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[ci] Update github actions (#4434)
* Update github actions * Fix missing dependency from somacore port * Disable linting error in setup.py
1 parent 2e54555 commit d0b669e

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+41
-40
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‎.github/workflows/build-cpp.yml‎

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@@ -15,14 +15,14 @@ jobs:
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runs-on: ${{ inputs.os }}
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steps:
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- name: Checkout TileDB-SOMA
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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- name: Build and install libtiledbsoma
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run: |
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./scripts/bld --no-tiledb-deprecated=true --werror=true --build ${{ inputs.build_type }}
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- name: Upload C++ build artifact
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uses: actions/upload-artifact@v4
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uses: actions/upload-artifact@v7
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with:
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# The name now includes the build type
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name: cpp-build-${{ inputs.build_type }}-${{ inputs.os }}

‎.github/workflows/ci-linters.yml‎

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@@ -10,15 +10,15 @@ jobs:
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runs-on: ubuntu-24.04
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steps:
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- name: Checkout TileDB-SOMA
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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- name: Set up Python
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: "3.12"
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- name: Restore pre-commit cache
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uses: actions/cache@v4
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uses: actions/cache@v5
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with:
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path: ~/.cache/pre-commit
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key: pre-commit-ubuntu-24.04-3.12-${{ hashFiles('.github/workflows/lint-python.yml', '.pre-commit-config.yaml') }}

‎.github/workflows/ci-r-python-interop.yml‎

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@@ -38,13 +38,13 @@ jobs:
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steps:
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- name: Checkout TileDB-SOMA
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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with:
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fetch-depth: 0 # Required to fetch tags: https://github.com/actions/checkout/issues/2199
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fetch-tags: true # Tags used for Python package version.
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- name: Download pre-built C++ library
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uses: actions/download-artifact@v4
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uses: actions/download-artifact@v8
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with:
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name: cpp-build-Release-${{ matrix.os }}
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@@ -100,7 +100,7 @@ jobs:
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run: Rscript -e 'tiledbsoma::show_package_versions()'
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- name: Set up Python 3.11
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: "3.11"
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cache: pip

‎.github/workflows/pkgdown.yaml‎

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@@ -23,7 +23,7 @@ jobs:
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v6
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- uses: r-lib/actions/setup-pandoc@v2
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‎.github/workflows/python-dependency-variation.yml‎

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@@ -46,13 +46,13 @@ jobs:
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steps:
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- name: Check out TileDB-SOMA
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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with:
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fetch-depth: 0 # Required to fetch tags: https://github.com/actions/checkout/issues/2199
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fetch-tags: true # Tags used for Python package version.
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- name: Checkout vcpkg
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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with:
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repository: microsoft/vcpkg
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path: vcpkg
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run: cat /proc/cpuinfo
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- name: Set up Python ${{ matrix.python_version }}
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python_version }}
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cache: pip

‎.github/workflows/python-dockers.yml‎

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@@ -45,7 +45,7 @@ jobs:
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name: ${{ matrix.img.name }}${{ matrix.os.suffix }}
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runs-on: ${{ matrix.os.runs-on }}
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v6
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- name: docker build
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run: |
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args=()
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if: (failure() || cancelled()) && github.event_name == 'schedule' && github.run_attempt == 1
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steps:
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- name: Checkout TileDB-SOMA `main`
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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- name: Create Issue if Build Fails
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uses: JasonEtco/create-an-issue@v2
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env:

