azure-pipelines.yml

# Schedule a build for every midnight Eastern time. This is visible to the pipeline as Build.Reason
schedules:
- cron: "0 4 * * *"
  displayName: Daily midnight build
  branches:
    include:
    - master

trigger:
  batch: true
  branches:
    include: ['master']

# 20200312: apparently this is now explicitly required for azure
pr:
  branches:
    include: ['master']

jobs:
- job: 'WindowsBuild'
  displayName: "End-to-end Windows build & package"
  timeoutInMinutes: 0
  cancelTimeoutInMinutes: 300

  pool:
    vmImage: 'vs2017-win2016'

  steps:
    - checkout: self  # self represents the repo where the initial Pipelines YAML file was found
      # fetchDepth: 1  # the depth of commits to ask Git to fetch; defaults to no limit

    # submodule 
    - bash: |
        git submodule update --init --recursive
        # ls -lt
        # ls ./src/applications/Preprocessing/greedy
      displayName: 'Git Submodule Init and Update'

    - script: |
        choco install doxygen.install nsis.install wget cmake git
      displayName: 'Install dependencies'

    # # Pull LFS
    # - bash: |
    #     export GIT_LFS_SKIP_SMUDGE=1
    #     # git lfs pull --include "binaries/precompiledApps/windows.zip"
    #     # git lfs pull --include "binaries/qt_5.12.1/windows.zip"
    #     #echo "Not doing this until quota is improved on GitHub"
    #   displayName: 'Pull LFS'
    #   condition: ne(variables.CACHE_RESTORED_WINDOWS, 'true')

    # - powershell: |
    #     wmic logicaldisk get size,freespace,caption
    #   displayName: 'Disk space check'

    - powershell: |
        wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/windows.zip -O binaries_windows.zip
        wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/windows.zip -O qt.zip
      displayName: 'Downloading via wget'

    # Moving LFS Files
    - bash: |
        mkdir -p bin
        cd bin
        mv ../binaries_windows.zip .
        mv ../qt.zip .
        # wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/windows.zip -O binaries_windows.zip
        # wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/windows.zip -O qt.zip
        rm -rf ../binaries/*
        rm -rf ../data/georgetown
        rm -rf ../data/georgetown
        rm -rf ../docs
        rm -rf ../.git
        ls -lt
      displayName: 'Moving LFS files to the appropriate location under bin and freeing up some space'

    - script: |
        cd bin
        call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
        cmake -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX="./installLibs" -DCMAKE_CONFIGURATION_TYPES="Release" ..
        # freeing up space
        rm -rf ../src/applications/individualApps/libra_source/doc
        rm -rf ../src/applications/individualApps/libra_source/LIBRA_Software_Manual.pdf
        # freeing up space
        setx PATH "%PATH%;$(Build.SourcesDirectory)/bin/qt/5.12.1/bin"
        cmake --build . --target ALL_BUILD --config Release
        rm -rf installLibs
        rm -rf qt.zip
        rm -rf install
      displayName: 'Configure and compile Superbuild'

    - bash: |
        git pull origin master
        git log -1
        cat CMakeLists.txt | grep -i "PROJECT_VERSION"
      displayName: 'Testing git pull and version'

    # - powershell: |
    #     wmic logicaldisk get size,freespace,caption
    #   displayName: 'Disk space check'

    - script: |
        cd bin
        call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
        cmake -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX="./install" -DCMAKE_CONFIGURATION_TYPES="Release" -DCAPTK_DISABLE_CWL=ON -DITK_DIR="$(Build.SourcesDirectory)/bin/ITK-build" -DDCMTK_DIR="$(Build.SourcesDirectory)/bin/DCMTK-build" -DBUILD_TESTING=OFF ..
        setx PATH "%PATH%;$(Build.SourcesDirectory)/bin/qt/5.12.1/bin"
        setx CMAKE_PREFIX_PATH "%CMAKE_PREFIX_PATH%;$(Build.SourcesDirectory)/bin/ITK-build;$(Build.SourcesDirectory)/bin/DCMTK-build;$(Build.SourcesDirectory)/bin/qt/5.12.1/lib/cmake/Qt5"
        rm -rf binaries_windows.zip

        rm -rf externalApps/binaries_windows/libra

        cmake --build . --target ALL_BUILD --config Release
        rm -rf externalApps
      displayName: 'Configure and compile CaPTk'

    # - powershell: |
    #     get-psdrive | Where Free*
    #     cd bin
    #     # Remove-Item install_manifest.txt
    #     pwd

