[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.15.6
+  rev: v0.16.3
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

setup.py

@@ -75,7 +75,7 @@ def build_cmake(self, ext):
             ext_modules=[CMakeExtension("biostrings")],
             cmdclass={"build_ext": build_ext},
         )
-    except:  # noqa
+    except:
         print(
             "\n\nAn error occurred while building the project, "
             "please ensure you have the most updated version of setuptools, "

src/biostrings/dnastring.py

@@ -2,7 +2,7 @@
 
 import re
 from copy import deepcopy
-from typing import Any, Dict, Optional, Union
+from typing import Any
 
 import biocutils as ut
 
@@ -34,8 +34,8 @@ class DNAString(ut.BiocObject):
 
     def __init__(
         self,
-        sequence: Union[str, bytes],
-        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+        sequence: str | bytes,
+        metadata: dict[str, Any] | ut.NamedList | None = None,
         _validate: bool = True,
     ):
         """Create a DNAString.
@@ -145,7 +145,7 @@ def __eq__(self, other) -> bool:
     #### Getitem/setitem ####
     #########################
 
-    def __getitem__(self, key: Union[int, slice]) -> DNAString:
+    def __getitem__(self, key: int | slice) -> DNAString:
         """Extract a subsequence (slicing).
 
         Args:

src/biostrings/dnastringset.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from copy import deepcopy
-from typing import Any, Dict, List, Optional, Union
+from typing import Any
 from warnings import warn
 
 import biocutils as ut
@@ -36,11 +36,11 @@ class DNAStringSet(ut.BiocObject):
 
     def __init__(
         self,
-        sequences: Optional[List[str]] = None,
-        names: Optional[Union[List[str], ut.Names]] = None,
-        _pool: Optional[bytes] = None,
-        _ranges: Optional[IRanges] = None,
-        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+        sequences: list[str] | None = None,
+        names: list[str] | ut.Names | None = None,
+        _pool: bytes | None = None,
+        _ranges: IRanges | None = None,
+        metadata: dict[str, Any] | ut.NamedList | None = None,
         _validate: bool = True,
     ):
         """Create a DNAStringSet.
@@ -141,7 +141,7 @@ def __deepcopy__(self, memo) -> DNAStringSet:
     #### Getter/setters ####
     ########################
 
-    def get_names(self) -> Optional[ut.Names]:
+    def get_names(self) -> ut.Names | None:
         """Get range names.
 
         Returns:
@@ -150,7 +150,7 @@ def get_names(self) -> Optional[ut.Names]:
         """
         return self._ranges.get_names()
 
-    def set_names(self, names: Optional[List[str]], in_place: bool = False) -> DNAStringSet:
+    def set_names(self, names: list[str] | None, in_place: bool = False) -> DNAStringSet:
         """
         Args:
             names:
@@ -169,12 +169,12 @@ def set_names(self, names: Optional[List[str]], in_place: bool = False) -> DNASt
         return output
 
     @property
-    def names(self) -> Optional[ut.Names]:
+    def names(self) -> ut.Names | None:
         """Return the names of the sequences."""
         return self._ranges.get_names()
 
     @names.setter
-    def names(self, new_names: List[str]):
+    def names(self, new_names: list[str]):
         """Set the names of the sequences."""
         warn(
             "Setting property 'names' is an in-place operation, use 'set_names' instead",
@@ -251,7 +251,7 @@ def width(self) -> np.ndarray:
         """Alias to :py:meth:`~.get_width`."""
         return self.get_width()
 
-    def __getitem__(self, key: Union[int, slice, List[int], np.ndarray]) -> Union[DNAString, DNAStringSet]:
+    def __getitem__(self, key: int | slice | list[int] | np.ndarray) -> DNAString | DNAStringSet:
         """Extract one or more sequences.
 
         Args:
@@ -278,7 +278,7 @@ def __getitem__(self, key: Union[int, slice, List[int], np.ndarray]) -> Union[DN
         else:
             raise TypeError(f"Index must be int, slice, or list, not {type(key)}")
 
-    def to_list(self) -> List[str]:
+    def to_list(self) -> list[str]:
         """Convert the set to a list of Python strings."""
         output = []
         for i in range(len(self._ranges)):

tests/test_dnastring.py

@@ -84,7 +84,6 @@ def test_reverse_complement_simple():
 
 
 def test_reverse_complement_iupac():
-    #
     dna = DNAString("ACGTRYSWKMBDHVN-")
     rc = dna.reverse_complement()
     # From our complement table

tests/test_dnastringset.py

@@ -12,7 +12,7 @@ def sample_seqs():
             "ACGT",
             "GATTACA",
             "",
-            "TTGAAAA-CTC-N",  #
+            "TTGAAAA-CTC-N",
             "ACGTACGT",
         ],
         "names": ["seq1", "seq2", "empty", "iupac", "seq5"],