Deprecate waterdynamics and replace with waterdynamics mdakit

[IAlibay]

Towards #4310

Changes made in this Pull Request:

• Remove local waterdynamics code and replace with mdakit import
• Remove local docs instead pointing to the mdakits docs

TODO

• add warning on module import + test
• remove local tests
• make decision on tests + docs (as per Deprecate PSA and replace with PathSimAnalysis mdakit #4403)
• fix py3.12 deployment Update deployment waterdynamics#28

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.

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📚 Documentation preview 📚: https://mdanalysis--4404.org.readthedocs.build/en/4404/

[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	✅ Passed

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/7486889600/job/20378150238

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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 (8ff8acc) 93.35% compared to head (37a59d5) 93.36%.

Additional details and impacted files

@@            Coverage Diff            @@
##           develop    #4404    +/-   ##
=========================================
  Coverage    93.35%   93.36%            
=========================================
  Files          171      185    +14     
  Lines        22003    22850   +847     
  Branches      4040     4012    -28     
=========================================
+ Hits         20541    21334   +793     
- Misses         966     1027    +61     
+ Partials       496      489     -7     

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[IAlibay]

This should be good to go - just waiting on conda-forge to refresh in a few hours.

[orbeckst]

Sorry, very quick, apart from py 3.12 failure look good.

3.12 is failing

This should be working.

 The following packages are incompatible
    ├─ pin-1 is installable and it requires
    │  └─ python 3.12.* , which can be installed;
    └─ waterdynamics is not installable because it requires
       └─ python >=3.9,<3.12  but there are no viable options
          ├─ python [3.10.0|3.10.1|...|3.9.9] conflicts with any installable versions previously reported;
          └─ python 3.12.0rc3 would require
             └─ _python_rc, which does not exist (perhaps a missing channel).
critical libmamba Could not solve for environment specs
Error: Process completed with exit code 1.

test_creating_multiple_universe_without_offset fails

This is one of our spurious multiprocessing failures IIRC and does not have to be addressed here.

[IAlibay]

Ah sorry @orbeckst I did the update prematurely, the py3.12 failure is just because it didn't filter through to conda-forge.

I cycled CI and everything passed.