaration as a string > > '''python ag: 'AtomGroup' ''' I expect...

Here is a common pattern that is annoying mypy : an attribute is set to None in init, it is given a value in prepare, single_frame and conclude assume that...

I would put that module on hold. @aya9aladdin is actively working on it so your work here is extremely prone to merge conflicts.

I have seen at least two shots given at the issue, one of them being from you if I well remember. They were dealing with CG universes, though. I am...

Looks simple enough to me that the maintenance burden should be minimal. On the contrary to other analyses, we all have a good understanding of what is happening and there...