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Merge branch 'master' into regressionv2
2 parents b1ad5a1 + c73a9e2 commit 0c3214b

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‎.github/workflows/build-linux-debug.yml

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@@ -28,12 +28,6 @@ jobs:
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steps:
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- name: Install SSH Key
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uses: shimataro/[email protected]
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with:
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key: ${{ secrets.SSH_PRIVATE_KEY }}
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known_hosts: ${{ secrets.KNOWN_HOSTS }}
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- name: Conda info
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run: conda info
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@@ -60,10 +54,6 @@ jobs:
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- name: Get tags
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run: git fetch --unshallow origin +refs/tags/*:refs/tags/*
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- name: Restore Caches
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shell: bash -l {0}
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run: .github/workflows/restore_caches.sh
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- name: Check space3
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run: df -h
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@@ -83,7 +73,7 @@ jobs:
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- name: cmake
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shell: bash -l {0}
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run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.2 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.1 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON ..
76+
run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.3 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.1 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON ..
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- name: Check space6
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run: df -h
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- name: make test
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shell: bash -l {0}
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run: conda activate shapeworks && source ./devenv.sh ./build/bin && cd build && ctest -VV
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- name: Store ccache
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shell: bash -l {0}
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run: .github/workflows/store_ccache.sh
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‎.github/workflows/build-linux.yml

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@@ -29,12 +29,6 @@ jobs:
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steps:
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- name: Install SSH Key
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uses: shimataro/[email protected]
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with:
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key: ${{ secrets.SSH_PRIVATE_KEY }}
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known_hosts: ${{ secrets.KNOWN_HOSTS }}
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- name: Conda info
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run: conda info
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- name: Check space3
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run: df -h
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- name: Restore Caches
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shell: bash -l {0}
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run: .github/workflows/restore_caches.sh
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- name: Conda Installs
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shell: bash -l {0}
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run: .github/workflows/gha_conda.sh
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- name: cmake
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shell: bash -l {0}
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run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.2 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.1 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..
75+
run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.3 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.1 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..
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- name: Check space5
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run: df -h
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shell: bash -l {0}
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run: conda activate shapeworks && source ./devenv.sh ./build/bin && cd build && ctest -VV
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- name: Copy artifact
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shell: bash -l {0}
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run: cd /__w/ShapeWorks/ShapeWorks/artifacts && ${GITHUB_WORKSPACE}/.github/workflows/copy_artifact.sh artifact-${{github.sha}}-linux *
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- uses: actions/upload-artifact@v2
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with:
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name: artifact-${{github.sha}}-linux
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title: "Development Build for Linux"
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files: |
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${{runner.workspace}}/ShapeWorks/artifacts/*.tar.gz
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- name: Store ccache
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shell: bash -l {0}
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run: .github/workflows/store_ccache.sh
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‎.github/workflows/build-mac-arm64.yml

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steps:
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- name: Install SSH Key
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uses: shimataro/ssh-key-action@v2
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with:
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key: ${{ secrets.SSH_PRIVATE_KEY }}
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known_hosts: ${{ secrets.KNOWN_HOSTS }}
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- name: Setup Miniconda
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uses: conda-incubator/[email protected]
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- name: Get tags
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run: git fetch --unshallow origin +refs/tags/*:refs/tags/*
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- name: Restore Caches
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shell: bash -l {0}
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run: .github/workflows/restore_caches.sh
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- name: Conda Installs
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shell: bash -l {0}
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run: .github/workflows/gha_conda.sh
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env:
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GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Store ccache
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shell: bash -l {0}
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run: .github/workflows/store_ccache.sh
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- name: Copy artifact
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shell: bash -l {0}
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run: cd ${{runner.workspace}}/ShapeWorks && ${GITHUB_WORKSPACE}/.github/workflows/copy_artifact.sh artifact-${{github.sha}}-mac-arm64 artifacts
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‎.github/workflows/build-mac.yml

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steps:
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- name: Install SSH Key
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uses: shimataro/ssh-key-action@v2
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with:
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key: ${{ secrets.SSH_PRIVATE_KEY }}
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known_hosts: ${{ secrets.KNOWN_HOSTS }}
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- name: OS Setup
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run: |
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ls /usr/local
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- name: Get tags
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run: git fetch --unshallow origin +refs/tags/*:refs/tags/*
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- name: Restore Caches
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shell: bash -l {0}
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run: .github/workflows/restore_caches.sh
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- name: Conda Installs
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run: .github/workflows/gha_conda.sh
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env:
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GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Store ccache
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shell: bash -l {0}
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run: .github/workflows/store_ccache.sh
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- name: Copy artifact
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shell: bash -l {0}
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run: cd ${{runner.workspace}}/ShapeWorks && ${GITHUB_WORKSPACE}/.github/workflows/copy_artifact.sh artifact-${{github.sha}}-mac artifacts
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‎.github/workflows/build-windows.yml

