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Merge pull request #1118 from julien-tierny/dev
[ci] upgrading to pv6
2 parents fbb8771 + a9f3bd1 commit 50d865f

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‎.github/actions/install-spectra-unix/action.yml‎

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name: 'Install dependencies for Unix'
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description: 'Install Spectra optional dependencies'
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runs:
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using: "composite"
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steps:
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- name: Install Spectra dependency
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shell: bash
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run: |
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wget https://github.com/yixuan/spectra/archive/v1.1.0.tar.gz
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tar xvf v1.1.0.tar.gz
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mkdir build_spectra && cd build_spectra
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cmake ../spectra-1.1.0
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sudo cmake --build . --target install --parallel

.github/actions/install-deps-unix/action.yml renamed to .github/actions/install-zfp-unix/action.yml

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name: 'Install dependencies for Unix'
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description: 'Install TTK optional dependencies on Ubuntu & macOS'
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description: 'Install ZFP optional dependencies'
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runs:
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using: "composite"
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steps:
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- name: Install Spectra dependency
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shell: bash
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run: |
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wget https://github.com/yixuan/spectra/archive/v1.1.0.tar.gz
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tar xvf v1.1.0.tar.gz
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mkdir build_spectra && cd build_spectra
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cmake ../spectra-1.1.0
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sudo cmake --build . --target install --parallel
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- name: Install ZFP dependency
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shell: bash
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run: |

‎.github/actions/test-ttk-macos/action.yml‎

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name: 'Test TTK for Unix'
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description: 'Test TTK standalone, examples & states on Ubuntu & macOS'
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runs:
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using: "composite"
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steps:
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- name: Test C++ example
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shell: bash
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run: |
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cd $GITHUB_WORKSPACE/examples/c++
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mkdir build && cd build
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cmake .. \
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-DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
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-DOpenMP_C_LIB_NAMES="omp" \
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-DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
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-DOpenMP_CXX_LIB_NAMES="omp" \
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-DOpenMP_omp_LIBRARY=/opt/homebrew/opt/libomp/lib/libomp.dylib \
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-DCMAKE_EXE_LINKER_FLAGS="-L/opt/homebrew/opt/libomp/lib -lomp"
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cmake --build . --parallel
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./ttkExample-c++ -i ../../data/inputData.off
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- name: Test VTK-C++ example
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shell: bash
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run: |
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cd $GITHUB_WORKSPACE/examples/vtk-c++
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mkdir build && cd build
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cmake .. \
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-DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
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-DOpenMP_C_LIB_NAMES="omp" \
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-DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
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-DOpenMP_CXX_LIB_NAMES="omp" \
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-DOpenMP_omp_LIBRARY=/opt/homebrew/opt/libomp/lib/libomp.dylib \
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-DCMAKE_EXE_LINKER_FLAGS="-L/opt/homebrew/opt/libomp/lib -lomp"
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cmake --build . --parallel
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./ttkExample-vtk-c++ -i ../../data/inputData.vtu
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- name: Test Python example
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shell: bash
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run: |
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cd $GITHUB_WORKSPACE/examples/python
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python3 example.py ../data/inputData.vtu
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- name: Test pvpython example
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shell: bash
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run: |
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cd $GITHUB_WORKSPACE/examples/pvpython
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pvpython example.py ../data/inputData.vtu
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- name: Test standalone
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shell: bash
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run: |
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cd $GITHUB_WORKSPACE
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ttkHelloWorldCmd -i examples/data/inputData.vtu

.github/actions/test-ttk-unix/action.yml renamed to .github/actions/test-ttk-ubuntu/action.yml

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‎.github/workflows/check.yml‎

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doxygen \
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clang-tidy
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- name: Install optional dependencies
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uses: ./.github/actions/install-deps-unix
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- name: Install optional Spectra dependency
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uses: ./.github/actions/install-spectra-unix
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- name: Install optional ZFP dependency
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uses: ./.github/actions/install-zfp-unix
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- name: Fetch TTK-ParaView headless Debian package
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run: |
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clang-tools \
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libomp-dev
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- name: Install optional dependencies
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uses: ./.github/actions/install-deps-unix
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- name: Install optional Spectra dependency
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uses: ./.github/actions/install-spectra-unix
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- name: Install optional ZFP dependency
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uses: ./.github/actions/install-zfp-unix
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- name: Fetch TTK-ParaView headless Debian package
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run: |

