macos.yml

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-13
    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 $(pwd)/libtiledbvcf/build \
            -D CMAKE_BUILD_TYPE=Debug \
            -D BUILD_SHARED_LIBS=ON \
            -D CMAKE_INSTALL_PREFIX=$(pwd)/dist \
            -D OVERRIDE_INSTALL_PREFIX=OFF \
            -D DOWNLOAD_TILEDB_PREBUILT=ON \
            -D TILEDBVCF_ENABLE_TESTS=ON \
            -D TILEDBVCF_SET_INSTALL_SUBPATH=OFF
      - 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 --install $(pwd)/libtiledbvcf/build --config Debug
      - name: Upload libtiledbvcf as artifact
        uses: actions/upload-artifact@v4
        with:
          name: libtiledbvcf
          path: dist/*
          retention-days: 14
          if-no-files-found: error
      - name: Confirm linking
        run: otool -L dist/lib/libtiledbvcf.dylib
      - name: libtiledbvcf version
        run: ./dist/bin/tiledbvcf version
      - name: Install bcftools
        run: brew install bcftools
      - name: Unit tests
        run: |
          ctest --test-dir libtiledbvcf/build
      - name: CLI tests (require bcftools)
        run: |
          # USAGE: run-cli-tests.sh <build-dir> <inputs-dir>
          libtiledbvcf/test/run-cli-tests.sh libtiledbvcf/build libtiledbvcf/test/inputs
  python:
    runs-on: macos-13
    needs: libtiledbvcf
    env:
      DYLD_LIBRARY_PATH: "${{ github.workspace }}/dist/tiledbvcf/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: Build tiledbvcf-py
        env:
          tiledbvcf_DIR: "${{ github.workspace }}/dist"
          TileDB_DIR: "/Users/runner/micromamba/envs/ci/lib/cmake/TileDB"
        run: |
          python -m pip install -v --no-deps --config-settings=cmake.define.TILEDBVCF_ONLY_PYTHON_BINDINGS=ON .[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-13
    needs: libtiledbvcf
    steps:
      - uses: actions/checkout@v4
      - name: Download libtiledbvcf artifact
        uses: actions/download-artifact@v4
        with:
          name: libtiledbvcf
          path: dist
      - name: Debug
        run: |
          ls -R dist
      - name: Build dependencies
        run: brew install autoconf automake
      - 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
  python-standalone:
    runs-on: macos-13
    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: Build tiledbvcf-py
        run: 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/lib/libtiledb.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