[python] Convert from Optional[Foo] to Foo | None

Convert `Optional` to [union
types](https://docs.python.org/3/library/stdtypes.html#union-type)

[SC-60887](https://app.shortcut.com/tiledb-inc/story/60887)

resolves #3334

apis/python/src/tiledbsoma/_collection.py

@@ -13,7 +13,6 @@
     Callable,
     ClassVar,
     Dict,
-    Optional,
     Tuple,
     Type,
     TypeVar,
@@ -67,9 +66,9 @@ def create(
         cls,
         uri: str,
         *,
-        platform_config: Optional[options.PlatformConfig] = None,
-        context: Optional[SOMATileDBContext] = None,
-        tiledb_timestamp: Optional[OpenTimestamp] = None,
+        platform_config: options.PlatformConfig | None = None,
+        context: SOMATileDBContext | None = None,
+        tiledb_timestamp: OpenTimestamp | None = None,
     ) -> Self:
         """Creates and opens a new SOMA collection in storage.
 
@@ -147,8 +146,8 @@ def add_new_collection(
         key: str,
         kind: None = None,
         *,
-        uri: Optional[str] = ...,
-        platform_config: Optional[options.PlatformConfig] = ...,
+        uri: str | None = ...,
+        platform_config: options.PlatformConfig | None = ...,
     ) -> "Collection[AnySOMAObject]": ...
 
     @overload
@@ -157,17 +156,17 @@ def add_new_collection(
         key: str,
         kind: Type[_Coll],
         *,
-        uri: Optional[str] = ...,
-        platform_config: Optional[options.PlatformConfig] = ...,
+        uri: str | None = ...,
+        platform_config: options.PlatformConfig | None = ...,
     ) -> _Coll: ...
 
     def add_new_collection(
         self,
         key: str,
-        kind: Optional[Type[CollectionBase]] = None,  # type: ignore[type-arg]
+        kind: Type[CollectionBase] | None = None,  # type: ignore[type-arg]
         *,
-        uri: Optional[str] = None,
-        platform_config: Optional[options.PlatformConfig] = None,
+        uri: str | None = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> AnyTileDBCollection:
         """Adds a new sub-collection to this collection.
 
@@ -226,7 +225,7 @@ def add_new_collection(
         DataFrame.create, exclude=("context", "tiledb_timestamp")
     )
     def add_new_dataframe(
-        self, key: str, *, uri: Optional[str] = None, **kwargs: Any
+        self, key: str, *, uri: str | None = None, **kwargs: Any
     ) -> DataFrame:
         """Adds a new DataFrame to this collection.
 
@@ -269,7 +268,7 @@ def add_new_dataframe(
 
     @_funcs.forwards_kwargs_to(NDArray.create, exclude=("context", "tiledb_timestamp"))
     def _add_new_ndarray(
-        self, cls: Type[_NDArr], key: str, *, uri: Optional[str] = None, **kwargs: Any
+        self, cls: Type[_NDArr], key: str, *, uri: str | None = None, **kwargs: Any
     ) -> _NDArr:
         """Internal implementation of common NDArray-adding operations."""
         return self._add_new_element(
@@ -361,7 +360,7 @@ def _add_new_element(
         key: str,
         kind: Type[_TDBO],
         factory: Callable[[str], _TDBO],
-        user_uri: Optional[str],
+        user_uri: str | None,
     ) -> _TDBO:
         """Handles the common parts of adding new elements.
 

apis/python/src/tiledbsoma/_common_nd_array.py

@@ -5,7 +5,9 @@
 
 """Common code shared by both NDArray implementations."""
 
-from typing import Optional, Sequence, Tuple, Union, cast
+from __future__ import annotations
+
+from typing import Sequence, Tuple, Union, cast
 
 import pyarrow as pa
 import somacore
@@ -32,9 +34,9 @@ def create(
         *,
         type: pa.DataType,
         shape: Sequence[Union[int, None]],
-        platform_config: Optional[options.PlatformConfig] = None,
-        context: Optional[SOMATileDBContext] = None,
-        tiledb_timestamp: Optional[OpenTimestamp] = None,
+        platform_config: options.PlatformConfig | None = None,
+        context: SOMATileDBContext | None = None,
+        tiledb_timestamp: OpenTimestamp | None = None,
     ) -> Self:
         """Creates a SOMA ``NDArray`` at the given URI.
 
