build-ants.yml

name: Build ANTs

on:
  pull_request:
    branches: [ master ]
  workflow_dispatch:
    inputs:
      git_ref:
        description: 'Upstream ANTsX/ANTs commit ref to check out when building'
        required: true
        default: 'b37e8b56e4e518b0f2947f80d0e3701a5ddfe120'

jobs:

  build:
    strategy:
      matrix:
        os: [ubuntu-20.04, ubuntu-18.04, macos-10.15]
    runs-on: ${{ matrix.os }}
    steps:
    # first, rewrite OS names to be safe for github artifacts.
    - name: names
      run: |
        OS="${{ matrix.os }}"
        OS=$(echo "$OS" | sed s/://)
        echo "ARTIFACT=$OS" >> $GITHUB_ENV
    - name: Downgrade OS X Version
      if: matrix.os == 'macos-10.15'
      run: |
        echo "CMAKE_CXX_FLAGS=-mmacosx-version-min=10.12" >> $GITHUB_ENV
    - uses: actions/checkout@v3
      with:
        repository: ANTsX/ANTs
        # NB: This commit mirrors the state of the kousu/ANTs repository
        #     at the time of https://github.com/kousu/ANTs/pull/5.
        ref: ${{ github.event.inputs.git_ref || 'b37e8b56e4e518b0f2947f80d0e3701a5ddfe120' }}
    # The step below sets an option inside the cmake file to use the `https` protocol, which addresses:
    # https://github.blog/2021-09-01-improving-git-protocol-security-github/#no-more-unauthenticated-git
    - name: Patch in fix for insecure git:// protocol
      run: |
        perl -pi -e 's/http instead." ON\)/http instead." OFF\)/g' SuperBuild.cmake
    - name: cmake generate
      run: |
        mkdir antsbin
        cd antsbin
        # TODO: check if cmake picks up CMAKE_CXX_FLAGS without being told about it
        # NB: `BUILD_TESTING=OFF` fixes https://github.com/ANTsX/ANTs/issues/1236
        cmake \
         -DBUILD_TESTING=OFF \
         -DBUILD_SHARED_LIBS=OFF \
         -DCMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS" \
         ../
    - name: make
      working-directory: antsbin
      run: |
        make VERBOSE=1 -j 4
      timeout-minutes: 300
      # for debugging, don't let a crash/timeout here fail the whole build
      # (github CI seems glitchy about giving reliable output about what happened on timeouts)
      continue-on-error: true
    - name: pre-package
      run: |
        mkdir fakeroot/
        cd antsbin/ANTS-build
        make VERBOSE=1 -j 4 DESTDIR="../../fakeroot" install
      continue-on-error: true
    - name: package
      run: |
        # snip out the apps we need for https://github.com/neuropoly/spinalcordtoolbox, since including all of ANTS is too much
        mkdir sct-apps/
        cp antsbin/ANTS-build/Examples/{antsRegistration,antsSliceRegularizedRegistration,antsApplyTransforms,ComposeMultiTransform} sct-apps
        (cd sct-apps; for i in *; do mv $i isct_$i; done)
        cp COPYING.txt sct-apps
        tar -zcvf sct-apps_${{ env.ARTIFACT }}.tar.gz sct-apps/
      continue-on-error: true
    - name: results (DEBUG)
      run: find .
    - name: Upload result
      uses: actions/upload-artifact@v2-preview
      with:
        name: sct-apps_${{ env.ARTIFACT }}
        #path: fakeroot/ # this is 2.3G large in this build
        path: sct-apps_${{ env.ARTIFACT }}.tar.gz