    #     switch((ls -r|measure -s Length).Sum) {
    #       {$_ -gt 1GB} {
    #         '{0:0.0} GiB' -f ($_/1GB)
    #         break
    #       }
    #       {$_ -gt 1MB} {
    #         '{0:0.0} MiB' -f ($_/1MB)
    #         break
    #       }
    #       {$_ -gt 1KB} {
    #         '{0:0.0} KiB' -f ($_/1KB)
    #         break
    #       }
    #       default { "$_ bytes" }
    #     }
    #   displayName: 'Disk space check'
    
- job: 'MacOSBuild'
  displayName: "End-to-end MacOS build & package"
  timeoutInMinutes: 0
  cancelTimeoutInMinutes: 300

  pool:
    vmImage: 'MacOS-10.14'

  steps:
    - checkout: self  # self represents the repo where the initial Pipelines YAML file was found
      # fetchDepth: 1  # the depth of commits to ask Git to fetch; defaults to no limit

    # submodule 
    - bash: |
        git submodule update --init --recursive
        # ls -lt
        # ls ./src/applications/Preprocessing/greedy
      displayName: 'Git Submodule Init and Update'

    - bash: |
        brew install make doxygen libomp openmpi glfw
        #brew install caskroom/cask/mactex # latex is not used for documentation right now
        export GIT_LFS_SKIP_SMUDGE=1
      displayName: 'Brew dependencies'

    # - bash: |
    #     brew install git-lfs
    #     git lfs install
    #   displayName: 'Brew dependency install LFS'
    #   condition: ne(variables['CACHE_RESTORED_MAC'], 'true')

    # # Pull LFS
    # - bash: |
    #     export GIT_LFS_SKIP_SMUDGE=1
    #     git lfs pull --include "binaries/precompiledApps/macos.zip"
    #     git lfs pull --include "binaries/qt_5.12.1/macos.zip"
    #     #echo "Not doing this until quota is improved on GitHub"
    #   displayName: 'Pull LFS'
    #   condition: ne(variables['CACHE_RESTORED_MAC'], 'true')

    # Moving LFS Files
    - bash: |
        mkdir -p bin
        cd bin
        wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/macos.zip -O binaries_macos.zip
        wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/macos.zip -O qt.zip
        # mv ../binaries/precompiledApps/macos.zip ./binaries_macos.zip
        # mv ../binaries/qt_5.12.1/macos.zip ./qt.zip
        ls -lt
      displayName: 'Downloading & Moving LFS files to the appropriate location under bin'
      # condition: ne(variables['CACHE_RESTORED_MAC'], 'true')

    - bash: |
        cd bin

        export CMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE
        export CMAKE_PREFIX_PATH="/Library/TeX/texbin"

        cmake ../ -DCMAKE_INSTALL_PREFIX="./install"

        make -j 2

        rm -rf install
      displayName: 'Configure and compile Superbuild'
      # condition: ne(variables['CACHE_RESTORED_MAC'], 'true')

     # Check qt
    - bash: |
        cd bin
        ls -a
        ls ./qt/
      displayName: 'Check qt'

    # - bash: |
    #     tar cvfz bin_macos_20200212.tar.gz bin
    #   displayName: 'Zipping Superbuild'

    - bash: |
        git pull origin master
        git log -1
        cat CMakeLists.txt | grep -i "PROJECT_VERSION"
      displayName: 'Testing git pull and version'

    - bash: |
        cd bin

        sudo rm -rf CaPTk_*

        cmake ../
        rm CMakeCache.txt
        export CMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE
        export CMAKE_PREFIX_PATH="/Library/TeX/texbin"

        export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/bin/ITK-build:$(Build.SourcesDirectory)/bin/DCMTK-build:$(Build.SourcesDirectory)/bin/qt/5.12.1/clang_64/lib/cmake/Qt5:$(Build.SourcesDirectory)/bin/qt/5.12.1/clang_64/lib/cmake/Qt5Core:$CMAKE_PREFIX_PATH
        cmake -DITK_DIR=./ITK-build -DDCMTK_DIR=./DCMTK-build ../

        rm -rf binaries_*.zip

        make -j 2
      displayName: 'Configure and compile CaPTk'

 #   - script: |
 #       cd bin

#        sudo rm -rf CaPTk_*

 #       cmake ../
 #       rm CMakeCache.txt
 #       export CMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE
 #       export CMAKE_PREFIX_PATH="/Library/TeX/texbin"