‎.github/workflows/package.yml‎

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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [macos-13, macos-14, macos-15]
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os: [macos-14, macos-15]
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env:
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DYLD_LIBRARY_PATH: /usr/local/lib
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [macos-13, macos-14, macos-15]
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os: [macos-14, macos-15]
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env:
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DYLD_LIBRARY_PATH: /usr/local/lib
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steps:
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# remove examples which fill up the memory
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rm python/topologicalOptimization_darkSky.py
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# some cases fail only with version 12
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if [[ "${{ matrix.os }}" == "macos-13" ]]; then
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rm python/contourTreeAlignment.py
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rm python/geometryApproximation.py
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rm python/harmonicSkeleton.py
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rm python/topologicalOptimization_torus.py
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fi
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# remove sklearn examples -- buggy on MacOS since sklearn-1.7
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rm python/1manifoldLearning.py python/clusteringKelvinHelmholtzInstabilities.py python/karhunenLoveDigits64Dimensions.py python/mergeTreeClustering.py python/persistentGenerators_householdAnalysis.py python/persistentGenerators_periodicPicture.py
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pvpython -u python/run.py
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file: ttk-ubuntu-24.04.deb/ttk.deb
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asset_name: ttk-$tag-ubuntu-24.04.deb
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- name: Upload MacOS 13 binary archives as Release Asset
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uses: svenstaro/upload-release-action@v2
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with:
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repo_token: ${{ secrets.GITHUB_TOKEN }}
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tag: ${{ github.ref }}
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file: ttk-macos-13.tar.gz/ttk.tar.gz
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asset_name: ttk-$tag-macos-13.tar.gz
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- name: Upload MacOS 14 binary archives as Release Asset
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uses: svenstaro/upload-release-action@v2
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with:

‎.github/workflows/test.yml‎

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cancel-in-progress: true
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env:
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PV_TAG: v5.13.0-headless
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PV_TAG: v6.0.1-headless
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PV_REPO: topology-tool-kit/ttk-paraview
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with:
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key: ${{ matrix.os }}-0
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- name: Install optional dependencies
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uses: ./.github/actions/install-deps-unix
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- name: Install optional Spectra dependency
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uses: ./.github/actions/install-spectra-unix
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- name: Install optional ZFP dependency
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uses: ./.github/actions/install-zfp-unix
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# TODO: try to replicate for mac
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- name: Install Torch
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run: sccache --show-stats
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- name: Run TTK tests
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uses: ./.github/actions/test-ttk-unix
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uses: ./.github/actions/test-ttk-ubuntu
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- name: Upload TTK .deb package for fast install in tests
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uses: actions/upload-artifact@v4
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [macos-13, macos-14, macos-15]
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os: [macos-14, macos-15]
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if: ${{ github.repository_owner == 'topology-tool-kit' || !contains(github.ref, 'heads') }}
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env:
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DYLD_LIBRARY_PATH: /usr/local/lib
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- uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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python-version: '3.13'
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- name: Install macOS dependencies
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run: |
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# ParaView dependencies
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brew install --cask xquartz
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brew install llvm lld ninja open-mpi
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brew install ninja open-mpi libomp
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#brew install llvm lld
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# TTK dependencies
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brew install boost cgal eigen graphviz spectra sqlite zlib numpy qhull
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brew install boost cgal eigen graphviz spectra sqlite numpy qhull
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- name: Install and setup sccache
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uses: f3d-app/sccache-setup-action@v1
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with:
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key: macos-0
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- name: Install optional dependencies
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uses: ./.github/actions/install-deps-unix
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- name: Install optional Spectra dependency
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uses: ./.github/actions/install-spectra-unix
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- name: Install optional ZFP dependency
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uses: ./.github/actions/install-zfp-unix
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- name: Fetch TTK-ParaView headless macOS binary archive
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run: |
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tar xzf ttk-paraview-headless.tar.gz
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sudo cp -r ttk-paraview/* /usr/local
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# pvpython does not embed the correct PYTHONPATH
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echo "PYTHONPATH=/usr/local/lib/python3.12/site-packages:$PYTHONPATH" >> $GITHUB_ENV
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echo "PYTHONPATH=/usr/local/lib/python3.13/site-packages:$PYTHONPATH" >> $GITHUB_ENV
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pvpython -m pip install --break-system-packages scikit-learn
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# pvpython is expecting a vtkpython executable at this path
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sudo ln -s /usr/local/bin/pvpython /Library/Frameworks/Python.framework/Versions/3.12/vtkpython
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- name: Set compilers as environment variables
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run: |
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echo "CC=$(brew --prefix llvm)/bin/clang" >> $GITHUB_ENV
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echo "CXX=$(brew --prefix llvm)/bin/clang++" >> $GITHUB_ENV
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echo "CPPFLAGS=$(brew --prefix llvm)/include" >> $GITHUB_ENV
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echo "LDFLAGS=-L$(brew --prefix llvm)/lib/c++ -L$(brew --prefix llvm)/lib/unwind -lunwind" >> $GITHUB_ENV
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sudo ln -s /usr/local/bin/pvpython /Library/Frameworks/Python.framework/Versions/3.13/vtkpython
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- name: Create & configure TTK build directory
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-DCMAKE_BUILD_TYPE=Release \
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-DCMAKE_C_COMPILER_LAUNCHER=sccache \
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-DCMAKE_CXX_COMPILER_LAUNCHER=sccache \
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-DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
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-DOpenMP_C_LIB_NAMES="omp" \
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-DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
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-DOpenMP_CXX_LIB_NAMES="omp" \
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-DOpenMP_omp_LIBRARY=/opt/homebrew/opt/libomp/lib/libomp.dylib \
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-DCMAKE_EXE_LINKER_FLAGS="-L/opt/homebrew/opt/libomp/lib -lomp" \
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-DTTK_BUILD_PARAVIEW_PLUGINS=TRUE \
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-DTTK_BUILD_VTK_WRAPPERS=TRUE \
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-DTTK_BUILD_STANDALONE_APPS=TRUE \
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-DTTK_ENABLE_KAMIKAZE=TRUE \
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-DTTK_ENABLE_MPI=TRUE \
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-DTTK_ENABLE_MPI=FALSE \
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-DTTK_ENABLE_CPU_OPTIMIZATION=FALSE \
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-DTTK_ENABLE_SHARED_BASE_LIBRARIES=TRUE \
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-DTTK_IMPLICIT_PRECONDITIONS_THRESHOLD=64*64*64 \
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run: sccache --show-stats
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- name: Run TTK tests
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uses: ./.github/actions/test-ttk-unix
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uses: ./.github/actions/test-ttk-macos
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- uses: actions/checkout@v4
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with:
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rm python/mpiExample.py
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rm python/topologicalOptimization_darkSky.py
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# remove examples using raster features
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rm python/geometryApproximation.py
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pvpython.exe -u python\run.py
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- name: Test ttk-data Python scripts results [NOT ENFORCED]

