[python] Various tiledb-py removals from pytest (#3170)

* `test_basic_anndata_io.py`
  - `test_null_obs`: Use arrow schema to check nullability
  - `test_export_obsm_with_holes`: Use `Experiment.metadata` directly
* `test_dataframe.py::test_enum_schema_report`: Remove redundant
   type checking against tiledb-py. Checks are already encompassed
   by Arrow schema check below
* `test_dense_nd_array.pytest_read_to_unwritten_array`: create expected
  data output by create a numpy array with the fill value rather than
  pulling from tiledb-py read query

apis/python/tests/test_basic_anndata_io.py

@@ -18,7 +18,6 @@
 from tiledbsoma import Experiment, _constants, _factory
 from tiledbsoma._soma_object import SOMAObject
 from tiledbsoma.io._common import _TILEDBSOMA_TYPE, UnsDict, UnsMapping
-import tiledb
 
 from ._util import TESTDATA, assert_adata_equal, make_pd_df
 
@@ -760,24 +759,24 @@ def test_null_obs(conftest_pbmc_small, tmp_path: Path):
     )
     assert_adata_equal(original, conftest_pbmc_small)
 
-    exp = tiledbsoma.Experiment.open(uri)
-    with tiledb.open(exp.obs.uri, "r") as obs:
-        #   Explicitly check columns created above
-        assert obs.attr("empty_categorical_all").isnullable
-        assert obs.attr("empty_categorical_partial").isnullable
-        assert obs.attr("empty_extension_all").isnullable
-        assert obs.attr("empty_extension_partial").isnullable
-        #   For every column in the data frame
-        #   ensure that `isnullable` reflects the null-ness
-        #   of the Pandas data frame
+    with tiledbsoma.Experiment.open(uri) as exp:
+        schema = exp.obs.schema.field
+
+        # Explicitly check columns created above
+        assert schema("empty_categorical_all").nullable
+        assert schema("empty_categorical_partial").nullable
+        assert schema("empty_extension_all").nullable
+        assert schema("empty_extension_partial").nullable
+
+        # For every column in the data frame ensure that `isnullable` reflects
+        # he null-ness of the Pandas data frame
         for k in conftest_pbmc_small.obs:
-            assert obs.attr(k).isnullable
+            assert schema(k).nullable
 
 
 def test_export_obsm_with_holes(h5ad_file_with_obsm_holes, tmp_path):
     adata = anndata.read_h5ad(h5ad_file_with_obsm_holes.as_posix())
     original = adata.copy()
-    assert 1 == 1
 
     # This data file is prepared such that obsm["X_pca"] has shape (2638, 50)
     # but its [0][0] element is a 0, so when it's stored as sparse, its nnz
@@ -790,48 +789,47 @@ def test_export_obsm_with_holes(h5ad_file_with_obsm_holes, tmp_path):
 
     assert_adata_equal(original, adata)
 
-    exp = tiledbsoma.Experiment.open(output_path)
-
     # Verify the bounding box on the SOMA SparseNDArray
-    with tiledb.open(exp.ms["RNA"].obsm["X_pca"].uri) as so:
-        assert so.meta["soma_dim_0_domain_lower"] == 0
-        assert so.meta["soma_dim_0_domain_upper"] == 2637
-        assert so.meta["soma_dim_1_domain_lower"] == 0
-        assert so.meta["soma_dim_1_domain_upper"] == 49
+    with tiledbsoma.Experiment.open(output_path) as exp:
+        meta = exp.ms["RNA"].obsm["X_pca"].metadata
+        assert meta["soma_dim_0_domain_lower"] == 0
+        assert meta["soma_dim_0_domain_upper"] == 2637
+        assert meta["soma_dim_1_domain_lower"] == 0
+        assert meta["soma_dim_1_domain_upper"] == 49
 
-    # With the bounding box present, all is well for outgest to AnnData format.
-    try1 = tiledbsoma.io.to_anndata(exp, "RNA")
-    assert try1.obsm["X_pca"].shape == (2638, 50)
+        # With the bounding box present, all is well for outgest to AnnData format.
+        try1 = tiledbsoma.io.to_anndata(exp, "RNA")
+        assert try1.obsm["X_pca"].shape == (2638, 50)
 
     # Now remove the bounding box to simulate reading older data that lacks a bounding box.
-    with tiledb.open(exp.ms["RNA"].obsm["X_pca"].uri, "w") as so:
-        del so.meta["soma_dim_0_domain_lower"]
-        del so.meta["soma_dim_0_domain_upper"]
-        del so.meta["soma_dim_1_domain_lower"]
-        del so.meta["soma_dim_1_domain_upper"]
+    with tiledbsoma.Experiment.open(output_path, "w") as exp:
+        meta = exp.ms["RNA"].obsm["X_pca"].metadata
+        del meta["soma_dim_0_domain_lower"]
+        del meta["soma_dim_0_domain_upper"]
+        del meta["soma_dim_1_domain_lower"]
+        del meta["soma_dim_1_domain_upper"]
 
