Updated tests to replace deprecated functions with assert_allclose an…

[0Shadow02]

Pull Request Description

Fixes #3743

Changes Made for mdanalysis/testsuite/MDAnalysisTests/analysis/test_base.py:

• Replaced deprecated assert_almost_equal with assert_allclose.
• Utilized pytest.approx for single float comparisons.
• Enhanced test coverage using pytest.mark.parametrize.
• Verified error handling for ValueError and IndexError.

PR Checklist:

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

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--4979.org.readthedocs.build/en/4979/

[github-actions]

Hello there first time contributor! Welcome to the MDAnalysis community! We ask that all contributors abide by our Code of Conduct and that first time contributors introduce themselves on GitHub Discussions so we can get to know you. You can learn more about participating here. Please also add yourself to package/AUTHORS as part of this PR.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.41%. Comparing base (66e7e5c) to head (8693842).
Report is 22 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4979      +/-   ##
===========================================
- Coverage    93.42%   93.41%   -0.02%     
===========================================
  Files          177      189      +12     
  Lines        21859    22925    +1066     
  Branches      3078     3078              
===========================================
+ Hits         20422    21415     +993     
- Misses         986     1059      +73     
  Partials       451      451              

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[orbeckst]

1. Please remove the comments that you inserted. We don't need an explanation like a LLM might give us on what was done.
2. Put back comments that you removed — these comments contain important information.
3. Format with black so that the linter passes.

Otherwise this looks good.

[orbeckst]

@yuxuanzhuang can you please be PR shepherd? I'll do the review but please keep an eye on the PR and feel free to ping me. Thanks.

[yuxuanzhuang]

@yuxuanzhuang can you please be PR shepherd? I'll do the review but please keep an eye on the PR and feel free to ping me. Thanks.

I think #4951 is addressing the same fix...in case I missed anything?

[orbeckst]

Aren’t the two PRs in different files?

[yuxuanzhuang]

Aren’t the two PRs in different files?

They both modified testsuite/MDAnalysisTests/analysis/test_base.py

[0Shadow02]

Hi @yuxuanzhuang, I've made the requested changes to the PR by removing unnecessary comments and formatting the code with black. Please let me know if there are any further adjustments needed. Thank you for your help!

[orbeckst]

@yuxuanzhuang you're right – this PR is addressing the same issue as PR #4951. Because PR #4951 started earlier and is active, we will not continue on this PR unless the other PR stalls and is closed.

Sorry @0Shadow02 , I hadn't realized that you were doing the same work as in PR #4951.

[0Shadow02]

Hi @orbeckst,

Thank you for the clarification regarding the overlap with PR #4951. I understand that since it was started earlier, this PR will not proceed unless the other one stalls.

If there are any updates or if I can assist in any way, please feel free to reach out. I appreciate your support and guidance.

Best regards,

0Shadow02

[orbeckst]

PR #4951 finally got merged so I am closing this PR as a duplicate.

Thank you for doing the work (it looked good) but we have to be fair.