 #       export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/bin/ITK-build:$(Build.SourcesDirectory)/bin/DCMTK-build:$(Build.SourcesDirectory)/bin/qt/5.12.1/clang_64/lib/cmake/Qt5:$(Build.SourcesDirectory)/bin/qt/5.12.1/clang_64/lib/cmake/Qt5Core:$CMAKE_PREFIX_PATH
 #       cmake -DITK_DIR=./ITK-build -DDCMTK_DIR=./DCMTK-build -DBUILD_TESTING=ON ../

 #       make -j 2
 #       make test
 #       rm -rf testing
 #     displayName: 'Performing the Tests'

- job: 'Windows_SelfHost_Windows_7'
  displayName: "Self-hosted agent on Windows 7"
  timeoutInMinutes: 0
  cancelTimeoutInMinutes: 300

  pool: 'Windows'

  steps:
    - checkout: self  

    # submodule 
    - powershell: |
        git submodule update --init --recursive

      displayName: 'Git Submodule Init and Update'


    - powershell: |
        Remove-Item -Recurse -Force -ErrorAction Ignore bin   
        mkdir bin     
      displayName: 'Reset bin'

    # Moving LFS Files
    - powershell: |
        cd bin
        [Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12
        wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/windows.zip -OutFile binaries_windows.zip
      displayName: 'Moving LFS files to the appropriate location under bin and freeing up some space'

    # - script: |
    #     cd bin
    #     call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Auxiliary\Build\vcvarsall.bat" x64
    #     cmake -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX="./installLibs" -DCMAKE_CONFIGURATION_TYPES="Release" ..
        
    #     setx PATH "$(Build.SourcesDirectory)/bin/qt/5.12.1/bin;%PATH%"
    #     cmake --build . --target ALL_BUILD --config Release

    #   displayName: 'Configure and compile Superbuild'

    # - powershell: |
    #     # Copy-Item -Recurse ../../../superbuild/ ./bin
    #     # cd bin
    #     # ls
        
    #     cd bin
    #     Copy-Item -Recurse ./ ../../../../superbuild
        
    #   displayName: 'Move superbuild and qt and compiled apps'
    
    - powershell: |
        $env:GIT_REDIRECT_STDERR = '2>&1'
        git pull origin master
        git log -1
        # cat CMakeLists.txt | grep -i "PROJECT_VERSION"
      displayName: 'Testing git pull and version'

    - script: |
        cd bin
        call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
        setx PATH "E:/LibsCaPTk/bin/qt/5.12.1/bin;%PATH%"
        setx CMAKE_PREFIX_PATH "E:/LibsCaPTk/ITK-build;E:/LibsCaPTk/DCMTK-build;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebView;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebEngineCore;%CMAKE_PREFIX_PATH%"
    
        cmake -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX="./install" -DCMAKE_CONFIGURATION_TYPES="Release" -DCAPTK_DISABLE_CWL=ON -DITK_DIR="E:/LibsCaPTk/ITK-build" -DDCMTK_DIR="E:/LibsCaPTk/DCMTK-build" -DQt5_DIR="E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5" -DQt5Core_DIR="E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core" -DBUILD_TESTING=OFF ..
        setx PATH "E:/LibsCaPTk/bin/qt/5.12.1/bin;%PATH%"
        setx CMAKE_PREFIX_PATH "E:/LibsCaPTk/ITK-build;E:/LibsCaPTk/DCMTK-build;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebView;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebEngineCore;%CMAKE_PREFIX_PATH%"

        rm -rf externalApps/binaries_windows/libra

        cmake --build . --target ALL_BUILD --config Release
        
      displayName: 'Configure and compile CaPTk'

    # - script: |
    #     cd bin
    #     export GIT_LFS_SKIP_SMUDGE=1
    #     git lfs pull --include "data/TestData.zip"
    #     call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
    #     setx PATH "E:/LibsCaPTk/bin/qt/5.12.1/bin;%PATH%"
    #     setx CMAKE_PREFIX_PATH "E:/LibsCaPTk/ITK-build;E:/LibsCaPTk/DCMTK-build;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebView;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebEngineCore;%CMAKE_PREFIX_PATH%"
    
    #     cmake -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX="./install" -DCMAKE_CONFIGURATION_TYPES="Release" -DCAPTK_DISABLE_CWL=ON -DITK_DIR="E:/LibsCaPTk/ITK-build" -DDCMTK_DIR="E:/LibsCaPTk/DCMTK-build" -DQt5_DIR="E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5" -DQt5Core_DIR="E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core" -DBUILD_TESTING=ON ..
    #     setx PATH "E:/LibsCaPTk/bin/qt/5.12.1/bin;%PATH%"
    #     setx CMAKE_PREFIX_PATH "E:/LibsCaPTk/ITK-build;E:/LibsCaPTk/DCMTK-build;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebView;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebEngineCore;%CMAKE_PREFIX_PATH%"
    
