azure-pipelines.yml

# https://aka.ms/yaml

trigger:
  - master

variables:
    regression: 1

jobs:
  - job: build_ubuntu_2004_userguide
    displayName: Ubuntu 2004 Userguide
    pool:
      vmImage: 'Ubuntu-20.04'
    steps:
      - checkout: "none"
      - script: |
          sudo apt-get update
          sudo apt-get -y install pandoc texlive-latex-recommended texlive-fonts-extra
        displayName: Install Dependencies
      - script: |
          cd ${SYSTEM_DEFAULTWORKINGDIRECTORY}
          git clone https://github.com/martin-steinegger/conterminator.wiki.git .
          .pandoc/make-pdf.sh
        displayName: Build Userguide
      - task: PublishPipelineArtifact@0
        inputs:
          targetPath: $(System.DefaultWorkingDirectory)/userguide.pdf
          artifactName: userguide
  - job: build_ubuntu_2004
    displayName: Ubuntu 2004 Conterminator
    pool:
      vmImage: 'Ubuntu-20.04'
    timeoutInMinutes: 120
    strategy:
      matrix:
        avx2:
          SIMD: 'AVX2'
          STATIC: 1
          MPI: 0
          BUILD_TYPE: RelWithDebInfo
        sse:
          SIMD: 'SSE4_1'
          STATIC: 1
          MPI: 0
          BUILD_TYPE: RelWithDebInfo
        asan:
          SIMD: 'AVX2'
          STATIC: 0
          MPI: 0
          BUILD_TYPE: ASanOpt
    steps:
      - script: |
          sudo apt-get update
          sudo apt-get -y install mpi-default-dev mpi-default-bin
        displayName: Install Dependencies
        condition: eq(variables['MPI'], 1)
      - script: |
          mkdir build && cd build
          if [ "${STATIC}" -eq "1" ]; then
              cmake -DHAVE_SANITIZER=1 -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DHAVE_TESTS=1 \
                -DBUILD_SHARED_LIBS=OFF \
                -DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc \
                -static-libstdc++" -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \
                -DENABLE_WERROR=1 -DHAVE_${SIMD}=1 -DHAVE_MPI=${MPI} ..
          else
              cmake -DHAVE_SANITIZER=1 -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DHAVE_TESTS=1 \
                -DENABLE_WERROR=1 -DHAVE_${SIMD}=1 -DHAVE_MPI=${MPI} ..
          fi

          make -j $(nproc --all)
        displayName: Build Conterminator
      - script: |
          export TTY=0
          if [ "${BUILD_TYPE}" = "ASan" ]; then
            echo "leak:libgomp1" > ${BUILD_SOURCESDIRECTORY}/ASan.supp
            export export ASAN_OPTIONS=suppressions=${BUILD_SOURCESDIRECTORY}/ASan.supp
          fi
          ${BUILD_SOURCESDIRECTORY}/build/src/conterminator dna ${BUILD_SOURCESDIRECTORY}/example/dna.fas ${BUILD_SOURCESDIRECTORY}/example/dna.mapping result tmp 
          ${BUILD_SOURCESDIRECTORY}/build/src/conterminator protein ${BUILD_SOURCESDIRECTORY}/example/prots.fas ${BUILD_SOURCESDIRECTORY}/example/prots.mapping result tmp 
        displayName: Run Regression Suite
        condition: eq(variables['regression'], 1)
      - task: PublishPipelineArtifact@0
        condition: eq(variables['STATIC'], 1)
        inputs:
          targetPath: $(Build.SourcesDirectory)/build/src/conterminator
          artifactName: conterminator-linux-$(SIMD)

  - job: upload_artifacts
    displayName: Upload Artifacts
    condition: and(succeeded(), ne(variables['Build.Reason'], 'PullRequest'))
    pool:
      vmImage: 'Ubuntu-20.04'
    dependsOn:
      - build_ubuntu_2004_userguide
      - build_ubuntu_2004
    steps:
      - script: |
          cd "${BUILD_SOURCESDIRECTORY}"
          mkdir conterminator
          cp -f README.md LICENCE.md conterminator
          cp -r examples conterminator
          mkdir conterminator/bin
      - task: DownloadPipelineArtifact@1
        inputs:
          artifactName: userguide
          targetPath: $(Build.SourcesDirectory)/conterminator
      - task: DownloadPipelineArtifact@1
        inputs:
          artifactName: conterminator-linux-SSE4_1
          targetPath: $(Build.SourcesDirectory)/conterminator/
      - script:
          chmod +x "${BUILD_SOURCESDIRECTORY}/conterminator/conterminator"
      - task: ArchiveFiles@2
        inputs:
          rootFolderOrFile: $(Build.SourcesDirectory)/conterminator
          archiveFile: $(Build.SourcesDirectory)/conterminator-linux-sse41.tar.gz
          includeRootFolder: true
          archiveType: tar
      - task: DownloadPipelineArtifact@1
        inputs:
          artifactName: conterminator-linux-AVX2
          targetPath: $(Build.SourcesDirectory)/conterminator/
      - script:
          chmod +x "${BUILD_SOURCESDIRECTORY}/conterminator/conterminator"
      - task: ArchiveFiles@2
        inputs:
          rootFolderOrFile: $(Build.SourcesDirectory)/conterminator
          archiveFile: $(Build.SourcesDirectory)/conterminator-linux-avx2.tar.gz
          includeRootFolder: true
          archiveType: tar
      - script:
          rm "${BUILD_SOURCESDIRECTORY}/conterminator/conterminator"
      - task: DownloadSecureFile@1
        inputs:
          secureFile: secretKeyPleaseDontSteal
        displayName: Get Deployment Key
      - script: |
          mkdir ~/.ssh && mv $DOWNLOADSECUREFILE_SECUREFILEPATH ~/.ssh/id_rsa
          chmod 700 ~/.ssh && chmod 600 ~/.ssh/id_rsa
          ssh-keyscan -t rsa uniclust.mmseqs.com >> ~/.ssh/known_hosts
          cd "${BUILD_SOURCESDIRECTORY}"
          ssh codeship@uniclust.mmseqs.com "mkdir -p \"/home/mirdita/repositories/mmseqs-webserver/archive/${BUILD_SOURCEVERSION}\""
          scp conterminator/userguide.pdf conterminator-linux-sse41.tar.gz conterminator-linux-avx2.tar.gz codeship@uniclust.mmseqs.com:"/home/mirdita/repositories/mmseqs-webserver/archive/${BUILD_SOURCEVERSION}"
          ssh codeship@uniclust.mmseqs.com "update-latest-conterminator.sh \"${BUILD_SOURCEVERSION}\""