Replace Union and Optional with Python 3.10+ typing

peterjc · peterjc · commit d9529227f806 · 2026-01-17T10:14:39.000Z
diff --git a/Bio/PDB/StructureAlignment.py b/Bio/PDB/StructureAlignment.py
@@ -25,12 +25,12 @@ class StructureAlignment:
 
     def __init__(
         self,
-        fasta_align: Optional[MultipleSeqAlignment | Alignment] = None,
+        fasta_align: MultipleSeqAlignment | Alignment | None = None,
         m1: Model | None = None,
         m2: Model | None = None,
         si: int = 0,
         sj: int = 1,
-        aligner: Optional[PairwiseAligner] = None,
+        aligner: PairwiseAligner | None = None,
     ) -> None:
         """Initialize.
 
diff --git a/Bio/PDB/internal_coords.py b/Bio/PDB/internal_coords.py
@@ -301,7 +301,7 @@
 
 HKT = tuple["AtomKey", "AtomKey", "AtomKey"]  # Hedron key tuple
 DKT = tuple["AtomKey", "AtomKey", "AtomKey", "AtomKey"]  # Dihedron Key Tuple
-EKT = Union[HKT, DKT]  # Edron Key Tuple
+EKT = HKT | DKT  # Edron Key Tuple
 BKT = tuple["AtomKey", "AtomKey"]  # Bond Key Tuple
 
 # HACS = Tuple[np.array, np.array, np.array]  # Hedron Atom Coord Set
diff --git a/Bio/SeqIO/Interfaces.py b/Bio/SeqIO/Interfaces.py
@@ -27,7 +27,7 @@
 
 # https://docs.python.org/3/glossary.html#term-path-like-object
 _PathLikeTypes = (PathLike, str, bytes)
-_IOSource = Union[IO[AnyStr], PathLike, str, bytes]
+_IOSource = IO[AnyStr] | PathLike | str | bytes
 _TextIOSource = _IOSource[str]
 _BytesIOSource = _IOSource[bytes]
 
diff --git a/Bio/SeqRecord.py b/Bio/SeqRecord.py
@@ -170,7 +170,7 @@ class SeqRecord:
 
     """
 
-    _AnnotationsDictValue = Union[str, int]
+    _AnnotationsDictValue = str | int
     _AnnotationsDict = dict[str, _AnnotationsDictValue]
 
     annotations: _AnnotationsDict
@@ -1072,7 +1072,7 @@ def __radd__(self, other: Union["Seq", "MutableSeq", str]) -> "SeqRecord":
         # Note can't transfer any per-letter-annotations
         offset = len(other)
         return type(self)(
-            cast(Union[Seq, MutableSeq], other + self.seq),
+            cast(Seq | MutableSeq, other + self.seq),
             id=self.id,
             name=self.name,
             description=self.description,
diff --git a/BioSQL/BioSeq.py b/BioSQL/BioSeq.py
@@ -18,8 +18,6 @@
 (like quality scores) in BioSQL.
 """
 
-from typing import Optional
-
 from Bio import SeqFeature
 from Bio.Seq import Seq
 from Bio.Seq import SequenceDataAbstractBaseClass
@@ -583,7 +581,7 @@ def annotations(self) -> SeqRecord._AnnotationsDict:
         return self._annotations
 
     @annotations.setter
-    def annotations(self, value: Optional[SeqRecord._AnnotationsDict]) -> None:
+    def annotations(self, value: SeqRecord._AnnotationsDict | None) -> None:
         if value:
             self._annotations = value
         else:
