Convert Optional[] to union types (#252)

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

[SC-61053](https://app.shortcut.com/tiledb-inc/story/61053)

resolves single-cell-data/TileDB-SOMA#3334

Author: mojaveazure

python-spec/src/somacore/_mixin.py

@@ -1,6 +1,8 @@
 """Tools for making mixins with SOMA Collections."""
 
-from typing import Generic, MutableMapping, Optional, Type, TypeVar, Union, overload
+from __future__ import annotations
+
+from typing import Generic, MutableMapping, Type, TypeVar, Union, overload
 
 import attrs
 
@@ -35,10 +37,10 @@ class FSCollection(FirstSecondMixin, CollectionBase):
         inst.second = 500
     """
 
-    typ: Optional[Type[_T]] = None
+    typ: Type[_T] | None = None
     """The type we expect to return from this field."""
 
-    item_name: Optional[str] = None
+    item_name: str | None = None
     """The name of the item we are getting (``x._backing["whatever"]``).
 
     This uses the name of the field by default but can be manually overridden.
@@ -59,7 +61,7 @@ def __get__(self, inst: None, owner: Type[_Coll]) -> "item[_T]": ...
     @overload
     def __get__(self, inst: _Coll, owner: Type[_Coll]) -> _T: ...
 
-    def __get__(self, inst: Optional[_Coll], owner: Type[_Coll]) -> Union["item", _T]:
+    def __get__(self, inst: _Coll | None, owner: Type[_Coll]) -> Union["item", _T]:
         del owner  # unused
         if not inst:
             return self

python-spec/src/somacore/base.py

@@ -4,8 +4,10 @@
 members will be exported to the ``somacore`` namespace.
 """
 
+from __future__ import annotations
+
 import abc
-from typing import Any, ClassVar, MutableMapping, Optional
+from typing import Any, ClassVar, MutableMapping
 
 from typing_extensions import LiteralString, Self
 
@@ -25,8 +27,8 @@ def open(
         uri: str,
         mode: options.OpenMode = "r",
         *,
-        context: Optional[Any] = None,
-        platform_config: Optional[options.PlatformConfig] = None,
+        context: Any | None = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> Self:
         """Opens the SOMA object of this type at the given URI.
 
@@ -43,7 +45,7 @@ def open(
 
     @classmethod
     @abc.abstractmethod
-    def exists(cls, uri: str, *, context: Optional[Any] = None) -> bool:
+    def exists(cls, uri: str, *, context: Any | None = None) -> bool:
         """Checks whether a SOMA object of this type is stored at the URI.
 
         Args:
@@ -66,7 +68,7 @@ def uri(self) -> str:
         raise NotImplementedError()
 
     @property
-    def context(self) -> Optional[types.ContextBase]:
+    def context(self) -> types.ContextBase | None:
         """A value storing implementation-specific configuration information.
 
         This contains long-lived (i.e., not call-specific) information that is

python-spec/src/somacore/collection.py

@@ -1,8 +1,9 @@
+from __future__ import annotations
+
 import abc
 from typing import (
     Any,
     MutableMapping,
-    Optional,
     Sequence,
     Tuple,
     Type,
@@ -43,8 +44,8 @@ def create(
         cls,
         uri: str,
         *,
-        platform_config: Optional[options.PlatformConfig] = None,
-        context: Optional[Any] = None,
+        platform_config: options.PlatformConfig | None = None,
+        context: Any | None = None,
     ) -> Self:
         """Creates a new collection of this type at the given URI.
 
@@ -69,8 +70,8 @@ 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": ...
 
     @overload
@@ -80,18 +81,18 @@ def add_new_collection(
         key: str,
         kind: Type[_CT],
         *,
-        uri: Optional[str] = ...,
-        platform_config: Optional[options.PlatformConfig] = ...,
+        uri: str | None = ...,
+        platform_config: options.PlatformConfig | None = ...,
     ) -> _CT: ...
 
