build.yml

name: Build & upload binaries

on:
  push:
    branches:
      - testactions
  workflow_dispatch:

env:
  regression: 1

jobs:
  build_macos:
    name: macOS
    runs-on: macos-12
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: true
            
      - name: Install Rust Toolchain
        run: |
          rustup update
          rustup target install x86_64-apple-darwin
          rustup target install aarch64-apple-darwin

      - name: Build
        run: |
          cd ${{ github.workspace }}
          ./util/build_osx.sh . build

      - name: Run Regression Suite
        if: ${{ env.regression == 1 }}
        run: |
          ${{ github.workspace }}/regression/run_regression.sh ${{ github.workspace }}/build/src/foldmason ${{ github.workspace }}/regression

      - name: Upload MacOS Universal
        uses: actions/upload-artifact@v3
        with:
          name: foldmason-darwin-universal
          path: ${{ github.workspace }}/build/foldmason

  build_ubuntu:
    name: Build Ubuntu
    runs-on: ubuntu-22.04
    timeout-minutes: 120
    strategy:
      matrix:
        include:
          - SIMD: AVX2
            STATIC: 1
            MPI: 0
            BUILD_TYPE: RelWithDebInfo
          - SIMD: SSE4_1
            STATIC: 1
            MPI: 0
            BUILD_TYPE: RelWithDebInfo
          - SIMD: SSE2
            STATIC: 1
            MPI: 0
            BUILD_TYPE: RelWithDebInfo
          - SIMD: AVX2_MPI
            STATIC: 0
            MPI: 1
            BUILD_TYPE: RelWithDebInfo
          - SIMD: AVX2
            STATIC: 0
            MPI: 0
            BUILD_TYPE: ASanOpt

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: true

      - name: Install G++
        run: |
          sudo apt-get update
          sudo apt-get install -y g++-12 rustc cargo

      - name: Install Dependencies
        if: matrix.MPI == 1
        run: |
          sudo apt-get update
          sudo apt-get -y install mpi-default-dev mpi-default-bin
         
      - name: Build Foldmason
        run: |
          mkdir build
          cd build
          export CC=gcc-12
          export CXX=g++-12
          WERROR=1
          if [ "${{ matrix.BUILD_TYPE }}" = "ASanOpt" ]; then
              WERROR=0
          fi
          if [ "${{ matrix.STATIC }}" -eq "1" ]; then
              cmake -DHAVE_SANITIZER=1 -DCMAKE_BUILD_TYPE=${{ matrix.BUILD_TYPE }} -DHAVE_TESTS=1 \
                -DBUILD_SHARED_LIBS=OFF \
                -DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc \
                -static-libstdc++" -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \
                -DENABLE_WERROR=$WERROR -DHAVE_${{ matrix.SIMD }}=1 -DHAVE_MPI=${{ matrix.MPI }} ..
          else
              cmake -DHAVE_SANITIZER=1 -DCMAKE_BUILD_TYPE=${{ matrix.BUILD_TYPE }} -DHAVE_TESTS=1 \
                -DENABLE_WERROR=$WERROR -DHAVE_${{ matrix.SIMD }}=1 -DHAVE_MPI=${{ matrix.MPI }} ..
          fi
          make -j $(nproc --all)

      - name: Run Regression Suite
        if: ${{ env.regression == 1 }}
        run: |
          export TTY=0
          if [ "${{ matrix.BUILD_TYPE }}" = "ASan" ]; then
            echo "leak:libgomp1" > ASan.supp
            export ASAN_OPTIONS=suppressions=ASan.supp
          fi
          ${{ github.workspace }}/regression/run_regression.sh ${{ github.workspace }}/build/src/foldmason ${{ github.workspace }}/regression

      - name: Upload Linux
        if: matrix.STATIC == 1
        uses: actions/upload-artifact@v3
        with:
          name: mmseqs-linux-${{ matrix.SIMD }}
          path: build/src/mmseqs
            
  build_ubuntu_cross:
    name: Ubuntu Cross-Compile
    runs-on: ubuntu-20.04
    timeout-minutes: 120
    strategy:
      matrix:
        include:
          - SIMD: ARM8
            ARCH: arm64
            CPREF: aarch64

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: true

      - name: Install Toolchain
        run: |
          sudo dpkg --add-architecture ${{ matrix.ARCH }}
          cat << HEREDOC | sudo tee /etc/apt/sources.list
          deb [arch=amd64,i386] http://archive.ubuntu.com/ubuntu/ focal main universe multiverse
          deb [arch=amd64,i386] http://archive.ubuntu.com/ubuntu/ focal-updates main universe multiverse
          deb [arch=amd64,i386] http://archive.ubuntu.com/ubuntu/ focal-backports main universe multiverse
          deb [arch=amd64,i386] http://security.ubuntu.com/ubuntu/ focal-security main universe multiverse
          deb [arch=${{ matrix.ARCH }}] http://ports.ubuntu.com/ubuntu-ports/ focal main universe multiverse
          deb [arch=${{ matrix.ARCH }}] http://ports.ubuntu.com/ubuntu-ports/ focal-updates main universe multiverse
          deb [arch=${{ matrix.ARCH }}] http://ports.ubuntu.com/ubuntu-ports/ focal-backports main universe multiverse
          deb [arch=${{ matrix.ARCH }}] http://ports.ubuntu.com/ubuntu-ports/ focal-security main universe multiverse
          HEREDOC
          sudo apt-get update
          sudo apt-get -y install -o APT::Immediate-Configure=false crossbuild-essential-${{ matrix.ARCH }} zlib1g-dev:${{ matrix.ARCH }} libbz2-dev:${{ matrix.ARCH }}
          rustup target add ${{ matrix.CPREF }}-unknown-linux-gnu

