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add Python API for sample deletion #426

add Python API for sample deletion

add Python API for sample deletion #426

Workflow file for this run

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