Add docstrings to SequenceDataAbstractBaseClass magic methods#5240
Add docstrings to SequenceDataAbstractBaseClass magic methods#5240LuciPengu wants to merge 2 commits into
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Add missing one-line docstrings to the 13 magic methods of SequenceDataAbstractBaseClass in Bio/Seq.py, which previously triggered ruff's D105 "Missing docstring in magic method" check. First batch towards issue biopython#2116. The D105 entry in the ruff ignore list in .pre-commit-config.yaml is left in place for now, since other modules still contain undocumented magic methods.
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That suggests to me the return is bytes (but it is a sequence object), does any alternative wording come to mind?
| # by _PartiallyDefinedSequenceData.__radd__ | ||
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| def __radd__(self, other): | ||
| """Return the concatenation of other and the sequence data as bytes.""" |
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You don't think something along the lines of 'add on the right' is relevant here - or following the Python string more closely?
| return bytes(self) >= other | ||
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| def __add__(self, other): | ||
| """Return the concatenation of the sequence data and other as bytes.""" |
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I think something modelled after the Python string's docstring would be nicer.
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Hi Neal, thank you for looking at this. I hope this question is just a formality, but is any of this AI generated? See ongoing discussion starting here: https://mailman.open-bio.org/pipermail/biopython/2026-April/017113.html |
I'm so sorry, I had no idea that generative AI wasn't allowed to be used in PRs, I used AI to help me understand the problem and I told it exactly what changes to do to the files as well as to help improve the markdown on my PR but nothing more than that |
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It isn't official policy yet, but it might well be shortly - see #5241. Until that's settled we're not merging any AI PRs (and potentially will have to just close those currently waiting in limbo). |
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I have read the
CONTRIBUTING.rstfile, have run the style checkslocally, and understand that continuous integration checks will be used to
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This is a first batch towards #2116 (ruff
D105, "Missing docstring in magic method").It adds one-line docstrings to the 13 magic methods of
SequenceDataAbstractBaseClassinBio/Seq.py, following the existingimperative docstring style used elsewhere in that file. Running
ruff check Bio/Seq.py --select=D105now reports no violations.No behaviour is changed. The
D105entry is intentionally left in the ruffignore list in
.pre-commit-config.yaml, since other modules still containundocumented magic methods; that ignore can be removed in a later PR once
they are all documented.
Towards #2116