Fix #3743: Modernize deprecated test assertions in hydrogen bond tests

[ShivansGupta25]

Summary

Modernize test assertions in test_hydrogenbonds_analysis.py by replacing deprecated NumPy testing helpers with current testing practices.

Changes

• Removed unused assert_almost_equal import.
• Replaced assert_almost_equal assertions with more appropriate modern alternatives.
• Replaced floating-point comparisons with numpy.testing.assert_allclose where applicable.
• Preserved existing test behavior and tolerances.
• Updated assertions to better match the type of values being tested.

Testing

pytest testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py -q

Result:

79 passed

AI Declaration

• I used AI assistance while working on this PR.

AI was used for:

• Understanding the issue requirements.
• Identifying deprecated testing patterns.
• Suggesting modern assertion alternatives.
• Reviewing proposed test changes.

All suggested changes were manually reviewed, verified, and tested by me before submission.

[IAlibay]

@ShivansGupta25 Thanks for opening this PR. However, before we can review we ask you put back and answer the AI declaration which was the in the PR template.

[IAlibay]

Blocking until relevant declarations are added back into the PR description.

[ShivansGupta25]

@ShivansGupta25 Thanks for opening this PR. However, before we can review we ask you put back and answer the AI declaration which was the in the PR template.

I've restored and completed the AI declaration section. All changes were reviewed and tested locally. Thanks for pointing it out sir.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.87%. Comparing base (941d679) to head (74e7bda).
⚠️ Report is 24 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5400      +/-   ##
===========================================
+ Coverage    93.85%   93.87%   +0.02%     
===========================================
  Files          182      182              
  Lines        22509    22522      +13     
  Branches      3202     3206       +4     
===========================================
+ Hits         21125    21143      +18     
+ Misses         922      917       -5     
  Partials       462      462              

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[orbeckst]

Thank you for your contribution. As a first-time contributor, please add yourself to AUTHORS.

Please address the formatting issues (in the file that you edited) that the linter raised.

[ShivansGupta25]

Thanks for the review sir @orbeckst !

I've addressed both requested changes:

• Added my name to package/AUTHORS.
• Ran Black on the modified file (testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py) and verified that black --check reports the file is correctly formatted.

The Black GitHub Action still appears to be failing on CI, but locally the modified file passes the formatting check. Please let me know if there's anything else I should update.

[oaksprout]

We can run this PR through an independent check if you want. The diff is applied to a clean copy at its base commit, your test suite and typechecks run in a locked-down container, and a separate pass reviews the change against #3743. Results come back as a comment with a record you can inspect. Free, no obligation, and we don't touch the PR itself.

AI agents do the checking; a human reviews everything before it's posted and answers replies. If that's useful, say so. If not, ignore this and we won't post again.

[ShivansGupta25]

Thanks, @oaksprout! Yes, I’d appreciate the independent check. Please go ahead and run it against the PR. I’d be happy to review the results and address any issues that come up.

[orbeckst]

Please read the AI Policy (at the repo root) to understand which uses of AI are acceptable in this project.

I’ll have a look at the PR again. Sorry for the delay.

You may have to merge current develop into this PR branch so that CI becomes all green. I’d like to see that happen before reviewing. On other recent PRs all listing and docs pass so you should also make it work here.

[orbeckst]

Ensure that all CI passes (linting and docs). You may have to merge current develop into this branch.

If after merging the CI still fails, look at the output and let me know why is failing and why this is not due to the changes you made.