(WIP) Initial spatial collection addition

apis/python/src/tiledbsoma/__init__.py

@@ -165,6 +165,7 @@
 )
 from ._indexer import IntIndexer, tiledbsoma_build_index
 from ._measurement import Measurement
+from ._scene import Scene
 from ._sparse_nd_array import SparseNDArray
 from .options import SOMATileDBContext, TileDBCreateOptions
 from .pytiledbsoma import (
@@ -204,6 +205,7 @@
     "SOMA_JOINID",
     "SOMAError",
     "SOMATileDBContext",
+    "Scene",
     "SparseNDArray",
     "TileDBCreateOptions",
     "tiledbsoma_build_index",

apis/python/src/tiledbsoma/_experiment.py

@@ -6,7 +6,7 @@
 """Implementation of a SOMA Experiment.
 """
 import functools
-from typing import Any, Optional
+from typing import Any, Optional, Union
 
 from somacore import experiment, query
 from typing_extensions import Self
@@ -15,6 +15,7 @@
 from ._dataframe import DataFrame
 from ._indexer import IntIndexer
 from ._measurement import Measurement
+from ._scene import Scene
 from ._tdb_handles import Wrapper
 from ._tiledb_object import AnyTileDBObject
 
@@ -24,6 +25,7 @@ class Experiment(  # type: ignore[misc]  # __eq__ false positive
     experiment.Experiment[  # type: ignore[type-var]
         DataFrame,
         Collection[Measurement],
+        Collection[Union[DataFrame, Scene]],
         AnyTileDBObject,
     ],
 ):
@@ -43,6 +45,8 @@ class Experiment(  # type: ignore[misc]  # __eq__ false positive
             defined in this dataframe.
         ms (Collection):
             A collection of named measurements.
+        spatial (Collection):
+            A collection of spatial scenes.
 
     Example:
         >>> import tiledbsoma
@@ -68,6 +72,7 @@ class Experiment(  # type: ignore[misc]  # __eq__ false positive
     _subclass_constrained_soma_types = {
         "obs": ("SOMADataFrame",),
         "ms": ("SOMACollection",),
+        "spatial": ("SOMACollection",),
     }
 
     @classmethod

apis/python/src/tiledbsoma/_scene.py

@@ -0,0 +1,39 @@
+# Copyright (c) 2024 TileDB, Inc.
+#
+# Licensed under the MIT License.
+
+"""Implementation of a SOMA Scene."""
+
+
+from typing import Union
+
+from somacore import scene
+
+from ._collection import Collection, CollectionBase
+from ._dataframe import DataFrame
+from ._dense_nd_array import DenseNDArray
+from ._sparse_nd_array import SparseNDArray
+from ._tiledb_object import AnyTileDBObject
+
+
+class Scene(  # type: ignore[misc]  # __eq__ false positive
+    CollectionBase[AnyTileDBObject],
+    scene.Scene[  # type: ignore[type-var]
+        Collection[
+            Union[DataFrame, DenseNDArray, SparseNDArray]
+        ],  # not just DataFrame and NDArray since NDArray does not have a common `read`
+        AnyTileDBObject,
+    ],
+):
+    """TODO: Add documentation for a Scene
+
+    Lifecycle:
+        Experimental.
+    """
+
+    __slots__ = ()
+
+    _subclass_constrained_soma_types = {
+        "exp": ("SOMACollection",),
+        "ms": ("SOMACollection",),
+    }

apis/python/tests/test_experiment_basic.py

@@ -90,6 +90,8 @@ def test_experiment_basic(tmp_path):
     measurement = ms.add_new_collection("RNA", soma.Measurement)
     assert soma.Measurement.exists(measurement.uri)
     assert not soma.Collection.exists(measurement.uri)
+    spatial = experiment.add_new_collection("spatial", soma.Collection)
+    assert soma.Collection.exists(spatial.uri)
 
     measurement["var"] = create_and_populate_var(urljoin(measurement.uri, "var"))
 
@@ -99,11 +101,13 @@ def test_experiment_basic(tmp_path):
     x.set("data", nda, use_relative_uri=False)
 
     # ----------------------------------------------------------------
-    assert len(experiment) == 2
+    assert len(experiment) == 3
     assert isinstance(experiment.obs, soma.DataFrame)
     assert isinstance(experiment.ms, soma.Collection)
+    assert isinstance(experiment.spatial, soma.Collection)
     assert "obs" in experiment
     assert "ms" in experiment
+    assert "spatial" in experiment
     assert "nonesuch" not in experiment
 
     assert experiment.obs == experiment["obs"]

libtiledbsoma/src/soma/soma_experiment.cc

@@ -59,12 +59,14 @@ void SOMAExperiment::create(
         platform_config,
         timestamp);
     SOMACollection::create(exp_uri + "/ms", ctx, timestamp);
+    SOMACollection::create(exp_uri + "/spatial", ctx, timestamp);
 
     auto name = std::string(std::filesystem::path(uri).filename());
     auto group = SOMAGroup::open(
         OpenMode::write, exp_uri, ctx, name, timestamp);
     group->set(exp_uri + "/obs", URIType::absolute, "obs");
     group->set(exp_uri + "/ms", URIType::absolute, "ms");
+    group->set(exp_uri + "/spatial", URIType::absolute, "spatial");
     group->close();
 }
 

libtiledbsoma/src/soma/soma_experiment.h

@@ -109,7 +109,10 @@ class SOMAExperiment : public SOMACollection {
 
     // A collection of named measurements
     std::shared_ptr<SOMACollection> ms_;
+
+    // A collection of spatial scenes
+    std::shared_ptr<SOMACollection> spatial_;
 };
 }  // namespace tiledbsoma
 
-#endif  // SOMA_EXPERIMENT
+#endif  // SOMA_EXPERIMENT