add ignore_same_residue kwarg to InterRDF

[orionarcher]

Changes made in this Pull Request:

This adds the ability to include the same residues in both g1 and g2 without blowing up the RDF calculation. Specifically, it adds a ignore_same_residue kwarg that excludes pairs of atoms with the same resindice from the distance calculation. This should be useful when a user wants to understand the correlation of a species with itself (as I do now).

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced? (N/A)

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📚 Documentation preview 📚: https://mdanalysis--4161.org.readthedocs.build/en/4161/

[github-actions]

Linter Bot Results:

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

Some issues were found with the formatting of your code.

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[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.01 🎉

Comparison is base (2e39563) 93.61% compared to head (29606f2) 93.62%.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4161      +/-   ##
===========================================
+ Coverage    93.61%   93.62%   +0.01%     
===========================================
  Files          193      193              
  Lines        25170    25295     +125     
  Branches      4059     4063       +4     
===========================================
+ Hits         23562    23683     +121     
- Misses        1092     1096       +4     
  Partials       516      516              

Impacted Files	Coverage Δ
package/MDAnalysis/analysis/rdf.py	100.00% <100.00%> (ø)

... and 11 files with indirect coverage changes

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[orionarcher]

Iterated slightly on this. Now users can select "residue", "segment", or "chain" to exclude. It will automatically map to the resindices, segindices, and chainID attributes (though I'm not sure chainid is the right option?). I feel this is a bit friendlier to new users than forcing them to understand the intricacies of 'residvsresindicesvsresname`, and covers the vast majority of use cases. Still happy to change it up if other implementations are preferred.

[hmacdope]

Quick comments.

[orionarcher]

Fixed @hmacdope's requested. Unless there are further requests for changes, this is ready to merge.

[hmacdope]

Few changes and a tiny bit more testing but almost there.

[orbeckst]

@hmacdope or @RMeli — could one of you assign the issue to yourself, please, just so that it's clear that someone is in charge following up on comments and eventually merging? Thanks.

[orionarcher]

I added new tests for segment and chain and added @RMeli cleanup suggestions. Thanks for all the feedback.

[RMeli]

Thanks @orionarcher. A few last nitpicks (sorry), otherwise LGTM.

[RMeli]

LGTM, thanks @orionarcher. I'll try to re-run the failed actions before approving, it failed because of time limits: https://dev.azure.com/mdanalysis/mdanalysis/_build/results?buildId=5981&view=logs&j=7a9c7d2c-346e-591b-84bb-5490fd358201

[RMeli]

/azp run

[azure-pipelines]

Azure Pipelines successfully started running 1 pipeline(s).

[RMeli]

Thanks @orionarcher. @hmacdope would you mind having the last look and merge? Thanks.

[hmacdope]

Looks great @orionarcher thanks so much. This is a great contribution and will be super useful to many.

[orionarcher]

Yay thanks y'all!