Replace deprecated assert_almost_equal with assert_allclose in GNM tests

[SRASHTI2004]

Fixes #3743

Changes made in this Pull Request:

• Replaced deprecated numpy.testing.assert_almost_equal with np.testing.assert_allclose in GNM tests.
• Added absolute tolerance (atol=1e-4) to ensure numerical comparisons remain stable across platforms and NumPy versions.
• Removed the deprecated import of assert_almost_equal.

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: no

PR Checklist

• Issue raised/referenced?
• Tests updated/added?
• Documentation updated/added?
• package/CHANGELOG file updated?
• Is your name in package/AUTHORS? (If it is not, add it!)
• LLM/AI disclosure was updated.

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--5290.org.readthedocs.build/en/5290/

[codecov]

Codecov Report

❌ Patch coverage is 94.14365% with 53 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.84%. Comparing base (9988556) to head (7c7aa79).
⚠️ Report is 2 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/coordinates/TRZ.py	89.69%	9 Missing and 1 partial ⚠️
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 ⚠️
package/MDAnalysis/analysis/bat.py	85.71%	1 Missing ⚠️
...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    #5290      +/-   ##
===========================================
+ Coverage    93.83%   93.84%   +0.01%     
===========================================
  Files          182      182              
  Lines        22501    22501              
  Branches      3195     3195              
===========================================
+ Hits         21113    21116       +3     
- Misses         925      928       +3     
+ Partials       463      457       -6     

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[BradyAJohnston]

Given we previously did from numpy.testing import assert_almost_equal, I suggest you keep that pattern and import assert_allclose as well.

[SRASHTI2004]

Thanks for the suggestion!
I’ll keep the same import pattern and add assert_allclose alongside it to maintain consistency with the existing style. I’ll push the update shortly.

[BradyAJohnston]

Don't know if we should be adding these - at the very least please add descriptions about what is being ignored & why like the rest of the file.

[SRASHTI2004]

Thanks for pointing that out!
I'll add proper descriptions explaining what is being ignored and why, to match the style used in the rest of the .gitignore file. I'll update the PR shortly.

[jeremyleung521]

There are 300 file changes (well, 299) in this PR, which I think are from a different linter that is not black~=24 (see docs and docs)? I would highly recommend fixing those and not including those changes here (esp. since the CI linter is throwing errors).

Again, it's making it really difficult tracking what you actually implemented, just like your previous PR.