4.1 and changelog #87
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| name: SPAdes release snapshot | |
| on: | |
| workflow_dispatch: | |
| push: | |
| tags: | |
| - '*' | |
| paths-ignore: | |
| - 'docs/**' | |
| - 'mkdocs.yml' | |
| env: | |
| INSTALL_DIR: ${{github.workspace}}/spades | |
| PKG_LINUX: SPAdes-*-Linux | |
| PKG_MAC: SPAdes-*-Darwin | |
| jobs: | |
| # We build inside a ManyLinux container, but run checks outside | |
| build-linux: | |
| name: '🐧 Build SPAdes inside ManyLinux 2.28 x86-64 container' | |
| runs-on: self-hosted | |
| # We use userns-remap on VM side | |
| container: | |
| image: quay.io/pypa/manylinux_2_28_x86_64 | |
| env: | |
| BUILD_TYPE: Release | |
| BUILD_DIR: './build' | |
| SRC_DIR: './src' | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install dependencies' | |
| run: > | |
| dnf install -y bzip2-devel | |
| - name: '⚙️ Configure CMake' | |
| run: > | |
| cmake | |
| -B $BUILD_DIR | |
| -S $SRC_DIR | |
| -DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=all | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build $BUILD_DIR | |
| -j16 | |
| -t package | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts-linux | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG_LINUX}}.tar.gz | |
| spades-1k-checks-linux: | |
| name: '🚬 E. coli 1k smoke checks' | |
| runs-on: self-hosted | |
| needs: build-linux | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-linux | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG_LINUX}}.tar.gz | |
| - name: '1k multi-cell' | |
| run: > | |
| $INSTALL_DIR/$PKG_LINUX/bin/spades.py --test | |
| - name: '1k single-cell' | |
| run: > | |
| $INSTALL_DIR/$PKG_LINUX/bin/spades.py --sc --test | |
| - name: '1k meta' | |
| run: > | |
| $INSTALL_DIR/$PKG_LINUX/bin/metaspades.py --test | |
| - name: '1k plasmid' | |
| run: > | |
| $INSTALL_DIR/$PKG_LINUX/bin/plasmidspades.py --test | |
| - name: '1k rna' | |
| run: > | |
| $INSTALL_DIR/$PKG_LINUX/bin/rnaspades.py --test | |
| - name: '1k corona' | |
| run: > | |
| $INSTALL_DIR/$PKG_LINUX/bin/coronaspades.py --test | |
| build-mac: | |
| strategy: | |
| matrix: | |
| include: | |
| - os: macos-13 | |
| arch: x86_64 | |
| - os: macos-14 | |
| arch: arm64 | |
| env: | |
| BUILD_TYPE: Release | |
| BUILD_DIR: './build' | |
| SRC_DIR: './src' | |
| name: '🍎 Build SPAdes for macOS' | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install dependencies' | |
| run: > | |
| brew install bzip2 mmv | |
| - name: '💩 Fix gcc / MacSDK trash' | |
| run: > | |
| rm -f /opt/homebrew/Cellar/gcc@13/*/lib/gcc/13/gcc/aarch64-apple*/13/include-fixed/AvailabilityInternal.h | |
| rm -f /usr/local/Cellar/gcc@13/*/lib/gcc/13/gcc/x86_64-apple*/13/include-fixed/AvailabilityInternal.h | |
| - name: '⚙️ Configure CMake' | |
| run: > | |
| cmake | |
| -B $BUILD_DIR | |
| -S $SRC_DIR | |
| -DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=all | |
| -DCMAKE_C_COMPILER=gcc-13 -DCMAKE_CXX_COMPILER=g++-13 | |
| -DSPADES_STATIC_BUILD=ON | |
| -DOpenMP_CXX_FLAGS:STRING=-fopenmp -DOpenMP_CXX_LIB_NAMES:STRING=gomp -DOpenMP_C_FLAGS:STRING=-fopenmp -DOpenMP_C_LIB_NAMES:STRING=gomp -DOpenMP_gomp_LIBRARY=libgomp.a | |
| -DCMAKE_EXE_LINKER_FLAGS="-Wl,-ld_classic" -DCMAKE_SHARED_LINKER_FLAGS="-Wl,-ld_classic" -DCMAKE_MODULE_LINKER_FLAGS="-Wl,-ld_classic" | |
| -DBZIP2_LIBRARIES=$(brew --prefix bzip2)/lib/libbz2.a | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build $BUILD_DIR | |
| -j16 | |
| -t package && mmv '${{env.BUILD_DIR}}/SPAdes-*-Darwin.tar.gz' '${{env.BUILD_DIR}}/SPAdes-#1-Darwin-${{ matrix.arch }}.tar.gz' | |
| - name: '🗂 Inspect directory before downloading artifacts' | |
| run: > | |
| ls -alFR ${{env.BUILD_DIR}}/*.tar.gz | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts-mac-${{ matrix.arch }} | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG_MAC}}-${{ matrix.arch }}.tar.gz | |
| spades-1k-checks-mac: | |
| name: '🚬 E. coli 1k smoke checks' | |
| strategy: | |
| matrix: | |
| include: | |
| - os: macos-13 | |
| arch: x86_64 | |
| - os: macos-14 | |
| arch: arm64 | |
| runs-on: ${{ matrix.os }} | |
| needs: build-mac | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-mac-${{ matrix.arch }} | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG_MAC}}*.tar.gz | |
| - name: '1k multi-cell' | |
| run: > | |
| $INSTALL_DIR/$PKG_MAC/bin/spades.py --test | |
| - name: '1k single-cell' | |
| run: > | |
| $INSTALL_DIR/$PKG_MAC/bin/spades.py --sc --test | |
| - name: '1k meta' | |
| run: > | |
| $INSTALL_DIR/$PKG_MAC/bin/metaspades.py --test | |
| - name: '1k plasmid' | |
| run: > | |
| $INSTALL_DIR/$PKG_MAC/bin/plasmidspades.py --test | |
| - name: '1k rna' | |
| run: > | |
| $INSTALL_DIR/$PKG_MAC/bin/rnaspades.py --test | |
| - name: '1k corona' | |
| run: > | |
| $INSTALL_DIR/$PKG_MAC/bin/coronaspades.py --test | |
| # Upload continuous build | |
| upload: | |
| name: '🗂 Create release and upload artifacts' | |
| needs: | |
| - spades-1k-checks-mac | |
| - spades-1k-checks-linux | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: '⚙️ Install dependencies' | |
| run: sudo apt-get install -y libfuse2 | |
| - name: '📥 Download artifacts' | |
| uses: actions/download-artifact@v4 | |
| - name: '🗂 Inspect directory after downloading artifacts' | |
| run: ls -alFR | |
| - name: '🚀 Create release and upload artifacts' | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| wget -q https://github.com/TheAssassin/pyuploadtool/releases/download/continuous/pyuploadtool-x86_64.AppImage | |
| chmod +x pyuploadtool-x86_64.AppImage | |
| ./pyuploadtool-x86_64.AppImage **/${{env.PKG_MAC}}*.tar.gz **/${{env.PKG_LINUX}}*.tar.gz |