[ci] upgrading to pv6

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

@@ -0,0 +1,14 @@
+name: 'Install dependencies for Unix'
+description: 'Install Spectra optional dependencies'
+runs:
+  using: "composite"
+  steps:
+
+    - name: Install Spectra dependency
+      shell: bash
+      run: |
+        wget https://github.com/yixuan/spectra/archive/v1.1.0.tar.gz
+        tar xvf v1.1.0.tar.gz
+        mkdir build_spectra && cd build_spectra
+        cmake ../spectra-1.1.0
+        sudo cmake --build . --target install --parallel

.github/actions/install-deps-unix/action.yml → .github/actions/install-zfp-unix/action.yml

@@ -1,18 +1,9 @@
 name: 'Install dependencies for Unix'
-description: 'Install TTK optional dependencies on Ubuntu & macOS'
+description: 'Install ZFP optional dependencies'
 runs:
   using: "composite"
   steps:
 
-    - name: Install Spectra dependency
-      shell: bash
-      run: |
-        wget https://github.com/yixuan/spectra/archive/v1.1.0.tar.gz
-        tar xvf v1.1.0.tar.gz
-        mkdir build_spectra && cd build_spectra
-        cmake ../spectra-1.1.0
-        sudo cmake --build . --target install --parallel
-
     - name: Install ZFP dependency
       shell: bash
       run: |

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

@@ -0,0 +1,53 @@
+name: 'Test TTK for Unix'
+description: 'Test TTK standalone, examples & states on Ubuntu & macOS'
+runs:
+  using: "composite"
+  steps:
+
+    - name: Test C++ example
+      shell: bash
+      run: |
+        cd $GITHUB_WORKSPACE/examples/c++
+        mkdir build && cd build
+        cmake .. \
+          -DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
+          -DOpenMP_C_LIB_NAMES="omp" \
+          -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
+          -DOpenMP_CXX_LIB_NAMES="omp" \
+          -DOpenMP_omp_LIBRARY=/opt/homebrew/opt/libomp/lib/libomp.dylib \
+          -DCMAKE_EXE_LINKER_FLAGS="-L/opt/homebrew/opt/libomp/lib -lomp" 
+        cmake --build . --parallel
+        ./ttkExample-c++ -i ../../data/inputData.off
+
+    - name: Test VTK-C++ example
+      shell: bash
+      run: |
+        cd $GITHUB_WORKSPACE/examples/vtk-c++
+        mkdir build && cd build
+        cmake .. \
+          -DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
+          -DOpenMP_C_LIB_NAMES="omp" \
+          -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
+          -DOpenMP_CXX_LIB_NAMES="omp" \
+          -DOpenMP_omp_LIBRARY=/opt/homebrew/opt/libomp/lib/libomp.dylib \
+          -DCMAKE_EXE_LINKER_FLAGS="-L/opt/homebrew/opt/libomp/lib -lomp" 
+        cmake --build . --parallel
+        ./ttkExample-vtk-c++ -i ../../data/inputData.vtu
+
+    - name: Test Python example
+      shell: bash
+      run: |
+        cd $GITHUB_WORKSPACE/examples/python
+        python3 example.py ../data/inputData.vtu
+
+    - name: Test pvpython example
+      shell: bash
+      run: |
+        cd $GITHUB_WORKSPACE/examples/pvpython
+        pvpython example.py ../data/inputData.vtu
+
+    - name: Test standalone
+      shell: bash
+      run: |
+        cd $GITHUB_WORKSPACE
+        ttkHelloWorldCmd -i examples/data/inputData.vtu

.github/workflows/check.yml

@@ -118,8 +118,11 @@ jobs:
           doxygen \
           clang-tidy
 
-    - name: Install optional dependencies
-      uses: ./.github/actions/install-deps-unix
+    - name: Install optional Spectra dependency
+      uses: ./.github/actions/install-spectra-unix
+
+    - name: Install optional ZFP dependency
+      uses: ./.github/actions/install-zfp-unix
 
     - name: Fetch TTK-ParaView headless Debian package
       run: |
@@ -207,8 +210,11 @@ jobs:
           clang-tools \
           libomp-dev
 
