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chore: add type annotation to Bio/File.py - #5088

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chore: add type annotation to Bio/File.py#5088
szabgab wants to merge 1 commit into
biopython:masterfrom
szabgab:szabgab/type-annotations-file

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@szabgab

@szabgab szabgab commented Oct 24, 2025

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  • I hereby agree to dual licence this and any previous contributions under both
    the Biopython License Agreement AND the BSD 3-Clause License.

  • I have read the CONTRIBUTING.rst file, have run pre-commit
    locally, 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
    NEWS.rst and CONTRIB.rst as part of this pull request, am listed
    already, or do not wish to be listed. (This acknowledgement is optional.)

Addresses #2236 and does not touch files that are addressed in #5057

@peterjc

peterjc commented Oct 26, 2025

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That's just a tiny fraction of the module - and a private bit of the API too - did you do more but forgot to push the work to GitHub?

@szabgab

szabgab commented Oct 26, 2025

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I thought smaller PRs would make it easier to review and accept.

@peterjc

peterjc commented Oct 26, 2025

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For type annotation, please do at least a whole file. Or most of it.

@szabgab
szabgab force-pushed the szabgab/type-annotations-file branch from fd22de7 to e0ab915 Compare October 29, 2025 12:35
@szabgab
szabgab requested a review from peterjc as a code owner October 29, 2025 12:35
@szabgab

szabgab commented Oct 29, 2025

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OK. I have made some progress. This still needs more work.

Comment thread Bio/SeqIO/Interfaces.py

from typing_extensions import TypeAlias
from typing import Callable
from _typeshed import FileDescriptorOrPath

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That's not in the standard library - see ModuleNotFoundError: No module named '_typeshed' errors in the CI testing.

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2 participants