    #     cmake --build . --target RUN_TESTS --config Release
    #   displayName: 'Performing the Tests'

    - script: |
        cd bin
        call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
        setx PATH "E:/LibsCaPTk/bin/qt/5.12.1/bin;%PATH%"
        setx CMAKE_PREFIX_PATH "E:/LibsCaPTk/ITK-build;E:/LibsCaPTk/DCMTK-build;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebView;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebEngineCore;%CMAKE_PREFIX_PATH%"
    
        cmake -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX="./install" -DCMAKE_CONFIGURATION_TYPES="Release" -DCAPTK_DISABLE_CWL=ON -DITK_DIR="E:/LibsCaPTk/ITK-build" -DDCMTK_DIR="E:/LibsCaPTk/DCMTK-build" -DQt5_DIR="E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5" -DQt5Core_DIR="E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core" -DBUILD_TESTING=OFF ..
        setx PATH "E:/LibsCaPTk/bin/qt/5.12.1/bin;%PATH%"
        setx CMAKE_PREFIX_PATH "E:/LibsCaPTk/ITK-build;E:/LibsCaPTk/DCMTK-build;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebView;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebEngineCore;%CMAKE_PREFIX_PATH%"
        
        cmake --build . --target PACKAGE --config Release

      displayName: 'Build & Package CaPTk'

    - powershell: |
        cd bin
        mv *_Installer.* $(Build.ArtifactStagingDirectory)
      displayName: 'Move installer to staging directory'

    - task: PublishBuildArtifacts@1
      inputs:
        pathtoPublish: '$(Build.ArtifactStagingDirectory)'
        artifactName: '$(Build.DefinitionName)_installer_Windows'

    - task: DownloadBuildArtifacts@0
      inputs:
        buildType: 'current'
        downloadType: 'single'
        artifactName: '$(Build.DefinitionName)_installer_Windows'
        downloadPath: '$(System.ArtifactsDirectory)'
    
    - task: CopyFilesOverSSH@0
      inputs:
        sshEndpoint: cbicaNITRC
        sourceFolder: $(Build.ArtifactStagingDirectory)
        contents: '*_Installer.*'
        targetFolder: /var/home/groups/captk/htdocs # previously /mnt/gforge-data/gforge/home/groups/captk/downloads
        cleanTargetFolder: false
        overwrite: true
        continueOnError: true
      displayName: Uploading to NITRC
      condition: and( eq(variables['Build.DefinitionName'], 'CBICA.CaPTk'), or( eq(variables['Build.Reason'], 'Manual'), eq(variables['Build.Reason'], 'Schedule')) )

- job: 'Linux_SelfHost_Ubuntu_1604'
  displayName: "Self-hosted agent on Ubuntu 16.04"
  timeoutInMinutes: 0
  cancelTimeoutInMinutes: 300

  pool: 'Ubuntu_16.04'

  steps:
    - checkout: self  # self represents the repo where the initial Pipelines YAML file was found

    # submodule 
    - bash: |
        git submodule update --init --recursive

        rm -rf bin
        ls
      displayName: 'Git Submodule Init and Update'

    # Moving LFS Files
    - bash: |
        rm -rf binaries

        mkdir -p bin
        cd bin
        wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/linux.zip -O binaries_linux.zip
        # wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/linux.zip -O qt.zip
    
        ls -lt
      displayName: 'Downloading & Moving LFS files to the appropriate location under bin'

    # Configure and build superbuild
    # - bash: |
    #     cd bin
    #     cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" ..
    #     make -j2
    #     rm -rf install

    #   displayName: 'Configure and compile Superbuild'

    # - bash: |
    #     # mkdir $(Build.SourcesDirectory)/../superbuild
    #     # cd bin
    #     # mv ./* $(Build.SourcesDirectory)/../superbuild
    #     # cd $(Build.SourcesDirectory)/..
    #     # ls
    #     # echo "Done cd"
    #     # tar cvfz superbuild.tar.gz superbuild
    #     # ls
    #     # echo "done tar"
    #     # rm -rf superbuild
    #     # ls
    #     # cd $(Build.SourcesDirectory)

