Enable python 3.12

.github/workflows/ci.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-12, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
       fail-fast: false
     env:
       # 11.7 necessary due to: https://github.com/actions/setup-python/issues/682#issuecomment-1604261330

.github/workflows/daily-test-build-numpy.yml

@@ -16,9 +16,11 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-12, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         include:
           # https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
+          - python-version: "3.12"
+            numpy-version: "1.26.4"
           - python-version: "3.11"
             numpy-version: "1.23.2"
           - python-version: "3.10"

misc/azure-release.yml

@@ -65,7 +65,7 @@ stages:
         condition: always()
         variables:
           cibw_test_requires: "pytest"
-          USE_CIBW_VERSION: 2.12.3
+          USE_CIBW_VERSION: 2.17.0
         strategy:
           matrix:
             linux_py:
@@ -79,7 +79,6 @@ stages:
               TILEDB_INSTALL: "$(Pipeline.Workspace)/.libtiledb_dist/$(LIBTILEDB_SHA)-macos-x86_64"
               CIBW_ARCHS_MACOS: "x86_64"
               CIBW_SKIP: "cp36-* cp37-* pp*"
-              CIBW_TEST_SKIP: "cp37-*"
               CIBW_BUILD_VERBOSITY: 3
             macOS_arm64_py:
               imageName: "macOS-12"

pyproject.toml

@@ -25,11 +25,12 @@ classifiers=[
     "Operating System :: POSIX :: Linux",
     "Operating System :: MacOS :: MacOS X",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.5",
-    "Programming Language :: Python :: 3.6",
     "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 dynamic = ["version", "dependencies"]
 

tiledb/libtiledb.pyx

@@ -1514,21 +1514,21 @@ cdef class Array(object):
         ...         A[:] = {"a1": a1_data, "l1": l1_data, "l2": l2_data, "l3": l3_data}
         ...
         ...     with tiledb.open(tmp, "r") as A:
-        ...         A.label_index(["l1"])[3:4]
-        ...         A.label_index(["l1", "l3"])[2, 0.5:1.0]
-        ...         A.label_index(["l2"])[:, -1:0]
-        ...         A.label_index(["l3"])[:, 0.5:1.0]
-        OrderedDict([('l1', array([4, 3])), ('a1', array([[1, 2, 3],
-               [4, 5, 6]]))])
-        OrderedDict([('l3', array([0.5, 1. ])), ('l1', array([2])), ('a1', array([[8, 9]]))])
-        OrderedDict([('l2', array([-1,  0])), ('a1', array([[ 1,  2],
-               [ 4,  5],
-               [ 7,  8],
-               [10, 11]]))])
-        OrderedDict([('l3', array([0.5, 1. ])), ('a1', array([[ 2,  3],
-               [ 5,  6],
-               [ 8,  9],
-               [11, 12]]))])
+        ...         A.label_index(["l1"])[3:4]  # doctest: +ELLIPSIS
+        ...         A.label_index(["l1", "l3"])[2, 0.5:1.0]  # doctest: +ELLIPSIS
+        ...         A.label_index(["l2"])[:, -1:0]  # doctest: +ELLIPSIS
+        ...         A.label_index(["l3"])[:, 0.5:1.0]  # doctest: +ELLIPSIS
+        OrderedDict(...'l1'... array([4, 3])..., ...'a1'... array([[1, 2, 3],
+                [4, 5, 6]])...)
+        OrderedDict(...'l3'... array([0.5, 1. ])..., ...'l1'... array([2])..., ...'a1'... array([[8, 9]])...)
+        OrderedDict(...'l2'... array([-1,  0])..., ...'a1'... array([[ 1,  2],
+                [ 4,  5],
+                [ 7,  8],
+                [10, 11]])...)
+        OrderedDict(...'l3'... array([0.5, 1. ])..., ...'a1'... array([[ 2,  3],
+                [ 5,  6],
+                [ 8,  9],
+                [11, 12]])...)
 