-    - name: Install optional dependencies
-      uses: ./.github/actions/install-deps-unix
+    - name: Install optional Spectra dependency
+      uses: ./.github/actions/install-spectra-unix
+
+    - name: Install optional ZFP dependency
+      uses: ./.github/actions/install-zfp-unix
 
     - name: Fetch TTK-ParaView headless Debian package
       run: |

.github/workflows/package.yml

@@ -181,7 +181,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-13, macos-14, macos-15]
+        os: [macos-14, macos-15]
     env:  
       DYLD_LIBRARY_PATH: /usr/local/lib
 
@@ -268,7 +268,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-13, macos-14, macos-15]
+        os: [macos-14, macos-15]
     env:
       DYLD_LIBRARY_PATH: /usr/local/lib
     steps:
@@ -344,12 +344,6 @@ jobs:
         # remove examples which fill up the memory
         rm python/topologicalOptimization_darkSky.py
         # some cases fail only with version 12
-        if [[ "${{ matrix.os }}" == "macos-13" ]]; then
-          rm python/contourTreeAlignment.py
-          rm python/geometryApproximation.py
-          rm python/harmonicSkeleton.py
-          rm python/topologicalOptimization_torus.py
-        fi
         # remove sklearn examples -- buggy on MacOS since sklearn-1.7
         rm python/1manifoldLearning.py python/clusteringKelvinHelmholtzInstabilities.py python/karhunenLoveDigits64Dimensions.py python/mergeTreeClustering.py python/persistentGenerators_householdAnalysis.py python/persistentGenerators_periodicPicture.py
         pvpython -u python/run.py
@@ -660,14 +654,6 @@ jobs:
         file: ttk-ubuntu-24.04.deb/ttk.deb
         asset_name: ttk-$tag-ubuntu-24.04.deb
 
-    - name: Upload MacOS 13 binary archives as Release Asset
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GITHUB_TOKEN }}
-        tag: ${{ github.ref }}
-        file: ttk-macos-13.tar.gz/ttk.tar.gz
-        asset_name: ttk-$tag-macos-13.tar.gz
-
     - name: Upload MacOS 14 binary archives as Release Asset
       uses: svenstaro/upload-release-action@v2
       with:

.github/workflows/test.yml

@@ -22,7 +22,7 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  PV_TAG: v5.13.0-headless
+  PV_TAG: v6.0.1-headless
   PV_REPO: topology-tool-kit/ttk-paraview
 
 
@@ -73,8 +73,11 @@ jobs:
       with:
         key: ${{ matrix.os }}-0
 
-    - name: Install optional dependencies
-      uses: ./.github/actions/install-deps-unix
+    - name: Install optional Spectra dependency
+      uses: ./.github/actions/install-spectra-unix
+
+    - name: Install optional ZFP dependency
+      uses: ./.github/actions/install-zfp-unix
 
     # TODO: try to replicate for mac
     - name: Install Torch
@@ -128,7 +131,7 @@ jobs:
       run: sccache --show-stats
 
     - name: Run TTK tests
-      uses: ./.github/actions/test-ttk-unix
+      uses: ./.github/actions/test-ttk-ubuntu
 
     - name: Upload TTK .deb package for fast install in tests
       uses: actions/upload-artifact@v4
@@ -272,7 +275,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-13, macos-14, macos-15]
+        os: [macos-14, macos-15]
     if: ${{ github.repository_owner == 'topology-tool-kit' || !contains(github.ref, 'heads') }}
     env:
       DYLD_LIBRARY_PATH: /usr/local/lib
@@ -283,23 +286,27 @@ jobs:
 
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.12'
+        python-version: '3.13'
 
     - name: Install macOS dependencies
       run: |
         # ParaView dependencies
         brew install --cask xquartz
-        brew install llvm lld ninja open-mpi
+        brew install ninja open-mpi libomp
+        #brew install llvm lld
         # TTK dependencies
-        brew install boost cgal eigen graphviz spectra sqlite zlib numpy qhull
+        brew install boost cgal eigen graphviz spectra sqlite numpy qhull
 
     - name: Install and setup sccache
       uses: f3d-app/sccache-setup-action@v1
       with:
         key: macos-0
 
