[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: v0.16.0
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

setup.py

@@ -12,7 +12,7 @@
 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/compressed_lists/__init__.py

@@ -15,12 +15,12 @@
 finally:
     del version, PackageNotFoundError
 
-from .partition import Partitioning
 from .base import CompressedList
-from .integer_list import CompressedIntegerList
-from .string_list import CompressedStringList, CompressedCharacterList
+from .biocframe_list import CompressedSplitBiocFrameList
 from .bool_list import CompressedBooleanList
 from .float_list import CompressedFloatList
+from .integer_list import CompressedIntegerList
 from .numpy_list import CompressedNumpyList
-from .biocframe_list import CompressedSplitBiocFrameList
+from .partition import Partitioning
 from .split_generic import splitAsCompressedList
+from .string_list import CompressedCharacterList, CompressedStringList

src/compressed_lists/base.py

@@ -1,11 +1,12 @@
 from __future__ import annotations
 
-from typing import Any, Callable, Dict, Iterator, List, Optional, Sequence, Union
+from collections.abc import Callable, Iterator, Sequence
+from typing import Any
 from warnings import warn
 
 import biocutils as ut
-from biocframe import BiocFrame
 import numpy as np
+from biocframe import BiocFrame
 
 from .partition import Partitioning
 
@@ -59,8 +60,8 @@ def __init__(
         unlist_data: Any,
         partitioning: Partitioning,
         element_type: Any = None,
-        element_metadata: Optional[BiocFrame] = None,
-        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+        element_metadata: BiocFrame | None = None,
+        metadata: dict[str, Any] | ut.NamedList | None = None,
         _validate: bool = True,
     ):
         """Initialize a CompressedList.
@@ -205,8 +206,8 @@ def __str__(self) -> str:
 
         output += f"partitioning: {ut.print_truncated_list(self._partitioning)}\n"
 
-        output += f"element_metadata({str(len(self._element_metadata))} rows): {ut.print_truncated_list(list(self._element_metadata.get_column_names()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
-        output += f"metadata({str(len(self._metadata))}): {ut.print_truncated_list(list(self._metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
+        output += f"element_metadata({len(self._element_metadata)!s} rows): {ut.print_truncated_list(list(self._element_metadata.get_column_names()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
+        output += f"metadata({len(self._metadata)!s}): {ut.print_truncated_list(list(self._metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
 
         return output
 
@@ -240,7 +241,7 @@ def paritioning(self) -> Partitioning:
     ######>> names <<######
     #######################
 
-    def get_names(self) -> Optional[ut.Names]:
+    def get_names(self) -> ut.Names | None:
         """Get the names of list elements."""
         return self._partitioning.get_names()
 
@@ -264,7 +265,7 @@ def set_names(self, names: Sequence[str], in_place: bool = False) -> CompressedL
         return output
 
     @property
-    def names(self) -> Optional[ut.Names]:
+    def names(self) -> ut.Names | None:
         """Alias for :py:attr:`~get_names`."""
         return self._partitioning.get_names()
 
@@ -379,7 +380,7 @@ def element_metadata(self, element_metadata: BiocFrame):
     ######>> accessors <<#####
     ##########################
 
-    def __getitem__(self, key: Union[int, str, slice]) -> Any:
+    def __getitem__(self, key: int | str | slice) -> Any:
         """Get an element or slice of elements from the list.
 
         Args:
@@ -458,8 +459,8 @@ def extract_range(self, start: int, end: int) -> Any:
     def from_list(
         cls,
         lst: Any,
-        names: Optional[Union[ut.Names, Sequence[str]]] = None,
-        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+        names: ut.Names | Sequence[str] | None = None,
+        metadata: dict[str, Any] | ut.NamedList | None = None,
     ) -> CompressedList:
         """Create a CompressedList from a regular list.
 
@@ -496,7 +497,7 @@ def from_list(
     ######>> coercions <<######
     ###########################
 
-    def to_list(self) -> List[List[Any]]:
+    def to_list(self) -> list[list[Any]]:
         """Convert to a regular Python list.
 
