Support a coordinate-to-accession map to a graph, mapping an annotation label+coordinate to an accession #4953
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| name: MetaGraph CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| tags: | |
| - 'v*' | |
| pull_request: | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| jobs: | |
| Linux: | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| alphabet: [DNA, Protein] | |
| build_type: [Debug, Release] | |
| compiler: [g++-11, g++-12, g++-13] | |
| build_static: [OFF, ON] | |
| with_avx: [OFF, ON] | |
| include: | |
| - compiler: g++-11 | |
| cxx: g++-11 | |
| cc: gcc-11 | |
| - compiler: g++-12 | |
| cxx: g++-12 | |
| cc: gcc-12 | |
| - compiler: g++-13 | |
| cxx: g++-13 | |
| cc: gcc-13 | |
| exclude: | |
| - alphabet: Protein | |
| compiler: g++-11 | |
| - alphabet: Protein | |
| compiler: g++-12 | |
| - compiler: g++-11 | |
| build_static: ON | |
| - compiler: g++-12 | |
| build_static: ON | |
| - build_type: Debug | |
| build_static: ON | |
| - build_type: Debug | |
| compiler: g++-11 | |
| - build_type: Debug | |
| compiler: g++-12 | |
| - with_avx: OFF | |
| build_static: OFF | |
| name: Linux (${{ matrix.alphabet }}, ${{ matrix.build_type }}, ${{ matrix.compiler }}${{ matrix.build_static == 'ON' && ', static' || '' }}${{ matrix.with_avx == 'OFF' && ', noAVX' || '' }}) | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: checkout submodules | |
| run: git submodule update --init --recursive | |
| - name: install dependencies | |
| run: | | |
| sudo apt-get update | |
| # If clang, use the default version. Otherwise the compiler install with apt-get. | |
| if [[ "${{ matrix.compiler }}" != "clang" ]]; then | |
| sudo apt-get install -y ${{ matrix.compiler }} | |
| fi | |
| sudo apt-get install -y cmake make libbz2-dev libjemalloc-dev libboost-all-dev libdeflate-dev libzstd-dev | |
| if [ "${{ matrix.build_static }}" = "ON" ]; then | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| fi | |
| echo "CC=$(which ${{ matrix.cc }})" >> $GITHUB_ENV | |
| echo "CXX=$(which ${{ matrix.cxx }})" >> $GITHUB_ENV | |
| - name: install dependencies for integration tests | |
| run: | | |
| pip3 install parameterized | |
| sudo apt-get install python3-venv | |
| - name: install sdsl-lite | |
| run: | | |
| cd metagraph/external-libraries/sdsl-lite | |
| ./install.sh $(pwd) | |
| - name: configure | |
| run: | | |
| mkdir metagraph/build | |
| cd metagraph/build | |
| cmake -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \ | |
| -DBUILD_STATIC=${{ matrix.build_static }} \ | |
| -DWITH_AVX=${{ matrix.with_avx }} -DWITH_MSSE42=${{ matrix.with_avx }} \ | |
| -DCMAKE_DBG_ALPHABET=${{ matrix.alphabet }} .. | |
| - name: build metagraph | |
| run: cd metagraph/build && make -j"$(getconf _NPROCESSORS_ONLN)" metagraph | |
| - name: build unit tests | |
| if: matrix.build_static == 'OFF' | |
| run: cd metagraph/build && make -j"$(getconf _NPROCESSORS_ONLN)" unit_tests | |
| - name: build other | |
| if: matrix.build_static == 'OFF' | |
| run: cd metagraph/build && make -j"$(getconf _NPROCESSORS_ONLN)" | |
| # for potential release | |
| - name: rename binary | |
| if: matrix.with_avx == 'OFF' | |
| run: mv metagraph/build/metagraph_${{ matrix.alphabet }} metagraph/build/metagraph_${{ matrix.alphabet }}_noAVX | |
| - name: upload static binary | |
| if: ${{ matrix.build_static == 'ON' && matrix.compiler == 'g++-13' }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: metagraph_${{ matrix.alphabet }}${{ matrix.with_avx == 'OFF' && '_noAVX' || '' }}_linux_x86 | |
| path: metagraph/build/metagraph_${{ matrix.alphabet }}${{ matrix.with_avx == 'OFF' && '_noAVX' || '' }} | |
| - name: run unit tests | |
| if: matrix.build_static == 'OFF' | |
