Add ASV benchmarks for MDAnalysis.lib core kernels

[Amarendra22]

Summary

This PR adds ASV benchmarks for several core computational kernels in MDAnalysis.lib.

The following functions are benchmarked:

• distance_array
• self_distance_array
• calc_dihedrals
• FastNS neighbor search
• AtomNeighborSearch

These functions are widely used across MDAnalysis analysis modules and are performance-critical components. Adding benchmarks helps track performance regressions and evaluate future optimizations.

Benchmarks added

• lib.distances.DistanceArrayBench.time_distance_array
• lib.distances.SelfDistanceArrayBench.time_self_distance_array
• lib.dihedrals.DihedralBench.time_calc_dihedrals
• lib.fastns.FastNSBench.time_fastns
• lib.neighborsearch.NeighborSearchBench.time_neighbor_search

Motivation

The MDAnalysis.lib module contains low-level computational kernels that are called repeatedly by higher-level analysis tools. Benchmarking these functions improves performance monitoring and supports future optimization work.

LLM / AI generated code disclosure

LLMs or other AI-powered tools were used in this contribution: No (used for research purpose only)

)

Developers Certificate of Origin

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--5292.org.readthedocs.build/en/5292/

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.83%. Comparing base (6e837a4) to head (20607e7).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5292      +/-   ##
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- Coverage    93.83%   93.83%   -0.01%     
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  Files          182      182              
  Lines        22501    22501              
  Branches      3195     3195              
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- Hits         21114    21113       -1     
- Misses         924      925       +1     
  Partials       463      463              

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[orbeckst]

There may be some overlap with potential GSOC projects so I am going to block this PR for the time being.