    #     pwd

    #     rm -rf bin

    #     mkdir bin
    #     cd bin
        
    #     cp -r $(Build.SourcesDirectory)/../superbuild.tar.gz ./
    #     ls
    #     echo "Done cp"
    #     tar xvfz superbuild.tar.gz
    #     rm -rf superbuild.tar.gz

    #     ls
    #     echo "Done tar"

    #     mv superbuild/* ./
    #     ls
    #   displayName: 'Move superbuild and qt and compiled apps'

    - bash: |
        git pull origin master
        git log -1
        cat CMakeLists.txt | grep -i "PROJECT_VERSION"
      displayName: 'Testing git pull and version'
          
    - bash: |
        rm -rf bin/qt.zip
        rm -rf bin/5.12.1
   
        df -k .
      displayName: 'Disk space check'

    # # Configure and build CaPTk
    # - bash: |
    #     cd bin
    #     export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/../../superbuild/bin/ITK-build:$(Build.SourcesDirectory)/../../superbuild/bin/DCMTK-build:$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH
    #     cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" -DITK_DIR=./ITK-build -DDCMTK_DIR=./DCMTK-build -DBUILD_TESTING=ON ..
    #     make -j2
    #   displayName: 'Configure and compile CaPTk with Testing enabled'

    # - script: |
    #    cd bin
    #    make test
    #    rm -rf testing
    #   displayName: 'Performing the Tests' 

    # Configure and build CaPTk
    - bash: |
        pwd
        cd bin
        ls $(Build.SourcesDirectory)/../../superbuild/bin
        export PATH=$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/bin:$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/libexec:$PATH
        export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/../../superbuild/bin/ITK-build:$(Build.SourcesDirectory)/../../superbuild/bin/DCMTK-build:$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH
        
        cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" -DITK_DIR="$(Build.SourcesDirectory)/../../superbuild/bin/ITK-build" -DDCMTK_DIR="$(Build.SourcesDirectory)/../../superbuild/bin/DCMTK-build" -DBUILD_TESTING=OFF ..
        
        rm -rf binaries_linux.zip
        rm -rf qt.zip
        rm -rf 5.12.1

        rm -rf externalApps/binaries_linux/libra

        make -j2
        make install/strip
      displayName: 'Configure and compile CaPTk'

    - bash: |
        rm -rf bin/qt.zip
        rm -rf bin/5.12.1
        rm -rf regression
        rm -rf binaries
        rm -rf bin_linux_*.tar.gz
        df -k .
      displayName: 'Disk space check'

    # Build a package
    - bash: |
        export PATH=$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/bin:$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/libexec:$PATH
        export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/../../superbuild/bin/ITK-build:$(Build.SourcesDirectory)/../../superbuild/bin/DCMTK-build:$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH

        rm -rf regression
        rm -rf binaries

        export PKG_FAST_MODE=1
        export ARCH=x86_64 appimagetool

        # export PKG_COPY_QT_LIBS=1
        ./scripts/captk-pkg

        mv *_Installer.* $(Build.ArtifactStagingDirectory)

        rm -rf bin
        df -k .

      displayName: 'Set up environment variables for packager and build a package'

    - task: PublishBuildArtifacts@1
      inputs:
        pathtoPublish: '$(Build.ArtifactStagingDirectory)'
        artifactName: '$(Build.DefinitionName)_installer_Linux_ubuntu1604'
        continueOnError: true

    - task: DownloadBuildArtifacts@0
      inputs:
        buildType: 'current'
        downloadType: 'single'
        artifactName: '$(Build.DefinitionName)_installer_Linux_ubuntu1604'
        downloadPath: '$(System.ArtifactsDirectory)'
        continueOnError: true

    - task: CopyFilesOverSSH@0
      inputs:
        sshEndpoint: cbicaNITRC
        sourceFolder: $(Build.ArtifactStagingDirectory)
        contents: '*_Installer.*'
        targetFolder: /var/home/groups/captk/htdocs # previously /mnt/gforge-data/gforge/home/groups/captk/downloads
        cleanTargetFolder: false
        overwrite: true
        continueOnError: true
      displayName: Uploading to NITRC 
      condition: and( eq(variables['Build.DefinitionName'], 'CBICA.CaPTk'), or( eq(variables['Build.Reason'], 'Manual'), eq(variables['Build.Reason'], 'Schedule')) )

# - job: 'macOS_SelfHost_1014'
  # displayName: "Self-hosted agent on macOS 10.14"
  # timeoutInMinutes: 0
  # cancelTimeoutInMinutes: 300

  # pool: 'macOS_10.14_alt' # Change to alt pool to try running this outside of Phuc's account -- possible permissions problems

