Revert old guessers and tables removal

[IAlibay]

Fixes #4751 #4753

TODO:

• Add tests back
• Add DeprecationWarning for old guessers and tables
• Make sure tables is still exposed in the right place

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--4752.org.readthedocs.build/en/4752/

[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/topology/guessers.py:

Line 28:80: E501 line too long (83 > 79 characters)
Line 29:58: W291 trailing whitespace
Line 43:80: E501 line too long (80 > 79 characters)
Line 101:80: E501 line too long (115 > 79 characters)
Line 136:80: E501 line too long (89 > 79 characters)
Line 141:80: E501 line too long (81 > 79 characters)
Line 162:80: E501 line too long (108 > 79 characters)
Line 177:80: E501 line too long (84 > 79 characters)
Line 197:31: E261 at least two spaces before inline comment
Line 200:1: E302 expected 2 blank lines, found 1
Line 226:52: E261 at least two spaces before inline comment
Line 226:53: E262 inline comment should start with '# '
Line 330:38: E713 test for membership should be 'not in'
Line 453:16: E713 test for membership should be 'not in'

• In the file testsuite/MDAnalysisTests/topology/test_guessers.py:

Line 100:1: W293 blank line contains whitespace
Line 110:21: W291 trailing whitespace
Line 156:1: E302 expected 2 blank lines, found 1
Line 158:80: E501 line too long (85 > 79 characters)
Line 164:1: E302 expected 2 blank lines, found 1
Line 171:1: E302 expected 2 blank lines, found 1

• In the file testsuite/MDAnalysisTests/topology/test_tables.py:

Line 35:1: W391 blank line at end of file

Comment last updated at 2024-10-25 19:30:05 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 84.32836% with 21 lines in your changes missing coverage. Please review.

Project coverage is 93.57%. Comparing base (d2729f7) to head (878aa5c).
Report is 3 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/topology/guessers.py	83.84%	18 Missing and 3 partials ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4752      +/-   ##
===========================================
- Coverage    93.65%   93.57%   -0.08%     
===========================================
  Files          175      189      +14     
  Lines        21565    22774    +1209     
  Branches      3023     3052      +29     
===========================================
+ Hits         20196    21311    +1115     
- Misses         925     1016      +91     
- Partials       444      447       +3     

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[orbeckst]

lgtm, thx

[orbeckst]

@IAlibay I'll assign the PR to you so you can merge when you need to.

[yuxuanzhuang]

Suggested change

[IAlibay]

I don't believe this is correct - removing that line would break the deprecation box (things render fine as-is here: https://mdanalysis--4752.org.readthedocs.build/en/4752/documentation_pages/topology/guessers.html)

[lilyminium]

LGTM, although I agree with @yuxuanzhuang's comments. Thanks @IAlibay!

[IAlibay]

@yuxuanzhuang I've addressed your review comments so I'll go ahead and dismiss it so we can more rapidly merge things ahead of the release.

Comments addressed