Add ASV benchmark for Contacts analysis

[Amarendra22]

Summary

This PR adds an ASV benchmark for the Contacts analysis module.

The benchmark measures the runtime of Contacts.run() using the PSF/DCD dataset from MDAnalysisTests. This allows tracking
performance changes in the native contacts analysis workflow across MDAnalysis versions.

Benchmark Added

analysis.contacts.ContactsBench.time_contacts_run

Motivation

The Contacts analysis is commonly used to calculate native contacts in molecular dynamics trajectories. Adding a benchmark
helps detect performance regressions and measure improvements in future optimizations.

LLM / AI generated code disclosure

LLMs or other AI-powered tools were used in this contribution: No

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📚 Documentation preview 📚: https://mdanalysis--5291.org.readthedocs.build/en/5291/

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.82%. Comparing base (50dc512) to head (b1f3e3e).

Additional details and impacted files

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##           develop    #5291   +/-   ##
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  Coverage    93.82%   93.82%           
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  Files          182      182           
  Lines        22487    22487           
  Branches      3196     3196           
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  Hits         21099    21099           
  Misses         925      925           
  Partials       463      463           

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[orbeckst]

Looks pretty good already. Please

• format with black
• add yourself to the end of AUTHORS (if you're not already in there)
• add an entry to CHANGELOG under Enhancements (see other examples of benchmarks)

EDIT: please also vary method='hard_cut' | 'soft_cut' | 'radius_cut' and pbc=True | False.

[orbeckst]

@Amarendra22 I've seen at least one other PR of yours. I encourage you to focus on one PR and try to get that merged. For MDAnalysis as a project it's much more important to get some work done well then all work started and never finished.

[Amarendra22]

I am sorry for the delayed response, I was occupied with some other work over the past few days. I have implemented the requested changes:

• format with black
• add yourself to the end of AUTHORS (if you're not already in there)
• add an entry to CHANGELOG under Enhancements (see other examples of benchmarks)
• vary method='hard_cut' | 'soft_cut' | 'radius_cut' and pbc=True | False

Please let me know if anything else should be improved.

[orbeckst]

Thank you for addressing my changes. However, the PR contains changes unrelated to ContactAnalysis benchmarks that should be removed — these belong into a separate PR.

Please also address the comments. Thanks.

[Amarendra22]

Thank you for the review and for pointing this out.
I have removed the unrelated changes so that the PR only contains the Contacts ASV benchmark along with the corresponding updates to AUTHORS and CHANGELOG. I have also addressed the remaining comments.

Please let me know if any further adjustments are needed.