         :param labels: List of labels to use when querying. Can only use at most one
             label per dimension.
@@ -1572,19 +1572,23 @@ cdef class Array(object):
         >>>
         >>> with tempfile.TemporaryDirectory() as tmp:
         ...    A = tiledb.from_numpy(tmp, np.eye(4) * [1,2,3,4])
-        ...    A.multi_index[1]
-        ...    A.multi_index[1,1]
+        ...    A.multi_index[1]  # doctest: +ELLIPSIS
+        ...    A.multi_index[1,1]  # doctest: +ELLIPSIS
         ...    # return row 0 and 2
-        ...    A.multi_index[[0,2]]
+        ...    A.multi_index[[0,2]]  # doctest: +ELLIPSIS
         ...    # return rows 0 and 2 intersecting column 2
-        ...    A.multi_index[[0,2], 2]
+        ...    A.multi_index[[0,2], 2]  # doctest: +ELLIPSIS
         ...    # return rows 0:2 intersecting columns 0:2
-        ...    A.multi_index[slice(0,2), slice(0,2)]
-        OrderedDict([('', array([[0., 2., 0., 0.]]))])
-        OrderedDict([('', array([[2.]]))])
-        OrderedDict([('', array([[1., 0., 0., 0.], [0., 0., 3., 0.]]))])
-        OrderedDict([('', array([[0.], [3.]]))])
-        OrderedDict([('', array([[1., 0., 0.], [0., 2., 0.], [0., 0., 3.]]))])
+        ...    A.multi_index[slice(0,2), slice(0,2)]  # doctest: +ELLIPSIS
+        OrderedDict(...''... array([[0., 2., 0., 0.]])...)
+        OrderedDict(...''... array([[2.]])...)
+        OrderedDict(...''... array([[1., 0., 0., 0.],
+                [0., 0., 3., 0.]])...)
+        OrderedDict(...''... array([[0.],
+                [3.]])...)
+        OrderedDict(...''... array([[1., 0., 0.],
+                [0., 2., 0.],
+                [0., 0., 3.]])...)
 
         """
         # Delayed to avoid circular import
@@ -2161,8 +2165,8 @@ cdef class DenseArrayImpl(Array):
         ...         A[0:10] = {"a1": np.zeros((10)), "a2": np.ones((10))}
         ...     with tiledb.DenseArray(tmp + "/array", mode='r') as A:
         ...         # Access specific attributes individually.
-        ...         A.query(attrs=("a1",))[0:5]
-        OrderedDict([('a1', array([0, 0, 0, 0, 0]))])
+        ...         A.query(attrs=("a1",))[0:5]  # doctest: +ELLIPSIS
+        OrderedDict(...'a1'... array([0, 0, 0, 0, 0])...)
 
         """
         if not self.isopen or self.mode != 'r':
@@ -2216,8 +2220,8 @@ cdef class DenseArrayImpl(Array):
         ...         A[0:10] = {"a1": np.zeros((10)), "a2": np.ones((10))}
         ...     with tiledb.DenseArray(tmp + "/array", mode='r') as A:
         ...         # A[0:5], attribute a1, row-major without coordinates
-        ...         A.subarray((slice(0, 5),), attrs=("a1",), coords=False, order='C')
-        OrderedDict([('a1', array([0, 0, 0, 0, 0]))])
+        ...         A.subarray((slice(0, 5),), attrs=("a1",), coords=False, order='C')  # doctest: +ELLIPSIS
+        OrderedDict(...'a1'... array([0, 0, 0, 0, 0])...)
 
         """
         from .subarray import Subarray
@@ -3154,11 +3158,10 @@ cdef class SparseArrayImpl(Array):
         ...                    "a2": np.array([3, 4])}
         ...     with tiledb.SparseArray(tmp + "/array", mode='r') as A:
         ...         # Return an OrderedDict with values and coordinates
-        ...         A[0:3, 0:10]
+        ...         A[0:3, 0:10]  # doctest: +ELLIPSIS
         ...         # Return just the "x" coordinates values
-        ...         A[0:3, 0:10]["x"]
-        OrderedDict([('a1', array([1, 2])), ('a2', array([3, 4])), ('y', array([0, 2], dtype=uint64)), ('x', array([0, 3], dtype=uint64))])
-        array([0, 3], dtype=uint64)
+        ...         A[0:3, 0:10]["x"]  # doctest: +ELLIPSIS
+        OrderedDict(...'a1'... array([1, 2])..., ...'a2'... array([3, 4])..., ...'y'... array([0, 2], dtype=uint64)..., ...'x'... array([0, 3], dtype=uint64)...)
 
         With a floating-point array domain, index bounds are inclusive, e.g.:
 
@@ -3231,8 +3234,8 @@ cdef class SparseArrayImpl(Array):
         ...         A[I, J] = {"a1": np.array([1, 2]),
         ...                    "a2": np.array([3, 4])}
         ...     with tiledb.SparseArray(tmp + "/array", mode='r') as A:
-        ...         A.query(attrs=("a1",), coords=False, order='G')[0:3, 0:10]
-        OrderedDict([('a1', array([1, 2]))])
+        ...         A.query(attrs=("a1",), coords=False, order='G')[0:3, 0:10]  # doctest: +ELLIPSIS
+        OrderedDict(...'a1'... array([1, 2])...)
 
