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BEN: Add HydrogenBondAnalysis benchmark for performance tracking#5309

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Dreamstick9 wants to merge 6 commits intoMDAnalysis:developfrom
Dreamstick9:benchmark/hydrogen-bond-analysis
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BEN: Add HydrogenBondAnalysis benchmark for performance tracking#5309
Dreamstick9 wants to merge 6 commits intoMDAnalysis:developfrom
Dreamstick9:benchmark/hydrogen-bond-analysis

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@Dreamstick9
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@Dreamstick9 Dreamstick9 commented Mar 14, 2026

Changes made in this Pull Request:

  • Added ASV benchmarks class "HydrogenBondAnalysisBenchmark" in mdanalysis/benchmarks/benchmarks/analysis/hbond_analysis.py
  • it benchmarks hbond.run() across different number of frames([2,5,10]) using waterPSF/waterDCD test files

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes / no
no

PR Checklist

  • Issue raised/referenced?
  • Tests updated/added?
  • Documentation updated/added?
  • package/CHANGELOG file updated?
  • Is your name in package/AUTHORS? (If it is not, add it!)
  • LLM/AI disclosure was updated.

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.


📚 Documentation preview 📚: https://mdanalysis--5309.org.readthedocs.build/en/5309/

@Dreamstick9
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For the second commit "Update CHANGELOG" i added the PR no. directly through github so the commit message was autogenerated by Co-pilot, i didn't notice this then but wanted to make it clear

@Dreamstick9
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hey @orbeckst this was my first time adding a benchmark, i would appreciate any feedback!

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codecov bot commented Mar 14, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.83%. Comparing base (50dc512) to head (1e348b2).

Additional details and impacted files
@@           Coverage Diff            @@
##           develop    #5309   +/-   ##
========================================
  Coverage    93.82%   93.83%           
========================================
  Files          182      182           
  Lines        22487    22487           
  Branches      3196     3196           
========================================
+ Hits         21099    21100    +1     
+ Misses         925      924    -1     
  Partials       463      463           

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@Dreamstick9 Dreamstick9 force-pushed the benchmark/hydrogen-bond-analysis branch from 5d9b75c to 3ed9564 Compare March 14, 2026 15:23
@Dreamstick9 Dreamstick9 force-pushed the benchmark/hydrogen-bond-analysis branch from a9617f6 to 1bc7e6d Compare March 14, 2026 15:27
@Dreamstick9 Dreamstick9 force-pushed the benchmark/hydrogen-bond-analysis branch from 7f07862 to 24b39ca Compare March 14, 2026 17:04
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