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[Backport release-0.27] Embedded 2.18.3 (#637)
* Embedded 2.18.3 (#635) * Migrate macOS CI to GitHub Actions --------- Co-authored-by: Adam Wenocur <[email protected]> Co-authored-by: John Blischak <[email protected]>
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‎.azure-pipelines.yml

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@@ -32,16 +32,6 @@ stages:
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BUILD_SPARK_API: OFF
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DOWNLOAD_TILEDB_PREBUILT: OFF
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ARTIFACT_NAME: linux_tiledb_source_build
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macos:
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imageName: 'macOS-12'
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python.version: '3.7'
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CXX: clang++
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BUILD_PYTHON_API: ON
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BUILD_SPARK_API: ON
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DOWNLOAD_TILEDB_PREBUILT: ON
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#SDKROOT: '/Applications/Xcode_10.3.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk'
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ARTIFACT_NAME: macos
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MACOSX_DEPLOYMENT_TARGET: '11'
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pool:
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vmImage: $(imageName)
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steps:

‎.github/workflows/macos.yml

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name: macOS
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on:
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push:
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paths:
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- '.github/workflows/macos.yml'
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- 'apis/**'
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- 'libtiledbvcf/**'
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pull_request:
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paths:
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- '.github/workflows/macos.yml'
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- 'apis/**'
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- 'libtiledbvcf/**'
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workflow_dispatch:
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env:
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MACOSX_DEPLOYMENT_TARGET: "11"
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jobs:
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libtiledbvcf:
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# Stuck on macos-11 because of the htslib dependency. The htslib
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# configuration step fails on macos-12 and macos-13
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runs-on: macos-11
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steps:
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- uses: actions/checkout@v3
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- name: Configure libtiledbvcf
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run: |
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cmake -S libtiledbvcf -B $(pwd)/libtiledbvcf/build \
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-D CMAKE_BUILD_TYPE=Debug \
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-D CMAKE_INSTALL_PREFIX=$(pwd)/dist \
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-D OVERRIDE_INSTALL_PREFIX=OFF \
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-D DOWNLOAD_TILEDB_PREBUILT=ON
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- name: Build libtiledbvcf
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run: cmake --build $(pwd)/libtiledbvcf/build -j 2 --config Debug
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- name: Upload coredump as artifact if build failed
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if: failure()
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uses: actions/upload-artifact@v3
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with:
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name: coredump
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path: libtiledbvcf/build/core
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retention-days: 14
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if-no-files-found: error
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- name: Install libtiledbvcf
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run: cmake --build $(pwd)/libtiledbvcf/build --config Debug --target install-libtiledbvcf
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- name: Upload libtiledbvcf as artifact
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uses: actions/upload-artifact@v3
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with:
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name: libtiledbvcf
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path: dist/*
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retention-days: 14
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if-no-files-found: error
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- name: Confirm linking
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run: otool -L dist/lib/libtiledbvcf.dylib
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- name: libtiledbvcf version
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run: ./dist/bin/tiledbvcf version
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- name: Install bcftools
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run: brew install bcftools
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- name: Unit tests
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run: |
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make -j 2 -C libtiledbvcf/build/libtiledbvcf tiledb_vcf_unit
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./libtiledbvcf/build/libtiledbvcf/test/tiledb_vcf_unit
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- name: CLI tests (require bcftools)
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run: |
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# USAGE: run-cli-tests.sh <build-dir> <inputs-dir>
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libtiledbvcf/test/run-cli-tests.sh libtiledbvcf/build libtiledbvcf/test/inputs
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python:
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runs-on: macos-11
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needs: libtiledbvcf
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env:
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DYLD_LIBRARY_PATH: "${{ github.workspace }}/dist/lib"
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0 # fetch everything for python setuptools_scm
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- name: Download libtiledbvcf artifact
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uses: actions/download-artifact@v3
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with:
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name: libtiledbvcf
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path: dist
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.11"
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- name: Install dependencies
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run: python -m pip install --prefer-binary \
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dask \
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distributed \
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'fsspec<2023.3.0' \
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pandas \
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pyarrow==10.0.1 \
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pyarrow-hotfix \
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pybind11 \
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pytest \
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setuptools \
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setuptools_scm \
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setuptools_scm_git_archive \
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wheel
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- name: Build tiledbvcf-py
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env:
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LIBTILEDBVCF_PATH: "${{ github.workspace }}/dist"
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run: |
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echo $DYLD_LIBRARY_PATH
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cd apis/python
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python -m pip install .
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- name: Confirm linking
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run: otool -L /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tiledbvcf/libtiledbvcf.cpython-*-darwin.so
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java:
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runs-on: macos-11
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needs: libtiledbvcf
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steps:
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- uses: actions/checkout@v3
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- name: Download libtiledbvcf artifact
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uses: actions/download-artifact@v3
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with:
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name: libtiledbvcf
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path: dist
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- name: Check format
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run: cd apis/java && ./gradlew checkFormat
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- name: Assemble
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run: cd apis/java && ./gradlew assemble
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- name: Test
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run: cd apis/java && ./gradlew test
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spark:
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runs-on: macos-11
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needs: libtiledbvcf
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steps:
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- uses: actions/checkout@v3
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- name: Download libtiledbvcf artifact
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uses: actions/download-artifact@v3
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with:
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name: libtiledbvcf
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path: dist
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- name: Assemble
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run: cd apis/spark && ./gradlew assemble
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- name: Jar
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run: cd apis/spark && ./gradlew jar
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- name: Test
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run: cd apis/spark && ./gradlew test
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- name: Check format
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run: cd apis/spark && ./gradlew checkFormat
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spark3:
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runs-on: macos-11
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needs: libtiledbvcf
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steps:
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- uses: actions/checkout@v3
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- name: Download libtiledbvcf artifact
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uses: actions/download-artifact@v3
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with:
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name: libtiledbvcf
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path: dist
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- name: Assemble
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run: cd apis/spark3 && ./gradlew assemble
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- name: Jar
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run: cd apis/spark3 && ./gradlew jar
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- name: Test
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run: cd apis/spark3 && ./gradlew test
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- name: Check format
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run: cd apis/spark3 && ./gradlew checkFormat
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python-standalone:
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runs-on: macos-11
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0 # fetch everything for python setuptools_scm
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.11"
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- name: Install dependencies
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run: python -m pip install --prefer-binary \
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dask \
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distributed \
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'fsspec<2023.3.0' \
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pandas \
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pyarrow==10.0.1 \
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pyarrow-hotfix \
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pybind11 \
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pytest \
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setuptools \
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setuptools_scm \
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setuptools_scm_git_archive \
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wheel
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- name: Build tiledbvcf-py
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run: cd apis/python && python -m pip install .
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- name: Confirm linking
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run: |
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otool -L /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tiledbvcf/libtiledbvcf.cpython-*-darwin.so
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otool -L /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tiledbvcf/libtiledbvcf.dylib
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otool -L /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tiledbvcf/libtiledb.dylib
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otool -L /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tiledbvcf/libhts.*.dylib
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- name: Version
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run: python -c "import tiledbvcf; print(tiledbvcf.version)"
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- name: Install bcftools (for tests)
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run: brew install bcftools
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- name: Install tiledb-py
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run: pip install tiledb
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- name: Test tiledbvcf-py
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run: cd apis/python && pytest