         """
         if not self.isopen or self.mode not in  ('r', 'd'):
@@ -3341,8 +3344,8 @@ cdef class SparseArrayImpl(Array):
         ...                    "a2": np.array([3, 4])}
         ...     with tiledb.SparseArray(tmp + "/array", mode='r') as A:
         ...         # A[0:3, 0:10], attribute a1, row-major without coordinates
-        ...         A.subarray((slice(0, 3), slice(0, 10)), attrs=("a1",), coords=False, order='G')
-        OrderedDict([('a1', array([1, 2]))])
+        ...         A.subarray((slice(0, 3), slice(0, 10)), attrs=("a1",), coords=False, order='G')  # doctest: +ELLIPSIS
+        OrderedDict(...'a1'... array([1, 2])...)
 
         """
         from .subarray import Subarray

tiledb/query_condition.py

@@ -15,9 +15,7 @@
 filtering query results on attribute and dimension values.
 """
 
-QueryConditionNodeElem = Union[
-    ast.Name, ast.Constant, ast.Call, ast.Num, ast.Str, ast.Bytes
-]
+QueryConditionNodeElem = Union[ast.Name, ast.Constant, ast.Call]
 
 
 @dataclass
@@ -280,8 +278,8 @@ def is_variable_node(self, variable: QueryConditionNodeElem) -> bool:
 
             return (
                 isinstance(variable.args[0], ast.Constant)
-                or isinstance(variable.args[0], ast.Str)
-                or isinstance(variable.args[0], ast.Bytes)
+                or isinstance(variable.args[0], ast.Constant)
+                or isinstance(variable.args[0], ast.Constant)
             )
 
         return isinstance(variable, ast.Name)
@@ -326,7 +324,9 @@ def get_variable_from_node(self, node: QueryConditionNodeElem) -> Any:
             variable = variable_node.id
         elif isinstance(variable_node, ast.Constant):
             variable = variable_node.value
-        elif isinstance(variable_node, ast.Str) or isinstance(variable_node, ast.Bytes):
+        elif isinstance(variable_node, ast.Constant) or isinstance(
+            variable_node, ast.Constant
+        ):
             # deprecated in 3.8
             variable = variable_node.s
         else:
@@ -363,13 +363,15 @@ def get_value_from_node(self, node: QueryConditionNodeElem) -> Any:
 
         if isinstance(value_node, ast.Constant):
             value = value_node.value
-        elif isinstance(value_node, ast.NameConstant):
+        elif isinstance(value_node, ast.Constant):
             # deprecated in 3.8
             value = value_node.value
-        elif isinstance(value_node, ast.Num):
+        elif isinstance(value_node, ast.Constant):
             # deprecated in 3.8
             value = value_node.n
-        elif isinstance(value_node, ast.Str) or isinstance(value_node, ast.Bytes):
+        elif isinstance(value_node, ast.Constant) or isinstance(
+            value_node, ast.Constant
+        ):
             # deprecated in 3.8
             value = value_node.s
         else:
@@ -491,7 +493,7 @@ def visit_UnaryOp(self, node: ast.UnaryOp, sign: int = 1):
         else:
             if isinstance(node.operand, ast.Constant):
                 node.operand.value *= sign
-            elif isinstance(node.operand, ast.Num):
+            elif isinstance(node.operand, ast.Constant):
                 node.operand.n *= sign
             else:
                 raise TileDBError(
@@ -500,18 +502,18 @@ def visit_UnaryOp(self, node: ast.UnaryOp, sign: int = 1):
 
             return node.operand
 
-    def visit_Num(self, node: ast.Num) -> ast.Num:
+    def visit_Num(self, node: ast.Constant) -> ast.Constant:
         # deprecated in 3.8
         return node
 
-    def visit_Str(self, node: ast.Str) -> ast.Str:
+    def visit_Str(self, node: ast.Constant) -> ast.Constant:
         # deprecated in 3.8
         return node
 
-    def visit_Bytes(self, node: ast.Bytes) -> ast.Bytes:
+    def visit_Bytes(self, node: ast.Constant) -> ast.Constant:
         # deprecated in 3.8
         return node
 