  # steps:
    # - checkout: self  # self represents the repo where the initial Pipelines YAML file was found

    # # submodule 
    # - bash: |
        # export GIT_LFS_SKIP_SMUDGE=1
        # git submodule update --init --recursive

      # displayName: 'Git Submodule Init and Update'

    # # Moving LFS Files
    # - bash: |
        # rm -rf bin
        # mkdir -p bin
        # cd bin
        # wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/macos.zip -O binaries_macos.zip
        # wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/macos.zip -O qt.zip
        # # mv ../binaries/precompiledApps/macos.zip ./binaries_macos.zip
        # # mv ../binaries/qt_5.12.1/macos.zip ./qt.zip
        # ls -lt
      # displayName: 'Downloading & Moving LFS files to the appropriate location under bin'

    # # - bash: |
    # #     cd bin

    # #     export CMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE
    # #     export CMAKE_PREFIX_PATH="/Library/TeX/texbin"

    # #     cmake ../ -DCMAKE_INSTALL_PREFIX="./install"

    # #     make -j 2

    # #   displayName: 'Configure and compile Superbuild'

    # # - bash: |
    # #     # mkdir $(Build.SourcesDirectory)/../superbuild
    # #     # cd bin
    # #     # mv ./* $(Build.SourcesDirectory)/../superbuild
    # #     # cd $(Build.SourcesDirectory)/..
    # #     # ls
    # #     # echo "Done cd"
    # #     # tar cvfz superbuild.tar.gz superbuild
    # #     # ls
    # #     # echo "done tar"
    # #     # rm -rf superbuild
    # #     # ls
    # #     # cd $(Build.SourcesDirectory)

    # #     pwd

    # #     cd $(Build.SourcesDirectory)/../../
    # #     ls
    # #     tar xvfz superbuild.tar.gz
    # #     rm -rf superbuild.tar.gz
    # #     cd $(Build.SourcesDirectory)/../../superbuild/bin
    # #     ls
    # #     echo "Done tar"
    # #   displayName: 'Move superbuild and qt and compiled apps'

    # - bash: |
        # git pull origin master
        # git log -1
        # cat CMakeLists.txt | grep -i "PROJECT_VERSION"
      # displayName: 'Testing git pull and version'

    # - bash: |
        # cd bin
        # pwd

        # rm -rf CaPTk_*

        # export CMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE
        # export CMAKE_PREFIX_PATH=/Users/Shared/superbuild/ITK-build:/Users/Shared/superbuild/DCMTK-build:/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5:/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5Core:$(pwd)/qt/5.12.1/clang_64/lib/cmake/Qt5:$(pwd)/qt/5.12.1/clang_64/lib/cmake/Qt5Core:$CMAKE_PREFIX_PATH
        # echo "[DEBUG] CMAKE_PREFIX_PATH: " $CMAKE_PREFIX_PATH
        # #cmake ../
        # #rm -f CMakeCache.txt
        
        # cmake -DITK_DIR="/Users/Shared/superbuild/ITK-build" -DDCMTK_DIR="/Users/Shared/superbuild/DCMTK-build" -DVTK_DIR="/Users/Shared/superbuild/VTK-build" -DCMAKE_INSTALL_PREFIX="./install" -DQt5_DIR=/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5 -DQt5Core_DIR=/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5Core ../
        
        # # Debug using vsts' cache
        # cp CMakeCache.txt /Users/Shared/debug-vsts-getkaa-cmakecache.txt 
        # make -j 2
         
      # displayName: 'Configure and compile CaPTk'

    # - bash: |
        # cd bin

        # version=$(grep -i -e "project_version:*" CMakeCache.txt | cut -c24-)

        # rm -rf CaPTk_$version.app/Contents/Resources/bin/ITK-SNAP.app

        # rm -rf CaPTk*.app

        # cmake ../
        # rm -f CMakeCache.txt
        # export CMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE
        # export CMAKE_PREFIX_PATH=/Users/Shared/superbuild/ITK-build:/Users/Shared/superbuild/DCMTK-build:/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5:/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5Core:/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5:/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5Core:$CMAKE_PREFIX_PATH
  
        
        # cmake -DITK_DIR="/Users/Shared/superbuild/ITK-build" -DDCMTK_DIR="/Users/Shared/superbuild/DCMTK-build" -DCMAKE_INSTALL_PREFIX="./install" -DQt5_DIR=/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5 -DQt5Core_DIR=/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5Core ../

