Merge pull request #368 from DEploid-dev/use_vcf_lib #249
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| name: Build and test | |
| on: | |
| push: | |
| branches: | |
| - "*" | |
| pull_request: | |
| branches: | |
| - "*" | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| name: [ubuntu-gcc-9, | |
| ubuntu-gcc-10, | |
| ubuntu-clang-15 | |
| ] | |
| include: | |
| - name: ubuntu-gcc-9 | |
| os: ubuntu-latest | |
| compiler: gcc | |
| version: "9" | |
| - name: ubuntu-gcc-10 | |
| os: ubuntu-latest | |
| compiler: gcc | |
| version: "10" | |
| - name: ubuntu-clang-15 | |
| os: ubuntu-latest | |
| compiler: clang | |
| version: "15" | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies (linux) | |
| if: runner.os == 'Linux' && matrix.name != 'windows' | |
| run: | | |
| sudo apt-get install libcppunit-dev valgrind r-base-core lcov doxygen graphviz ccache | |
| if [ "${{ matrix.compiler }}" = "gcc" ]; then | |
| sudo apt-get install -y g++-${{ matrix.version }} | |
| echo "CC=ccache gcc-${{ matrix.version }}" >> $GITHUB_ENV | |
| echo "CXX=ccache g++-${{ matrix.version }}" >> $GITHUB_ENV | |
| else | |
| sudo apt-get install -y clang-${{ matrix.version }} | |
| echo "CC=ccache clang-${{ matrix.version }}" >> $GITHUB_ENV | |
| echo "CXX=ccache clang++-${{ matrix.version }}" >> $GITHUB_ENV | |
| fi | |
| - name: Install dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install cppunit r lcov doxygen graphviz ccache coreutils automake | |
| echo "DEVELOPER_DIR=/Applications/Xcode_${{ matrix.version }}.app/Contents/Developer" >> $GITHUB_ENV | |
| echo "CC=ccache clang" >> $GITHUB_ENV | |
| echo "CXX=ccache clang++" >> $GITHUB_ENV | |
| ccache --set-config=cache_dir=$HOME/.ccache | |
| - name: Install python packages | |
| run: python3 -mpip install cpp-coveralls cpplint | |
| - name: Check style | |
| run: cpplint --version # .ci/style.sh | |
| - name: Prepare ccache timestamp | |
| id: ccache_cache_timestamp | |
| run: | | |
| if [ "$RUNNER_OS" = "Linux" ]; then | |
| stamp=$(date '+%s') | |
| else | |
| stamp=$(gdate '+%s') | |
| fi | |
| echo "${stamp}" | |
| echo "::set-output name=timestamp::${stamp}" | |
| - name: ccache cache files | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/.ccache | |
| key: ${{ matrix.name }}-ccache-${{ steps.ccache_cache_timestamp.outputs.timestamp }} | |
| restore-keys: | | |
| ${{ matrix.name }}-ccache- | |
| - name: configure | |
| run: ./bootstrap | |
| - name: make | |
| run: make -j2 | |
| - name: make check | |
| run: make -j2 check | |
| - name: make install | |
| run: sudo make install | |
| - name: test | |
| run: | | |
| # Mac OS does not have valgrind! | |
| if [ "$RUNNER_OS" == Linux ]; then echo ::group::binary ; ./tests/test_binary.sh; fi | |
| echo ::group::POS | |
| ./tests/testPOS.sh | |
| echo ::group::binaryVcf | |
| ./tests/test_binaryVcfVsTxt.sh | |
| echo ::group::test-against-previous-version | |
| ./tests/test-against-previous-version.sh | |
| echo ::group::binary reproducible | |
| ./tests/test_binaryReproducible.sh | |
| - name: docs | |
| run: if [ $TRAVIS_OS_NAME == linux ]; then cd docs/doxygen; doxygen Doxyfile; fi | |
| - name: run coverage | |
| if: matrix.name == 'ubuntu-gcc-9' | |
| run: | | |
| tests/test-coverage-coverall.sh | |
| # See: https://github.com/marketplace/actions/coveralls-github-action | |
| - name: Coveralls | |
| if: matrix.name == 'ubuntu-gcc-9' | |
| uses: coverallsapp/[email protected] | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| #run: coveralls --exclude lib --exclude tests --exclude src/random --exclude src/codeCogs/ --exclude src/export/ --exclude src/gzstream/ --gcov-options '\-lp' |