-
Notifications
You must be signed in to change notification settings - Fork 16
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
[Backport release-0.27] Embedded 2.18.3 (#637)
* Embedded 2.18.3 (#635) * Migrate macOS CI to GitHub Actions --------- Co-authored-by: Adam Wenocur <[email protected]> Co-authored-by: John Blischak <[email protected]>
- Loading branch information
3 people
authored
Dec 15, 2023
1 parent
3e7e9a1
commit e258193
Showing
3 changed files
with
205 additions
and
20 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,195 @@ | ||
| name: macOS | ||
| on: | ||
| push: | ||
| 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@v3 | ||
| - 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@v3 | ||
| with: | ||
| name: coredump | ||
| path: libtiledbvcf/build/core | ||
| retention-days: 14 | ||
| if-no-files-found: error | ||
| - name: Install libtiledbvcf | ||
| run: cmake --build $(pwd)/libtiledbvcf/build --config Debug --target install-libtiledbvcf | ||
| - name: Upload libtiledbvcf as artifact | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: libtiledbvcf | ||
| path: dist/* | ||
| retention-days: 14 | ||
| if-no-files-found: error | ||
| - name: Confirm linking | ||
| run: otool -L dist/lib/libtiledbvcf.dylib | ||
| - name: libtiledbvcf version | ||
| run: ./dist/bin/tiledbvcf version | ||
| - name: Install bcftools | ||
| run: brew install bcftools | ||
| - name: Unit tests | ||
| run: | | ||
| make -j 2 -C libtiledbvcf/build/libtiledbvcf tiledb_vcf_unit | ||
| ./libtiledbvcf/build/libtiledbvcf/test/tiledb_vcf_unit | ||
| - name: CLI tests (require bcftools) | ||
| run: | | ||
| # USAGE: run-cli-tests.sh <build-dir> <inputs-dir> | ||
| libtiledbvcf/test/run-cli-tests.sh libtiledbvcf/build libtiledbvcf/test/inputs | ||
| python: | ||
| runs-on: macos-11 | ||
| needs: libtiledbvcf | ||
| env: | ||
| DYLD_LIBRARY_PATH: "${{ github.workspace }}/dist/lib" | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| with: | ||
| fetch-depth: 0 # fetch everything for python setuptools_scm | ||
| - name: Download libtiledbvcf artifact | ||
| uses: actions/download-artifact@v3 | ||
| with: | ||
| name: libtiledbvcf | ||
| path: dist | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.11" | ||
| - name: Install dependencies | ||
| run: python -m pip install --prefer-binary \ | ||
| dask \ | ||
| distributed \ | ||
| 'fsspec<2023.3.0' \ | ||
| pandas \ | ||
| pyarrow==10.0.1 \ | ||
| pyarrow-hotfix \ | ||
| pybind11 \ | ||
| pytest \ | ||
| setuptools \ | ||
| setuptools_scm \ | ||
| setuptools_scm_git_archive \ | ||
| wheel | ||
| - name: Build tiledbvcf-py | ||
| env: | ||
| LIBTILEDBVCF_PATH: "${{ github.workspace }}/dist" | ||
| run: | | ||
| echo $DYLD_LIBRARY_PATH | ||
| cd apis/python | ||
| python -m pip install . | ||
| - 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@v3 | ||
| - name: Download libtiledbvcf artifact | ||
| uses: actions/download-artifact@v3 | ||
| 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@v3 | ||
| - name: Download libtiledbvcf artifact | ||
| uses: actions/download-artifact@v3 | ||
| 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@v3 | ||
| - name: Download libtiledbvcf artifact | ||
| uses: actions/download-artifact@v3 | ||
| 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@v3 | ||
| with: | ||
| fetch-depth: 0 # fetch everything for python setuptools_scm | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.11" | ||
| - name: Install dependencies | ||
| run: python -m pip install --prefer-binary \ | ||
| dask \ | ||
| distributed \ | ||
| 'fsspec<2023.3.0' \ | ||
| pandas \ | ||
| pyarrow==10.0.1 \ | ||
| pyarrow-hotfix \ | ||
| pybind11 \ | ||
| pytest \ | ||
| setuptools \ | ||
| setuptools_scm \ | ||
| setuptools_scm_git_archive \ | ||
| wheel | ||
| - name: Build tiledbvcf-py | ||
| run: cd apis/python && python -m pip install . | ||
| - 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: Install tiledb-py | ||
| run: pip install tiledb | ||
| - name: Test tiledbvcf-py | ||
| run: cd apis/python && pytest |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters