Standardize atomicdistances to use results

[charity-g]

Fixes #4819

Changes made in this Pull Request:

• MDAnalysis.analysis.atomicdistances.AtomicDistances results are now consistent with expectedanalysis documentation data type = Results (Issue analysis.atomicdistances.AtomicDistances does not use Results #4819)

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: no

PR Checklist

• Issue raised/referenced?
• Tests updated/added?
• Documentation updated/added?
• package/CHANGELOG file updated?
• Is your name in package/AUTHORS? (If it is not, add it!)
• LLM/AI disclosure was updated.

Developers Certificate of Origin

I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

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📚 Documentation preview 📚: https://mdanalysis--5347.org.readthedocs.build/en/5347/

[BradyAJohnston]

Some suggestions that should fix the issues with running tests.

The black formatter is also failing. You can run it like this:

uvx black~=24.0 package

[orbeckst]

@charity-g based on discussion in #4822 (comment) we will continue with this PR. Have a look at @BradyAJohnston 's comments and feel free to take it out of draft mode.

[orbeckst]

The first thing is to make the code (and tests) run, following Brady's comments. Then please address my inline comments. Focus this PR just on the API change. CHANGELOG and docs must be very clear.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.84%. Comparing base (379d296) to head (ccf4761).
⚠️ Report is 1 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #5347   +/-   ##
========================================
  Coverage    93.84%   93.84%           
========================================
  Files          182      182           
  Lines        22497    22499    +2     
  Branches      3200     3200           
========================================
+ Hits         21113    21115    +2     
  Misses         922      922           
  Partials       462      462           

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[orbeckst]

There are two doc/changelog fixes that I'll add. Otherwise looks good to me! Thank you!

[talagayev]

LGTM, good job @charity-g 😸

[orbeckst]

@BradyAJohnston does this look good to you?

@talagayev are you keeping an eye on the PR so that you can squash-merge when everybody is happy?

p.s.: I messed up the merge of the latest develop into this branch (must have forgotten to actually accept my edits) and needed to manually fix.

[orbeckst]

@talagayev oops — you were reviewing while I was typing ⚡

[talagayev]

@talagayev oops — you were reviewing while I was typing ⚡

All good no worries :) was checking and going that PR on Sunday and looked good to me, added the checkboxes for some of the files, but had to focus on preparing something for work so forgot to approve it. Saw you pushing now the commits so double checked the files and finished checking the remaining boxes to approve the PR :)