Deprecate lib.util.which

[IAlibay]

Fixes #3649

Notes:

• Not switching over x3dna because that code doesn't even work.
• Separate PR has been opened in hole2-mdakit

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

Developers certificate of origin

• I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

---

📚 Documentation preview 📚: https://mdanalysis--4340.org.readthedocs.build/en/4340/

[pep8speaks]

Hello @IAlibay! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file testsuite/MDAnalysisTests/util.py:

Line 35:1: E402 module level import not at top of file

Comment last updated at 2023-11-05 12:37:53 UTC

[github-actions]

Linter Bot Results:

Hi @IAlibay! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	⚠️ Possible failure
testsuite	⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/6761340134/job/18376120039

---

Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (cb26ebc) 93.37% compared to head (3914925) 93.36%.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4340      +/-   ##
===========================================
- Coverage    93.37%   93.36%   -0.02%     
===========================================
  Files          170      184      +14     
  Lines        22299    23410    +1111     
  Branches      4075     4075              
===========================================
+ Hits         20822    21856    +1034     
- Misses         962     1036      +74     
- Partials       515      518       +3     

Files	Coverage Δ
package/MDAnalysis/analysis/hole2/hole.py	83.11% <100.00%> (+0.04%)	⬆️
package/MDAnalysis/lib/util.py	89.14% <100.00%> (-0.51%)	⬇️

... and 14 files with indirect coverage changes

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[IAlibay]

not looking to add tests to cover these if the migration is also being done in hole2-mdakit

[hmacdope]

LGTM, thanks @IAlibay