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Merge branch 'dev' into jpd/wkt-wkb-support
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‎.github/workflows/ci.yml

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@@ -15,11 +15,11 @@ jobs:
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strategy:
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matrix:
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os: [ubuntu-latest, macos-12, windows-latest]
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python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
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fail-fast: false
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env:
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# 11.7 necessary due to: https://github.com/actions/setup-python/issues/682#issuecomment-1604261330
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MACOSX_DEPLOYMENT_TARGET: ${{ matrix.os == 'macos-12' && contains(fromJSON('["3.7", "3.8"]'), matrix.python-version) && '11.7' || '11' }}
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MACOSX_DEPLOYMENT_TARGET: ${{ matrix.os == 'macos-12' && matrix.python-version == '3.8' && '11.7' || '11' }}
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#MACOSX_DEPLOYMENT_TARGET: "10.11"
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# On windows-2019 we are using the Visual Studio generator, which is multi-config and places the build artifacts in a subdirectory
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steps:
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with:
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python-version: ${{ matrix.python-version }}
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- run: rm -rf $RUNNER_TOOL_CACHE/Python/3.7.17
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if: matrix.os == 'macos-12' && matrix.python-version == '3.7'
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- uses: actions/setup-python@v4
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with:
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python-version: 3.7.17
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if: matrix.os == 'macos-12' && matrix.python-version == '3.7'
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- name: Print Python version
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run: |
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which python
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- name: "Check build directory"
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run: ls -Rl
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- name: "Install libfaketime (linux and macOS)"
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if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-12'
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run: |
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git clone https://github.com/wolfcw/libfaketime/
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cd libfaketime
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sudo make install
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cd ..
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- name: "Run tests"
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run: pytest -vv --showlocals
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‎.github/workflows/daily-test-build-numpy.yml

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name: TileDB Python CI - With Earliest Supported Version of NumPy
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# on: [push]
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on:
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schedule:
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# runs every day at 5:00 UTC (1:00AM EST / Midnight CST)
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- cron: "0 5 * * *"
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workflow_dispatch:
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workflow_call:
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inputs:
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libtiledb_version:
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required: true
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type: string
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jobs:
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test:
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strategy:
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matrix:
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os: [ubuntu-latest, macos-12, windows-latest]
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python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
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include:
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# https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
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- python-version: "3.12"
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numpy-version: "1.26.4"
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- python-version: "3.11"
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numpy-version: "1.23.2"
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- python-version: "3.10"
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numpy-version: "1.19.3"
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- python-version: "3.8"
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numpy-version: "1.17.3"
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- python-version: "3.7"
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numpy-version: "1.16.5"
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fail-fast: false
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env:
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TILEDB_VERSION: 'release-2.20'
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TILEDB_VERSION: ${{ github.event.inputs.libtiledb_version }}
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# 11.7 necessary due to: https://github.com/actions/setup-python/issues/682#issuecomment-1604261330
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#MACOSX_DEPLOYMENT_TARGET: "10.15"
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MACOSX_DEPLOYMENT_TARGET: ${{ matrix.os == 'macos-11' && contains(fromJson('["3.7", "3.8"]'), matrix.python-version) && '11.7' || '11' }}
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MACOSX_DEPLOYMENT_TARGET: ${{ matrix.os == 'macos-12' && matrix.python-version == '3.8' ? '11.7' : '11' }}
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VCPKG_BINARY_SOURCES: 'clear;x-gha,readwrite'
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steps:
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- name: Checkout TileDB-Py `dev`
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- name: Create Issue if Build Fails
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uses: TileDB-Inc/github-actions/open-issue@main
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with:
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name: nightly build with earilest supported numpy
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name: nightly build with earliest supported numpy
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label: bug,nightly-failure
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assignee: nguyenv,ihnorton
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assignee: kounelisagis,nguyenv,KiterLuc,ihnorton

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

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name: Daily Test Build TileDB-Py Against Core
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#on: [push]
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on:
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workflow_dispatch:
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schedule:
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# runs every day at 5:00 UTC (1:00AM EST / Midnight CST)
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- cron: "0 5 * * *"
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workflow_call:
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inputs:
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libtiledb_version:
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required: true
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type: string
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jobs:
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test-wheels-on-azure:
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strategy:
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matrix:
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os: [ubuntu-latest, macos-12, windows-latest]
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libtiledb_version: ["dev", "release-2.19", "release-2.20"]
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uninstall_pandas: [true, false]
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fail-fast: false
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env:
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TILEDB_VERSION: ${{ matrix.libtiledb_version }}
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TILEDB_VERSION: ${{ github.event.inputs.libtiledb_version }}
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MACOSX_DEPLOYMENT_TARGET: "11"
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VCPKG_BINARY_SOURCES: 'clear;x-gha,readwrite'
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with:
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name: nightly build
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label: bug,nightly-failure
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assignee: nguyenv,ihnorton
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assignee: kounelisagis,nguyenv,KiterLuc,ihnorton