‎libtiledbvcf/cmake/Modules/FindTileDB_EP.cmake

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# Try to download prebuilt artifacts unless the user specifies to build from source
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if(DOWNLOAD_TILEDB_PREBUILT)
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if (WIN32) # Windows
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.2/tiledb-windows-x86_64-2.18.2-9ae6e1a.zip")
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SET(DOWNLOAD_SHA1 "c440403fde701e5014a7ffa046d38bb49b141e55")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.3/tiledb-windows-x86_64-2.18.3-8f8b766.zip")
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SET(DOWNLOAD_SHA1 "313cc237c8cab22edaf2745014471d231f185926")
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elseif(APPLE) # OSX
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if (CMAKE_OSX_ARCHITECTURES STREQUAL x86_64 OR CMAKE_SYSTEM_PROCESSOR MATCHES "(x86_64)|(AMD64|amd64)|(^i.86$)")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.2/tiledb-macos-x86_64-2.18.2-9ae6e1a.tar.gz")
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SET(DOWNLOAD_SHA1 "6ba986407b2d0e25fb5df19d08ed22fefeac1c2a")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.3/tiledb-macos-x86_64-2.18.3-8f8b766.tar.gz")
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SET(DOWNLOAD_SHA1 "fbd7515172de977c8ebd553427b7c136a73df299")
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elseif (CMAKE_OSX_ARCHITECTURES STREQUAL arm64 OR CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64" OR CMAKE_SYSTEM_PROCESSOR MATCHES "^arm")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.2/tiledb-macos-arm64-2.18.2-9ae6e1a.tar.gz")
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SET(DOWNLOAD_SHA1 "4395a283db57844a944f02dab5bd0f0001eb7e30")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.3/tiledb-macos-arm64-2.18.3-8f8b766.tar.gz")
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SET(DOWNLOAD_SHA1 "8109bbac66824ee5806cbea93386d66f5b874bc2")
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endif()
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else() # Linux
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.2/tiledb-linux-x86_64-2.18.2-9ae6e1a.tar.gz")
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SET(DOWNLOAD_SHA1 "6386504a58d52330f41fa688a2b259b67824e2c8")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.3/tiledb-linux-x86_64-2.18.3-8f8b766.tar.gz")
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SET(DOWNLOAD_SHA1 "22ccf17c67532ca80fe2c6f06350a267bc839e81")
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endif()
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ExternalProject_Add(ep_tiledb
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else() # Build from source
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ExternalProject_Add(ep_tiledb
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PREFIX "externals"
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URL "https://github.com/TileDB-Inc/TileDB/archive/2.18.2.zip"
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URL_HASH SHA1=70bb2e9a7603675849830b763d1a0d17fce4bafa
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URL "https://github.com/TileDB-Inc/TileDB/archive/2.18.3.zip"
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URL_HASH SHA1=12edfe14b78f1d0119d2e4229daf83a06d37e440
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DOWNLOAD_NAME "tiledb.zip"
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CMAKE_ARGS
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-DCMAKE_INSTALL_PREFIX=${EP_INSTALL_PREFIX}

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