‎CMake/cpack_config.cmake‎

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set(CPACK_RESOURCE_FILE_README ${PROJECT_BINARY_DIR}/Readme.txt)
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endif()
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set(CPACK_DEBIAN_PACKAGE_DEPENDS
22-
"ttk-paraview (= 5.13.0), libboost-system-dev, libeigen3-dev, libgraphviz-dev, libsqlite3-dev, graphviz, python3-sklearn, zlib1g-dev, libqhull-dev, python3-dev, libgl1-mesa-dev")
22+
"ttk-paraview (= 6.0.1), libboost-system-dev, libeigen3-dev, libgraphviz-dev, libsqlite3-dev, graphviz, python3-sklearn, zlib1g-dev, libqhull-dev, python3-dev, libgl1-mesa-dev")
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# autogenerate dependency information
2424
set (CPACK_DEBIAN_PACKAGE_SHLIBDEPS ON)
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# package will be installed under %ProgramFiles%\${CPACK_PACKAGE_INSTALL_DIRECTORY} on Windows

‎ChangeLog.md‎

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- Distributed computation of persistent homology!
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- New backend for TrackingFromFields (critical point based)
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- Fast planar Rips filtration persistence computation
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- CI updates
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89
### 1.3.0
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- Wasserstein Auto-Encoders of Merge Trees / Pers. Diagrams (IEEE TVCG 2024)

‎paraview/patch/headless.yml‎

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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [macos-13, macos-14, macos-15]
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os: [macos-14, macos-15]
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env:
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CCACHE_DIR: /Users/runner/work/ttk/.ccache
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CCACHE_MAXSIZE: 200M
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# ParaView dependencies
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brew install --cask xquartz
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brew install ninja open-mpi
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brew install llvm lld ninja open-mpi
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- name: Set compilers as environment variables
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run: |
95+
echo "CC=$(brew --prefix llvm)/bin/clang" >> $GITHUB_ENV
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echo "CXX=$(brew --prefix llvm)/bin/clang++" >> $GITHUB_ENV
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echo "CPPFLAGS=$(brew --prefix llvm)/include" >> $GITHUB_ENV
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echo "LDFLAGS=-L$(brew --prefix llvm)/lib/c++ -L$(brew --prefix llvm)/lib/unwind -lunwind" >> $GITHUB_ENV
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- name: Create & configure ParaView build directory
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run: |
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file: ttk-paraview-headless-macos-14/ttk-paraview.tar.gz
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asset_name: ttk-paraview-headless-macos-14.tar.gz
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- name: Upload MacOS 13 .tar.gz as Release Asset
274-
uses: svenstaro/upload-release-action@v2
275-
with:
276-
repo_token: ${{ secrets.GITHUB_TOKEN }}
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tag: ${{ github.ref }}
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file: ttk-paraview-headless-macos-13/ttk-paraview.tar.gz
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asset_name: ttk-paraview-headless-macos-13.tar.gz
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- name: Upload .exe as Release Asset
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uses: svenstaro/upload-release-action@v2
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with:

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