Relax blaze cache size assertion. Likely we will not have CPUs with L… #139
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: SPAdes basic tests | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| - next | |
| tags: | |
| - '*' | |
| paths-ignore: | |
| - 'docs/**' | |
| - 'mkdocs.yml' | |
| pull_request: | |
| paths-ignore: | |
| - 'docs/**' | |
| - 'mkdocs.yml' | |
| env: | |
| BUILD_TYPE: Release | |
| BUILD_DIR: './build' | |
| SRC_DIR: './src' | |
| INSTALL_DIR: ${{github.workspace}}/spades | |
| PKG_LINUX: SPAdes-*-Linux | |
| PKG_MAC: SPAdes-*-Darwin | |
| jobs: | |
| build-linux: | |
| runs-on: self-hosted | |
| name: '🐧 Build SPAdes for Linux' | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install ccache' | |
| uses: hendrikmuhs/[email protected] | |
| with: | |
| variant: sccache | |
| key: sccache-${{env.BUILD_TYPE}}-linux | |
| - name: '⚙️ Configure CMake' | |
| run: > | |
| cmake | |
| -B $BUILD_DIR | |
| -S $SRC_DIR | |
| -DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=all | |
| -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build ${{env.BUILD_DIR}} | |
| -j16 | |
| -t package include_test debruijn_test | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts-linux | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG_LINUX}}.tar.gz | |
| ${{env.BUILD_DIR}}/bin/debruijn_test | |
| ${{env.BUILD_DIR}}/bin/include_test | |
| 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 $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 | |
| spades-unittests-linux: | |
| name: 'SPAdes unittests' | |
| runs-on: self-hosted | |
| needs: build-linux | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-linux | |
| path: ${{env.BUILD_DIR}} | |
| - name: '🔎 Include tests' | |
| working-directory: ${{github.workspace}} | |
| run: > | |
| chmod +x $BUILD_DIR/bin/include_test && | |
| $BUILD_DIR/bin/include_test | |
| - name: '🔎 De-Bruijn tests' | |
| working-directory: ${{github.workspace}} | |
| run: > | |
| chmod +x $BUILD_DIR/bin/debruijn_test && | |
| $BUILD_DIR/bin/debruijn_test | |
| build-mac: | |
| strategy: | |
| matrix: | |
| include: | |
| - os: macos-13 | |
| arch: x86_64 | |
| - os: macos-14 | |
| arch: arm64 | |
| name: '🍎 Build SPAdes for macOS' | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install dependencies' | |
| run: > | |
| brew install llvm libomp bzip2 | |
| - name: '⚙️ Install ccache' | |
| uses: hendrikmuhs/[email protected] | |
| with: | |
| variant: sccache | |
| key: sccache-${{env.BUILD_TYPE}}-${{ matrix.os }} | |
| - name: '⚙️ Configure CMake' | |
| run: > | |
| cmake | |
| -B $BUILD_DIR | |
| -S $SRC_DIR | |
| -DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=all | |
| -DCMAKE_C_COMPILER=$(brew --prefix llvm)/bin/clang | |
| -DCMAKE_CXX_COMPILER=$(brew --prefix llvm)/bin/clang++ | |
| -DCMAKE_EXE_LINKER_FLAGS=-L$(brew --prefix llvm)/lib/c++ | |
| -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build $BUILD_DIR | |
| -j16 | |
| -t package include_test debruijn_test | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts-mac-${{ matrix.arch }} | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG_MAC}}.tar.gz | |
| ${{env.BUILD_DIR}}/bin/debruijn_test | |
| ${{env.BUILD_DIR}}/bin/include_test | |
| 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: ${{ matrix.os }} | |
| needs: build-mac | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '⚙️ Install dependencies' | |
| run: > | |
| brew install llvm libomp bzip2 | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-mac-${{ 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 | |
| spades-unittests-mac: | |
| name: 'SPAdes unittests' | |
| strategy: | |
| matrix: | |
| include: | |
| - os: macos-13 | |
| arch: x86_64 | |
| - os: macos-14 | |
| arch: arm64 | |
| runs-on: ${{ matrix.os }} | |
| needs: build-mac | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-mac-${{ matrix.arch }} | |
| path: ${{env.BUILD_DIR}} | |
| - name: '⚙️ Install dependencies' | |
| run: > | |
| brew install llvm libomp bzip2 | |
| - name: '🔎 Include tests' | |
| working-directory: ${{github.workspace}} | |
| run: > | |
| chmod +x $BUILD_DIR/bin/include_test && | |
| $BUILD_DIR/bin/include_test | |
| - name: '🔎 De-Bruijn tests' | |
| working-directory: ${{github.workspace}} | |
| run: > | |
| chmod +x $BUILD_DIR/bin/debruijn_test && | |
| $BUILD_DIR/bin/debruijn_test |