     # Re-open to simulate opening afresh a bounding-box-free array.
-    exp = tiledbsoma.Experiment.open(output_path)
-
-    with tiledb.open(exp.ms["RNA"].obsm["X_pca"].uri) as so:
+    with tiledbsoma.Experiment.open(output_path) as exp:
+        meta = exp.ms["RNA"].obsm["X_pca"].metadata
         with pytest.raises(KeyError):
-            so.meta["soma_dim_0_domain_lower"]
+            meta["soma_dim_0_domain_lower"]
         with pytest.raises(KeyError):
-            so.meta["soma_dim_0_domain_upper"]
+            meta["soma_dim_0_domain_upper"]
         with pytest.raises(KeyError):
-            so.meta["soma_dim_1_domain_lower"]
+            meta["soma_dim_1_domain_lower"]
         with pytest.raises(KeyError):
-            so.meta["soma_dim_1_domain_upper"]
-        assert so.meta["soma_object_type"] == "SOMASparseNDArray"
+            meta["soma_dim_1_domain_upper"]
+        assert meta["soma_object_type"] == "SOMASparseNDArray"
 
-    # Now try the remaining options for outgest.
-    with pytest.raises(tiledbsoma.SOMAError):
-        tiledbsoma.io.to_anndata(exp, "RNA")
+        # Now try the remaining options for outgest.
+        with pytest.raises(tiledbsoma.SOMAError):
+            tiledbsoma.io.to_anndata(exp, "RNA")
 
-    try3 = tiledbsoma.io.to_anndata(
-        exp, "RNA", obsm_varm_width_hints={"obsm": {"X_pca": 50}}
-    )
-    assert try3.obsm["X_pca"].shape == (2638, 50)
+        try3 = tiledbsoma.io.to_anndata(
+            exp, "RNA", obsm_varm_width_hints={"obsm": {"X_pca": 50}}
+        )
+        assert try3.obsm["X_pca"].shape == (2638, 50)
 
 
 def test_X_empty(h5ad_file_X_empty):

apis/python/tests/test_dataframe.py

@@ -12,7 +12,6 @@
 from pandas.api.types import union_categoricals
 
 import tiledbsoma as soma
-import tiledb
 
 from tests._util import raises_no_typeguard
 
@@ -1593,25 +1592,6 @@ def test_enum_schema_report(tmp_path):
         arrow_table = pa.Table.from_pandas(pandas_df, preserve_index=False)
         sdf.write(arrow_table)
 
-    # Double-check against TileDB-Py reporting
-    with tiledb.open(uri) as A:
-        for i in range(A.schema.nattr):
-            attr = A.schema.attr(i)
-            try:
-                index_type = attr.dtype
-                value_type = A.enum(attr.name).dtype
-            except tiledb.cc.TileDBError:
-                pass  # not an enum attr
-            if attr.name == "int_cat":
-                assert index_type.name == "int8"
-                assert value_type.name == "int64"
-            elif attr.name == "str_cat":
-                assert index_type.name == "int8"
-                assert value_type.name == "str32"
-            elif attr.name == "byte_cat":
-                assert index_type.name == "int8"
-                assert value_type.name == "bytes8"
-
     # Verify SOMA Arrow schema
     with soma.open(uri) as sdf:
         f = sdf.schema.field("int_cat")

apis/python/tests/test_dataframe_index_columns.py

@@ -1898,6 +1898,6 @@ def test_types_read_errors(
     with soma.DataFrame.open(uri, "w") as sdf:
         sdf.write(arrow_table)
 
-    with pytest.raises((soma.SOMAError)):
+    with pytest.raises(soma.SOMAError):
         with soma.DataFrame.open(uri, "r") as sdf:
             sdf.read(coords=coords).concat()

apis/python/tests/test_dense_nd_array.py

@@ -494,10 +494,5 @@ def test_read_to_unwritten_array(tmp_path, shape):
 
     soma.DenseNDArray.create(uri, type=pa.uint8(), shape=shape)
 
-    with tiledb.open(uri, "r") as A:
-        expected = A[:]["soma_data"]
-
     with soma.DenseNDArray.open(uri, "r") as A:
-        actual = A.read().to_numpy()
-
-    assert np.array_equal(expected, actual)
+        assert np.array_equal(np.ones(shape) * 255, A.read().to_numpy())

apis/python/tests/test_experiment_query.py

@@ -1,3 +1,4 @@
+import re
 from concurrent import futures
 from contextlib import nullcontext
 from typing import Tuple
@@ -15,7 +16,6 @@
 from tiledbsoma import SOMATileDBContext, _factory
 from tiledbsoma._collection import CollectionBase
 from tiledbsoma.experiment_query import X_as_series
-import tiledb
 
 from tests._util import raises_no_typeguard
 
@@ -950,11 +950,11 @@ def test_empty_categorical_query(conftest_pbmc_small_exp):
         measurement_name="RNA", obs_query=AxisQuery(value_filter='groups == "foo"')
     )
     # Empty query on a categorical column raised ArrowInvalid before TileDB 2.21; see https://github.com/single-cell-data/TileDB-SOMA/pull/2299
-    ctx = (
-        nullcontext()
-        if tiledb.libtiledb.version() >= (2, 21)
-        else pytest.raises(ArrowInvalid)
-    )
+    m = re.fullmatch(r"libtiledb=(\d+\.\d+\.\d+)", soma.pytiledbsoma.version())
+    version = m.group(1).split(".")
+    major, minor = int(version[0]), int(version[1])
+
+    ctx = nullcontext() if (major, minor) >= (2, 21) else pytest.raises(ArrowInvalid)
     with ctx:
         obs = q.obs().concat()
         assert len(obs) == 0