‎.github/workflows/daily-tests.yml

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name: Daily Tests TileDB-Py
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on:
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schedule:
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# runs every day at 5:00 UTC (1:00AM EST / Midnight CST)
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- cron: "0 5 * * *"
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workflow_dispatch:
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jobs:
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ci1:
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uses: ./.github/workflows/daily-test-build.yml
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with:
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libtiledb_version: 'dev'
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ci2:
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uses: ./.github/workflows/daily-test-build.yml
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with:
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libtiledb_version: 'release-2.23'
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ci3:
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uses: ./.github/workflows/daily-test-build.yml
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with:
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libtiledb_version: 'release-2.22'
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ci4:
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uses: ./.github/workflows/daily-test-build-numpy.yml
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with:
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libtiledb_version: 'release-2.22'

‎.github/workflows/issue-if-azure-fail.yml

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with:
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name: nightly Azure wheel
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label: bug,nightly-azure-failure
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assignee: nguyenv,ihnorton
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assignee: KiterLuc,kounelisagis,nguyenc,ihnorton

‎.gitignore

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# IntelliJ
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.idea
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# Visual Studio Code
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.vscode/
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*.DS_Store

‎HISTORY.md

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# Next
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# Release 0.29.0
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3+
* TileDB-Py 0.29.0 includes TileDB Embedded [2.23.0](https://github.com/TileDB-Inc/TileDB/releases/tag/2.23.0)
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5+
## Improvements
6+
7+
* Migrate away from deprecated TileDB C++ APIs by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1958
8+
* Pybind11 Config should honor prefix for iter by @Shelnutt2 in https://github.com/TileDB-Inc/TileDB-Py/pull/1962
9+
* Fix test skipping by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1957
10+
* Make timestamp overrides optional in tests and add faketime test by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1953
11+
* Wrap tiledb_array_consolidate_fragments from pybind11 by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1948
12+
13+
## Build system changes
14+
15+
* Enable python 3.12 by @dudoslav in https://github.com/TileDB-Inc/TileDB-Py/pull/1959
16+
* Add .vscode to .gitignore by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1952
17+
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# Release 0.28.0
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## TileDB Embedded updates
21+
22+
* TileDB-Py 0.28.0 includes TileDB Embedded [2.22.0](https://github.com/TileDB-Inc/TileDB/releases/tag/2.22.0)
23+
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## Improvements
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26+
* Update type signature for VFS::readinto by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1937
27+
* Show enumerated value-types in enum-printer by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1936
28+
* Add wrapping for new consolidation plan API by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1935
29+
* Add test for Group constructor invalid uri object type by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1941
30+
* Update doc for tiledb.consolidate by @ihnorton in https://github.com/TileDB-Inc/TileDB-Py/pull/1946
31+
* Improve documentation of from_numpy function by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1942
32+
33+
## Build system changes
34+
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* Exclude .pytest_cache and .hypothesis files by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1932
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* Remove modular building option by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1938
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* Fix wrong version number for Python API docs by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1947
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* Remove conditional code for TileDB < 2.16 by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1949
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* Update nightly test target to 2.21 by @ihnorton in https://github.com/TileDB-Inc/TileDB-Py/pull/1950
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# Release 0.27.1
42+
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## TileDB Embedded updates
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* TileDB-Py 0.27.1 includes TileDB Embedded [2.21.1](https://github.com/TileDB-Inc/TileDB/releases/tag/2.21.1)
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## Improvements
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* Add tests to ensure empty result on query condition for invalid enum. [1882](https://github.com/TileDB-Inc/TileDB-Py/pull/1882)
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# Release 0.27.0
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* TileDB-Py 0.27.0 includes TileDB Embedded [2.21.0](https://github.com/TileDB-Inc/TileDB/releases/tag/2.21.0)
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# Release 0.26.4
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## Bug Fixes
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* Fix VFS `read`, `seek` with numpy integer sizes. [#1927](https://github.com/TileDB-Inc/TileDB-Py/pull/1927)
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* Remove erroneous `_ctx` check for GroupMetadata [#1925](https://github.com/TileDB-Inc/TileDB-Py/pull/1925)
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# Release 0.26.3
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## Improvements
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* Fix vfs readinto when buff is not bytes. [#1915](https://github.com/TileDB-Inc/TileDB-Py/pull/1915)
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* Update daily test builds to use single source of truth for libtiledb target versions. [1910](https://github.com/TileDB-Inc/TileDB-Py/pull/1910)
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* Remove Python 3.7 CI jobs. [1916](https://github.com/TileDB-Inc/TileDB-Py/pull/1916)
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# Release 0.26.2
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## Improvements
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* For compatibility with fsspec and rasterio, `isdir()`, `isfile()`, and `size()` aliases have been added to the `VFS` class (#1902).
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* Added API support for TileDB aggregates. [#1889](https://github.com/TileDB-Inc/TileDB-Py/pull/1889)
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* For compatibility with fsspec and rasterio, `isdir()`, `isfile()`, and `size()` aliases have been added to the `VFS` class. [#1902](https://github.com/TileDB-Inc/TileDB-Py/pull/1902).
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# Release 0.26.1
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‎doc/requirements_doc.txt

