ingest somacore classes

.pre-commit-config.yaml

@@ -18,7 +18,8 @@ repos:
         # Pandas 2.x types (e.g. `pd.Series[Any]`). See `_types.py` or https://github.com/single-cell-data/TileDB-SOMA/issues/2839
         # for more info.
         - "pandas-stubs>=2"
-        - "somacore==1.0.23"
+        # Temporary, for PR: see https://github.com/single-cell-data/SOMA/pull/244
+        - "git+https://github.com/single-cell-data/soma@9e81f07"
         - types-setuptools
       args: ["--config-file=apis/python/pyproject.toml", "apis/python/src", "apis/python/devtools"]
       pass_filenames: false

apis/python/setup.py

@@ -336,8 +336,8 @@ def run(self):
         "pyarrow",
         "scanpy>=1.9.2",
         "scipy",
-        # Note: the somacore version is in .pre-commit-config.yaml too
-        "somacore==1.0.23",
+        # Temporary, for PR: see https://github.com/single-cell-data/SOMA/pull/244
+        "somacore @ git+https://github.com/single-cell-data/soma@rw/abcs",
         "typing-extensions",  # Note "-" even though `import typing_extensions`
     ],
     extras_require={

apis/python/src/tiledbsoma/_experiment.py

@@ -9,13 +9,13 @@
 from typing import Optional
 
 from somacore import experiment, query
-from typing_extensions import Self
 
 from . import _tdb_handles
 from ._collection import Collection, CollectionBase
 from ._dataframe import DataFrame
 from ._indexer import IntIndexer
 from ._measurement import Measurement
+from ._query import ExperimentAxisQuery
 from ._scene import Scene
 from ._soma_object import AnySOMAObject
 
@@ -83,13 +83,11 @@ def axis_query(  # type: ignore
         *,
         obs_query: Optional[query.AxisQuery] = None,
         var_query: Optional[query.AxisQuery] = None,
-    ) -> query.ExperimentAxisQuery[Self]:  # type: ignore
+    ) -> ExperimentAxisQuery:
         """Creates an axis query over this experiment.
         Lifecycle: Maturing.
         """
-        # mypy doesn't quite understand descriptors so it issues a spurious
-        # error here.
-        return query.ExperimentAxisQuery(  # type: ignore
+        return ExperimentAxisQuery(
             self,
             measurement_name,
             obs_query=obs_query or query.AxisQuery(),

apis/python/src/tiledbsoma/_indexer.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, List, Optional, Union
+from typing import List, Optional, Union
 
 import numpy as np
 import numpy.typing as npt
@@ -11,9 +11,7 @@
 from tiledbsoma import pytiledbsoma as clib
 
 from ._types import PDSeries
-
-if TYPE_CHECKING:
-    from .options import SOMATileDBContext
+from .options import SOMATileDBContext
 
 IndexerDataType = Union[
     npt.NDArray[np.int64],
@@ -27,7 +25,7 @@
 
 
 def tiledbsoma_build_index(
-    data: IndexerDataType, *, context: Optional["SOMATileDBContext"] = None
+    data: IndexerDataType, *, context: Optional[SOMATileDBContext] = None
 ) -> IndexLike:
     """Initialize re-indexer for provided indices (deprecated).
 
@@ -54,7 +52,7 @@ class IntIndexer:
     """
 
     def __init__(
-        self, data: IndexerDataType, *, context: Optional["SOMATileDBContext"] = None
+        self, data: IndexerDataType, *, context: Optional[SOMATileDBContext] = None
     ):
         """Initialize re-indexer for provided indices.
 
@@ -73,15 +71,15 @@ def __init__(
         )
         self._reindexer.map_locations(data)
 
-    def get_indexer(self, target: IndexerDataType) -> Any:
+    def get_indexer(self, target: IndexerDataType) -> npt.NDArray[np.intp]:
         """Compute underlying indices of index for target data.
 
         Compatible with Pandas' Index.get_indexer method.
 
         Args:
             target: Data to return re-index data for.
         """
-        return (
+        return (  # type: ignore[no-any-return]
             self._reindexer.get_indexer_pyarrow(target)
             if isinstance(target, (pa.Array, pa.ChunkedArray))
             else self._reindexer.get_indexer_general(target)