MAINT: Replace deprecated numpy assertions in coordinates/base.py

[Dreamstick9]

Contributes to #3743

Changes made in this Pull Request:

• Replaced deprecated assert_almost_equal and assert_array_almost_equal with assert_allclose in testsuite/MDAnalysisTests/coordinates/base.py.
• Converted decimal precision to atol=10**(-decimal) and rtol=0 to maintain original test strictness.
• Added contributor name to package/AUTHORS.

PR Checklist

• [x] Issue raised/referenced?
• [ ] Tests updated/added?
• [ ] Documentation updated/added?
• [x] package/CHANGELOG file updated?
• [x] Is your name in package/AUTHORS?

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Documentation preview : https://mdanalysis--5156.org.readthedocs.build/en/5156/

[codecov[bot]]

Codecov Report

:white_check_mark: All modified and coverable lines are covered by tests. :white_check_mark: Project coverage is 92.72%. Comparing base (5c11b50) to head (b35276c). :warning: Report is 5 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #5156   +/-   ##
========================================
  Coverage    92.72%   92.72%           
========================================
  Files          180      180           
  Lines        22457    22472   +15     
  Branches      3186     3188    +2     
========================================
+ Hits         20823    20837   +14     
  Misses        1177     1177           
- Partials       457      458    +1     

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[Dreamstick9]

Hi! The Windows test failed in test_density.py with a MaybeEncodingError (unrelated to my changes). Could you please trigger a re-run?

[IAlibay]

/azp run

[azure-pipelines[bot]]

Azure Pipelines successfully started running 1 pipeline(s).

[Dreamstick9]

@IAlibay Hi, if you get some free time please review this PR and if there are any other changes that you would like please let me know!

[Dreamstick9]

@marinegor Thanks for the review!

I have applied all your suggested commits (reverting ref.prec in those spots and fixing the 0.01 tolerance).

Regarding the other places where I used 1e-3—do you want me to do a bulk revert of all those back to ref.prec as well, or are the remaining ones acceptable as they are?

[marinegor]

Since the issue you're solving doesn't assume changing test logic at all, I'd suggest you revert the ref.spec wherever it was used.

[Dreamstick9]

@marinegor Done! I've reverted the remaining 19 instances of the hardcoded 1e-3 tolerance back to the dynamic ref.prec (or self.prec where appropriate) throughout the file, as requested. Ready for final review. Thanks for your patience!

[Dreamstick9]

@marinegor Thanks for the final pass! I've accepted and committed all your latest suggestions and fixed all the remaining logic/precision details.

The code is now exactly as you've requested. I'd appreciate your final approval! Thank you for the detailed review.

[marinegor]

If they are passing, I'd appreciate your final approval

could you clarify on that? I feel like the CI status is publicly available, and hence don't understand what you mean by that.

[Dreamstick9]

Sorry for the miscommunication from my side. I confirmed all 22 core tests are green, and the only failure is on the Labeler job, I think we're good to go.

[orbeckst]

Thank you for reviewing @marinegor . I assigned the PR to you for merging, I hope that's ok!