remove unnecessary and problematic lines from CLI test (#722) #44
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| name: macOS | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - 'release-*' | |
| paths: | |
| - '.github/workflows/macos.yml' | |
| - 'apis/**' | |
| - 'libtiledbvcf/**' | |
| pull_request: | |
| paths: | |
| - '.github/workflows/macos.yml' | |
| - 'apis/**' | |
| - 'libtiledbvcf/**' | |
| workflow_dispatch: | |
| env: | |
| MACOSX_DEPLOYMENT_TARGET: "11" | |
| jobs: | |
| libtiledbvcf: | |
| # Stuck on macos-11 because of the htslib dependency. The htslib | |
| # configuration step fails on macos-12 and macos-13 | |
| runs-on: macos-11 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Configure libtiledbvcf | |
| run: | | |
| cmake -S libtiledbvcf -B $(pwd)/libtiledbvcf/build \ | |
| -D CMAKE_BUILD_TYPE=Debug \ | |
| -D CMAKE_INSTALL_PREFIX=$(pwd)/dist \ | |
| -D OVERRIDE_INSTALL_PREFIX=OFF \ | |
| -D DOWNLOAD_TILEDB_PREBUILT=ON | |
| - name: Build libtiledbvcf | |
| run: cmake --build $(pwd)/libtiledbvcf/build -j 2 --config Debug | |
| - name: Upload coredump as artifact if build failed | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coredump | |
| path: libtiledbvcf/build/core | |
| retention-days: 14 | |
| if-no-files-found: error | |
| - name: Install libtiledbvcf | |
| run: cmake --build $(pwd)/libtiledbvcf/build --config Debug --target install-libtiledbvcf | |
| - name: Upload libtiledbvcf as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: libtiledbvcf | |
| path: dist/* | |
| retention-days: 14 | |
| if-no-files-found: error | |
| - name: Confirm linking | |
| run: otool -L dist/lib/libtiledbvcf.dylib | |
| - name: libtiledbvcf version | |
| run: ./dist/bin/tiledbvcf version | |
| - name: Install bcftools | |
| run: brew install bcftools | |
| - name: Unit tests | |
| run: | | |
| make -j 2 -C libtiledbvcf/build/libtiledbvcf tiledb_vcf_unit | |
| ./libtiledbvcf/build/libtiledbvcf/test/tiledb_vcf_unit | |
| - name: CLI tests (require bcftools) | |
| run: | | |
| # USAGE: run-cli-tests.sh <build-dir> <inputs-dir> | |
| libtiledbvcf/test/run-cli-tests.sh libtiledbvcf/build libtiledbvcf/test/inputs | |
| python: | |
| runs-on: macos-11 | |
| needs: libtiledbvcf | |
| env: | |
| DYLD_LIBRARY_PATH: "${{ github.workspace }}/dist/lib" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # fetch everything for python setuptools_scm | |
| - name: Download libtiledbvcf artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: libtiledbvcf | |
| path: dist | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install libtiledb | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: ci | |
| create-args: tiledb | |
| - name: Install dependencies | |
| run: python -m pip install --prefer-binary pyarrow==10.0.1 | |
| - name: Build tiledbvcf-py | |
| env: | |
| LIBTILEDBVCF_PATH: "${{ github.workspace }}/dist" | |
| TileDB_DIR: "/Users/runner/micromamba/envs/ci/lib/cmake/TileDB" | |
| run: | | |
| echo $DYLD_LIBRARY_PATH | |
| echo $TileDB_DIR | |
| cd apis/python | |
| python -m pip install -v .[test] | |
| - name: Confirm linking | |
| run: otool -L /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tiledbvcf/libtiledbvcf.cpython-*-darwin.so | |
| java: | |
| runs-on: macos-11 | |
| needs: libtiledbvcf | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Download libtiledbvcf artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: libtiledbvcf | |
| path: dist | |
| - name: Check format | |
| run: cd apis/java && ./gradlew checkFormat | |
| - name: Assemble | |
| run: cd apis/java && ./gradlew assemble | |
| - name: Test | |
| run: cd apis/java && ./gradlew test | |
| spark: | |
| runs-on: macos-11 | |
| needs: libtiledbvcf | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Download libtiledbvcf artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: libtiledbvcf | |
| path: dist | |
| - name: Assemble | |
| run: cd apis/spark && ./gradlew assemble | |
| - name: Jar | |
| run: cd apis/spark && ./gradlew jar | |
| - name: Test | |
| run: cd apis/spark && ./gradlew test | |
| - name: Check format | |
| run: cd apis/spark && ./gradlew checkFormat | |
| spark3: | |
| runs-on: macos-11 | |
| needs: libtiledbvcf | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Download libtiledbvcf artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: libtiledbvcf | |
| path: dist | |
| - name: Assemble | |
| run: cd apis/spark3 && ./gradlew assemble | |
| - name: Jar | |
| run: cd apis/spark3 && ./gradlew jar | |
| - name: Test | |
| run: cd apis/spark3 && ./gradlew test | |
| - name: Check format | |
| run: cd apis/spark3 && ./gradlew checkFormat | |
| python-standalone: | |
| runs-on: macos-11 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # fetch everything for python setuptools_scm | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: python -m pip install --prefer-binary pyarrow==10.0.1 | |
| - name: Build tiledbvcf-py | |
| run: cd apis/python && python -m pip install -v .[test] | |
| - name: Confirm linking | |
| run: | | |
| otool -L /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tiledbvcf/libtiledbvcf.cpython-*-darwin.so | |
| otool -L /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tiledbvcf/libtiledbvcf.dylib | |
| otool -L /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tiledbvcf/libtiledb.dylib | |
| otool -L /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tiledbvcf/libhts.*.dylib | |
| - name: Version | |
| run: python -c "import tiledbvcf; print(tiledbvcf.version)" | |
| - name: Install bcftools (for tests) | |
| run: brew install bcftools | |
| - name: Test tiledbvcf-py | |
| run: cd apis/python && pytest |