Fixes #3743: Modernize test assertions in test_msd.py

[tanii1125]

Summary of Changes-

This PR Modernize test assertions in testsuite\MDAnalysisTests\analysis\test_msd.py

Changes made-

1. Replaced deprecated assert_almost_equal with assert_allclose using tolerances equivalent to the previous decimal keyword.
2. Replaced scalar floating-point comparisons with pytest.approx() where appropriate.
3. Cleaned up imports (removed unused deprecated functions).
4. Ensured all updated assertions preserve original test behavior.

Thanks, and please let me know if any further adjustments are needed.

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📚 Documentation preview 📚: https://mdanalysis--5169.org.readthedocs.build/en/5169/

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.15%. Comparing base (bbcef1b) to head (d17591b).

❗ There is a different number of reports uploaded between BASE (bbcef1b) and HEAD (d17591b). Click for more details.

HEAD has 3 uploads less than BASE

Flag	BASE (bbcef1b)	HEAD (d17591b)
	5	2

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5169      +/-   ##
===========================================
- Coverage    92.72%   86.15%   -6.57%     
===========================================
  Files          180      180              
  Lines        22472    22472              
  Branches      3188     3188              
===========================================
- Hits         20837    19361    -1476     
- Misses        1177     2658    +1481     
+ Partials       458      453       -5     

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