Import pyarrow-hotfix #256
Workflow file for this run
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| name: Nightly | |
| # High-level notes: | |
| # * Installs libtiledb and libtiledbvcf into ./install/ | |
| # * Manually updates library path so that tiledbvcf-py can link to | |
| # the shared objects in ./install/ | |
| on: | |
| push: | |
| paths: | |
| - '.github/workflows/nightly.yml' | |
| - 'ci/nightly/**' | |
| pull_request: | |
| paths: | |
| - '.github/workflows/nightly.yml' | |
| - 'ci/nightly/**' | |
| schedule: | |
| - cron: "0 3 * * *" # Every night at 3 AM UTC (10 PM EST; 11 PM EDT) | |
| workflow_dispatch: | |
| jobs: | |
| nightly: | |
| runs-on: ${{ matrix.os }} | |
| name: ${{ matrix.os }}-libtiledb-${{ matrix.branches.libtiledb }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-12, ubuntu-latest] | |
| branches: | |
| - {libtiledb: release-2.20, tiledb-py: release-0.26.1} | |
| - {libtiledb: dev, tiledb-py: dev} | |
| env: | |
| MACOSX_DEPLOYMENT_TARGET: 10.15 | |
| steps: | |
| - name: Clone TileDB | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: TileDB-Inc/TileDB | |
| ref: ${{ matrix.branches.libtiledb }} | |
| path: TileDB | |
| - name: Clone TileDB-Py | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: TileDB-Inc/TileDB-Py | |
| ref: ${{ matrix.branches.tiledb-py }} | |
| path: TileDB-Py | |
| - name: Clone TileDB-VCF | |
| uses: actions/checkout@v3 | |
| with: | |
| path: TileDB-VCF | |
| fetch-depth: 0 # fetch everything for python setuptools_scm | |
| - name: Build libtiledb | |
| run: bash TileDB-VCF/ci/nightly/build-libtiledb.sh | |
| - name: Setup to build htslib from source (macOS) | |
| if: runner.os == 'macOS' | |
| run: brew install autoconf automake | |
| - name: Build libtiledbvcf | |
| run: bash TileDB-VCF/ci/nightly/build-libtiledbvcf.sh | |
| - name: Confirm linking (Linux) | |
| if: runner.os == 'Linux' | |
| run: | | |
| ldd install/lib/libtiledb.so | |
| ldd install/lib/libtiledbvcf.so | |
| - name: Confirm linking (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| otool -L install/lib/libtiledb.dylib | |
| otool -L install/lib/libtiledbvcf.dylib | |
| - name: Install bcftools (for tests) (Linux) | |
| if: runner.os == 'Linux' | |
| run: sudo apt install bcftools | |
| - name: Install bcftools (for tests) (macOS) | |
| if: runner.os == 'macOS' | |
| run: brew install bcftools | |
| - name: Test libtiledbvcf | |
| run: bash TileDB-VCF/ci/nightly/test-libtiledbvcf.sh | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --prefer-binary \ | |
| -r TileDB-VCF/ci/nightly/requirements.txt \ | |
| -r TileDB-VCF/ci/nightly/requirements-test.txt | |
| pip list | |
| - name: Build tiledb-py from source | |
| run: | | |
| cd TileDB-Py/ | |
| python setup.py develop --tiledb=../install/ | |
| python -c "import tiledb; print('successful import')" | |
| python -c "import tiledb; print(tiledb.libtiledb.version())" | |
| python -c "import tiledb; print(tiledb.version())" | |
| - name: Build (and test) tiledbvcf-py | |
| run: bash TileDB-VCF/ci/nightly/build-tiledbvcf-py.sh | |
| issue: | |
| permissions: | |
| issues: write | |
| runs-on: ubuntu-latest | |
| needs: nightly | |
| if: ( failure() || cancelled() ) && github.repository_owner == 'TileDB-Inc' && github.event_name == 'schedule' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Open Issue | |
| uses: TileDB-Inc/github-actions/open-issue@main | |
| with: | |
| name: nightly build | |
| label: nightly-failure | |
| assignee: awenocur,gspowley,ihnorton,Shelnutt2 | |
| env: | |
| TZ: "America/New_York" |