update vcf submodule #251
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: 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' |