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| name: Nightly build against nightly libtiledb | |
| # 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/ | |
| # * The Python dependencies are handled differently per OS | |
| # * linux: conda binaries | |
| # * osx: PyPI wheels | |
| 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: | |
| linux: | |
| runs-on: ubuntu-latest | |
| name: linux-libtiledb-${{ matrix.libtiledb_version }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| libtiledb_version: [release-2.19, dev] | |
| steps: | |
| - name: Clone TileDB | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: TileDB-Inc/TileDB | |
| ref: ${{ matrix.libtiledb_version }} | |
| path: TileDB | |
| - name: Clone TileDB-VCF | |
| uses: actions/checkout@v3 | |
| with: | |
| path: TileDB-VCF | |
| fetch-depth: 0 # fetch everything for python setuptools_scm | |
| - name: Build libtiledb | |
| run: bash TileDB-VCF/ci/nightly/build-libtiledb.sh | |
| - name: Build libtiledbvcf | |
| run: bash TileDB-VCF/ci/nightly/build-libtiledbvcf.sh | |
| - name: Confirm linking | |
| run: | | |
| ldd install/lib/libtiledb.so | |
| ldd install/lib/libtiledbvcf.so | |
| - name: Install bcftools (for tests) | |
| run: sudo apt install bcftools | |
| - name: Test libtiledbvcf | |
| run: bash TileDB-VCF/ci/nightly/test-libtiledbvcf.sh | |
| - name: Setup conda env | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: TileDB-VCF/ci/nightly/environment.yaml | |
| cache-environment: true | |
| - name: Build (and test) tiledbvcf-py | |
| # need -l to activate conda env | |
| shell: bash -l {0} | |
| run: bash TileDB-VCF/ci/nightly/build-tiledbvcf-py.sh | |
| osx: | |
| runs-on: macos-12 | |
| name: osx-libtiledb-${{ matrix.libtiledb_version }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| libtiledb_version: [release-2.19, dev] | |
| env: | |
| MACOSX_DEPLOYMENT_TARGET: 10.15 | |
| steps: | |
| - name: Clone TileDB | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: TileDB-Inc/TileDB | |
| ref: ${{ matrix.libtiledb_version }} | |
| path: TileDB | |
| - 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 | |
| run: brew install autoconf automake | |
| - name: Build libtiledbvcf | |
| run: bash TileDB-VCF/ci/nightly/build-libtiledbvcf.sh | |
| - name: Confirm linking | |
| run: | | |
| otool -L install/lib/libtiledb.dylib | |
| otool -L install/lib/libtiledbvcf.dylib | |
| - name: Install bcftools (for tests) | |
| 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 | |
| - 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: [linux, osx] | |
| 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" |