  build-manylinuxes: # Github only supports Ubuntu natively; for other Linuxes, we need to use Docker
    strategy:
      matrix:
        os: ['centos:7']  # 'quay.io/centos/centos:stream8', 'archlinux']
        # 'centos:stream8' and 'archlinux' are currently broken. However, we don't currently use either build in our
        # `spinalcordtoolbox-binaries` repo. So, we just temporarily disable for now.
    runs-on: ubuntu-latest
    container: ${{ matrix.os }}
    steps:
    - name: install centos toolchain
      if: contains(matrix.os, 'centos')
      run: |
        yum install -y make gcc gcc-c++ git zlib-devel
    - name: install centos toolchain
      if: contains(matrix.os, 'centos:stream8')
      run: |
        yum install -y cmake
    - name: install centos toolchain
      if: contains(matrix.os, 'centos:7')
      run: |
        # centos7 has a new enough cmake available, but it's not in the default repo
        yum install -y epel-release
        yum install -y cmake3
        ln -s /usr/bin/cmake3 /usr/bin/cmake # make it the default
    - name: install archlinux toolchain
      if: contains(matrix.os, 'archlinux')
      run: |
        pacman -Syy --noconfirm make cmake gcc git libffi
    # first, rewrite OS names to be safe for github artifacts.
    - name: names
      run: |
        OS="${{ matrix.os }}"
        OS=$(echo "$OS" | sed s/://)
        echo "ARTIFACT=$OS" >> $GITHUB_ENV
    - uses: actions/checkout@v3
      with:
        repository: ANTsX/ANTs
        # NB: This commit mirrors the state of the kousu/ANTs repository
        #     at the time of https://github.com/kousu/ANTs/pull/5.
        ref: ${{ github.event.inputs.git_ref || 'b37e8b56e4e518b0f2947f80d0e3701a5ddfe120' }}
    # The step below sets an option inside the cmake file to use the `https` protocol, which addresses:
    # https://github.blog/2021-09-01-improving-git-protocol-security-github/#no-more-unauthenticated-git
    - name: Patch in fix for insecure git:// protocol
      run: |
        perl -pi -e 's/http instead." ON\)/http instead." OFF\)/g' SuperBuild.cmake
    - name: context
      run: |
        set -x
        set
        pwd
        whoami
        hostname || true
        df -h || true
        uname -a
        gcc -v
        cmake --version
        ifconfig
        curl ifconfig.me
      continue-on-error: true
    - name: cmake generate
      run: |
        mkdir antsbin
        cd antsbin
        # NB: `BUILD_TESTING=OFF` fixes https://github.com/ANTsX/ANTs/issues/1236
        cmake \
         -DBUILD_TESTING=OFF \
         -DBUILD_SHARED_LIBS=OFF \
         ../
    - name: make
      working-directory: antsbin
      run: |
        make VERBOSE=1 -j 4
      timeout-minutes: 300
      # for debugging, don't let a crash/timeout here fail the whole build
      # (github CI seems glitchy about giving reliable output about what happened on timeouts)
      continue-on-error: true
    - name: pre-package
      run: |
        mkdir fakeroot/
        cd antsbin/ANTS-build
        make VERBOSE=1 -j 4 DESTDIR="../../fakeroot" install
      continue-on-error: true
    - name: package
      run: |
        # snip out the apps we need for https://github.com/neuropoly/spinalcordtoolbox, since including all of ANTS is too much
        mkdir sct-apps/
        cp antsbin/ANTS-build/Examples/{antsRegistration,antsSliceRegularizedRegistration,antsApplyTransforms,ComposeMultiTransform} sct-apps
        (cd sct-apps; for i in `ls`; do mv $i isct_$i; done)
        cp COPYING.txt sct-apps
        tar -zcvf sct-apps_${{ env.ARTIFACT }}.tar.gz sct-apps/
      continue-on-error: true
    - name: results (DEBUG)
      run: find .
    - name: Upload result
      uses: actions/upload-artifact@v2-preview
      with:
        name: sct-apps_${{ env.ARTIFACT }}
        #path: fakeroot/ # this is 2.3G large in this build
        path: sct-apps_${{ env.ARTIFACT }}.tar.gz

  build-windows:
    strategy:
      matrix:
        os: [ windows-2019 ]
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash
    steps:
    # first, rewrite OS names to be safe for github artifacts.
    - name: names
      run: |
        OS="${{ matrix.os }}"
        OS=$(echo "$OS" | sed s/://)
        echo "ARTIFACT=$OS" >> $GITHUB_ENV
    - uses: actions/checkout@v3
      with:
        repository: ANTsX/ANTs
        # NB: This commit mirrors the state of the kousu/ANTs repository
        #     at the time of https://github.com/kousu/ANTs/pull/5.
        ref: ${{ github.event.inputs.git_ref || 'b37e8b56e4e518b0f2947f80d0e3701a5ddfe120' }}
    # The step below sets an option inside the cmake file to use the `https` protocol, which addresses:
    # https://github.blog/2021-09-01-improving-git-protocol-security-github/#no-more-unauthenticated-git
    - name: Patch in fix for insecure git:// protocol
      run: |
        perl -pi -e 's/http instead." ON\)/http instead." OFF\)/g' SuperBuild.cmake