     @abc.abstractmethod
     def add_new_collection(
         self,
         key: str,
-        kind: Optional[Type["BaseCollection"]] = None,
+        kind: Type["BaseCollection"] | None = None,
         *,
-        uri: Optional[str] = None,
-        platform_config: Optional[options.PlatformConfig] = None,
+        uri: str | None = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> "BaseCollection":
         """Creates a new sub-collection of this collection.
         To add an existing collection as a sub-element of this collection,
@@ -151,11 +152,11 @@ def add_new_dataframe(
         self,
         key: str,
         *,
-        uri: Optional[str] = None,
+        uri: str | None = None,
         schema: pa.Schema,
         index_column_names: Sequence[str] = (options.SOMA_JOINID,),
-        domain: Optional[Sequence[Optional[Tuple[Any, Any]]]] = None,
-        platform_config: Optional[options.PlatformConfig] = None,
+        domain: Sequence[Tuple[Any, Any] | None] | None = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> data.DataFrame:
         """Creates a new DataFrame as a child of this collection.
 
@@ -174,10 +175,10 @@ def add_new_dense_ndarray(
         self,
         key: str,
         *,
-        uri: Optional[str] = None,
+        uri: str | None = None,
         type: pa.DataType,
         shape: Sequence[int],
-        platform_config: Optional[options.PlatformConfig] = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> data.DenseNDArray:
         """Creates a new dense NDArray as a child of this collection.
 
@@ -196,10 +197,10 @@ def add_new_sparse_ndarray(
         self,
         key: str,
         *,
-        uri: Optional[str] = None,
+        uri: str | None = None,
         type: pa.DataType,
         shape: Sequence[int],
-        platform_config: Optional[options.PlatformConfig] = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> data.SparseNDArray:
         """Creates a new sparse NDArray as a child of this collection.
 
@@ -219,7 +220,7 @@ def __setitem__(self, key: str, value: _Elem) -> None:
 
     @abc.abstractmethod
     def set(
-        self, key: str, value: _Elem, *, use_relative_uri: Optional[bool] = None
+        self, key: str, value: _Elem, *, use_relative_uri: bool | None = None
     ) -> Self:
         """Sets an entry of this collection.
 

python-spec/src/somacore/coordinates.py

@@ -1,9 +1,11 @@
 """Definitions of types related to coordinate systems."""
 
+from __future__ import annotations
+
 import abc
 import collections.abc
 import itertools
-from typing import Iterable, Optional, Sequence, Tuple, Union
+from typing import Iterable, Sequence, Tuple, Union
 
 import attrs
 import numpy as np
@@ -23,7 +25,7 @@ class Axis:
 
     name: str
     """Name of the axis."""
-    unit: Optional[str] = None
+    unit: str | None = None
     """Optional string name for the units of the axis."""
 
 

python-spec/src/somacore/data.py

@@ -6,13 +6,14 @@
 Default values are provided here as a reference for implementors.
 """
 
+from __future__ import annotations
+
 import abc
 from typing import (
     Any,
     ClassVar,
     Iterator,
     List,
-    Optional,
     Sequence,
     Tuple,
     TypeVar,
@@ -51,9 +52,9 @@ def create(
         *,
         schema: pa.Schema,
         index_column_names: Sequence[str] = (options.SOMA_JOINID,),
-        domain: Optional[Sequence[Optional[Tuple[Any, Any]]]] = None,
-        platform_config: Optional[options.PlatformConfig] = None,
-        context: Optional[Any] = None,
+        domain: Sequence[Tuple[Any, Any] | None] | None = None,
+        platform_config: options.PlatformConfig | None = None,
+        context: Any | None = None,
     ) -> Self:
         """Creates a new ``DataFrame`` at the given URI.
 
@@ -112,13 +113,13 @@ def create(
     def read(
         self,
         coords: options.SparseDFCoords = (),
-        column_names: Optional[Sequence[str]] = None,
+        column_names: Sequence[str] | None = None,
         *,
         batch_size: options.BatchSize = options.BatchSize(),
-        partitions: Optional[options.ReadPartitions] = None,
+        partitions: options.ReadPartitions | None = None,
         result_order: options.ResultOrderStr = _RO_AUTO,
-        value_filter: Optional[str] = None,
-        platform_config: Optional[options.PlatformConfig] = None,
+        value_filter: str | None = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> "ReadIter[pa.Table]":
         """Reads a user-defined slice of data into Arrow tables.
 