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jinja2==3.0.0
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sphinx-rtd-theme==2.0.0
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-r ../requirements_dev.txt

‎doc/source/conf.py

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import os
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import sys
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from os.path import abspath, dirname, join
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import sphinx_rtd_theme
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from importlib.metadata import version as get_version
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sys.path.insert(0, abspath(join(dirname(__file__))))
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# -- Project information -----------------------------------------------------
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project = "TileDB-Py"
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copyright = "2020, TileDB, Inc."
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copyright = "2024, TileDB, Inc."
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author = "TileDB, Inc."
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# The short X.Y version
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version = "0.6"
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# The full version, including alpha/beta/rc tags
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release = "0.6.5"
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release: str = get_version("tiledb")
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# The short X.Y version
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version: str = ".".join(release.split(".")[:2])
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# -- General configuration ---------------------------------------------------
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# -- Options for HTML output -------------------------------------------------
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html_static_path = ["_static"]
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html_title = "TileDB Python API Reference — TileDB-Py %s documentation" % version
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html_logo = "_static/[email protected]"
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html_favicon = "_static/favicon.ico"
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if readthedocs:
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html_theme = "default"
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else:
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import sphinx_rtd_theme
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html_theme = "sphinx_rtd_theme"
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html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
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html_theme = "sphinx_rtd_theme"
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html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
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# -- Options for HTMLHelp output ---------------------------------------------
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‎misc/azure-release.yml

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LIBTILEDB_VERSION: dev
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LIBTILEDB_SHA: dev
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${{ else }}:
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TILEDBPY_VERSION: 0.26.0
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TILEDBPY_VERSION: 0.29.0
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# NOTE: *must* update both LIBTILEDB_VERSION and LIBTILEDB_SHA
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LIBTILEDB_VERSION: "2.20.1"
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LIBTILEDB_VERSION: "2.23.0"
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# NOTE: *must* update both LIBTILEDB_VERSION and LIBTILEDB_SHA
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LIBTILEDB_SHA: 249c02481ed261a643b7fc63b748a90bce060e70
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# kick the hash
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LIBTILEDB_SHA: 152093bed1f25f219fc91f31456c26b04a67dd63
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LIBTILEDB_REPO: https://github.com/TileDB-Inc/TileDB
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TILEDB_SRC: "$(Build.Repository.Localpath)/tiledb_src"
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TILEDB_BUILD: "$(Build.Repository.Localpath)/tiledb_build"
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condition: always()
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variables:
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cibw_test_requires: "pytest"
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USE_CIBW_VERSION: 2.12.3
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USE_CIBW_VERSION: 2.17.0
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strategy:
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matrix:
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imageName: "ubuntu-latest"
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CIBW_SKIP: "cp36-* *_i686 pp* *musllinux*"
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CIBW_SKIP: "cp36-* cp37-* *_i686 pp* *musllinux*"
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CIBW_BUILD_VERBOSITY: 3
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CIBW_ARCHS_MACOS: ""
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MACOSX_DEPLOYMENT_TARGET: 11
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TILEDB_INSTALL: "$(Pipeline.Workspace)/.libtiledb_dist/$(LIBTILEDB_SHA)-macos-x86_64"
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CIBW_ARCHS_MACOS: "x86_64"
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CIBW_SKIP: "cp36-* pp*"
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CIBW_TEST_SKIP: "cp37-*"
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CIBW_SKIP: "cp36-* cp37-* pp*"
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imageName: "macOS-12"
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CIBW_SKIP: "cp36-* *-win32 pp*"
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CIBW_SKIP: "cp36-* cp37-* *-win32 pp*"
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CIBW_BUILD_VERBOSITY: 3
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CIBW_ARCHS_MACOS: ""
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pool:

‎misc/requirements_wheel.txt

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#-------------------------------
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cmake >= 3.23
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cython < 3.0
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cython
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pybind11
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setuptools>=42
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setuptools_scm >= 1.5.4
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setuptools >= 64
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setuptools_scm >= 8
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wheel >= 0.30
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contextvars ;python_version<"3.7"

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