    ########################################## START OF ITK WORKAROUND ###############################################
    # ITK v5.1 has an upstream bug (https://github.com/InsightSoftwareConsortium/ITK/issues/1967) that prevents
    # building ITK with MS Visual Studio 2019 (which is what the `windows-2019` GitHub Actions runner uses). This bug
    # was fixed in ITK v5.2.
    #
    # Normally, to pull in an upstream fix, we would update ANTs, which in turn would update ITK (because the `make`
    # step for ANTs clones ITK to a specific commit, hardcoded by ANTs in its External_ITKv5.cmake file). However,
    # updating ANTs to pull in the ITK v5.2 fix has the side effect of changing the registration results on SCT's end.
    #
    # So, we need a way to apply a fix for the ITK issue that *doesn't* involve updating ANTs. Luckily, there is a
    # quick and dirty workaround, described here: https://github.com/SuperElastix/SimpleElastix/pull/425#issuecomment-878516818
    #
    # In order to apply the workaround, we have to manually clone ITK ourselves (prior to the ANTs `make` step),
    # then apply the fix, then continue on with building ANTs normally.
    #
    # TODO: Remove this fix after we update ANTs to a version that uses ITK v5.2 or higher.
    ##################################################################################################################
    - name: 'WORKAROUND: Manually clone ITK'
      run: |
        mkdir antsbin
        cd antsbin
        git clone https://github.com/InsightSoftwareConsortium/ITK.git ITKv5
        cd ITKv5
        git checkout 1e708db2f586997e408cfdc2cea5114ae5575892  # This commit corresponds to:
        # https://github.com/ANTsX/ANTs/blob/b37e8b56e4e518b0f2947f80d0e3701a5ddfe120/SuperBuild/External_ITKv5.cmake#L154
        # i.e. the ITK commit specified by the version of ANTs we're currently using.
    - name: 'WORKAROUND: Apply fix for `lrintf` issue in ITK dependency'
      run: sed -i '93,120d' antsbin/ITKv5/Modules/ThirdParty/OpenJPEG/src/openjpeg/opj_includes.h
    - name: 'WORKAROUND: Skip ITK clone in Superbuild'
      run: |
        # These `sed` commands remove the git project settings from the `ExternalProject_Add` cmake function call
        sed -i '/    GIT_REPOSITORY ${${proj}_REPOSITORY}/d' SuperBuild/External_ITKv5.cmake
        sed -i '/    GIT_TAG ${${proj}_GIT_TAG}/d' SuperBuild/External_ITKv5.cmake
    ########################################### END OF ITK WORKAROUND ################################################

    - name: cmake generate
      run: |
        cd antsbin
        # NB: `BUILD_TESTING=OFF` fixes https://github.com/ANTsX/ANTs/issues/1236
        cmake \
         -DBUILD_TESTING=OFF \
         -DBUILD_SHARED_LIBS=OFF \
         -DZLIB_INCLUDE_DIR=D:\lib\zlib \
         -DZLIB_LIBRARY=D:\lib\zlib\libz.dll.a \
         ../
    - name: Add msbuild to PATH
      uses: microsoft/setup-msbuild@v1.1
      with:
        msbuild-architecture: x64
    - name: make
      working-directory: antsbin
      shell: cmd
      run: |
        msbuild ALL_BUILD.vcxproj -property:Configuration=Release
      timeout-minutes: 300
      # for debugging, don't let a crash/timeout here fail the whole build
      # (github CI seems glitchy about giving reliable output about what happened on timeouts)
      continue-on-error: true
    - name: package
      run: |
        # snip out the apps we need for https://github.com/neuropoly/spinalcordtoolbox, since including all of ANTS is too much
        mkdir sct-apps/
        cp antsbin/ANTS-build/Examples/Release/{antsRegistration,antsSliceRegularizedRegistration,antsApplyTransforms,ComposeMultiTransform}.exe sct-apps
        (cd sct-apps; for i in `ls`; do mv $i isct_$i; done)
        cp COPYING.txt sct-apps
        tar -zcvf sct-apps_${{ env.ARTIFACT }}.tar.gz sct-apps/
      continue-on-error: true
    - name: results (DEBUG)
      run: find .
    - name: Upload result
      uses: actions/upload-artifact@v2-preview
      with:
        name: sct-apps_${{ env.ARTIFACT }}
        path: sct-apps_${{ env.ARTIFACT }}.tar.gz