         Returns:
@@ -511,7 +512,7 @@ def to_list(self) -> List[List[Any]]:
 
         return result
 
-    def as_list(self) -> List[List[Any]]:
+    def as_list(self) -> list[list[Any]]:
         """Alias to :py:meth:`~to_list`"""
         return self.to_list()
 

src/compressed_lists/biocframe_list.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
-from typing import Any, Dict, List, Optional, Sequence, Union
+from collections.abc import Sequence
+from typing import Any
 
 import biocutils as ut
 from biocframe import BiocFrame
@@ -23,8 +24,8 @@ def __init__(
         self,
         unlist_data: BiocFrame,
         partitioning: Partitioning,
-        element_metadata: Optional[dict] = None,
-        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+        element_metadata: dict | None = None,
+        metadata: dict[str, Any] | ut.NamedList | None = None,
         **kwargs,
     ):
         """Initialize a CompressedSplitBiocFrameList.
@@ -55,9 +56,9 @@ def __init__(
     @classmethod
     def from_list(
         cls,
-        lst: List[BiocFrame],
-        names: Optional[Union[ut.Names, Sequence[str]]] = None,
-        metadata: Optional[dict] = None,
+        lst: list[BiocFrame],
+        names: ut.Names | Sequence[str] | None = None,
+        metadata: dict | None = None,
     ) -> CompressedSplitBiocFrameList:
         """Create a `CompressedSplitBiocFrameList` from a regular list.
 
@@ -82,7 +83,7 @@ def from_list(
         partitioning = Partitioning.from_list(lst, names)
         return cls(unlist_data, partitioning, metadata=metadata)
 
-    def __getitem__(self, key: Union[int, str, slice]):
+    def __getitem__(self, key: int | str | slice):
         """Override to handle column extraction using `splitAsCompressedList`."""
         if isinstance(key, str):
             column_data = self._unlist_data.get_column(key)
@@ -154,8 +155,8 @@ def __str__(self) -> str:
 
         output += f"partitioning: {ut.print_truncated_list(self._partitioning)}\n"
 
-        output += f"element_metadata({str(len(self._element_metadata))} rows): {ut.print_truncated_list(list(self._element_metadata.get_column_names()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
-        output += f"metadata({str(len(self._metadata))}): {ut.print_truncated_list(list(self._metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
+        output += f"element_metadata({len(self._element_metadata)!s} rows): {ut.print_truncated_list(list(self._element_metadata.get_column_names()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
+        output += f"metadata({len(self._metadata)!s}): {ut.print_truncated_list(list(self._metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
 
         return output
 
@@ -179,9 +180,9 @@ def empty(cls, n: int):
 @splitAsCompressedList.register
 def _(
     data: BiocFrame,
-    groups_or_partitions: Union[list, Partitioning],
-    names: Optional[Union[ut.Names, Sequence[str]]] = None,
-    metadata: Optional[dict] = None,
+    groups_or_partitions: list | Partitioning,
+    names: ut.Names | Sequence[str] | None = None,
+    metadata: dict | None = None,
 ) -> CompressedSplitBiocFrameList:
     """Handle lists of BiocFrame objects."""
 

src/compressed_lists/bool_list.py

@@ -1,4 +1,5 @@
-from typing import Any, Dict, Optional, Sequence, Union
+from collections.abc import Sequence
+from typing import Any
 from warnings import warn
 
 import biocutils as ut
@@ -19,8 +20,8 @@ def __init__(
         self,
         unlist_data: ut.BooleanList,
         partitioning: Partitioning,
-        element_metadata: Optional[dict] = None,
-        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+        element_metadata: dict | None = None,
+        metadata: dict[str, Any] | ut.NamedList | None = None,
         **kwargs,
     ):
         """Initialize a CompressedBooleanList.
@@ -57,9 +58,9 @@ def __init__(
 @splitAsCompressedList.register
 def _(
     data: ut.BooleanList,
-    groups_or_partitions: Union[list, Partitioning],
-    names: Optional[Union[ut.Names, Sequence[str]]] = None,
-    metadata: Optional[dict] = None,
+    groups_or_partitions: list | Partitioning,
+    names: ut.Names | Sequence[str] | None = None,
+    metadata: dict | None = None,
 ) -> CompressedBooleanList:
     """Handle lists of booleans."""
 

