mdanalysis

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use AtomGroup in place of selection strings

4

**Is your feature request related to a problem? Please describe.** Many analysis methods (`Contacts`, old and new H-bond analysis PR #2237, ...) require the user to provide _selection strings_ and...

orbeckst

Guessing a read attribute

3

## Is your feature request related to a problem? ## continuing on the context-aware guesser project on #3753 I'm wondering what is the most suitable action to take if the...

aya9aladdin

MAINT: improve auto-labeling

2

I should mention that the approach to auto-labeling that we currently use for PRs and stuff was rejected upstream and replaced with something that is supposed to work better re:...

tylerjereddy

Change order of arguments for adding auxiliary data for 3.0 release

2

## Is your feature request related to a problem? ## Currently, auxiliary data is added as such: ```python aux = mda.auxiliary.EDR.EDRReader(edr_file) u.trajectory.add_auxiliary(aux_spec, aux) ``` i.e. ```python u.trajectory.add_auxiliary({"temp": "Temperature"}, aux) ```...

BFedder

# Is your feature request related to a problem? If a residue has multiple atoms with the same name, they are silently skipped over without any warnings. One can provide...

ozyo

Long term solution for units in AuxReaders and in general

9

## Is your feature request related to a problem? ## Some discussions on #3749 brought up conversion of units in the `AuxReaders`. Our current solution used in the coordinate readers...

hmacdope

Consolidate TopologyAttrs with consistent meanings

6

TopologyAttrs are a bit of a mess right now, and the documentation is not up-to-date. This is a list of some inconsistencies I found. ## atomiccharge The GAMESS parser uses...

lilyminium

Type hint for visualization module

3

Fixes # Changes made in this Pull Request: - PR Checklist ------------ - [ ] Tests? - [ ] Docs? - [ ] CHANGELOG updated? - [ ] Issue raised/referenced?

umak1106

Make Cython a build requirement

6

We've been saying we'd do this for ages but never go around to it. Making Cython required at build time (which is sorta is because of pyproject.toml) would make deployment...

IAlibay

Follow up from #1901 For 3.0 we should remove the tempfactor aliases.

IAlibay