      - name: Build Cross
        run: |
          mkdir build && cd build
          CC=${{ matrix.CPREF }}-linux-gnu-gcc CXX=${{ matrix.CPREF }}-linux-gnu-g++ \
          cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -DHAVE_TESTS=1 \
            -DBUILD_SHARED_LIBS=OFF \
            -DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc -static-libstdc++" \
            -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \
            -DRust_CARGO_TARGET=${{ matrix.CPREF }}-unknown-linux-gnu \
            -DENABLE_WERROR=1 -DHAVE_${{ matrix.SIMD }}=1 ..
          make -j $(nproc --all)

      - name: Upload Linux Artifact
        uses: actions/upload-artifact@v3
        with:
          name: mmseqs-linux-${{ matrix.SIMD }}
          path: build/src/foldmason

  upload_artifacts:
    name: Upload Artifacts
    runs-on: ubuntu-latest
    needs: [build_macos, build_ubuntu, build_ubuntu_cross]
    if: github.event_name != 'pull_request'
    steps:
      - uses: actions/checkout@v4

      - name: Prepare Artifacts Directory
        run: |
          mkdir foldmason
          cp -f README.md LICENSE.md foldmason
          mkdir mmseqs/bin

      - name: Download Userguide Artifact
        uses: actions/download-artifact@v3
        with:
          name: userguide
          path: foldmason

      - name: Download foldmason-darwin-universal Artifact
        uses: actions/download-artifact@v3
        with:
          name: foldmason-darwin-universal
          path: foldmason/bin

      - name: Set Executable Permissions on macOS Binary
        run: chmod +x foldmason/bin/foldmason

      - name: Archive macOS Binary
        run: tar -czvf foldmason-osx-universal.tar.gz -C foldmason .

      - name: Download foldmason-linux-SSE4_1 Artifact
        uses: actions/download-artifact@v3
        with:
          name: foldmason-linux-SSE4_1
          path: foldmason/bin

      - name: Set Executable Permissions on SSE4_1 Binary
        run: chmod +x foldmason/bin/foldmason

      - name: Archive SSE4_1 Binary
        run: tar -czvf foldmason-linux-sse41.tar.gz -C foldmason .

#     - name: Get Deployment Key
#       uses: actions/download-artifact@v3
#       with:
#         name: secretKeyPleaseDontSteal

#     - name: Sign and Upload Artifacts
#       run: |
#         mkdir -p $HOME/.ssh && mv secretKeyPleaseDontSteal $HOME/.ssh/id_rsa
#         chmod 700 $HOME/.ssh && chmod 600 $HOME/.ssh/id_rsa
#         ssh-keygen -f $HOME/.ssh/id_rsa -y > $HOME/.ssh/id_rsa.pub
#         cp mmseqs/userguide.pdf userguide.pdf
#         ssh-keygen -Y sign -f $HOME/.ssh/id_rsa -n file userguide.pdf mmseqs-osx-universal.tar.gz mmseqs-linux-sse2.tar.gz mmseqs-linux-sse41.tar.gz mmseqs-linux-avx2.tar.gz mmseqs-linux-arm64.tar.gz mmseqs-linux-ppc64le-power8.tar.gz mmseqs-linux-ppc64le-power9.tar.gz mmseqs-win64.zip
#         curl --retry 5 --retry-all-errors -X POST \
#           -F file[]=@userguide.pdf -F signature[]=@userguide.pdf.sig \
#           -F file[]=@mmseqs-osx-universal.tar.gz -F signature[]=@mmseqs-osx-universal.tar.gz.sig \
#           -F file[]=@mmseqs-linux-sse2.tar.gz -F signature[]=@mmseqs-linux-sse2.tar.gz.sig \
#           -F file[]=@mmseqs-linux-sse41.tar.gz -F signature[]=@mmseqs-linux-sse41.tar.gz.sig \
#           -F file[]=@mmseqs-linux-avx2.tar.gz -F signature[]=@mmseqs-linux-avx2.tar.gz.sig \
#           -F file[]=@mmseqs-linux-arm64.tar.gz -F signature[]=@mmseqs-linux-arm64.tar.gz.sig \
#           -F file[]=@mmseqs-linux-ppc64le-power8.tar.gz -F signature[]=@mmseqs-linux-pp