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@@ -39,7 +39,7 @@ jobs:
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- name: Init conda
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run: /c/Miniconda/condabin/conda.bat init --all
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# - name: link
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# shell: bash -l {0}
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# run: cd /usr/bin && ln -s /c/Miniconda/condabin/conda.bat conda
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# with:
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# miniconda-version: 'latest'
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- name: Install SSH Key
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uses: shimataro/ssh-key-action@v2
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with:
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key: ${{ secrets.SSH_PRIVATE_KEY }}
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known_hosts: ${{ secrets.KNOWN_HOSTS }}
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- name: Checkout code
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uses: actions/checkout@v3
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with:
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- name: Get tags
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run: git fetch --unshallow origin +refs/tags/*:refs/tags/*
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- name: Download test data
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shell: bash -l {0}
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run: .github/workflows/download_test_data.sh
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- name: Get NSIS
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working-directory: ${{runner.workspace}}
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run: |
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curl -o nsis.zip http://www.sci.utah.edu/~amorris/NSISPortable_3.04.zip
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Expand-Archive -LiteralPath nsis.zip -DestinationPath .
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- name: Restore Caches
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shell: bash -l {0}
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run: .github/workflows/restore_caches.sh
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- name: Conda Installs
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run: .github/workflows/gha_conda.sh
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# Note the current convention is to use the -S and -B options here to specify source
116110
# and build directories, but this is only available with CMake 3.13 and higher.
117111
# The CMake binaries on the Github Actions machines are (as of this writing) 3.12
118-
run: conda activate shapeworks && cmake $GITHUB_WORKSPACE -DCMAKE_CXX_FLAGS="-FS" -DCMAKE_C_FLAGS="-FS" -DCMAKE_CXX_FLAGS_RELEASE="-FS /Zm500 /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_C_FLAGS_RELEASE="-FS /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_SHARED_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_EXE_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DITK_DIR="C:\deps\lib\cmake\ITK-5.2" -DVTK_DIR="C:\deps\lib\cmake\vtk-9.1" -DXLNT_DIR="C:\deps" -DLIBIGL_DIR="C:\deps" -DJKQTCommonSharedLib_DIR="C:/deps/lib/cmake/JKQTCommonSharedLib" -DJKQTMathTextSharedLib_DIR="C:/deps/lib/cmake/JKQTMathTextSharedLib" -DJKQTPlotterSharedLib_DIR="C:/deps/lib/cmake/JKQTPlotterSharedLib" -DOpenVDB_DIR="C:\deps\lib\cmake\OpenVDB" -DGEOMETRYCENTRAL_DIR="C:\deps" -DACVD_DIR="C:\deps" -DBuild_Studio=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET
112+
run: conda activate shapeworks && cmake $GITHUB_WORKSPACE -DCMAKE_CXX_FLAGS="-FS" -DCMAKE_C_FLAGS="-FS" -DCMAKE_CXX_FLAGS_RELEASE="-FS /Zm500 /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_C_FLAGS_RELEASE="-FS /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_SHARED_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_EXE_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DITK_DIR="C:\deps\lib\cmake\ITK-5.3" -DVTK_DIR="C:\deps\lib\cmake\vtk-9.1" -DXLNT_DIR="C:\deps" -DLIBIGL_DIR="C:\deps" -DJKQTCommonSharedLib_DIR="C:/deps/lib/cmake/JKQTCommonSharedLib" -DJKQTMathTextSharedLib_DIR="C:/deps/lib/cmake/JKQTMathTextSharedLib" -DJKQTPlotterSharedLib_DIR="C:/deps/lib/cmake/JKQTPlotterSharedLib" -DOpenVDB_DIR="C:\deps\lib\cmake\OpenVDB" -DGEOMETRYCENTRAL_DIR="C:\deps" -DACVD_DIR="C:\deps" -DBuild_Studio=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET
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- name: Build
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working-directory: "C:/build"
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title: "Development Build for Windows"
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files: |
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d:/a/ShapeWorks/ShapeWorks/artifacts/*.exe
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- name: Copy artifact
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shell: bash -l {0}
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run: cd /d/a/ShapeWorks/ShapeWorks/artifacts && ${GITHUB_WORKSPACE}/.github/workflows/copy_artifact.sh artifact-${{github.sha}}-windows *
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‎.github/workflows/download_test_data.sh