src/compressed_lists/float_list.py

@@ -1,4 +1,5 @@
-from typing import Any, Dict, Optional, Sequence, Union
+from collections.abc import Sequence
+from typing import Any
 from warnings import warn
 
 import biocutils as ut
@@ -19,8 +20,8 @@ def __init__(
         self,
         unlist_data: ut.FloatList,
         partitioning: Partitioning,
-        element_metadata: Optional[dict] = None,
-        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+        element_metadata: dict | None = None,
+        metadata: dict[str, Any] | ut.NamedList | None = None,
         **kwargs,
     ):
         """Initialize a CompressedFloatList.
@@ -57,9 +58,9 @@ def __init__(
 @splitAsCompressedList.register
 def _(
     data: ut.FloatList,
-    groups_or_partitions: Union[list, Partitioning],
-    names: Optional[Union[ut.Names, Sequence[str]]] = None,
-    metadata: Optional[dict] = None,
+    groups_or_partitions: list | Partitioning,
+    names: ut.Names | Sequence[str] | None = None,
+    metadata: dict | None = None,
 ) -> CompressedFloatList:
     """Handle lists of floats."""
 

src/compressed_lists/integer_list.py

@@ -1,4 +1,5 @@
-from typing import Any, Dict, Optional, Sequence, Union
+from collections.abc import Sequence
+from typing import Any
 from warnings import warn
 
 import biocutils as ut
@@ -19,8 +20,8 @@ def __init__(
         self,
         unlist_data: ut.IntegerList,
         partitioning: Partitioning,
-        element_metadata: Optional[dict] = None,
-        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+        element_metadata: dict | None = None,
+        metadata: dict[str, Any] | ut.NamedList | None = None,
         **kwargs,
     ):
         """Initialize a CompressedIntegerList.
@@ -57,9 +58,9 @@ def __init__(
 @splitAsCompressedList.register
 def _(
     data: ut.IntegerList,
-    groups_or_partitions: Union[list, Partitioning],
-    names: Optional[Union[ut.Names, Sequence[str]]] = None,
-    metadata: Optional[dict] = None,
+    groups_or_partitions: list | Partitioning,
+    names: ut.Names | Sequence[str] | None = None,
+    metadata: dict | None = None,
 ) -> CompressedIntegerList:
     """Handle lists of integers."""
 

src/compressed_lists/numpy_list.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
-from typing import Any, Dict, List, Optional, Sequence, Union
+from collections.abc import Sequence
+from typing import Any
 from warnings import warn
 
 import biocutils as ut
@@ -22,8 +23,8 @@ def __init__(
         self,
         unlist_data: np.ndarray,
         partitioning: Partitioning,
-        element_metadata: Optional[dict] = None,
-        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+        element_metadata: dict | None = None,
+        metadata: dict[str, Any] | ut.NamedList | None = None,
         **kwargs,
     ):
         """Initialize a CompressedNumpyList.
@@ -62,9 +63,9 @@ def __init__(
     @classmethod
     def from_list(
         cls,
-        lst: List[np.ndarray],
-        names: Optional[Union[ut.Names, Sequence[str]]] = None,
-        metadata: Optional[dict] = None,
+        lst: list[np.ndarray],
+        names: ut.Names | Sequence[str] | None = None,
+        metadata: dict | None = None,
     ) -> CompressedNumpyList:
         """
         Create a `CompressedNumpyList` from a list of NumPy vectors.
@@ -95,9 +96,9 @@ def from_list(
 @splitAsCompressedList.register
 def _(
     data: np.ndarray,
-    groups_or_partitions: Union[list, Partitioning],
-    names: Optional[Union[ut.Names, Sequence[str]]] = None,
-    metadata: Optional[dict] = None,
+    groups_or_partitions: list | Partitioning,
+    names: ut.Names | Sequence[str] | None = None,
+    metadata: dict | None = None,
 ) -> CompressedNumpyList:
     """Handle NumPy arrays."""