Release 0.19.0 Against 2.13.0

.github/workflows/ci.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-11, windows-latest]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
       fail-fast: false
     env:
       MACOSX_DEPLOYMENT_TARGET: "10.15"

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

@@ -16,9 +16,11 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-11, windows-latest]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
         include:
           # https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
+          - python-version: "3.11"
+            numpy-version: "1.23.2"
           - python-version: "3.10"
             numpy-version: "1.21.6"
           - python-version: "3.9"

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

@@ -46,7 +46,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Print Python version
         run: |

HISTORY.md

@@ -1,4 +1,10 @@
-# In Progress
+# Release 0.19.0
+
+## Packaging Notes
+* Added support for Python 3.11
+
+## TileDB Embedded updates:
+* TileDB-Py 0.19.0 includes TileDB Embedded [TileDB 2.13.0](https://github.com/TileDB-Inc/TileDB/releases/tag/2.13.0)
 
 ## API Changes
 * Support Boolean types for query conditions [#1432](https://github.com/TileDB-Inc/TileDB-Py/pull/1432)
@@ -10,6 +16,7 @@
 ## Bug Fixes
 * Fix issue where queries in delete mode error out on arrays with string dimensions [#1473](https://github.com/TileDB-Inc/TileDB-Py/pull/1473)
 * Fix representation of nullable integers in dataframe when using PyArrow path [#1439](https://github.com/TileDB-Inc/TileDB-Py/pull/1439)
+* Check for uninitialized query state after submit and error out if uninitialized [#1483](https://github.com/TileDB-Inc/TileDB-Py/pull/1483)
 
 # Release 0.18.3
 

examples/query_condition_dense.py

@@ -32,8 +32,6 @@
 import tiledb
 import numpy as np
 from pprint import pprint
-import tempfile
-import string
 
 uri = "query_condition_dense"
 
@@ -67,14 +65,14 @@ def read_array(path):
         print()
 
     with tiledb.open(uri) as arr:
-        qc = tiledb.QueryCondition("(2 < attr1 < 6) and (attr2 < 0.5 or attr2 > 0.85)")
+        qc = "(2 < attr1 < 6) and (attr2 < 0.5 or attr2 > 0.85)"
         print(f"--- with query condition {qc}:")
 
         print(f"--- the fill value for attr1 is {arr.attr('attr1').fill}")
         print(f"--- the fill value for attr1 is {arr.attr('attr2').fill}")
 
         print()
-        res = arr.query(attr_cond=qc)[:]
+        res = arr.query(cond=qc)[:]
         pprint(res)
 
 

examples/query_condition_sparse.py

@@ -32,8 +32,6 @@
 import tiledb
 import numpy as np
 from pprint import pprint
-import tempfile
-import string
 
 uri = "query_condition_sparse"
 
@@ -67,10 +65,10 @@ def read_array(path):
         print()
 
     with tiledb.open(uri) as arr:
-        qc = tiledb.QueryCondition("(2 < attr1 < 6) and (attr2 < 0.5 or attr2 > 0.85)")
+        qc = "(2 < attr1 < 6) and (attr2 < 0.5 or attr2 > 0.85)"
         print(f"--- with query condition {qc}:")
         print()
-        res = arr.query(attr_cond=qc)[:]
+        res = arr.query(cond=qc)[:]
         pprint(res)
 
 

examples/query_condition_string.py

@@ -52,10 +52,8 @@ def create_array(path):
 
 def read_array(path, cond):
     with tiledb.open(path) as arr:
-        qc = tiledb.QueryCondition(cond)
-
-        print("QueryCondition is: ", qc)
-        res = arr.query(attr_cond=qc)[:]
+        print("QueryCondition is: ", cond)
+        res = arr.query(cond=cond)[:]
         return res
 
 

examples/vfs.py

@@ -76,37 +76,34 @@ def write():
     # Create TileDB VFS
     vfs = tiledb.VFS()
 
-    # Create VFS file handle
-    f = vfs.open("tiledb_vfs.bin", "wb")
-
     # Write binary data
-    vfs.write(f, struct.pack("f", 153.0))
-    vfs.write(f, "abcd".encode("utf-8"))
-    vfs.close(f)
+    with vfs.open("tiledb_vfs.bin", "wb") as f:
+        f.write(struct.pack("f", 153.0))
+        f.write("abcd".encode("utf-8"))
 
     # Write binary data again - this will overwrite the previous file
-    f = vfs.open("tiledb_vfs.bin", "wb")
-    vfs.write(f, struct.pack("f", 153.1))
-    vfs.write(f, "abcdef".encode("utf-8"))
-    vfs.close(f)
+    with vfs.open("tiledb_vfs.bin", "wb") as f:
+        f.write(struct.pack("f", 153.1))
+        f.write("abcdef".encode("utf-8"))
 
     # Append binary data to existing file (this will NOT work on S3)
-    f = vfs.open("tiledb_vfs.bin", "ab")
-    vfs.write(f, "ghijkl".encode("utf-8"))
-    vfs.close(f)
+    with vfs.open("tiledb_vfs.bin", "ab") as f:
+        f.write("ghijkl".encode("utf-8"))
 
 
 def read():
     # Create TileDB VFS
     vfs = tiledb.VFS()
 