        # make -j 2

      # displayName: 'Ensure documentation is picked up properly'


    # - bash: |
        # cd bin

        # version=$(grep -i -e "project_version:*" CMakeCache.txt | cut -c24-)
        # pkgname="_Installer"
        # pkgname="$version$pkgname"

        # rm -rf *.pkg
        # rm -rf install_manifest.txt
        # make package
        
        # # print dir tree for debug
        # ls -R _CPack_Packages

        # pkgpath=""
        # if [ -d "$(Build.SourcesDirectory)/bin/_CPack_Packages/OSX/DragNDrop/CaPTk_$version/ALL_IN_ONE/CaPTk_$version.app/" ]; then pkgpath="$(Build.SourcesDirectory)/bin/_CPack_Packages/OSX/DragNDrop/CaPTk_$version/ALL_IN_ONE/CaPTk_$version.app/"; else pkgpath="$(Build.SourcesDirectory)/bin/_CPack_Packages/OSX/DragNDrop/CaPTk_$version/CaPTk_$version.app/"; fi
        
        # # Try patching Utilities as late as possible. Seems to be necessary for Utilities specifically.
        # install_name_tool -change /usr/local/opt/libomp/lib/libomp.dylib  @rpath/libomp.dylib $pkgpath/Contents/Resources/bin/Utilities
        
        # pkgbuild --version $version --identifier com.cbica.captk --install-location /Applications --component $pkgpath ./CaPTk_$version.pkg

        # productbuild --synthesize --package CaPTk_$version.pkg ./distribution.xml

        # xml='<?xml version="1.0" encoding="utf-8"?>
        # <installer-gui-script minSpecVersion="1">
            # <title>CaPTk_'"$version"'</title>
            # <license file="Combined.txt"></license>
            # <pkg-ref id="com.cbica.captk"/>
            # <options customize="never" require-scripts="false"/>
            # <choices-outline>
                # <line choice="default">
                    # <line choice="com.cbica.captk"/>
                # </line>
            # </choices-outline>
            # <choice id="default"/>
            # <choice id="com.cbica.captk" visible="false">
                # <pkg-ref id="com.cbica.captk"/>
            # </choice>
            # <pkg-ref id="com.cbica.captk" version="$version" onConclusion="none">CaPTk_'"$version"'.pkg</pkg-ref>
        # </installer-gui-script>'

        # echo $xml > "./distribution.xml"

        # productbuild --distribution ./distribution.xml --resources $(Build.SourcesDirectory)/bin/_CPack_Packages/OSX/DragNDrop/CaPTk_$version/ALL_IN_ONE/CaPTk_$version.app/Contents/Resources/license/ --package-path . ./CaPTk_$pkgname.pkg

        # mv *_Installer* $(Build.ArtifactStagingDirectory)

      # displayName: 'Package CaPTk (.dmg and .pkg)'

    # - task: PublishBuildArtifacts@1
      # inputs:
        # pathtoPublish: '$(Build.ArtifactStagingDirectory)'
        # artifactName: '$(Build.DefinitionName)_installer_macOS'

    # - task: DownloadBuildArtifacts@0
      # inputs:
        # buildType: 'current'
        # downloadType: 'single'
        # artifactName: '$(Build.DefinitionName)_installer_macOS'
        # downloadPath: '$(System.ArtifactsDirectory)'

    # - task: CopyFilesOverSSH@0
      # inputs:
        # sshEndpoint: cbicaNITRC
        # sourceFolder: $(Build.ArtifactStagingDirectory)
        # contents: '*_Installer.*'
        # targetFolder: /var/home/groups/captk/htdocs # previously /mnt/gforge-data/gforge/home/groups/captk/downloads
        # cleanTargetFolder: false
        # overwrite: true
        # continueOnError: true
      # displayName: Uploading to NITRC
      # condition: and( eq(variables['Build.DefinitionName'], 'CBICA.CaPTk'), or( eq(variables['Build.Reason'], 'Manual'), eq(variables['Build.Reason'], 'Schedule')) )

# - job: 'Linux_SelfHost_CentOS7'
#   displayName: "Self-hosted agent on CentOS 7"
#   timeoutInMinutes: 0
#   cancelTimeoutInMinutes: 300

#   pool: 'CentOS7'

#   steps:
#     - checkout: self  # self represents the repo where the initial Pipelines YAML file was found

#     # submodule 
#     - bash: |
#         git submodule update --init --recursive

#         rm -rf bin
#         ls
#       displayName: 'Git Submodule Init and Update'

#     # Moving LFS Files
#     - bash: |
#         rm -rf binaries

#         mkdir -p bin
#         cd bin
#         wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/linux.zip -O binaries_linux.zip
#         # wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/linux.zip -O qt.zip
    