@@ -154,7 +156,7 @@ def tiledbsoma_has_upgraded_shape(self) -> bool:
     def _dim_capacity_and_extent(
         cls,
         dim_name: str,
-        dim_shape: Optional[int],
+        dim_shape: int | None,
         ndim: int,
         create_options: TileDBCreateOptions,
     ) -> Tuple[int, int]:

apis/python/src/tiledbsoma/_dataframe.py

@@ -6,12 +6,14 @@
 """
 Implementation of a SOMA DataFrame
 """
+
+from __future__ import annotations
+
 import inspect
 from typing import (
     Any,
     Dict,
     List,
-    Optional,
     Sequence,
     Tuple,
     Union,
@@ -151,10 +153,10 @@ def create(
         *,
         schema: pa.Schema,
         index_column_names: Sequence[str] = (SOMA_JOINID,),
-        domain: Optional[Domain] = None,
-        platform_config: Optional[options.PlatformConfig] = None,
-        context: Optional[SOMATileDBContext] = None,
-        tiledb_timestamp: Optional[OpenTimestamp] = None,
+        domain: Domain | None = None,
+        platform_config: options.PlatformConfig | None = None,
+        context: SOMATileDBContext | None = None,
+        tiledb_timestamp: OpenTimestamp | None = None,
     ) -> "DataFrame":
         """Creates the data structure on disk/S3/cloud.
 
@@ -407,7 +409,7 @@ def count(self) -> int:
         return cast(DataFrameWrapper, self._handle).count
 
     @property
-    def _maybe_soma_joinid_shape(self) -> Optional[int]:
+    def _maybe_soma_joinid_shape(self) -> int | None:
         """An internal helper method that returns the shape
         value along the ``soma_joinid`` index column, if the ``DataFrame
         has one, else ``None``.
@@ -419,7 +421,7 @@ def _maybe_soma_joinid_shape(self) -> Optional[int]:
         return self._handle.maybe_soma_joinid_shape
 
     @property
-    def _maybe_soma_joinid_maxshape(self) -> Optional[int]:
+    def _maybe_soma_joinid_maxshape(self) -> int | None:
         """An internal helper method that returns the maxshape
         value along the ``soma_joinid`` index column, if the ``DataFrame
         has one, else ``None``.
@@ -657,13 +659,13 @@ def __len__(self) -> int:
     def read(
         self,
         coords: options.SparseDFCoords = (),
-        column_names: Optional[Sequence[str]] = None,
+        column_names: Sequence[str] | None = None,
         *,
         result_order: options.ResultOrderStr = options.ResultOrder.AUTO,
-        value_filter: Optional[str] = None,
+        value_filter: str | None = None,
         batch_size: options.BatchSize = _UNBATCHED,
-        partitions: Optional[options.ReadPartitions] = None,
-        platform_config: Optional[options.PlatformConfig] = None,
+        partitions: options.ReadPartitions | None = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> TableReadIter:
         """Reads a user-defined subset of data, addressed by the dataframe indexing columns,
         optionally filtered, and return results as one or more `Arrow tables <https://arrow.apache.org/docs/python/generated/pyarrow.Table.html>`_.
@@ -732,7 +734,7 @@ def read(
         )
 
     def write(
-        self, values: pa.Table, platform_config: Optional[options.PlatformConfig] = None
+        self, values: pa.Table, platform_config: options.PlatformConfig | None = None
     ) -> Self:
         """Writes an `Arrow table <https://arrow.apache.org/docs/python/generated/pyarrow.Table.html>`_
         to the persistent object. As duplicate index values are not allowed, index values already

apis/python/src/tiledbsoma/_dense_nd_array.py

@@ -7,7 +7,9 @@
 Implementation of SOMA DenseNDArray.
 """
 
-from typing import List, Optional, Sequence, Tuple, Union
+from __future__ import annotations
+
+from typing import List, Sequence, Tuple, Union
 
 import numpy as np
 import pyarrow as pa
@@ -93,9 +95,9 @@ def create(
         *,
         type: pa.DataType,
         shape: Sequence[Union[int, None]],
-        platform_config: Optional[options.PlatformConfig] = None,
-        context: Optional[SOMATileDBContext] = None,
-        tiledb_timestamp: Optional[OpenTimestamp] = None,
+        platform_config: options.PlatformConfig | None = None,
+        context: SOMATileDBContext | None = None,
+        tiledb_timestamp: OpenTimestamp | None = None,
     ) -> Self:
         context = _validate_soma_tiledb_context(context)
 
@@ -173,8 +175,8 @@ def read(
         coords: options.DenseNDCoords = (),
         *,
         result_order: options.ResultOrderStr = somacore.ResultOrder.ROW_MAJOR,
-        partitions: Optional[options.ReadPartitions] = None,
-        platform_config: Optional[options.PlatformConfig] = None,
+        partitions: options.ReadPartitions | None = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> pa.Tensor:
         """Reads a user-defined dense slice of the array and return as an Arrow ``Tensor``.
 