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# based on root folder
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cd /
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# if platform is windows, install wget
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if [ "$PLATFORM" == "windows" ]; then
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choco install wget --no-progress
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fi
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# Tiny test data downloads
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for run in {1..5}; do
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if [ ! -f /tmp/tiny_test_cache.tar.gz ] ; then
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scp runner@${CACHE_HOST}:github/tiny_test_cache.tar.gz /tmp || true
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cd /tmp
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wget https://www.sci.utah.edu/~shapeworks/doc-resources/zips/tiny_test_cache.tar.gz || true
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‎.github/workflows/gha_conda.sh

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# run install
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source ./install_shapeworks.sh --developer
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conda clean -p -t -y
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echo "Create and store cache"
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cd /
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compress_file /tmp/${CONDA_FILE} "${CONDA_PATH}"
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scp /tmp/${CONDA_FILE} runner@${CACHE_HOST}:github
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rm /tmp/${CONDA_FILE}
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‎.github/workflows/gha_deps.sh

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rm -rf $BUILD_DIR
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echo "Create and store cache"
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cd /
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compress_file ${FILE} "${DEP_PATH}"
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scp ${FILE} runner@${CACHE_HOST}:github
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rm ${FILE}
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fi

‎CMakeLists.txt

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find_package (Eigen3 3.3 REQUIRED NO_MODULE)
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### ITK
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FIND_PACKAGE(ITK 5.2.1 REQUIRED)
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FIND_PACKAGE(ITK 5.3.0 REQUIRED)
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IF (ITK_FOUND)
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INCLUDE(${ITK_USE_FILE})
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‎Examples/Python/Data/femur_pvalues.zip

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version https://git-lfs.github.com/spec/v1
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oid sha256:9105d2c3e61ffd4cbff59584258807ee2250b8723ceff519a37694cbcad8033b
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size 350473

‎Examples/Python/Data/supershapes_1mode_contour.zip

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version https://git-lfs.github.com/spec/v1
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oid sha256:1b1dc6d05a3450976b0102926716d44708849d0d31f5da24a187408ba499ec3e
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size 121224

‎Examples/Python/ellipsoid_fd.py

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We define dataset_name which determines which dataset to download from
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the portal and the directory to save output from the use case in.
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"""
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dataset_name = "ellipsoid_fd"
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dataset_name = "ellipsoid_fd_multiscale"
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output_directory = "Output/ellipsoid_fd/"
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‎Examples/Python/femur_pvalues.py

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import numpy as np
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import pandas as pd
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import json
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import zipfile
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def Run_Pipeline(args):
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dataset_name = 'femur_pvalues'
13-
sw.download_dataset(dataset_name, output_directory)
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# unzip Data/femur_pvalues.zip
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zip_file = 'Data/femur_pvalues.zip'
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with zipfile.ZipFile(zip_file, 'r') as zip_ref:
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zip_ref.extractall("Output/")
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csvfile = convert_swproj_to_csv(swproj_file)
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data = pd.read_csv(csvfile)

‎Examples/Python/supershapes_1mode_contour.py

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import shapeworks as sw
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import zipfile
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2224
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25-
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zip_file = 'Data/supershapes_1mode_contour.zip'
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with zipfile.ZipFile(zip_file, 'r') as zip_ref:
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zip_ref.extractall("Output/")
31+
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2632
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contour_files = sorted(glob.glob(output_directory + dataset_name + "/contours/*.vtp"))
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‎Libs/Analyze/Shape.cpp

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -558,8 +558,8 @@ void Shape::load_feature(DisplayMode display_mode, std::string feature) {
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group.meshes()[d]->apply_feature_map(feature, image);
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apply_feature_to_points(feature, image);
561-
} catch (itk::ExceptionObject& excep) {
562-
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561+
} catch (std::exception& ex) {
562+
SW_ERROR("Unable to open file \"{}\": {}", filename, ex.what());
563563
}
564564
}
565565
}
@@ -582,7 +582,7 @@ std::shared_ptr<Image> Shape::get_image_volume(std::string image_volume_name) {
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image_volume_ = image;
583583
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584584
} catch (std::exception& ex) {
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}
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}
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‎Libs/Common/CMakeLists.txt

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@@ -3,14 +3,12 @@ set(Common_sources
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Shapeworks.cpp
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ShapeworksUtils.cpp
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Region.cpp
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Exception.cpp
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Logging.cpp
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)
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set(Common_headers
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Shapeworks.h
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ShapeworksUtils.h
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Region.h
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Exception.h
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Logging.h
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)
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add_library(Common STATIC

‎Libs/Common/Exception.cpp

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