-    - name: Install optional dependencies
-      uses: ./.github/actions/install-deps-unix
+    - name: Install optional Spectra dependency
+      uses: ./.github/actions/install-spectra-unix
+
+    - name: Install optional ZFP dependency
+      uses: ./.github/actions/install-zfp-unix
 
     - name: Fetch TTK-ParaView headless macOS binary archive
       run: |
@@ -311,17 +318,10 @@ jobs:
         tar xzf ttk-paraview-headless.tar.gz
         sudo cp -r ttk-paraview/* /usr/local
         # pvpython does not embed the correct PYTHONPATH
-        echo "PYTHONPATH=/usr/local/lib/python3.12/site-packages:$PYTHONPATH" >> $GITHUB_ENV
+        echo "PYTHONPATH=/usr/local/lib/python3.13/site-packages:$PYTHONPATH" >> $GITHUB_ENV
         pvpython -m pip install --break-system-packages scikit-learn
         # pvpython is expecting a vtkpython executable at this path
-        sudo ln -s /usr/local/bin/pvpython /Library/Frameworks/Python.framework/Versions/3.12/vtkpython
-
-    - name: Set compilers as environment variables
-      run: |
-        echo "CC=$(brew --prefix llvm)/bin/clang" >> $GITHUB_ENV
-        echo "CXX=$(brew --prefix llvm)/bin/clang++" >> $GITHUB_ENV
-        echo "CPPFLAGS=$(brew --prefix llvm)/include" >> $GITHUB_ENV
-        echo "LDFLAGS=-L$(brew --prefix llvm)/lib/c++ -L$(brew --prefix llvm)/lib/unwind -lunwind" >> $GITHUB_ENV
+        sudo ln -s /usr/local/bin/pvpython /Library/Frameworks/Python.framework/Versions/3.13/vtkpython
 
     - name: Create & configure TTK build directory
       run: |
@@ -331,11 +331,17 @@ jobs:
           -DCMAKE_BUILD_TYPE=Release \
           -DCMAKE_C_COMPILER_LAUNCHER=sccache \
           -DCMAKE_CXX_COMPILER_LAUNCHER=sccache \
+          -DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
+          -DOpenMP_C_LIB_NAMES="omp" \
+          -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
+          -DOpenMP_CXX_LIB_NAMES="omp" \
+          -DOpenMP_omp_LIBRARY=/opt/homebrew/opt/libomp/lib/libomp.dylib \
+          -DCMAKE_EXE_LINKER_FLAGS="-L/opt/homebrew/opt/libomp/lib -lomp" \
           -DTTK_BUILD_PARAVIEW_PLUGINS=TRUE \
           -DTTK_BUILD_VTK_WRAPPERS=TRUE \
           -DTTK_BUILD_STANDALONE_APPS=TRUE \
           -DTTK_ENABLE_KAMIKAZE=TRUE \
-          -DTTK_ENABLE_MPI=TRUE \
+          -DTTK_ENABLE_MPI=FALSE \
           -DTTK_ENABLE_CPU_OPTIMIZATION=FALSE \
           -DTTK_ENABLE_SHARED_BASE_LIBRARIES=TRUE \
           -DTTK_IMPLICIT_PRECONDITIONS_THRESHOLD=64*64*64 \
@@ -356,7 +362,7 @@ jobs:
       run: sccache --show-stats
 
     - name: Run TTK tests
-      uses: ./.github/actions/test-ttk-unix
+      uses: ./.github/actions/test-ttk-macos
 
     - uses: actions/checkout@v4
       with:
@@ -589,6 +595,8 @@ jobs:
         rm python/mpiExample.py
         # remove examples which fill up the memory
         rm python/topologicalOptimization_darkSky.py
+        # remove examples using raster features
+        rm python/geometryApproximation.py
         pvpython.exe -u python\run.py
 
     - name: Test ttk-data Python scripts results [NOT ENFORCED]

