clean API pages batch 1to4

[namiroues]

Fixes #4998

The edits in this PR only apply to non-autogenerated API documentation pages. I did not modify any auto-generated API reference files (e.g., those populated via automodule, autoclass, autofunction, etc.).

All changes were made to manually written .rst files that provide curated narrative content or structured overviews (e.g., analysis.rst, topology.rst, parallelization.rst). These are not overwritten by Sphinx during builds and are safe to edit directly.

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--4999.org.readthedocs.build/en/4999/

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.41%. Comparing base (35d9d2e) to head (cff9772).
Report is 4 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4999      +/-   ##
===========================================
- Coverage    93.42%   93.41%   -0.02%     
===========================================
  Files          177      189      +12     
  Lines        21859    22931    +1072     
  Branches      3078     3079       +1     
===========================================
+ Hits         20422    21421     +999     
- Misses         986     1059      +73     
  Partials       451      451              

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[orbeckst]

I probably won't get to reviewing for a while because there's too much GSOC to do, sorry. Please find another reviewer.

[RMeli]

LGTM!

Only a few very minor comments and nitpicks. (I'm not a native speaker, so please disregard as you see fit.)

[namiroues]

Thanks @RMeli for the comments. I made the changes.

[orbeckst]

lgtm

[orbeckst]

@micaela-matta can you please shepherd the PR to completion?

[orbeckst]

@namiroues when someone approves your PR, you don't need to ask for their review again. They trusted you you'd do the right thing and they might not have time to just say "yes" again — people often don't have 5 minutes to open a PR and look at it for a LGTM. EDIT: It's also bad for getting your PR merged because the re-request deletes their previous approval and then your perfectly fine PR shows up as "no approvals". I added my approval a few days ago, just so that there's a "ok" on it because @RMeli had already signed off. We probably could have merged this PR 2 weeks ago.

I'll now leave the actual finalizing/merging to @micaela-matta .

EDIT: I was wrong, the approval is recorded and not deleted... it's just confusing when you look at the reviewer list and nobody has green tickmark.

[RMeli]

Sorry, I missed this re-review request!

I agree with @orbeckst that it is not necessary to re-request a review on approval (unless you completely change the PR).

[RMeli]

EDIT: I was wrong, the approval is recorded and not deleted... it's just confusing when you look at the reviewer list and nobody has green tickmark.

I don't think you were wrong. The approval is indeed recorded in the PR history, but it doesn't show up in the top level (PR reviewers, PR list, etc.) and I don't think it counts as a required review to allow merge.