Fix for First argument to super() is not enclosing class#5418
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| :attr:`angles` results are now stored in a | ||
| :class:`MDAnalysis.analysis.base.Results` instance. | ||
| """ | ||
| super(Ramachandran, self).__init__( |
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This looks horrible but is actually correct.
AnalysisBase's init is special so I also need to change the arguments when calling Ramachandran.
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additionally, Janin does not want to call Ramachandran's init; it's a bit of a mess
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It's actually correct as is. The code would need some refactoring or at least a comment... |
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Fixes #
Changes made in this Pull Request:
Fixes incorrect call of super in the Janin analysis class.
This error was detected when doing a trial run of CodeQL, see https://github.com/MDAnalysis/mdanalysis/security/quality and in particular https://github.com/MDAnalysis/mdanalysis/security/quality/rules/py%2Fsuper-not-enclosing-class
The "generate fix" disregards our standard PR template and adds the text below. For compliance, I manually inserted the PR text from
LLM / AI generated code disclosure
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes
The fix was auto-generated, i.e., full AI use. However, that was simply faster than me making the equivalent edit.
PR Checklist
package/CHANGELOGfile updated?package/AUTHORS? (If it is not, add it!)Developers Certificate of Origin
I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.
Autofix-generated text
The fix is to make the
super()call reference the enclosing class (Janin) so object initialization follows the correct MRO and calls the intended base-class constructor.Best minimal fix (no behavior change beyond correcting initialization): in
package/MDAnalysis/analysis/dihedrals.py, replace:super(Ramachandran, self).__init__(...)with:
super(Janin, self).__init__(...)No new imports, methods, or dependencies are required.
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