WIP: nearest N particle search

[richardjgowers]

Fixes #

Changes made in this Pull Request:

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[richardjgowers]

@hmacdope I think if you get your head round how the results container is keeping track of the "best" N results, then how the cubeiter works the actual search function isn't that nasty tbh. It's currently failing because of a double free somewhere, so I think I've got my cython wrong somewhere but I'll track that down.

[codecov]

Codecov Report

Merging #3382 (a98e29d) into develop (8f9f402) will increase coverage by 0.01%.
The diff coverage is 96.73%.

@@             Coverage Diff             @@
##           develop    #3382      +/-   ##
===========================================
+ Coverage    93.62%   93.63%   +0.01%     
===========================================
  Files          176      176              
  Lines        22839    22915      +76     
  Branches      3225     3227       +2     
===========================================
+ Hits         21382    21456      +74     
- Misses        1406     1408       +2     
  Partials        51       51              

Impacted Files	Coverage Δ
package/MDAnalysis/lib/distances.py	97.83% <77.77%> (-0.58%)	⬇️
package/MDAnalysis/lib/nsgrid.pyx	97.88% <98.79%> (+0.23%)	⬆️
package/MDAnalysis/coordinates/PQR.py	95.23% <0.00%> (+0.91%)	⬆️

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[pep8speaks]

Hello @richardjgowers! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file testsuite/MDAnalysisTests/lib/test_distances.py:

Line 1393:1: W293 blank line contains whitespace
Line 1400:80: E501 line too long (88 > 79 characters)
Line 1405:80: E501 line too long (94 > 79 characters)
Line 1409:1: W391 blank line at end of file

[cbouy]

I'm a bit late to the party but doesn't the KDTree query from scipy already do what you need?

[richardjgowers]

Yes, but KDTree won’t (ever) do periodic boundaries

…

On Wed, Jan 12, 2022 at 11:42, Cédric Bouysset ***@***.***> wrote: I'm a bit late to the party but doesn't the KDTree <https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.cKDTree.html> query <https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.cKDTree.query.html> from scipy already do what you need? — Reply to this email directly, view it on GitHub <#3382 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACGSGBZLPOUODOVAXRVCPDLUVVSJVANCNFSM5BQORAGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[orbeckst]

use KDTree as suggested by @cbouy ?