Deprecate fetch mmtf

[IAlibay]

Fixes #4634

Changes made in this Pull Request:

• Remove fetch_mmtf method
• Deprecate MMTFReader

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--4639.org.readthedocs.build/en/4639/

[pep8speaks]

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

• In the file package/MDAnalysis/coordinates/MMTF.py:

Line 60:80: E501 line too long (83 > 79 characters)

Comment last updated at 2024-07-24 14:17:41 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	✅ 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/10078393665/job/27863215540

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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 ✅

Project coverage is 93.59%. Comparing base (b227f17) to head (42841e8).
Report is 33 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4639      +/-   ##
===========================================
- Coverage    93.61%   93.59%   -0.03%     
===========================================
  Files          171      183      +12     
  Lines        21250    22320    +1070     
  Branches      3936     3937       +1     
===========================================
+ Hits         19893    20890     +997     
- Misses         898      971      +73     
  Partials       459      459              

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[IAlibay]

RDKit failures being fixed in #4640

[hmacdope]

Content LGTM @IAlibay

[RMeli]

LGTM

[orbeckst]

@RMeli or @IAlibay please merge when you need to. If there's a reason not merge leave a comment, please.

[RMeli]

@orbeckst CI is not in a good state. There was one of the usual timeouts, but I think this PR is blocked by #4640.