release.yml

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