rebase onto current main

apis/python/src/tiledbsoma/__init__.py

@@ -97,42 +97,6 @@
 import os
 import sys
 
-from somacore import AxisColumnNames, AxisQuery, ExperimentAxisQuery
-from somacore.options import ResultOrder
-
-from ._collection import Collection
-from ._constants import SOMA_JOINID
-from ._dataframe import DataFrame
-from ._dense_nd_array import DenseNDArray
-from ._exception import (
-    AlreadyExistsError,
-    DoesNotExistError,
-    NotCreateableError,
-    SOMAError,
-)
-from ._experiment import Experiment
-from ._factory import open
-from ._general_utilities import (
-    get_implementation,
-    get_implementation_version,
-    get_SOMA_version,
-    get_storage_engine,
-    show_package_versions,
-)
-from ._indexer import IntIndexer, tiledbsoma_build_index
-from ._measurement import Measurement
-from ._sparse_nd_array import SparseNDArray, SparseNDArrayRead
-from .options import SOMATileDBContext, TileDBCreateOptions, TileDBWriteOptions
-from .pytiledbsoma import (
-    tiledbsoma_stats_disable,
-    tiledbsoma_stats_dump,
-    tiledbsoma_stats_enable,
-    tiledbsoma_stats_reset,
-)
-from .stats import (
-    tiledbsoma_stats_as_py,
-    tiledbsoma_stats_json,
-)
 
 # Load native libraries. On wheel builds, we may have a shared library
 # already linked. In this case, we can import directly
@@ -171,6 +135,49 @@
         # Otherwise try loading by name only.
         ctypes.CDLL(libtiledbsoma_name)
 
+from somacore import AxisColumnNames, AxisQuery, ExperimentAxisQuery
+from somacore.options import ResultOrder
+
+# This is important since we need to do the above dll/dylib/so business
+# _before_ imports, but, ruff will tell us that imports need to be
+# at the top of the file:
+#
+# ruff: noqa
+
+from ._collection import Collection
+from ._constants import SOMA_JOINID
+from ._dataframe import DataFrame
+from ._dense_nd_array import DenseNDArray
+from ._exception import (
+    AlreadyExistsError,
+    DoesNotExistError,
+    NotCreateableError,
+    SOMAError,
+)
+from ._experiment import Experiment
+from ._factory import open
+from ._general_utilities import (
+    get_implementation,
+    get_implementation_version,
+    get_SOMA_version,
+    get_storage_engine,
+    show_package_versions,
+)
+from ._indexer import IntIndexer, tiledbsoma_build_index
+from ._measurement import Measurement
+from ._sparse_nd_array import SparseNDArray, SparseNDArrayRead
+from .options import SOMATileDBContext, TileDBCreateOptions, TileDBWriteOptions
+from .pytiledbsoma import (
+    tiledbsoma_stats_disable,
+    tiledbsoma_stats_dump,
+    tiledbsoma_stats_enable,
+    tiledbsoma_stats_reset,
+)
+from .stats import (
+    tiledbsoma_stats_as_py,
+    tiledbsoma_stats_json,
+)
+
 __version__ = get_implementation_version()
 
 __all__ = [
@@ -205,6 +212,6 @@
     "tiledbsoma_stats_dump",
     "tiledbsoma_stats_enable",
     "tiledbsoma_stats_reset",
-    "tiledbsoma_stats_json",
     "tiledbsoma_stats_as_py",
+    "tiledbsoma_stats_json",
 ]

apis/python/src/tiledbsoma/_dataframe.py

@@ -14,7 +14,7 @@
 from somacore import options
 from typing_extensions import Self
 
-from tiledbsoma._flags import _new_shape_feature_flag_enabled
+from tiledbsoma._flags import NEW_SHAPE_FEATURE_FLAG_ENABLED
 
 from . import _arrow_types, _util
 from . import pytiledbsoma as clib
@@ -293,7 +293,7 @@ def create(
             # [4] core current domain hi
 
             index_column_schema.append(pa_field)
-            if _new_shape_feature_flag_enabled():
+            if NEW_SHAPE_FEATURE_FLAG_ENABLED:
 
                 index_column_data[pa_field.name] = [
                     *slot_core_max_domain,

apis/python/src/tiledbsoma/_flags.py

@@ -5,14 +5,9 @@
 
 import os
 
-# Temporary for https://github.com/single-cell-data/TileDB-SOMA/issues/2407
-_new_shape_feature_flag = os.getenv("SOMA_PY_NEW_SHAPE") is not None
+# This is temporary for
+# https://github.com/single-cell-data/TileDB-SOMA/issues/2407.  It will be
+# removed once https://github.com/single-cell-data/TileDB-SOMA/issues/2407 is
+# complete.
 
