ENH: Add PDB reader benchmark to track parsing performance

[Dreamstick9]

Changes made in this Pull Request:

• Contributes to performance benchmarks #1023
• Added PDBReaderBench class to benchmarks/benchmarks/traj_reader.py.
• it benchmarks PDB format reading and parsing across different number of frames ([10, 100, 500]) using the standard PDB test file.

LLM / AI generated code disclosure

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

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• 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.

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[read-the-docs-community]

Documentation build overview

📚 MDAnalysis | 🛠️ Build #33265929 | 📁 Comparing 529bbcf against latest (941d679)

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• index.html
• documentation_pages/units.html
• documentation_pages/analysis/density.html
• documentation_pages/analysis/dihedrals.html
• documentation_pages/analysis/distances.html
• documentation_pages/analysis/hbond_autocorrel.html
• documentation_pages/analysis/rms.html
• documentation_pages/analysis/wbridge_analysis.html
• documentation_pages/coordinates/TRJ.html
• documentation_pages/lib/pkdtree.html
• and 4 more...

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@@             Coverage Diff             @@
##           develop    #5394      +/-   ##
===========================================
- Coverage    93.85%   86.13%   -7.72%     
===========================================
  Files          182      182              
  Lines        22509    22509              
  Branches      3202     3202              
===========================================
- Hits         21125    19388    -1737     
- Misses         922     2668    +1746     
+ Partials       462      453       -9     

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[Dreamstick9]

I believe all these tests that are failing are due to something messed up in develop, I will try to trace the root cause and will report on discord about this

[orbeckst]

The CI failures are being addressed in other PRs. Apart from PR #5404 all quick-fix PRs are merged. You can pull the current develop branch and merge it into your add-pdb-benchmark.

Can you please locally run the trajectory benchmarks and paste the output so that I can see that the new PDB one is running with everything else?

[orbeckst]

Changes look good.

Can you please locally run the trajectory benchmarks and paste the output so that I can see that the new PDB one is running with everything else?

[Dreamstick9]

The CI failures are being addressed in other PRs. Apart from PR #5404 all quick-fix PRs are merged. You can pull the current develop branch and merge it into your add-pdb-benchmark.

Can you please locally run the trajectory benchmarks and paste the output so that I can see that the new PDB one is running with everything else?

· Discovering benchmarks
· Running 2 total benchmarks (1 commits * 1 environments * 2 benchmarks)
[ 0.00%] ·· Benchmarking existing-py_usr_local_bin_python3
[25.00%] ··· traj_reader.TrajReaderCreation.time_reads                                                                                                                                                   ok
[25.00%] ··· ============= ==========
              traj_format            
             ------------- ----------
                  XTC       4.09±0ms 
                  TRR       13.4±0ms 
                  DCD       1.64±0ms 
                  NCDF      5.69±0ms 
                  TRC       3.55±0ms 
                  PDB       6.70±0ms 
             ============= ==========

[50.00%] ··· traj_reader.TrajReaderIteration.time_strides                                                                                                                                                ok
[50.00%] ··· ============= ==========
              traj_format            
             ------------- ----------
                  XTC       8.07±0ms 
                  TRR       56.9±0ms 
                  DCD       4.01±0ms 
                  NCDF      1.80±0ms 
                  TRC       3.46±0ms 
                  PDB       5.40±0ms 
             ============= ==========

[orbeckst]

LGTM, thank you for the new benchmarks!

[Dreamstick9]

LGTM, thank you for the new benchmarks!

Thanks!, also I have started to work on another benchmark, maybe XYZ format