| run: | | |
| export LD_LIBRARY_PATH="/usr/local/lib/:$LD_LIBRARY_PATH" | |
| cd metagraph/build && ./unit_tests | |
| - name: run integration tests | |
| uses: nick-fields/retry@v2 | |
| with: | |
| timeout_minutes: 1000 | |
| max_attempts: 5 | |
| retry_on: error | |
| command: | | |
| export LD_LIBRARY_PATH="/usr/local/lib/:$LD_LIBRARY_PATH" | |
| cd metagraph/build && make integration_tests | |
| MacOS: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # Apple Silicon Release | |
| - alphabet: DNA | |
| build_type: Release | |
| platform: macos-latest | |
| target_arch: arm64 | |
| # Intel Release | |
| - alphabet: DNA | |
| build_type: Release | |
| platform: macos-15-intel | |
| target_arch: x86_64 | |
| # Apple Silicon runner + Rosetta for x86_64 | |
| - alphabet: DNA | |
| build_type: Release | |
| platform: macos-latest | |
| target_arch: x86_64 | |
| # Debug run on Apple Silicon | |
| - alphabet: DNA | |
| build_type: Debug | |
| platform: macos-latest | |
| target_arch: arm64 | |
| runs-on: ${{ matrix.platform }} | |
| defaults: | |
| run: | |
| shell: arch -${{ matrix.target_arch }} /bin/bash -eo pipefail {0} | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: checkout submodules | |
| run: git submodule update --init --recursive | |
| - name: (Only for arm64 -> x86_64) Install Rosetta Homebrew in /usr/local | |
| if: ${{ matrix.platform == 'macos-latest' && matrix.target_arch == 'x86_64' }} | |
| run: | | |
| # Install Intel Homebrew into /usr/local if missing | |
| if [[ ! -d /usr/local/Homebrew ]]; then | |
| echo "Installing Intel Homebrew to /usr/local under Rosetta..." | |
| arch -x86_64 /bin/bash -lc '/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"' | |
| fi | |
| # Replace any legacy wrapper that points to /usr/local/Library/Homebrew | |
| if [[ -f /usr/local/bin/brew ]] && grep -q '/usr/local/Library/Homebrew' /usr/local/bin/brew; then | |
| echo "Replacing legacy brew wrapper..." | |
| sudo rm -f /usr/local/bin/brew | |
| fi | |
| # Ensure wrapper points to the modern repo location | |
| if [[ ! -f /usr/local/bin/brew ]]; then | |
| sudo ln -s /usr/local/Homebrew/bin/brew /usr/local/bin/brew | |
| fi | |
| echo "/usr/local/bin" >> "$GITHUB_PATH" | |
| echo "/usr/local/sbin" >> "$GITHUB_PATH" | |
| - name: install dependencies | |
| run: brew install bzip2 libomp boost jemalloc autoconf automake libdeflate icu4c zstd | |
| - name: install dependencies for integration tests | |
| run: pip3 install parameterized --break-system-packages --user | |
| - name: install sdsl-lite | |
| run: | | |
| cd metagraph/external-libraries/sdsl-lite | |
| ./install.sh $(pwd) | |
| - name: configure | |
| run: | | |
| mkdir metagraph/build | |
| cd metagraph/build | |
| cmake -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \ | |
| -DCMAKE_DBG_ALPHABET=${{ matrix.alphabet }} \ | |
| .. | |
| - name: build metagraph | |
| run: cd metagraph/build && make -j"$(getconf _NPROCESSORS_ONLN)" metagraph | |
| - name: build unit tests | |
| run: cd metagraph/build && make -j"$(getconf _NPROCESSORS_ONLN)" unit_tests | |
| - name: build other | |
| run: cd metagraph/build && make -j"$(getconf _NPROCESSORS_ONLN)" | |
| - name: run unit tests | |
| run: cd metagraph/build && ./unit_tests | |
| - name: run integration tests | |
| run: cd metagraph/build && make integration_tests | |
| Metagraph-Workflows: | |
| name: Test metagraph workflows | |
| runs-on: ubuntu-22.04 | |
| needs: [Linux] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.10.18 | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.10.18 | |
| - name: fetch static binary | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: artifacts | |
| - name: setup metagraph binary | |
| run: | | |
