Frankenatom fix

[MattTDavies]

Made the "Frankenatom" protection more robust.
Since indexing initialises a new GroupBase, moving the dimension check to initialisation is more robust as it will also capture incorrectly created atomgroups using the AtomGroup(indices, universe) initialisation as well as just when indexing a preexisting atomgroup as was covered previously.

Fixes #4647

Changes made in this Pull Request:

• Added index dimension check to GroupBase initialisation
• Added test for improperly indexed AtomGroup initialisation
• Removed dimension check during GroupBase indexing
• Added integral check to CompontBase initialisation index value
• Added test for improperly indexed Atom initialisation

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

Developers certificate of origin

• I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

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📚 Documentation preview 📚: https://mdanalysis--4692.org.readthedocs.build/en/4692/

[pep8speaks]

Hello @MattTDavies! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file package/MDAnalysis/core/groups.py:

Line 4254:80: E501 line too long (81 > 79 characters)

Comment last updated at 2024-09-05 09:05:59 UTC

[github-actions]

Linter Bot Results:

Hi @MattTDavies! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	⚠️ Possible failure
testsuite	⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/10717324275/job/29716780262

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Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.60%. Comparing base (489905f) to head (10b6c76).
Report is 1 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4692      +/-   ##
===========================================
- Coverage    93.62%   93.60%   -0.03%     
===========================================
  Files          173      185      +12     
  Lines        21419    22488    +1069     
  Branches      3978     3979       +1     
===========================================
+ Hits         20053    21049     +996     
- Misses         903      976      +73     
  Partials       463      463              

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[richardjgowers]

lgtm @MattTDavies can you add yourself to the CHANGELOG file authors for 2.8.0?

[hmacdope]

LGTM @MattTDavies, could you just check the Developer Certificate of Origin box and then we can merge.