Support new GenomicsDB query_variant_calls api that uses QueryConfiguration protobuf #161
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Build and Test | |
| on: | |
| push: | |
| paths-ignore: | |
| - '**/*.md' | |
| - '**/*.rst' | |
| pull_request: | |
| paths-ignore: | |
| - '**/*.md' | |
| - '**/*.rst' | |
| env: | |
| GENOMICSDB_BUILD_DIR: ${{github.workspace}} | |
| GENOMICSDB_HOME: ${{github.workspace}}/install | |
| GENOMICSDB_BRANCH: develop | |
| jobs: | |
| native-build: | |
| name: GenomicsDB Build | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Cache Native GenomicsDB | |
| uses: actions/cache@v3 | |
| env: | |
| GENOMICSDB_TARBALL: ${{env.GENOMICSDB_HOME}}_${{env.GENOMICSDB_BRANCH}}.tar | |
| with: | |
| path: ${{env.GENOMICSDB_TARBALL}} | |
| key: ${{env.GENOMICSDB_TARBALL}}.v1 | |
| - name: Native Build | |
| env: | |
| GENOMICSDB_TARBALL: ${{env.GENOMICSDB_HOME}}_${{env.GENOMICSDB_BRANCH}}.tar | |
| run: | | |
| echo "GENOMICSDB_TARBALL=$GENOMICSDB_TARBALL" >> $GITHUB_ENV | |
| if [[ ! -f ${GENOMICSDB_TARBALL} ]]; then | |
| sudo apt-get update -q && sudo apt install -y libcurl4-openssl-dev curl | |
| git clone https://github.com/GenomicsDB/GenomicsDB.git -b $GENOMICSDB_BRANCH $GENOMICSDB_BUILD_DIR | |
| cd $GENOMICSDB_BUILD_DIR | |
| cmake -S . -B build -DBUILD_FOR_PYTHON=1 -DCMAKE_INSTALL_PREFIX=$GENOMICSDB_HOME | |
| cd build && make -j4 && make install | |
| cd $(dirname $GENOMICSDB_HOME) | |
| tar -cvf ${GENOMICSDB_TARBALL} $(basename $GENOMICSDB_HOME) | |
| fi | |
| - name: Upload GenomicsDB Tarball | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: GenomicsDB-Tarball-${{runner.os}} | |
| path: ${{env.GENOMICSDB_TARBALL}} | |
| retention-days: 5 | |
| python-build: | |
| name: GenomicsDB Python Build | |
| needs: native-build | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Download GenomicsDB Tarball | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: GenomicsDB-Tarball-${{runner.os}} | |
| - name: Extract GenomicsDB from Tarball | |
| env: | |
| GENOMICSDB_TARBALL: ${{env.GENOMICSDB_HOME}}_${{env.GENOMICSDB_BRANCH}}.tar | |
| run: tar -xvf ${GENOMICSDB_TARBALL} -C $(dirname $GENOMICSDB_HOME) | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -r requirements_dev.txt | |
| - name: Build | |
| run: make install-dev | |
| - name: Test | |
| run: | | |
| PYTHONPATH=. pytest | |
| PYTHONPATH=. python test/test.py |