gcc.yml

name: SPAdes GCC & Python versions

on:
  workflow_dispatch:
  pull_request:
    paths-ignore:
      - 'docs/**'
      - 'mkdocs.yml'
  push:
    tags:
      - '*'
  schedule:
    - cron: '30 23 6,12,18,24,30 * *'

env:
  BUILD_TYPE: Release
  BUILD_DIR: ${{github.workspace}}/build
  INSTALL_DIR: ${{github.workspace}}/spades
  SRC_DIR: ${{github.workspace}}/src
  PKG: SPAdes-*-Linux

jobs:
  build-gcc9:
    runs-on:
      labels: [self-hosted, worker-1]
    name: '🚧 Build SPAdes with GCC9'

    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}}-gcc9

      - name: '⚙️ Configure CMake'
        run: >
          cmake
          -B ${{env.BUILD_DIR}}
          -S ${{env.SRC_DIR}}
          -DCMAKE_C_COMPILER=gcc-9 -DCMAKE_CXX_COMPILER=g++-9
          -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
          -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}
          -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC9-Linux

      - name: '🚧 Build'
        run: >
          cmake
          --build ${{env.BUILD_DIR}}
          -j16
          -t package

      - name: '📦 Package'
        uses: actions/upload-artifact@v4
        with:
          name: build-artifacts-gcc9
          path: |
            ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz

  spades-test-python38:
    name: 'E. coli 1k run with Python3.8'
    runs-on:
      labels: [self-hosted, worker-1]
    needs: build-gcc9

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts-gcc9
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'E.coli 1K with Python 3.8'
        run: >
          python3.8 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test

  build-gcc10:
    runs-on:
      labels: [self-hosted, worker-1]
    name: '🚧 Build SPAdes with GCC10'

    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}}-gcc10

      - name: '⚙️ Configure CMake'
        run: >
          cmake
          -B ${{env.BUILD_DIR}}
          -S ${{env.SRC_DIR}}
          -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10
          -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
          -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}
          -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC10-Linux

      - name: '🚧 Build'
        run: >
          cmake
          --build ${{env.BUILD_DIR}}
          -j16
          -t package

      - name: '📦 Package'
        uses: actions/upload-artifact@v4
        with:
          name: build-artifacts-gcc10
          path: |
            ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz

  spades-test-python39:
    name: 'E. coli 1k run with Python3.9'
    runs-on:
      labels: [self-hosted, worker-1]
    needs: build-gcc10

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts-gcc10
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'E.coli 1K SC with Python 3.9'
        run: >
          python3.9 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --sc

  build-gcc11:
    runs-on:
      labels: [self-hosted, worker-1]
    name: '🚧 Build SPAdes with GCC11'

    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}}-gcc11

      - name: '⚙️ Configure CMake'
        run: >
          cmake
          -B ${{env.BUILD_DIR}}
          -S ${{env.SRC_DIR}}
          -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
          -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
          -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}
          -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC11-Linux

      - name: '🚧 Build'
        run: >
          cmake
          --build ${{env.BUILD_DIR}}
          -j16
          -t package

      - name: '📦 Package'
        uses: actions/upload-artifact@v4
        with:
          name: build-artifacts-gcc11
          path: |
            ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz

  spades-test-python310:
    name: 'E. coli 1k run with Python3.10'
    runs-on:
      labels: [self-hosted, worker-1]
    needs: build-gcc11

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts-gcc11
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'E.coli 1K meta with Python 3.10'
        run: >
          python3.10 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --meta

  build-gcc12:
    runs-on:
      labels: [self-hosted, worker-1]
    name: '🚧 Build SPAdes with GCC12'

    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}}-gcc12

      - name: '⚙️ Configure CMake'
        run: >
          cmake
          -B ${{env.BUILD_DIR}}
          -S ${{env.SRC_DIR}}
          -DCMAKE_C_COMPILER=/home/ubuntu/bin/gcc12/bin/gcc -DCMAKE_CXX_COMPILER=/home/ubuntu/bin/gcc12/bin/g++
          -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
          -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}
          -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC12-Linux

      - name: '🚧 Build'
        run: >
          cmake
          --build ${{env.BUILD_DIR}}
          -j16
          -t package

      - name: '📦 Package'
        uses: actions/upload-artifact@v4
        with:
          name: build-artifacts-gcc12
          path: |
            ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz

  spades-test-python311:
    name: 'E. coli 1k run with Python3.11'
    runs-on:
      labels: [self-hosted, worker-1]
    needs: build-gcc12

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts-gcc12
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'E.coli 1K RNA with Python 3.11'
        run: >
          python3.11 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --rna

  build-gcc13:
    runs-on:
      labels: [self-hosted, worker-1]
    name: '🚧 Build SPAdes with GCC13'

    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}}-gcc13

      - name: '⚙️ Configure CMake'
        run: >
          cmake
          -B ${{env.BUILD_DIR}}
          -S ${{env.SRC_DIR}}
          -DCMAKE_C_COMPILER=/home/ubuntu/bin/gcc13/bin/gcc -DCMAKE_CXX_COMPILER=/home/ubuntu/bin/gcc13/bin/g++
          -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
          -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}
          -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC13-Linux

      - name: '🚧 Build'
        run: >
          cmake
          --build ${{env.BUILD_DIR}}
          -j16
          -t package

      - name: '📦 Package'
        uses: actions/upload-artifact@v4
        with:
          name: build-artifacts-gcc13
          path: |
            ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz

  spades-test-python312:
    name: 'E. coli 1k run with Python3.12'
    runs-on:
      labels: [self-hosted, worker-1]
    needs: build-gcc13

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts-gcc13
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'E.coli 1K Isolate with Python 3.13'
        run: >
          python3.12 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --isolate