-
-def _new_shape_feature_flag_enabled() -> bool:
-    """
-    This is temporary only and will be removed once
-    https://github.com/single-cell-data/TileDB-SOMA/issues/2407
-    is complete.
-    """
-    return _new_shape_feature_flag
+NEW_SHAPE_FEATURE_FLAG_ENABLED = os.getenv("SOMA_PY_NEW_SHAPE") is not None

apis/python/src/tiledbsoma/_sparse_nd_array.py

@@ -26,7 +26,7 @@
 from somacore.options import PlatformConfig
 from typing_extensions import Self
 
-from tiledbsoma._flags import _new_shape_feature_flag_enabled
+from tiledbsoma._flags import NEW_SHAPE_FEATURE_FLAG_ENABLED
 
 from . import _util
 
@@ -163,7 +163,7 @@ def create(
             # [3] core current domain lo
             # [4] core current domain hi
 
-            if _new_shape_feature_flag_enabled():
+            if NEW_SHAPE_FEATURE_FLAG_ENABLED:
                 dim_capacity, dim_extent = cls._dim_capacity_and_extent(
                     dim_name,
                     # The user specifies current domain -- this is the max domain

apis/python/tests/test_dataframe.py

@@ -93,7 +93,7 @@ def test_dataframe(tmp_path, arrow_schema):
         # More to come on https://github.com/single-cell-data/TileDB-SOMA/issues/2407
         assert (
             sdf.tiledbsoma_has_upgraded_domain
-            == soma._flags._new_shape_feature_flag_enabled()
+            == soma._flags.NEW_SHAPE_FEATURE_FLAG_ENABLED
         )
 
         with pytest.raises(AttributeError):

apis/python/tests/test_shape.py

@@ -48,7 +48,7 @@ def test_sparse_nd_array_basics(
         # More to come on https://github.com/single-cell-data/TileDB-SOMA/issues/2407
         assert (
             snda.tiledbsoma_has_upgraded_shape
-            == tiledbsoma._flags._new_shape_feature_flag_enabled()
+            == tiledbsoma._flags.NEW_SHAPE_FEATURE_FLAG_ENABLED
         )
 
         # Before current-domain support: shape is maxshape.
@@ -58,7 +58,7 @@ def test_sparse_nd_array_basics(
         # involving R compatibility, and leaving room for a single tile
         # capacity, etc ...  we could check for some magic value but it suffices
         # to check that it's over 2 billion.)
-        if tiledbsoma._flags._new_shape_feature_flag_enabled():
+        if tiledbsoma._flags.NEW_SHAPE_FEATURE_FLAG_ENABLED:
             for e in snda.maxshape:
                 assert e > 2_000_000_000
         else:
@@ -89,7 +89,7 @@ def test_sparse_nd_array_basics(
     with tiledbsoma.SparseNDArray.open(uri) as snda:
         assert snda.shape == arg_shape
         # This will change with current-domain support
-        if tiledbsoma._flags._new_shape_feature_flag_enabled():
+        if tiledbsoma._flags.NEW_SHAPE_FEATURE_FLAG_ENABLED:
             for e in snda.maxshape:
                 assert e > 2_000_000_000
         else:
@@ -113,7 +113,7 @@ def test_sparse_nd_array_basics(
     with tiledbsoma.SparseNDArray.open(uri) as snda:
         assert snda.shape == arg_shape
 
-    if tiledbsoma._flags._new_shape_feature_flag_enabled():
+    if tiledbsoma._flags.NEW_SHAPE_FEATURE_FLAG_ENABLED:
 
         # Test resize down
         new_shape = tuple([arg_shape[i] - 50 for i in range(ndim)])
@@ -267,11 +267,11 @@ def test_dataframe_basics(tmp_path, soma_joinid_domain, index_column_names):
         has_sjid_dim = "soma_joinid" in index_column_names
         if has_sjid_dim:
             assert sdf._maybe_soma_joinid_shape == 1 + soma_joinid_domain[1]
-            if not tiledbsoma._flags._new_shape_feature_flag_enabled():
+            if not tiledbsoma._flags.NEW_SHAPE_FEATURE_FLAG_ENABLED:
                 assert sdf._maybe_soma_joinid_maxshape == 1 + soma_joinid_domain[1]
         else:
             assert sdf._maybe_soma_joinid_shape is None
-            if not tiledbsoma._flags._new_shape_feature_flag_enabled():
+            if not tiledbsoma._flags.NEW_SHAPE_FEATURE_FLAG_ENABLED:
                 assert sdf._maybe_soma_joinid_maxshape is None
 
         assert len(sdf.non_empty_domain()) == len(index_column_names)

apis/python/tests/test_sparse_nd_array.py

@@ -1088,7 +1088,7 @@ def test_tile_extents(tmp_path):
     ).close()
 
     with tiledb.open(uri) as A:
-        if soma._flags._new_shape_feature_flag_enabled():
+        if soma._flags.NEW_SHAPE_FEATURE_FLAG_ENABLED:
             assert A.schema.domain.dim(0).tile == 2048
             assert A.schema.domain.dim(1).tile == 2048
         else:

apis/r/DESCRIPTION

@@ -35,7 +35,6 @@ Imports:
     stats,
     bit64,
     tiledb (>= 0.30.0),
-    tiledb (<= 0.30.99),
     arrow (>= 14.0.0),
     utils,
     fs,

apis/r/R/Init.R

@@ -15,7 +15,7 @@
     if (rpkg_lib_version != soma_lib_version) {
         msg <- sprintf("TileDB Core version %s used by TileDB-R package, but TileDB-SOMA uses %s",
                        sQuote(rpkg_lib_version), sQuote(soma_lib_version))
-        stop(msg, call. = FALSE)
+        packageStartupMessage(msg)
     }
 
     # This is temporary for https://github.com/single-cell-data/TileDB-SOMA/issues/2407