-    def visit_NameConstant(self, node: ast.NameConstant) -> ast.NameConstant:
+    def visit_NameConstant(self, node: ast.Constant) -> ast.Constant:
         # deprecated in 3.8
         return node

tiledb/tests/test_compat.py

@@ -46,7 +46,10 @@ def test_compat_tiledb_py_0_5_anon_attr_dense(self):
 
         path = self.path("tiledb_py_0_6_anon_attr")
         with tarfile.open(fileobj=io.BytesIO(base64.b64decode(array_tgz))) as tf:
-            tf.extractall(path)
+            try:
+                tf.extractall(path, filter="fully_trusted")
+            except TypeError:
+                tf.extractall(path)
 
         with tiledb.open(path) as A:
             self.assertEqual(A.schema.attr(0).name, "")
@@ -85,7 +88,11 @@ def test_compat_py_0_5_anon_attr_sparse(self):
 
         path = self.path("test_tiledb_py_0_5_anon_attr_sparse")
         with tarfile.open(fileobj=io.BytesIO(base64.b64decode(test_array))) as tf:
-            tf.extractall(path)
+            try:
+                tf.extractall(path, filter="fully_trusted")
+            except TypeError:
+                tf.extractall(path)
+
         with tiledb.open(path) as A:
             assert_array_equal(A[:][""], np.array([1.0, 2.0, 5.0]))
 
@@ -108,7 +115,11 @@ def test_tiledb_py_0_6_anon_attr(self):
 
         path = self.path("0_6_anon_sparse")
         with tarfile.open(fileobj=io.BytesIO(base64.b64decode(tgz_sparse))) as tf:
-            tf.extractall(path)
+            try:
+                tf.extractall(path, filter="fully_trusted")
+            except TypeError:
+                tf.extractall(path)
+
         with tiledb.open(path) as A:
             if A.schema.sparse:
                 assert_array_equal(A[:][""], np.array([1.0, 2.0, 5.0]))
@@ -158,7 +169,11 @@ def test_tiledb_py_0_6_anon_attr(self):
 
         path = self.path("0_6_anon_dense")
         with tarfile.open(fileobj=io.BytesIO(base64.b64decode(tgz_dense))) as tf:
-            tf.extractall(path)
+            try:
+                tf.extractall(path, filter="fully_trusted")
+            except TypeError:
+                tf.extractall(path)
+
         with tiledb.open(path) as A:
             self.assertEqual(A.schema.attr(0).name, "")
             self.assertEqual(A.schema.attr(0)._internal_name, "__attr")

tiledb/tests/test_fork_ctx.py

@@ -36,6 +36,7 @@ def test_no_warning_fork_without_ctx():
 @pytest.mark.skipif(
     sys.platform == "win32", reason="fork() is not available on Windows"
 )
+@pytest.mark.filterwarnings("ignore::DeprecationWarning")
 def test_warning_fork_with_ctx():
     """Get a warning if we fork after creating a tiledb context."""
     _ = tiledb.Ctx()
@@ -50,6 +51,7 @@ def test_warning_fork_with_ctx():
 @pytest.mark.skipif(
     sys.platform == "win32", reason="fork() is not available on Windows"
 )
+@pytest.mark.filterwarnings("ignore::DeprecationWarning")
 def test_warning_fork_with_default_ctx():
     """Get a warning if we fork after creating a default context."""
     _ = tiledb.default_ctx()
@@ -60,8 +62,6 @@ def test_warning_fork_with_default_ctx():
         else:
             os.wait()
 
-    pass
-
 
 @pytest.mark.skipif(
     sys.platform == "win32", reason="fork() is not available on Windows"
@@ -79,6 +79,7 @@ def test_no_warning_multiprocessing_without_ctx():
 @pytest.mark.skipif(
     sys.platform == "win32", reason="fork() is not available on Windows"
 )
+@pytest.mark.filterwarnings("ignore::DeprecationWarning")
 def test_warning_multiprocessing_with_ctx():
     """Get a warning if we fork after creating a tiledb context."""
     _ = tiledb.Ctx()
@@ -92,6 +93,7 @@ def test_warning_multiprocessing_with_ctx():
 @pytest.mark.skipif(
     sys.platform == "win32", reason="fork() is not available on Windows"
 )
+@pytest.mark.filterwarnings("ignore::DeprecationWarning")
 def test_warning_multiprocessing_with_default_ctx():
     """Get a warning if we fork after creating a default context."""
     _ = tiledb.default_ctx()

tiledb/tests/test_libtiledb.py

@@ -327,7 +327,10 @@ def test_upgrade_version(self):
         path = self.path("test_upgrade_version")
 
         with tarfile.open(fileobj=io.BytesIO(base64.b64decode(tgz_sparse))) as tf:
-            tf.extractall(path)
+            try:
+                tf.extractall(path, filter="fully_trusted")
+            except TypeError:
+                tf.extractall(path)
 
         with tiledb.open(path) as A:
             assert A.schema.version == 5