     # Read binary data
-    f = vfs.open("tiledb_vfs.bin", "rb")
-    f1 = struct.unpack("f", vfs.read(f, 0, 4))[0]
-    s1 = bytes.decode(vfs.read(f, 4, 12), "utf-8")
-    print("Binary read:\n{}\n{}".format(f1, s1))
+    with vfs.open("tiledb_vfs.bin", "rb") as f:
+        # Read the first 4 bytes (bytes [0:4])
+        f1 = struct.unpack("f", f.read(4))[0]
+
+        # Read the next 8 bytes (bytes [4:12])
+        s1 = bytes.decode(f.read(8), "utf-8")
 
-    vfs.close(f)
+        print(f"Binary read:\n{f1}\n{s1}")
 
 
 dirs_files()

misc/azure-ci.yml

@@ -9,14 +9,14 @@ stages:
           matrix:
             mac:
               imageName: "macOS-11"
-              python.version: "3.10"
+              python.version: "3.11"
               MACOSX_DEPLOYMENT_TARGET: 10.15
             windows:
               imageName: "windows-latest"
-              python.version: "3.10"
+              python.version: "3.11"
             linux_py3:
               imageName: "ubuntu-latest"
-              python.version: "3.10"
+              python.version: "3.11"
           maxParallel: 4
         timeoutInMinutes: 120
 

misc/azure-release.yml

@@ -6,9 +6,9 @@ stages:
         LIBTILEDB_VERSION: dev
         LIBTILEDB_SHA: dev
       ${{ else }}:
-        TILEDBPY_VERSION: 0.18.3
-        LIBTILEDB_VERSION: 2.12.3
-        LIBTILEDB_SHA: fdfc2ee106caffe7e3a373b8728a04eabc4d89a5
+        TILEDBPY_VERSION: 0.19.0
+        LIBTILEDB_VERSION: 2.13.0
+        LIBTILEDB_SHA: db00e709701fa1787dce68c7563f775d6a0770ad
       LIBTILEDB_REPO: https://github.com/TileDB-Inc/TileDB
       TILEDB_SRC: "$(Build.Repository.Localpath)/tiledb_src"
       TILEDB_BUILD: "$(Build.Repository.Localpath)/tiledb_build"
@@ -70,7 +70,7 @@ stages:
         steps:
           - task: UsePythonVersion@0
             inputs:
-              versionSpec: "3.10"
+              versionSpec: "3.11"
             condition: and(succeeded(), eq(variables['Agent.OS'], 'Darwin'))
 
           - script: git tag -f $(TILEDBPY_VERSION)

misc/pypi_linux/build.sh

@@ -63,8 +63,21 @@ auditwheel repair dist/*.whl
 /opt/python/cp310-cp310/bin/python3.10 -m pip install wheelhouse/*.whl
 cd tiledb/tests
 
+# build python311 wheel
+cd /home/tiledb
+git clone $TILEDB_PY_REPO TileDB-Py311
+git -C TileDB-Py311 checkout $TILEDBPY_VERSION
+
+cd /home/tiledb/TileDB-Py311
+/opt/python/cp311-cp311m/bin/python3.10 -m pip install -r misc/requirements_wheel.txt
+/opt/python/cp311-cp311/bin/python3.10 setup.py build_ext bdist_wheel --tiledb=/usr/local
+auditwheel repair dist/*.whl
+/opt/python/cp311-cp311/bin/python3.10 -m pip install wheelhouse/*.whl
+cd tiledb/tests
+
 # copy build products out
 cp /home/tiledb/TileDB-Py37/wheelhouse/* /wheels
 cp /home/tiledb/TileDB-Py38/wheelhouse/* /wheels
 cp /home/tiledb/TileDB-Py39/wheelhouse/* /wheels
 cp /home/tiledb/TileDB-Py310/wheelhouse/* /wheels
+cp /home/tiledb/TileDB-Py311/wheelhouse/* /wheels

misc/requirements_wheel.txt

@@ -6,6 +6,7 @@ numpy==1.19.4 ; python_version == "3.9" and platform_machine !='aarch64'
 # NOTE: oldest-supported-numpy (1.19.2) had forward ABI compat problems
 numpy==1.20.* ; python_version < "3.10" and platform_machine=='aarch64'
 numpy==1.21.* ; python_version >= "3.10"
+numpy>=1.23.0 ; python_version >= "3.11"
 
 #-------------------------------
 # Note 11/23/2021: the current version of the AWS sdk does not work with cmake 3.22

requirements.txt

@@ -1,6 +1,7 @@
 numpy>=1.16.5 ; python_version < "3.10" and platform_machine != 'aarch64'
 numpy>=1.19.2 ; python_version < "3.10" and platform_machine == 'aarch64'
 numpy>=1.21.0 ; python_version >= "3.10"
+numpy>=1.23.0 ; python_version >= "3.11"
 packaging
 
 contextvars ;python_version<"3.7"