[fmt] core

[RMeli]

---

📚 Documentation preview 📚: https://mdanalysis--4874.org.readthedocs.build/en/4874/

[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/core/groups.py:

Line 3776:80: E501 line too long (80 > 79 characters)

• In the file testsuite/MDAnalysisTests/core/test_atomselections.py:

Line 82:80: E501 line too long (84 > 79 characters)
Line 91:80: E501 line too long (87 > 79 characters)
Line 168:80: E501 line too long (88 > 79 characters)
Line 1292:80: E501 line too long (82 > 79 characters)

• In the file testsuite/MDAnalysisTests/core/test_group_traj_access.py:

Line 439:80: E501 line too long (81 > 79 characters)

• In the file testsuite/MDAnalysisTests/core/test_groups.py:

Line 1016:80: E501 line too long (156 > 79 characters)
Line 1308:80: E501 line too long (82 > 79 characters)
Line 1431:80: E501 line too long (94 > 79 characters)

Comment last updated at 2025-01-07 17:15:32 UTC

[RMeli]

The test failure here seems real. I'm not very familiar with this part of the code, but I think it is due to the following assumption:

mdanalysis/package/MDAnalysis/core/topologyattrs.py

Lines 226 to 227 in 453be6c

	# The first line of the original docstring is not indented, but the
	# subsequent lines are. We want to dedent the whole docstring.

From black documentation:

Black cleans up leading and trailing whitespace of docstrings, re-indenting them if needed. It’s been one of the most popular user-reported features for the formatter to fix whitespace issues with docstrings. While the result is technically an AST difference, due to the various possibilities of forming docstrings, all real-world uses of docstrings that we’re aware of sanitize indentation and leading/trailing whitespace anyway.

[RMeli]

The following change appears to fix things:

-    # The first line of the original docstring is not indented, but the
-    # subsequent lines are. We want to dedent the whole docstring.
-    first_line, other_lines = method.__doc__.split("\n", 1)
-    stub_method.__doc__ = (
-        first_line + "\n" + textwrap.dedent(other_lines) + "\n\n" + annotation
-    )
+    # The original docstring is arrumed to be formatted with black
+    stub_method.__doc__ = textwrap.dedent(method.__doc__) + "\n\n" + annotation

[codecov]

Codecov Report

Attention: Patch coverage is 97.71529% with 13 lines in your changes missing coverage. Please review.

Project coverage is 93.63%. Comparing base (1eca9f2) to head (de6e3d0).
Report is 1 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/core/groups.py	95.75%	5 Missing and 4 partials ⚠️
package/MDAnalysis/core/topologyattrs.py	99.31%	2 Missing ⚠️
package/MDAnalysis/core/_get_readers.py	90.90%	1 Missing ⚠️
package/MDAnalysis/core/topologyobjects.py	96.96%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4874      +/-   ##
===========================================
- Coverage    93.66%   93.63%   -0.03%     
===========================================
  Files          177      189      +12     
  Lines        21796    22861    +1065     
  Branches      3067     3067              
===========================================
+ Hits         20415    21407     +992     
- Misses         929     1002      +73     
  Partials       452      452              

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

[RMeli]

This one is also good to go IMO. Please check the change described in #4874 (comment).

[orbeckst]

I am updating the comment on the doc-dedent code change (good that you found this interaction — in a way that's been pretty brittle as it required that doc strings were written in a specific way).

Otherwise I did spot checks and believe it's fine.

[marinegor]

Retrospective LGTM (except for one trailing comma, but it's non-blocking especially given that PR is already merged)

[marinegor]

perhaps should be this:

coords = np.array([[1, 1, 1], [2, 1, 1], [3, 1, 1],], dtype=np.float32)

(with a trailing comma to maintain 3x3 format)