[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -33,7 +33,7 @@ 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

@@ -10,7 +10,7 @@
 if __name__ == "__main__":
     try:
         setup(use_scm_version={"version_scheme": "no-guess-dev"})
-    except:  # noqa
+    except:
         print(
             "\n\nAn error occurred while building the project, "
             "please ensure you have the most updated version of setuptools, "

src/biocutils/BooleanList.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
-from typing import Any, Iterable, Optional, Sequence, Union
+from collections.abc import Iterable, Sequence
+from typing import Any
 
 from .NamedList import NamedList
 from .Names import Names
@@ -23,7 +24,7 @@ def __init__(self, data: Sequence) -> None:
         """
         self._data = data
 
-    def __getitem__(self, index: int) -> Optional[bool]:
+    def __getitem__(self, index: int) -> bool | None:
         """Get an item and coerce it to boolean.
 
         Args:
@@ -46,8 +47,8 @@ class BooleanList(NamedList):
 
     def __init__(
         self,
-        data: Optional[Sequence] = None,
-        names: Optional[Names] = None,
+        data: Sequence | None = None,
+        names: Names | None = None,
         _validate: bool = True,
     ):
         """
@@ -76,15 +77,15 @@ def __init__(
 
         super().__init__(data, names, _validate=_validate)
 
-    def set_value(self, index: Union[int, str], value: Any, in_place: bool = False) -> BooleanList:
+    def set_value(self, index: int | str, value: Any, in_place: bool = False) -> BooleanList:
         """Calls :py:meth:`~biocutils.NamedList.NamedList.set_value` after coercing ``value`` to a boolean."""
         return super().set_value(index, _coerce_to_bool(value), in_place=in_place)
 
     def set_slice(self, index: SubscriptTypes, value: Sequence, in_place: bool = False) -> BooleanList:
         """Calls :py:meth:`~biocutils.NamedList.NamedList.set_slice` after coercing ``value`` to booleans."""
         return super().set_slice(index, _SubscriptCoercer(value), in_place=in_place)
 
-    def safe_insert(self, index: Union[int, str], value: Any, in_place: bool = False) -> BooleanList:
+    def safe_insert(self, index: int | str, value: Any, in_place: bool = False) -> BooleanList:
         """Calls :py:meth:`~biocutils.NamedList.NamedList.safe_insert` after coercing ``value`` to a boolean."""
         return super().safe_insert(index, _coerce_to_bool(value), in_place=in_place)
 

src/biocutils/Factor.py

@@ -1,8 +1,8 @@
 from __future__ import annotations
 
 import warnings
+from collections.abc import Sequence
 from copy import copy, deepcopy
-from typing import Optional, Sequence, Union
 
 import numpy
 
@@ -78,7 +78,7 @@ def __iter__(self) -> FactorIterator:
         """
         return self
 
-    def __next__(self) -> Union[str, None]:
+    def __next__(self) -> str | None:
         """
         Returns:
             Level corresponding to the code at the current position, or None
@@ -102,10 +102,10 @@ class Factor:
 
     def __init__(
         self,
-        codes: Union[numpy.ndarray, Sequence[int]],
-        levels: Union[StringList, Sequence[str]],
+        codes: numpy.ndarray | Sequence[int],
+        levels: StringList | Sequence[str],
         ordered: bool = False,
-        names: Optional[Union[Names, Sequence[str]]] = None,
+        names: Names | Sequence[str] | None = None,
         _validate: bool = True,
     ):
         """Initialize a Factor object.
@@ -246,7 +246,7 @@ def names(self) -> Names:
         """Alias for :py:meth:`~get_names`."""
         return self.get_names()
 
-    def set_names(self, names: Optional[Names], in_place: bool = False) -> "NamedList":
+    def set_names(self, names: Names | None, in_place: bool = False) -> NamedList:
         """
         Args:
             names:
@@ -341,7 +341,7 @@ def __eq__(self, other: Factor):
     #####>>>> Slicing <<<<#####
     ###########################
 
-    def get_value(self, index: Union[str, int]) -> Union[str, None]:
+    def get_value(self, index: str | int) -> str | None:
         """
         Args:
             index:
@@ -380,7 +380,7 @@ def get_slice(self, index: SubscriptTypes) -> Factor:
             output._names = subset_sequence(self._names, index)
         return output
 
-    def __getitem__(self, index: SubscriptTypes) -> Union[str, Factor]:
+    def __getitem__(self, index: SubscriptTypes) -> str | Factor:
         """
         If ``index`` is a scalar, this is an alias for :py:meth:`~get_value`.
 