@@ -262,7 +264,7 @@ def write(
         coords: options.DenseNDCoords,
         values: pa.Tensor,
         *,
-        platform_config: Optional[options.PlatformConfig] = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> Self:
         """Writes a subarray, defined by ``coords`` and ``values``. Will overwrite existing
         values in the array.
@@ -326,7 +328,7 @@ def write(
     def _dim_capacity_and_extent(
         cls,
         dim_name: str,
-        dim_shape: Optional[int],
+        dim_shape: int | None,
         ndim: int,
         create_options: TileDBCreateOptions,
     ) -> Tuple[int, int]:

apis/python/src/tiledbsoma/_eager_iter.py

@@ -1,5 +1,7 @@
+from __future__ import annotations
+
 from concurrent import futures
-from typing import Iterator, Optional, TypeVar
+from typing import Iterator, TypeVar
 
 _T = TypeVar("_T")
 
@@ -8,7 +10,7 @@ class EagerIterator(Iterator[_T]):
     def __init__(
         self,
         iterator: Iterator[_T],
-        pool: Optional[futures.Executor] = None,
+        pool: futures.Executor | None = None,
     ):
         super().__init__()
         self.iterator = iterator

apis/python/src/tiledbsoma/_experiment.py

@@ -5,8 +5,10 @@
 
 """Implementation of a SOMA Experiment.
 """
+
+from __future__ import annotations
+
 import functools
-from typing import Optional
 
 from somacore import experiment, query
 
@@ -81,8 +83,8 @@ def axis_query(  # type: ignore
         self,
         measurement_name: str,
         *,
-        obs_query: Optional[query.AxisQuery] = None,
-        var_query: Optional[query.AxisQuery] = None,
+        obs_query: query.AxisQuery | None = None,
+        var_query: query.AxisQuery | None = None,
     ) -> ExperimentAxisQuery:
         """Creates an axis query over this experiment.
         Lifecycle: Maturing.

apis/python/src/tiledbsoma/_factory.py

@@ -7,10 +7,11 @@
 Collection.
 """
 
+from __future__ import annotations
+
 from typing import (
     Callable,
     Dict,
-    Optional,
     Type,
     TypeVar,
     Union,
@@ -55,9 +56,9 @@ def open(
     uri: str,
     mode: options.OpenMode = ...,
     *,
-    soma_type: Optional[str] = None,
-    context: Optional[SOMATileDBContext] = None,
-    tiledb_timestamp: Optional[OpenTimestamp] = None,
+    soma_type: str | None = None,
+    context: SOMATileDBContext | None = None,
+    tiledb_timestamp: OpenTimestamp | None = None,
 ) -> AnySOMAObject: ...
 
 
@@ -67,8 +68,8 @@ def open(
     mode: options.OpenMode,
     *,
     soma_type: Type[_Obj],
-    context: Optional[SOMATileDBContext] = None,
-    tiledb_timestamp: Optional[OpenTimestamp] = None,
+    context: SOMATileDBContext | None = None,
+    tiledb_timestamp: OpenTimestamp | None = None,
 ) -> _Obj: ...
 
 
@@ -78,8 +79,8 @@ def open(
     mode: options.OpenMode = "r",
     *,
     soma_type: Union[Type[SOMAObject], str, None] = None,  # type: ignore[type-arg]
-    context: Optional[SOMATileDBContext] = None,
-    tiledb_timestamp: Optional[OpenTimestamp] = None,
+    context: SOMATileDBContext | None = None,
+    tiledb_timestamp: OpenTimestamp | None = None,
 ) -> AnySOMAObject:
     """Opens a TileDB SOMA object.
 
@@ -145,12 +146,12 @@ def open(
 
 def _open_internal(
     opener: Callable[
-        [str, options.OpenMode, SOMATileDBContext, Optional[OpenTimestamp]], _Wrapper
+        [str, options.OpenMode, SOMATileDBContext, OpenTimestamp | None], _Wrapper
     ],
     uri: str,
     mode: options.OpenMode,
     context: SOMATileDBContext,
-    timestamp: Optional[OpenTimestamp],
+    timestamp: OpenTimestamp | None,
 ) -> SOMAObject[_Wrapper]:
     """Lower-level open function for internal use only."""
     handle = opener(uri, mode, context, timestamp)