  release:
    needs: [build, build-manylinuxes, build-windows]
    runs-on: ubuntu-latest
    steps:
      - name: Create Release
        id: create_release
        uses: actions/create-release@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          # name the release with the run_id to allow multiple builds on the same branch/tag
          # https://github.com/actions/create-release/issues/2#issuecomment-613591846
          tag_name: ${{ github.ref }}-${{github.run_id }}
          release_name: Release ${{ github.sha }}
          draft: true
          prerelease: true


      - uses: actions/download-artifact@v1
        with:
          name: sct-apps_centos7
        continue-on-error: true
      - name: checkin # DEBUG
        run: find .
      - name: Upload Release Asset
        uses: actions/upload-release-asset@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
          asset_path: ./sct-apps_centos7/sct-apps_centos7.tar.gz
          asset_name: sct-apps_centos7.tar.gz
          asset_content_type: application/gzip
        continue-on-error: true

#      - uses: actions/download-artifact@v1
#        with:
#          name: sct-apps_centos8
#        continue-on-error: true
#      - name: checkin # DEBUG
#        run: find .
#      - name: Upload Release Asset
#        uses: actions/upload-release-asset@v1
#        env:
#          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
#        with:
#          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
#          asset_path: ./sct-apps_centos8/sct-apps_centos8.tar.gz
#          asset_name: sct-apps_centos8.tar.gz
#          asset_content_type: application/gzip
#        continue-on-error: true
#
#      - uses: actions/download-artifact@v1
#        with:
#          name: sct-apps_archlinux
#        continue-on-error: true
#      - name: Upload Release Asset
#        uses: actions/upload-release-asset@v1
#        env:
#          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
#        with:
#          upload_url: ${{ steps.create_release.outputs.upload_url }}
#          asset_path: ./sct-apps_archlinux/sct-apps_archlinux.tar.gz
#          asset_name: sct-apps_archlinux.tar.gz
#          asset_content_type: application/gzip
#        continue-on-error: true

      - uses: actions/download-artifact@v1
        with:
          name: sct-apps_ubuntu-20.04
        continue-on-error: true
      - name: Upload Release Asset
        uses: actions/upload-release-asset@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          upload_url: ${{ steps.create_release.outputs.upload_url }}
          asset_path: ./sct-apps_ubuntu-20.04/sct-apps_ubuntu-20.04.tar.gz
          asset_name: sct-apps_ubuntu-20.04.tar.gz
          asset_content_type: application/gzip
        continue-on-error: true

      - uses: actions/download-artifact@v1
        with:
          name: sct-apps_ubuntu-18.04
        continue-on-error: true
      - name: Upload Release Asset
        uses: actions/upload-release-asset@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          upload_url: ${{ steps.create_release.outputs.upload_url }}
          asset_path: ./sct-apps_ubuntu-18.04/sct-apps_ubuntu-18.04.tar.gz
          asset_name: sct-apps_ubuntu-18.04.tar.gz
          asset_content_type: application/gzip
        continue-on-error: true

      - uses: actions/download-artifact@v1
        with:
          name: sct-apps_macos-10.15
        continue-on-error: true
      - name: Upload Release Asset
        uses: actions/upload-release-asset@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          upload_url: ${{ steps.create_release.outputs.upload_url }}
          asset_path: ./sct-apps_macos-10.15/sct-apps_macos-10.15.tar.gz
          asset_name: sct-apps_macos-10.15.tar.gz
          asset_content_type: application/gzip
        continue-on-error: true

      - uses: actions/download-artifact@v1
        with:
          name: sct-apps_windows-2019
        continue-on-error: true
      - name: Upload Release Asset
        uses: actions/upload-release-asset@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          upload_url: ${{ steps.create_release.outputs.upload_url }}
          asset_path: ./sct-apps_windows-2019/sct-apps_windows-2019.tar.gz
          asset_name: sct-apps_windows-2019.tar.gz
          asset_content_type: application/gzip
        continue-on-error: true