@@ -392,7 +392,7 @@ def __getitem__(self, index: SubscriptTypes) -> Union[str, Factor]:
         else:
             return self.get_slice(NormalizedSubscript(index))
 
-    def set_value(self, index: Union[str, int], value: Union[str, None], in_place: bool = False) -> Factor:
+    def set_value(self, index: str | int, value: str | None, in_place: bool = False) -> Factor:
         """
         Args:
             index:
@@ -482,7 +482,7 @@ def set_slice(self, index: SubscriptTypes, value: Factor, in_place: bool = False
 
         return output
 
-    def __setitem__(self, index: SubscriptTypes, value: Union[str, Factor]):
+    def __setitem__(self, index: SubscriptTypes, value: str | Factor):
         """
         If ``index`` is a scalar, this is an alias for :py:meth:`~set_value`.
 
@@ -588,7 +588,7 @@ def replace_levels(
         output._levels = new_levels
         return output
 
-    def set_levels(self, levels: Union[str, Sequence[str]], remap: bool = True, in_place: bool = False) -> Factor:
+    def set_levels(self, levels: str | Sequence[str], remap: bool = True, in_place: bool = False) -> Factor:
         """
         Alias for :py:meth:`~remap_levels` if ``remap = True``, otherwise an
         alias for :py:meth:`~replace_levels`. The first alias is deprecated and
@@ -600,7 +600,7 @@ def set_levels(self, levels: Union[str, Sequence[str]], remap: bool = True, in_p
         else:
             return self.replace_levels(levels, in_place=in_place)
 
-    def remap_levels(self, levels: Union[str, Sequence[str]], in_place: bool = False) -> Factor:
+    def remap_levels(self, levels: str | Sequence[str], in_place: bool = False) -> Factor:
         """Remap codes to a replacement list of levels. Each entry of the
         remapped ``Factor`` will refer to the same string across the old and
         new levels, provided that string is present in both sets of levels.
@@ -723,10 +723,10 @@ def to_pandas(self):
     @staticmethod
     def from_sequence(
         x: Sequence[str],
-        levels: Optional[Sequence[str]] = None,
+        levels: Sequence[str] | None = None,
         sort_levels: bool = True,
         ordered: bool = False,
-        names: Optional[Sequence[str]] = None,
+        names: Sequence[str] | None = None,
         **kwargs,
     ) -> Factor:
         """Convert a sequence of hashable values into a factor.
@@ -776,7 +776,7 @@ def as_list(self) -> list:
         """
         return [self._levels[c] if c >= 0 else None for c in self._codes]
 
-    def safe_delete(self, index: Union[int, str, slice], in_place: bool = False) -> Factor:
+    def safe_delete(self, index: int | str | slice, in_place: bool = False) -> Factor:
         """
         Args:
             index:
@@ -810,11 +810,11 @@ def safe_delete(self, index: Union[int, str, slice], in_place: bool = False) ->
 
         return output
 
-    def delete(self, index: Union[int, str, slice]):
+    def delete(self, index: int | str | slice):
         """Alias for :py:meth:`~safe_delete` with ``in_place = True``."""
         self.safe_delete(index, in_place=True)
 
-    def __delitem__(self, index: Union[int, str, slice]):
+    def __delitem__(self, index: int | str | slice):
         """Alias for :py:meth:`~delete`."""
         self.delete(index)
 

src/biocutils/FloatList.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
-from typing import Any, Iterable, Optional, Sequence, Union
+from collections.abc import Iterable, Sequence
+from typing import Any
 
 from .NamedList import NamedList
 from .Names import Names
@@ -27,7 +28,7 @@ def __init__(self, data: Sequence) -> None:
         """
         self._data = data
 
-    def __getitem__(self, index: int) -> Optional[float]:
+    def __getitem__(self, index: int) -> float | None:
         """Get an item and coerce it to float.
 
