added type annotations to most common oublic methods for Bio/Align, A…#5057
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dimi1729 wants to merge 2 commits intobiopython:masterfrom
Closed
added type annotations to most common oublic methods for Bio/Align, A…#5057dimi1729 wants to merge 2 commits intobiopython:masterfrom
dimi1729 wants to merge 2 commits intobiopython:masterfrom
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…lignIO, Graphics, HMM, KEGG, and PDB
dimi1729
requested review from
JoaoRodrigues,
mdehoon and
peterjc
as code owners
mdehoon
approved these changes
Sep 6, 2025
Member
|
Looks like there are still 3 mypy errors? |
peterjc
reviewed
Sep 11, 2025
| """ | ||
| self.alignment = alignment | ||
| self.ic_vector = [] | ||
| self.ic_vector: list[float] = [] |
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Should this be broader than just list? Arrays? (I don't know)
Member
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It would have been easier to review this in chunks, especially when multiple code owners are involed. |
This was referenced Oct 24, 2025
peterjc
reviewed
Oct 26, 2025
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| seq = seq if strand == ref_first_strand else seq.reverse_complement() | ||
| if strand != ref_first_strand: | ||
| sequence = Seq(sequence.reverse_complement()) |
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This is a change from just using the method - why?
Member
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I'm going to close this, but encourage you to resubmit this in smaller chunks like just Graphics, just HMM, just KEGG, etc - once the automated checks are all passing for you locally. This will be easier to review - and easier to assign for review. Thank you. |
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…lignIO, Graphics, HMM, KEGG, and PDB
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the Biopython License Agreement AND the BSD 3-Clause License.
I have read the
CONTRIBUTING.rstfile, have runpre-commitlocally, and understand that continuous integration checks will be used to
confirm the Biopython unit tests and style checks pass with these changes.
I have added my name to the alphabetical contributors listings in the files
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Addresses #2236
Added type annotations to most getter functions in Align, AlignIO, Graphics, HMM, KEGG, and PDB modules. While this is not a completed effort, it will hopefully be useful to people who use these modules and like type hints. Since no added functionality was added and very little actual logic was changed, no additional tests were created, but all existing tests were ran.