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Misc mypy fixes/clean-up#5248
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peterjc wants to merge 3 commits into
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Solves this typing complaint:
Bio/Align/__init__.py: note: In member "from_alignments_with_same_reference" of class "Alignment":
Bio/Align/__init__.py:1253:27: error: Incompatible types in assignment (expression has type
"ndarray[Any, Any]", variable has type "list[list[Any]]") [assignment]
msa_coordinates = np.array(msa_coordinates).transpose()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Solves these three with mypy 1.16.1:
Bio/PDB/Atom.py: note: In member "set_sigatm" of class "Atom":
Bio/PDB/Atom.py:333:29: error: Incompatible types in assignment (expression has type
"ndarray[tuple[Any, ...], dtype[Any]] | None", variable has type "None") [assignment]
self.sigatm_array = sigatm_array
^~~~~~~~~~~~
Bio/PDB/Atom.py: note: In member "set_siguij" of class "Atom":
Bio/PDB/Atom.py:341:29: error: Incompatible types in assignment (expression has type
"ndarray[tuple[Any, ...], dtype[Any]] | None", variable has type "None") [assignment]
self.siguij_array = siguij_array
^~~~~~~~~~~~
Bio/PDB/Atom.py: note: In member "set_anisou" of class "Atom":
Bio/PDB/Atom.py:349:29: error: Incompatible types in assignment (expression has type
"ndarray[tuple[Any, ...], dtype[Any]] | None", variable has type "None") [assignment]
self.anisou_array = anisou_array
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mdehoon
approved these changes
Jun 26, 2026
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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.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.
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This addresses most of the issues flagged by running mypy 1.16.1 which is in the pre-commit configuration but not run on the pre-commit CI due to time concerns. It seems some recent work had not been validated with the mypy setup.
There is still one issue in
Bio/PDB/Atom.pywith some mixing of single-element-arrays vs booleans I think:Found while testing with zuban as a possible faster alternative to mypy: https://github.com/zubanls/zuban/