         Args:
@@ -49,8 +50,8 @@ class FloatList(NamedList):
 
     def __init__(
         self,
-        data: Optional[Sequence] = None,
-        names: Optional[Names] = None,
+        data: Sequence | None = None,
+        names: Names | None = None,
         _validate: bool = True,
     ):
         """
@@ -79,15 +80,15 @@ def __init__(
 
         super().__init__(data, names, _validate=_validate)
 
-    def set_value(self, index: Union[int, str], value: Any, in_place: bool = False) -> FloatList:
+    def set_value(self, index: int | str, value: Any, in_place: bool = False) -> FloatList:
         """Calls :py:meth:`~biocutils.NamedList.NamedList.set_value` after coercing ``value`` to a float."""
         return super().set_value(index, _coerce_to_float(value), in_place=in_place)
 
     def set_slice(self, index: SubscriptTypes, value: Sequence, in_place: bool = False) -> FloatList:
         """Calls :py:meth:`~biocutils.NamedList.NamedList.set_slice` after coercing ``value`` to floats."""
         return super().set_slice(index, _SubscriptCoercer(value), in_place=in_place)
 
-    def safe_insert(self, index: Union[int, str], value: Any, in_place: bool = False) -> FloatList:
+    def safe_insert(self, index: int | str, value: Any, in_place: bool = False) -> FloatList:
         """Calls :py:meth:`~biocutils.NamedList.NamedList.safe_insert` after coercing ``value`` to a float."""
         return super().safe_insert(index, _coerce_to_float(value), in_place=in_place)
 

src/biocutils/IntegerList.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
-from typing import Any, Iterable, Optional, Sequence, Union
+from collections.abc import Iterable, Sequence
+from typing import Any
 
 from .NamedList import NamedList
 from .Names import Names
@@ -28,7 +29,7 @@ def __init__(self, data: Sequence) -> None:
         """
         self._data = data
 
-    def __getitem__(self, index: int) -> Optional[int]:
+    def __getitem__(self, index: int) -> int | None:
         """Get an item and coerce it to integer.
 
         Args:
@@ -51,8 +52,8 @@ class IntegerList(NamedList):
 
     def __init__(
         self,
-        data: Optional[Sequence] = None,
-        names: Optional[Names] = None,
+        data: Sequence | None = None,
+        names: Names | None = None,
         _validate: bool = True,
     ):
         """
@@ -80,15 +81,15 @@ def __init__(
                     data = list(_coerce_to_int(item) for item in original)
         super().__init__(data, names, _validate=_validate)
 
-    def set_value(self, index: Union[int, str], value: Any, in_place: bool = False) -> IntegerList:
+    def set_value(self, index: int | str, value: Any, in_place: bool = False) -> IntegerList:
         """Calls :py:meth:`~biocutils.NamedList.NamedList.set_value` after coercing ``value`` to a integer."""
         return super().set_value(index, _coerce_to_int(value), in_place=in_place)
 
     def set_slice(self, index: SubscriptTypes, value: Sequence, in_place: bool = False) -> IntegerList:
         """Calls :py:meth:`~biocutils.NamedList.NamedList.set_slice` after coercing ``value`` to integers."""
         return super().set_slice(index, _SubscriptCoercer(value), in_place=in_place)
 
-    def safe_insert(self, index: Union[int, str], value: Any, in_place: bool = False) -> IntegerList:
+    def safe_insert(self, index: int | str, value: Any, in_place: bool = False) -> IntegerList:
         """Calls :py:meth:`~biocutils.NamedList.NamedList.safe_insert` after coercing ``value`` to a integer."""
         return super().safe_insert(index, _coerce_to_int(value), in_place=in_place)