#         ls -lt
#       displayName: 'Downloading & Moving LFS files to the appropriate location under bin'

#     # Configure and build superbuild
#     # - bash: |
#     #     cd bin
#     #     cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" ..
#     #     make -j2
#     #     rm -rf install

#     #   displayName: 'Configure and compile Superbuild'

#     # - bash: |
        
#     #   displayName: 'Move superbuild and qt and compiled apps'

#     - bash: |
#         git pull origin master
#         git log -1
#         cat CMakeLists.txt | grep -i "PROJECT_VERSION"
#       displayName: 'Testing git pull and version'
          
#     # - bash: |
#     #     rm -rf bin/qt.zip
#     #     rm -rf bin/5.12.1
   
#     #     df -k .
#     #   displayName: 'Disk space check'

#     # # Configure and build CaPTk
#     # - bash: |
#     #     cd bin
#     #     export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/bin/ITK-build:$(Build.SourcesDirectory)/bin/DCMTK-build:$(Build.SourcesDirectory)/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH
#     #     cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" -DITK_DIR=./ITK-build -DDCMTK_DIR=./DCMTK-build -DBUILD_TESTING=ON ..
#     #     make -j2
#     #   displayName: 'Configure and compile CaPTk with Testing enabled'

#     # - script: |
#     #    cd bin
#     #    make test
#     #    rm -rf testing
#     #   displayName: 'Performing the Tests'

#     # Configure and build CaPTk
#     - bash: |
#         cd bin
#         # export PATH=$(Build.SourcesDirectory)/bin/qt/5.12.1/bin:$(Build.SourcesDirectory)/bin/qt/5.12.1/libexec:$PATH
#         # export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/bin/ITK-build:$(Build.SourcesDirectory)/bin/DCMTK-build:$(Build.SourcesDirectory)/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH
        
#         cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" -DBUILD_TESTING=OFF ..
        
#         rm -rf binaries_linux.zip
#         rm -rf qt.zip
#         rm -rf 5.12.1

#         rm -rf externalApps/binaries_linux/libra

#         make -j2
#         make install/strip
#       displayName: 'Configure and compile CaPTk'

#     # - bash: |
#     #     rm -rf bin/qt.zip
#     #     rm -rf bin/5.12.1
#     #     rm -rf regression
#     #     rm -rf binaries
#     #     rm -rf bin_linux_*.tar.gz
#     #     df -k .
#     #   displayName: 'Disk space check'

#     # Build a package
#     - bash: |
#         # export PATH=$(Build.SourcesDirectory)/bin/qt/5.12.1/bin:$(Build.SourcesDirectory)/bin/qt/5.12.1/libexec:$PATH
#         # export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/bin/ITK-build:$(Build.SourcesDirectory)/bin/DCMTK-build:$(Build.SourcesDirectory)/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH

#         # rm -rf regression
#         # rm -rf binaries

#         export PKG_FAST_MODE=1
#         export ARCH=x86_64 appimagetool

#         # export PKG_COPY_QT_LIBS=1
#         ./scripts/captk-pkg

#         rm -rf src
#         rm -rf docs*

#         rm -rf scripts

#         mv *_Installer.* $(Build.ArtifactStagingDirectory)

#         rm -rf bin
#         df -k .

#       displayName: 'Set up environment variables for packager and build a package'

#     - task: PublishBuildArtifacts@1
#       inputs:
#         pathtoPublish: '$(Build.ArtifactStagingDirectory)'
#         artifactName: '$(Build.DefinitionName)_installer_Linux_centos7'
#         continueOnError: true

#     - task: DownloadBuildArtifacts@0
#       inputs:
#         buildType: 'current'
#         downloadType: 'single'
#         artifactName: '$(Build.DefinitionName)_installer_Linux_centos7'
#         downloadPath: '$(System.ArtifactsDirectory)'
#         continueOnError: true

#     - task: CopyFilesOverSSH@0
#       inputs:
#         sshEndpoint: cbicaNITRC
#         sourceFolder: $(Build.ArtifactStagingDirectory)
#         contents: '*_Installer.*'
#         targetFolder: /mnt/gforge-data/gforge/home/groups/captk/downloads
#         cleanTargetFolder: false
#         overwrite: true
#         continueOnError: true
#       displayName: Uploading to NITRC 
#       condition: eq(variables['Build.DefinitionName'], 'CBICA.CaPTk')