@@ -218,7 +219,7 @@ def write(
         self,
         values: Union[pa.RecordBatch, pa.Table],
         *,
-        platform_config: Optional[options.PlatformConfig] = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> Self:
         """Writes the data from an Arrow table to the persistent object.
 
@@ -283,9 +284,9 @@ def create(
         uri: str,
         *,
         type: pa.DataType,
-        shape: Sequence[Optional[int]],
-        platform_config: Optional[options.PlatformConfig] = None,
-        context: Optional[Any] = None,
+        shape: Sequence[int | None],
+        platform_config: options.PlatformConfig | None = None,
+        context: Any | None = None,
     ) -> Self:
         """Creates a new ND array of the current type at the given URI.
 
@@ -376,9 +377,9 @@ def read(
         self,
         coords: options.DenseNDCoords = (),
         *,
-        partitions: Optional[options.ReadPartitions] = None,
+        partitions: options.ReadPartitions | None = None,
         result_order: options.ResultOrderStr = _RO_AUTO,
-        platform_config: Optional[options.PlatformConfig] = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> pa.Tensor:
         """Reads the specified subarray as a Tensor.
 
@@ -432,7 +433,7 @@ def write(
         coords: options.DenseNDCoords,
         values: pa.Tensor,
         *,
-        platform_config: Optional[options.PlatformConfig] = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> Self:
         """Writes an Arrow tensor to a subarray of the persistent object.
 
@@ -476,9 +477,9 @@ def read(
         coords: options.SparseNDCoords = (),
         *,
         batch_size: options.BatchSize = options.BatchSize(),
-        partitions: Optional[options.ReadPartitions] = None,
+        partitions: options.ReadPartitions | None = None,
         result_order: options.ResultOrderStr = _RO_AUTO,
-        platform_config: Optional[options.PlatformConfig] = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> "SparseRead":
         """Reads the specified subarray in batches.
 
@@ -537,7 +538,7 @@ def write(
         self,
         values: SparseArrowData,
         *,
-        platform_config: Optional[options.PlatformConfig] = None,
+        platform_config: options.PlatformConfig | None = None,
     ) -> Self:
         """Writes a Tensor to a subarray of the persistent object.
 

python-spec/src/somacore/experiment.py

@@ -1,6 +1,8 @@
+from __future__ import annotations
+
 from abc import ABC
 from abc import abstractmethod
-from typing import Generic, Optional, TypeVar
+from typing import Generic, TypeVar
 
 from typing_extensions import Final
 
@@ -71,8 +73,8 @@ def axis_query(
         self,
         measurement_name: str,
         *,
-        obs_query: Optional[query.AxisQuery] = None,
-        var_query: Optional[query.AxisQuery] = None,
+        var_query: query.AxisQuery | None = None,
+        obs_query: query.AxisQuery | None = None,
     ) -> ExperimentAxisQuery:
         """Creates an axis query over this experiment.
 

python-spec/src/somacore/options.py

@@ -4,8 +4,10 @@
 SOMA types that require them, not reimplemented by the implementing package.
 """
 
+from __future__ import annotations
+
 import enum
-from typing import Any, Dict, Mapping, Optional, Sequence, TypeVar, Union
+from typing import Any, Dict, Mapping, Sequence, TypeVar, Union
 
 import attrs
 import numpy as np
@@ -89,9 +91,9 @@ class BatchSize:
         Experimental
     """
 
-    count: Optional[int] = attrs.field(default=None)
+    count: int | None = attrs.field(default=None)
     """``arrow.Table``s with this number of rows will be returned."""
-    bytes: Optional[int] = attrs.field(default=None)
+    bytes: int | None = attrs.field(default=None)
     """Data of up to this size in bytes will be returned."""
 
     @count.validator

python-spec/src/somacore/query/axis.py

@@ -1,4 +1,6 @@
-from typing import Optional, Sequence, Tuple
+from __future__ import annotations
+
+from typing import Sequence, Tuple
 
 import attrs
 import numpy as np
@@ -81,7 +83,7 @@ class AxisQuery:
     Lifecycle: maturing
     """
 
-    value_filter: Optional[str] = attrs.field(
+    value_filter: str | None = attrs.field(
         default=None,
         validator=attrs.validators.optional(attrs.validators.instance_of(str)),
     )