Build ANTs #21
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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/[email protected] | |
| 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 |