CMake/cpack_config.cmake

@@ -19,7 +19,7 @@ else()
   set(CPACK_RESOURCE_FILE_README ${PROJECT_BINARY_DIR}/Readme.txt)
 endif()
 set(CPACK_DEBIAN_PACKAGE_DEPENDS
-  "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")
+  "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")
 # autogenerate dependency information
 set (CPACK_DEBIAN_PACKAGE_SHLIBDEPS ON)
 # package will be installed under %ProgramFiles%\${CPACK_PACKAGE_INSTALL_DIRECTORY} on Windows

ChangeLog.md

@@ -4,6 +4,7 @@
 - Distributed computation of persistent homology!
 - New backend for TrackingFromFields (critical point based)
 - Fast planar Rips filtration persistence computation
+- CI updates
 
 ### 1.3.0
 - Wasserstein Auto-Encoders of Merge Trees / Pers. Diagrams (IEEE TVCG 2024)

paraview/patch/headless.yml

@@ -72,7 +72,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-13, macos-14, macos-15]
+        os: [macos-14, macos-15]
     env:
       CCACHE_DIR: /Users/runner/work/ttk/.ccache
       CCACHE_MAXSIZE: 200M
@@ -88,7 +88,14 @@ jobs:
       run: |
         # ParaView dependencies
         brew install --cask xquartz
-        brew install ninja open-mpi
+        brew install llvm lld ninja open-mpi
+
+    - name: Set compilers as environment variables
+      run: |
+        echo "CC=$(brew --prefix llvm)/bin/clang" >> $GITHUB_ENV
+        echo "CXX=$(brew --prefix llvm)/bin/clang++" >> $GITHUB_ENV
+        echo "CPPFLAGS=$(brew --prefix llvm)/include" >> $GITHUB_ENV
+        echo "LDFLAGS=-L$(brew --prefix llvm)/lib/c++ -L$(brew --prefix llvm)/lib/unwind -lunwind" >> $GITHUB_ENV
 
     - name: Create & configure ParaView build directory
       run: |
@@ -270,15 +277,6 @@ jobs:
         file: ttk-paraview-headless-macos-14/ttk-paraview.tar.gz
         asset_name: ttk-paraview-headless-macos-14.tar.gz
 
-    - name: Upload MacOS 13 .tar.gz as Release Asset
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GITHUB_TOKEN }}
-        tag: ${{ github.ref }}
-        file: ttk-paraview-headless-macos-13/ttk-paraview.tar.gz
-        asset_name: ttk-paraview-headless-macos-13.tar.gz
-
-
     - name: Upload .exe as Release Asset
       uses: svenstaro/upload-release-action@v2
       with:

paraview/patch/package.yml

@@ -75,7 +75,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-13, macos-14, macos-15]
+        os: [macos-14, macos-15]
     env:
       CCACHE_DIR: /Users/runner/work/ttk/.ccache
       CCACHE_MAXSIZE: 200M
@@ -91,7 +91,14 @@ jobs:
       run: |
         # ParaView dependencies
         brew install --cask xquartz
-        brew install mesa glew qt@5 ninja 
+        brew install llvm lld mesa glew qt@5 ninja 
+
+    - name: Set compilers as environment variables
+      run: |
+        echo "CC=$(brew --prefix llvm)/bin/clang" >> $GITHUB_ENV
+        echo "CXX=$(brew --prefix llvm)/bin/clang++" >> $GITHUB_ENV
+        echo "CPPFLAGS=$(brew --prefix llvm)/include" >> $GITHUB_ENV
+        echo "LDFLAGS=-L$(brew --prefix llvm)/lib/c++ -L$(brew --prefix llvm)/lib/unwind -lunwind" >> $GITHUB_ENV
 
     - name: Create & configure ParaView build directory
       run: |
@@ -271,14 +278,6 @@ jobs:
         file: ttk-paraview-macos-14/ttk-paraview.tar.gz
         asset_name: ttk-paraview-$tag-macos-14.tar.gz
 
-    - name: Upload MacOS 13 .tar.gz as Release Asset
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GITHUB_TOKEN }}
-        tag: ${{ github.ref }}
-        file: ttk-paraview-macos-13/ttk-paraview.tar.gz
-        asset_name: ttk-paraview-$tag-macos-13.tar.gz
-
     - name: Upload .exe as Release Asset
       uses: svenstaro/upload-release-action@v2
       with: