add Python API for sample deletion #426
Workflow file for this run
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
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: | |
runs-on: macos-12 | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Setup to build htslib from source | |
run: brew install autoconf automake | |
- 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 $(pwd)/libtiledbvcf/build --config Debug --target install-libtiledbvcf | |
- name: Upload libtiledbvcf as artifact | |
uses: actions/upload-artifact@v4 | |
with: | |
name: libtiledbvcf | |
path: dist/* | |
retention-days: 14 | |
if-no-files-found: error | |
- name: Confirm linking | |
run: otool -L dist/lib/libtiledbvcf.dylib | |
- name: libtiledbvcf version | |
run: ./dist/bin/tiledbvcf version | |
- name: Install bcftools | |
run: brew install bcftools | |
- name: Unit tests | |
run: | | |
make -j 2 -C libtiledbvcf/build/libtiledbvcf tiledb_vcf_unit | |
./libtiledbvcf/build/libtiledbvcf/test/tiledb_vcf_unit | |
- name: CLI tests (require bcftools) | |
run: | | |
# USAGE: run-cli-tests.sh <build-dir> <inputs-dir> | |
libtiledbvcf/test/run-cli-tests.sh libtiledbvcf/build libtiledbvcf/test/inputs | |
python: | |
runs-on: macos-12 | |
needs: libtiledbvcf | |
env: | |
DYLD_LIBRARY_PATH: "${{ 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-12 | |
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-12 | |
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-12 | |
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-12 | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 # fetch everything for python setuptools_scm | |
- name: Setup to build htslib from source | |
run: brew install autoconf automake | |
- 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 |