DOC: fix doctests in universe.py for newer NumPy and optional rdkit

[Kd1880]

Fixes part of #3925

Changes made in this Pull Request:

• Updated expected doctest output for u.atoms.tempfactors in universe.py — newer NumPy returns array([..., shape=(3341,)) instead of array([...])
• Added # doctest: +SKIP to all from_smiles() examples that require optional rdkit library

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes
(Claude by Anthropic was used to help identify and understand the fixes. Actual code changes were made manually.)

PR Checklist

• Issue raised/referenced?
• Tests updated/added? (documentation-only change, no new tests needed)
• Documentation updated/added?
• package/CHANGELOG file updated?
• Is your name in package/AUTHORS?
• 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--5297.org.readthedocs.build/en/5297/

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.82%. Comparing base (9531c6e) to head (afd647f).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #5297   +/-   ##
========================================
  Coverage    93.82%   93.82%           
========================================
  Files          182      182           
  Lines        22483    22483           
  Branches      3195     3195           
========================================
  Hits         21095    21095           
  Misses         925      925           
  Partials       463      463           

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[BradyAJohnston]

Skipping lines isn't a solution to doctests. If it's in the docs it should be runnable code. The environment for running the tests just needs the optional packages installed.