‎.github/workflows/python-packaging.yml‎

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@@ -18,7 +18,7 @@ jobs:
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runs-on: ubuntu-24.04
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steps:
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- name: Checkout TileDB-SOMA
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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with:
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fetch-depth: 0 # Required to fetch tags: https://github.com/actions/checkout/issues/2199
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fetch-tags: true # Tags needed for python API version number
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- name: Upload sdist artifact to GitHub Actions storage
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uses: actions/upload-artifact@v4
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uses: actions/upload-artifact@v7
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with:
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name: sdist
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path: apis/python/dist/
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python_version: ["3.9", "3.10", "3.11", "3.12"]
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steps:
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- name: Set up Python ${{ matrix.python_version }}
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python_version }}
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- name: Download sdist artifact
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uses: actions/download-artifact@v4
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uses: actions/download-artifact@v8
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with:
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name: sdist
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path: apis/python/dist/
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steps:
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- name: Checkout TileDB-SOMA
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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with:
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fetch-depth: 0 # Required to fetch tags: https://github.com/actions/checkout/issues/2199
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fetch-tags: true # Tags needed for python API version number
@@ -118,7 +118,7 @@ jobs:
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pip list
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- name: Build wheels
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uses: pypa/cibuildwheel@v3.1.1
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uses: pypa/cibuildwheel@v3.4.0
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with:
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package-dir: apis/python/
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output-dir: wheelhouse
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run: ls -l ./wheelhouse/*.whl
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- name: Upload wheel-${{ matrix.python_name }}-${{ matrix.platform }}
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uses: actions/upload-artifact@v4
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uses: actions/upload-artifact@v7
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with:
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name: wheel-${{ matrix.python_name }}-${{ matrix.platform }}
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path: ./wheelhouse/*.whl
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fail-fast: false
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steps:
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- name: Set up Python ${{ matrix.python_version }}
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python_version }}
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- name: Download artifacts
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uses: actions/download-artifact@v4
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uses: actions/download-artifact@v8
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with:
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name: wheel-${{ matrix.python_name }}-${{ matrix.platform }}
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- name: Install numba to prevent building from source
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if: github.event_name == 'workflow_dispatch'
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steps:
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- name: Download artifacts
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uses: actions/download-artifact@v4
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uses: actions/download-artifact@v8
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- name: Create dist
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run: |
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set -x
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if: github.event_name == 'release'
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steps:
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- name: Download artifacts
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uses: actions/download-artifact@v4
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uses: actions/download-artifact@v8
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- name: Create dist
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run: |
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set -x
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if: (failure() || cancelled()) && github.event_name != 'workflow_dispatch' && github.event_name != 'pull_request' && github.run_attempt == 1
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steps:
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- name: Checkout TileDB-SOMA `main`
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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- name: Create Issue if Build Fails
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uses: JasonEtco/create-an-issue@v2
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env:

‎.github/workflows/python-remote-storage.yml‎

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@@ -45,7 +45,7 @@ jobs:
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v6
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- name: Show matrix OS
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run: echo "matrix.os:" ${{ matrix.os }}
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run: cat /proc/cpuinfo
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- name: Set up Python ${{ matrix.python_version }}
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python_version }}
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cache: pip
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cache-dependency-path: ./apis/python/setup.py
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- name: Check out TileDB-SOMA
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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with:
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fetch-depth: 0 # ensure we get all tags to inform package version determination
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- name: Download pre-built C++ library
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uses: actions/download-artifact@v4
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uses: actions/download-artifact@v8
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with:
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name: cpp-build-Release-${{ matrix.os }}
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‎.github/workflows/r-valgrind.yaml‎

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container:
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image: rocker/r2u:latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v6
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- name: SessionInfo
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run: R -q -e 'sessionInfo()'

‎.github/workflows/test-cpp.yml‎

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@@ -24,7 +24,7 @@ jobs:
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- uses: actions/checkout@v4
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- name: Download pre-built C++ library
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uses: actions/download-artifact@v4
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uses: actions/download-artifact@v8
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with:
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name: cpp-build-Release-${{ inputs.os }}
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- uses: actions/checkout@v4
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- name: Download C++ ASAN build artifact
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uses: actions/download-artifact@v4
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uses: actions/download-artifact@v8
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with:
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name: cpp-build-ASAN-${{ inputs.os }}
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