spades/.github/workflows/basic.yml at 93bc08969a5250dbe24ec457bbb305c313d4ab98 · ablab/spades · GitHub

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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/ccache-action@v1.2
        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

  spades-mpi-1k-checks-linux:
    name: '🚬 E. coli 1k smoke checks (MPI)'
    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 meta'
        run: >
          $INSTALL_DIR/$PKG_LINUX/bin/spades.py --test --grid-engine=mpi

      - name: 'slurm configs only'
        run: >
          $INSTALL_DIR/$PKG_LINUX/bin/spades.py --test --grid-engine=slurm --only-generate-config --grid-extra=\"--gres=gpu:0\"


  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 openmpi

      - name: '⚙️ Install ccache'
        uses: hendrikmuhs/ccache-action@v1.2
        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