Implement scipy.spatial.cKDTree for orthorhombic and no PBC

[Aryaman-Chaudhri]

Fixes #5114

Changes made in this Pull Request:

-Added benchmarks/benchmarks/neighbors.py proving scipy.spatial.cKDTree is faster than the existing Implemetation.

-Implemented scipy.spatial.cKDTree backend in package/MDAnalysis/lib/pkdtree.py by building a new class.

-Updated testsuite/MDAnalysisTests/lib/test_pkdtree.py to verify both PeriodicKDTree (for API stability) and AugmentedPKDTree.

-Updated package/AUTHORS and package/CHANGELOG to reflect the contribution.

PR Checklist

• Issue raised/referenced?(Fixes Use native scipy periodic KDTree for orthorhombic boxes? #5114 )
• Tests updated/added?(Yes, in test_pkdtree.py)
• Documentation updated/added?(might need improvement based on feedback)
• package/CHANGELOG file updated?
• Is your name in package/AUTHORS? (If it is not, add it!)

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--5193.org.readthedocs.build/en/5193/

[BradyAJohnston]

Thanks for working on this. Before we do any kind of review we need you to address the currently failing tests and also format using black to pass the linting checks.

[codecov]

Codecov Report

❌ Patch coverage is 82.14286% with 20 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.75%. Comparing base (9cbc8ea) to head (68a7f40).
⚠️ Report is 9 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/lib/pkdtree.py	82.14%	10 Missing and 10 partials ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5193      +/-   ##
===========================================
+ Coverage    92.72%   93.75%   +1.02%     
===========================================
  Files          180      180              
  Lines        22475    22583     +108     
  Branches      3190     3218      +28     
===========================================
+ Hits         20841    21172     +331     
+ Misses        1177      937     -240     
- Partials       457      474      +17     

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[Aryaman-Chaudhri]

Hi @BradyAJohnston , just a quick question , during working on this task , I was wondering why is 'nsgrid' not implemented anywhere , based on documentation it does have a few flaws but seems to be a well optimized and a fast function (also O(N)) atleast on paper.

[orbeckst]

@BradyAJohnston do you want to take on shepherding this PR? If so, please assign it to you.

I am happy to review (once linters pass).

[Aryaman-Chaudhri]

Hi @BradyAJohnston , @orbeckst , I think this is ready for a review .