[fmt] Format topology module and tests

[RMeli]

Format topology module and tests. Some files from active PRs might be excluded (see #4815).

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📚 Documentation preview 📚: https://mdanalysis--4849.org.readthedocs.build/en/4849/

[pep8speaks]

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

• In the file package/MDAnalysis/topology/CRDParser.py:

Line 129:21: W503 line break before binary operator

• In the file package/MDAnalysis/topology/ExtendedPDBParser.py:

Line 63:80: E501 line too long (80 > 79 characters)
Line 64:80: E501 line too long (80 > 79 characters)

• In the file package/MDAnalysis/topology/FHIAIMSParser.py:

Line 103:80: E501 line too long (82 > 79 characters)

• In the file package/MDAnalysis/topology/GMSParser.py:

Line 112:80: E501 line too long (139 > 79 characters)

• In the file package/MDAnalysis/topology/LAMMPSParser.py:

Line 682:13: W503 line break before binary operator
Line 683:13: W503 line break before binary operator
Line 684:13: W503 line break before binary operator
Line 685:13: W503 line break before binary operator
Line 686:13: W503 line break before binary operator
Line 687:13: W503 line break before binary operator

• In the file package/MDAnalysis/topology/PSFParser.py:

Line 270:9: E731 do not assign a lambda expression, use a def

• In the file package/MDAnalysis/topology/guessers.py:

Line 164:80: E501 line too long (87 > 79 characters)
Line 343:17: W503 line break before binary operator
Line 343:59: E713 test for membership should be 'not in'
Line 344:17: W503 line break before binary operator
Line 345:17: W503 line break before binary operator

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

Line 74:13: W503 line break before binary operator
Line 75:13: W503 line break before binary operator
Line 76:13: W503 line break before binary operator

• In the file testsuite/MDAnalysisTests/topology/test_mol2.py:

Line 274:9: W503 line break before binary operator
Line 275:9: W503 line break before binary operator
Line 276:9: W503 line break before binary operator
Line 277:9: W503 line break before binary operator
Line 278:9: W503 line break before binary operator
Line 279:9: W503 line break before binary operator
Line 280:9: W503 line break before binary operator
Line 281:9: W503 line break before binary operator
Line 282:9: W503 line break before binary operator

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

Line 95:13: W503 line break before binary operator
Line 103:13: W503 line break before binary operator
Line 154:21: W503 line break before binary operator
Line 155:21: W503 line break before binary operator
Line 156:21: W503 line break before binary operator
Line 389:80: E501 line too long (81 > 79 characters)
Line 390:80: E501 line too long (81 > 79 characters)
Line 491:70: E231 missing whitespace after ','
Line 793:80: E501 line too long (98 > 79 characters)

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

Line 148:13: E126 continuation line over-indented for hanging indent
Line 152:9: E121 continuation line under-indented for hanging indent
Line 165:9: W503 line break before binary operator
Line 166:9: W503 line break before binary operator
Line 167:9: W503 line break before binary operator
Line 168:9: W503 line break before binary operator
Line 169:9: W503 line break before binary operator
Line 170:9: W503 line break before binary operator
Line 186:9: W503 line break before binary operator
Line 187:9: W503 line break before binary operator
Line 188:9: W503 line break before binary operator
Line 189:9: W503 line break before binary operator
Line 190:9: W503 line break before binary operator
Line 191:9: W503 line break before binary operator
Line 192:9: W503 line break before binary operator
Line 197:9: W503 line break before binary operator
Line 198:9: W503 line break before binary operator
Line 199:9: W503 line break before binary operator
Line 200:9: W503 line break before binary operator
Line 201:9: W503 line break before binary operator
Line 316:9: E126 continuation line over-indented for hanging indent
Line 319:5: E121 continuation line under-indented for hanging indent

Comment last updated at 2024-12-29 22:02:08 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 91.87500% with 26 lines in your changes missing coverage. Please review.

Project coverage is 93.63%. Comparing base (b710e57) to head (ca27dec).
Report is 1 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/topology/GSDParser.py	16.66%	10 Missing ⚠️
package/MDAnalysis/topology/HoomdXMLParser.py	71.42%	2 Missing and 2 partials ⚠️
package/MDAnalysis/topology/ITPParser.py	93.10%	2 Missing and 2 partials ⚠️
package/MDAnalysis/topology/PSFParser.py	82.35%	3 Missing ⚠️
package/MDAnalysis/topology/CRDParser.py	90.90%	1 Missing ⚠️
package/MDAnalysis/topology/LAMMPSParser.py	97.72%	0 Missing and 1 partial ⚠️
package/MDAnalysis/topology/MOL2Parser.py	94.11%	1 Missing ⚠️
package/MDAnalysis/topology/PQRParser.py	91.66%	0 Missing and 1 partial ⚠️
package/MDAnalysis/topology/guessers.py	94.73%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4849      +/-   ##
===========================================
- Coverage    93.66%   93.63%   -0.03%     
===========================================
  Files          177      189      +12     
  Lines        21787    22853    +1066     
  Branches      3067     3067              
===========================================
+ Hits         20406    21399     +993     
- Misses         929     1002      +73     
  Partials       452      452              

☔ View full report in Codecov by Sentry.
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[RMeli]

The web UI was really slow with this one. I hope all the review comments were saved.

[orbeckst]

blanket LGTM — please merge when you're happy with it @RMeli

🎄 🎁

[RMeli]

Wait for #4866 before merging this one.

[RMeli]

@marinegor this should be good for final review.

[RMeli]

Wait for #4873 before merging.

[marinegor]

retrospective LGTM