[fmt] Coordinates

[RMeli]

---

📚 Documentation preview 📚: https://mdanalysis--4856.org.readthedocs.build/en/4856/

[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/coordinates/FHIAIMS.py:

Line 145:24: E713 test for membership should be 'not in'
Line 147:80: E501 line too long (118 > 79 characters)
Line 162:80: E501 line too long (82 > 79 characters)
Line 173:80: E501 line too long (108 > 79 characters)
Line 179:80: E501 line too long (99 > 79 characters)
Line 183:80: E501 line too long (83 > 79 characters)
Line 238:80: E501 line too long (80 > 79 characters)
Line 241:80: E501 line too long (211 > 79 characters)

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

Line 326:80: E501 line too long (108 > 79 characters)
Line 329:80: E501 line too long (156 > 79 characters)

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

Line 183:80: E501 line too long (88 > 79 characters)
Line 219:80: E501 line too long (88 > 79 characters)
Line 393:21: W503 line break before binary operator
Line 406:21: W503 line break before binary operator
Line 407:21: W503 line break before binary operator
Line 680:13: W503 line break before binary operator
Line 681:13: W503 line break before binary operator

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

Line 302:12: E713 test for membership should be 'not in'

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

Line 331:25: W503 line break before binary operator
Line 340:25: W503 line break before binary operator

• In the file testsuite/MDAnalysisTests/coordinates/test_chainreader.py:

Line 69:80: E501 line too long (110 > 79 characters)
Line 75:80: E501 line too long (93 > 79 characters)
Line 577:9: W503 line break before binary operator
Line 583:9: W503 line break before binary operator

• In the file testsuite/MDAnalysisTests/coordinates/test_copying.py:

Line 292:19: E712 comparison to False should be 'if cond is False:' or 'if not cond:'

• In the file testsuite/MDAnalysisTests/coordinates/test_dlpoly.py:

Line 98:34: E712 comparison to False should be 'if cond is False:' or 'if not cond:'
Line 101:30: E712 comparison to False should be 'if cond is False:' or 'if not cond:'

• In the file testsuite/MDAnalysisTests/coordinates/test_fhiaims.py:

Line 90:80: E501 line too long (93 > 79 characters)
Line 105:80: E501 line too long (101 > 79 characters)
Line 115:80: E501 line too long (171 > 79 characters)
Line 180:80: E501 line too long (85 > 79 characters)

• In the file testsuite/MDAnalysisTests/coordinates/test_lammps.py:

Line 191:9: W503 line break before binary operator
Line 708:13: W503 line break before binary operator
Line 713:13: W503 line break before binary operator

• In the file testsuite/MDAnalysisTests/coordinates/test_memory.py:

Line 351:13: W503 line break before binary operator
Line 357:13: W503 line break before binary operator

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

Line 108:80: E501 line too long (110 > 79 characters)

• In the file testsuite/MDAnalysisTests/coordinates/test_pdb.py:

Line 818:21: W503 line break before binary operator

• In the file testsuite/MDAnalysisTests/coordinates/test_pdbqt.py:

Line 59:80: E501 line too long (85 > 79 characters)
Line 93:80: E501 line too long (81 > 79 characters)

• In the file testsuite/MDAnalysisTests/coordinates/test_writer_api.py:

Line 32:5: W503 line break before binary operator
Line 59:9: W503 line break before binary operator
Line 67:9: W503 line break before binary operator
Line 93:9: W503 line break before binary operator
Line 122:9: W503 line break before binary operator

• In the file testsuite/MDAnalysisTests/coordinates/test_xdr.py:

Line 331:80: E501 line too long (82 > 79 characters)

• In the file testsuite/MDAnalysisTests/coordinates/test_xyz.py:

Line 122:80: E501 line too long (81 > 79 characters)
Line 202:54: E741 ambiguous variable name 'l'

Comment last updated at 2024-12-24 12:56:12 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 94.03509% with 17 lines in your changes missing coverage. Please review.

Project coverage is 93.63%. Comparing base (29deccc) to head (c141360).
Report is 1 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/coordinates/GSD.py	30.00%	7 Missing ⚠️
package/MDAnalysis/coordinates/LAMMPS.py	96.80%	3 Missing ⚠️
package/MDAnalysis/coordinates/CRD.py	92.00%	2 Missing ⚠️
package/MDAnalysis/coordinates/DMS.py	81.81%	2 Missing ⚠️
package/MDAnalysis/coordinates/GRO.py	95.12%	2 Missing ⚠️
package/MDAnalysis/coordinates/PDBQT.py	95.23%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4856      +/-   ##
===========================================
- Coverage    93.65%   93.63%   -0.03%     
===========================================
  Files          177      189      +12     
  Lines        21779    22845    +1066     
  Branches      3064     3064              
===========================================
+ Hits         20398    21391     +993     
- Misses         929     1002      +73     
  Partials       452      452              

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

[RMeli]

Fixed trading commas. Good to go IMO.

[orbeckst]

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

🎄 🎁

[marinegor]

hey @RMeli sorry it took so long on my side -- LGTM too, no big issues.

Perhaps a little suggestion: could you limit the formatting PRs to ~20-25 files each? Petty reason but my browser keeps crushing during the review process :)