Updated atom ID representation order to match AtomGroup

[ztimol]

Fixes #4181

Changes made in this Pull Request:

• Removed check that reorders atom indices - confirmed that this is okay (see original issue).
• Return topology object representation in order of underlying AtomGroup indices
• Updated tests - topology object representation now matches order of AtomGroup indices

PR Checklist

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

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📚 Documentation preview 📚: https://mdanalysis--4191.org.readthedocs.build/en/4191/

[github-actions]

Linter Bot Results:

Hi @ztimol! 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/5718701996/job/15495053589

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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

Patch and project coverage have no change.

Comparison is base (ac30c88) 93.62% compared to head (4f71bdc) 93.62%.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #4191   +/-   ##
========================================
  Coverage    93.62%   93.62%           
========================================
  Files          193      193           
  Lines        25294    25295    +1     
  Branches      4063     4063           
========================================
+ Hits         23682    23683    +1     
  Misses        1096     1096           
  Partials       516      516           

Files Changed	Coverage Δ
package/MDAnalysis/core/topologyobjects.py	98.16% <ø> (ø)

... and 1 file with indirect coverage changes

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[IAlibay]

Could you add an entry to changelog and I think this is your first PR? (I can only see a closed in in the history), if so please also add yourself to AUTHORS.

[IAlibay]

Couple of minor changes and then I think we're good to go.

[IAlibay]

Sorry about the delay and thanks for the contribution!

I'll merge once CI returns green (had some codecov issues earlier today)

[ztimol]

Not sure if you've picked this up already but two tests seemed to have timed out. Can you reinitialise them when you get the chance. Thanks.

[ztimol]

Took a while but CI tests have finally all passed. Wondering if it was just an issue on the GH side of things. Would be great if this could be merged into develop. Thanks.

[IAlibay]

@ztimol the CI issues are related to #4209 I worked on it all weekend but unfortunately we've not really been able to work out what's up here.

Re; merge - unfortunately we are blocked by #4219, I'm hoping we'll merge it tonight and then we can start merging PRs again.

In the meantime, @ztimol could you please confirm that you agree to releasing this code under the terms of the LGPLv2.1 and that your contribution also adheres to the developer certificate of origion?

[IAlibay]

Blocking for license agreement

[ztimol]

No worries. Agree to LGPLv2.1 and can confirm adherence to developer certificate of origion.

[IAlibay]

All good, thanks for your patience @ztimol !

[IAlibay]

Just to clarify @ztimol this is LGPLv2.1+ (I typoed), i.e. you it may be relased under LGPLv2.1 or any later version.