Modernize assertions in test_distances.py (part of #3743)

[Pranay096]

Contributes to #3743

Changes made in this Pull Request:

• Modernized assertions in testsuite/MDAnalysisTests/analysis/test_distances.py
• Replaced deprecated assert_almost_equal / assert_array_almost_equal with numpy.testing.assert_allclose and assert_array_equal where appropriate
• Replaced old float comparison patterns with modern NumPy/PyTest assertions
• Ensured no behavioural changes to distance calculations

PR Checklist

• Issue raised/referenced? (Contributes to modernize testing code #3743)
• Tests updated/added? (Updated test assertions)
• 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.

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📚 Documentation preview 📚: https://mdanalysis--5158.org.readthedocs.build/en/5158/

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.71%. Comparing base (6b51eac) to head (b329d19).
⚠️ Report is 4 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5158      +/-   ##
===========================================
- Coverage    92.72%   92.71%   -0.02%     
===========================================
  Files          180      180              
  Lines        22458    22457       -1     
  Branches      3186     3186              
===========================================
- Hits         20824    20820       -4     
- Misses        1177     1179       +2     
- Partials       457      458       +1     

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[Pranay096]

This PR is ready for review.

All tests pass locally, and the only CI failure was a cancelled job due to duplicate workflow runs by GitHub.

@orbeckst @RMeli @marinegor — Please let me know if anything else is needed. Thanks!

[marinegor]

@Pranay096 thanks for the PR, this one is also accepted.

If you're planning to work on them file by file, I'd be in favor of choosing some strategy to chunk them together, since there are 70 files that need modernization, and 860 occurrences total. I'd think about splitting them logically (i.e. by module or finer) into ~10-ish PRs, because 70 PRs would be quite overwhelming in terms of review time (but perhaps it's just me -- @MDAnalysis/coredevs ?)