| sudo ln -s $(pwd)/artifacts/metagraph_DNA_linux_x86/metagraph_DNA /usr/local/bin/metagraph | |
| sudo chmod +rx /usr/local/bin/metagraph | |
| /usr/local/bin/metagraph --help | |
| metagraph --help | |
| - name: Install python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest | |
| pip install -r metagraph/workflows/requirements.txt | |
| - name: Test metagraph-workflows pytest | |
| run: | | |
| cd metagraph/workflows | |
| pytest | |
| Build-and-Push-Docker: | |
| # adapted from https://docs.github.com/en/actions/guides/publishing-docker-images#publishing-images-to-github-packages | |
| needs: [Linux, Metagraph-Workflows] | |
| runs-on: ubuntu-22.04 | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: checkout submodules | |
| run: git submodule update --init --recursive | |
| - name: Log in to the Container registry | |
| uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract metadata (tags, labels) for Docker | |
| id: meta | |
| uses: docker/metadata-action@v3 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| - name: Build Docker image | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: . | |
| push: false | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| - name: Build and push Docker image | |
| if: github.event_name != 'pull_request' | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: . | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| Release: | |
| name: Create Release | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| runs-on: ubuntu-22.04 | |
| needs: [Linux, Metagraph-Workflows] | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: checkout submodules | |
| run: git submodule update --init --recursive | |
| - name: fetch static binary | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: artifacts | |
| - name: Tag name | |
| id: tag_name | |
| run: | | |
| echo ::set-output name=TAG::${GITHUB_REF#refs/tags/} | |
| echo ::set-output name=VER::${GITHUB_REF#refs/tags/v} | |
| # from https://stackoverflow.com/a/61919791/6869319 | |
| - name: read current version | |
| id: read_version | |
| run: | | |
| content=`cat package.json` | |
| # the following lines are only required for multi line json | |
| content="${content//'%'/'%25'}" | |
| content="${content//$'\n'/'%0A'}" | |
| content="${content//$'\r'/'%0D'}" | |
| # end of optional handling for multi line json | |
| echo "::set-output name=packageJson::$content" | |
| - name: build source archive including submodules | |
| run: | | |
| [[ v${{fromJson(steps.read_version.outputs.packageJson).version}} == ${{ steps.tag_name.outputs.TAG }} ]] \ | |
| || (echo "::error file=package.json::Version in package.json (v${{fromJson(steps.read_version.outputs.packageJson).version}}) does not match tag ${{ steps.tag_name.outputs.TAG }}. Update package.json and set the tag again."; \ | |
| exit 1) | |
| mkdir -p artifacts/sources | |
| tag=${{ steps.tag_name.outputs.TAG }} | |
| bash .github/workflows/git-archive-all.sh --format tar.gz artifacts/sources/${tag}-sources-with-submodules.tar.gz | |
| bash .github/workflows/git-archive-all.sh --format zip artifacts/sources/${tag}-sources-with-submodules.zip | |
| - name: create release with static binaries | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| release_name: Version ${{ steps.tag_name.outputs.VER }} | |
| body: | | |
| The pre-compiled binaries (only for Linux) are statically linked and hence don't require additional libraries to be installed. | |
| The *_noAVX binaries are compiled without the modern AVX2 and MSSE4.2 instructions and should be used when the processor does not support these instructions. | |
| file: 'artifacts/*/*' | |
| file_glob: true | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| tag: ${{ github.ref }} | |
| prerelease: true |