tests: modernize deprecated numpy assertions in test_gnm.py (ref #3743)

[shubhammittal2241]

Modernize deprecated NumPy assertions in test_gnm.py (ref #3743)

This PR updates deprecated NumPy testing functions in test_gnm.py:

• Replaces assert_almost_equal and assert_array_almost_equal
  with numpy.testing.assert_allclose
• Uses pytest.approx for scalar floating point comparisons
• Preserves existing tolerances and test behavior

All tests pass locally.

Contributes to issue #3743.

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📚 Documentation preview 📚: https://mdanalysis--5174.org.readthedocs.build/en/5174/

[github-actions]

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[codecov]

Codecov Report

❌ Patch coverage is 93.28108% with 60 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.70%. Comparing base (bbcef1b) to head (74cefc3).

Files with missing lines	Patch %	Lines
package/MDAnalysis/coordinates/TRZ.py	89.69%	9 Missing and 1 partial ⚠️
package/MDAnalysis/converters/ParmEd.py	0.00%	8 Missing ⚠️
package/MDAnalysis/visualization/streamlines_3D.py	64.70%	6 Missing ⚠️
package/MDAnalysis/analysis/align.py	50.00%	4 Missing ⚠️
package/MDAnalysis/coordinates/base.py	93.44%	4 Missing ⚠️
package/MDAnalysis/lib/transformations.py	42.85%	4 Missing ⚠️
...ckage/MDAnalysis/analysis/encore/confdistmatrix.py	62.50%	2 Missing and 1 partial ⚠️
package/MDAnalysis/analysis/encore/utils.py	33.33%	1 Missing and 1 partial ⚠️
package/MDAnalysis/topology/tpr/utils.py	92.59%	1 Missing and 1 partial ⚠️
...e/MDAnalysis/analysis/encore/clustering/cluster.py	75.00%	0 Missing and 1 partial ⚠️
... and 16 more

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5174      +/-   ##
===========================================
- Coverage    92.72%   92.70%   -0.02%     
===========================================
  Files          180      180              
  Lines        22472    22472              
  Branches      3188     3188              
===========================================
- Hits         20837    20833       -4     
- Misses        1177     1184       +7     
+ Partials       458      455       -3     

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