time tracking : backend with critical points

Author: thom-dani

.github/workflows/package.yml

@@ -180,43 +180,44 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-12, macos-14]
+        os: [macos-13, macos-14, macos-15]
     env:  
       DYLD_LIBRARY_PATH: /usr/local/lib
 
     steps:
     - uses: actions/checkout@v4
       name: Checkout TTK source code
 
-    - name: Remove hosted Python
-      run: |
-        sudo rm -rf /Library/Frameworks/Python.framework/
-        sudo rm -rf /usr/local/Frameworks/Python.framework/
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
 
     - name: Install macOS dependencies
       run: |
         # ParaView dependencies
-        brew reinstall python
         brew install --cask xquartz
         brew install llvm mesa glew qt@5 ninja 
         # TTK dependencies
         brew install boost eigen graphviz spectra sqlite zlib 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: Fetch & install TTK-ParaView
       run: |
-        if [[ "${{ matrix.os }}" == "macos-12" ]]; then
-          wget https://github.com/${{ env.PV_REPO }}/releases/download/${{ env.PV_TAG }}/ttk-paraview-${{ env.PV_TAG }}-${{ matrix.os }}.tar.gz
-          tar xzf ttk-paraview-${{ env.PV_TAG }}-${{ matrix.os }}.tar.gz
-        fi
-        if [[ "${{ matrix.os }}" == "macos-14" ]]; then
-          wget https://github.com/${{ env.PV_REPO }}/releases/download/${{ env.PV_TAG }}/ttk-paraview-${{ env.PV_TAG }}-${{ matrix.os }}-arm64.tar.gz
-          tar xzf ttk-paraview-${{ env.PV_TAG }}-${{ matrix.os }}-arm64.tar.gz
-        fi
+        wget https://github.com/${{ env.PV_REPO }}/releases/download/${{ env.PV_TAG }}/ttk-paraview-${{ env.PV_TAG }}-${{ matrix.os }}.tar.gz
+        tar xzf ttk-paraview-${{ env.PV_TAG }}-${{ matrix.os }}.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
         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: |
@@ -230,8 +231,6 @@ jobs:
         cmake \
           -DCMAKE_BUILD_TYPE=Release \
           -DQt5_DIR=$(brew --prefix qt@5)/lib/cmake/Qt5 \
-          -DPython3_FIND_STRATEGY=LOCATION \
-          -DPython3_ROOT_DIR=$(brew --prefix python) \
           -DTTK_BUILD_PARAVIEW_PLUGINS=TRUE \
           -DTTK_BUILD_VTK_WRAPPERS=TRUE \
           -DTTK_BUILD_STANDALONE_APPS=TRUE \
@@ -266,36 +265,36 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-12, macos-14]
+        os: [macos-13, macos-14, macos-15]
     env:
       DYLD_LIBRARY_PATH: /usr/local/lib
     steps:
     - uses: actions/checkout@v4
       name: Checkout TTK source code
 
-    - name: Remove hosted Python
-      run: |
-        sudo rm -rf /Library/Frameworks/Python.framework
-        sudo rm -rf /usr/local/Frameworks/Python.framework
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
 
     - name: Install macOS dependencies
       run: |
         # ParaView dependencies
-        brew reinstall python
         brew install --cask xquartz
         brew install llvm mesa glew qt@5 ninja 
         # TTK dependencies
         brew install boost eigen graphviz spectra sqlite zlib 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: Fetch TTK-ParaView
       run: |
-        if [[ "${{ matrix.os }}" == "macos-12" ]]; then
-          wget -O ttk-paraview.tar.gz https://github.com/${{ env.PV_REPO }}/releases/download/${{ env.PV_TAG }}/ttk-paraview-${{ env.PV_TAG }}-${{ matrix.os }}.tar.gz
-        fi
-        if [[ "${{ matrix.os }}" == "macos-14" ]]; then
-          wget -O ttk-paraview.tar.gz https://github.com/${{ env.PV_REPO }}/releases/download/${{ env.PV_TAG }}/ttk-paraview-${{ env.PV_TAG }}-${{ matrix.os }}-arm64.tar.gz
-        fi
-
+        wget -O ttk-paraview.tar.gz https://github.com/${{ env.PV_REPO }}/releases/download/${{ env.PV_TAG }}/ttk-paraview-${{ env.PV_TAG }}-${{ matrix.os }}.tar.gz
 
     - name: Fetch TTK .tar.gz artifact
       uses: actions/download-artifact@v4.1.7
@@ -317,6 +316,8 @@ jobs:
         echo "CMAKE_PREFIX_PATH=$(brew --prefix qt@5)/lib/cmake:$CMAKE_PREFIX_PATH" >> $GITHUB_ENV
         # pvpython does not embed the correct PYTHONPATH
         echo "PYTHONPATH=/usr/local/lib/python3.12/site-packages:$PYTHONPATH" >> $GITHUB_ENV
+        # 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: Run TTK tests
       uses: ./.github/actions/test-ttk-unix
@@ -337,7 +338,7 @@ jobs:
         # remove examples which fill up the memory
         rm python/topologicalOptimization_darkSky.py
         # some cases fail only with version 12
-        if [[ "${{ matrix.os }}" == "macos-12" ]]; then
+        if [[ "${{ matrix.os }}" == "macos-13" ]]; then
           rm python/contourTreeAlignment.py
           rm python/geometryApproximation.py
           rm python/harmonicSkeleton.py
@@ -659,21 +660,29 @@ jobs:
         file: ttk-ubuntu-24.04.deb/ttk.deb
         asset_name: ttk-$tag-ubuntu-24.04.deb
 
-    - name: Upload MacOS 12 binary archives as Release Asset
+    - name: Upload MacOS 13 binary archives as Release Asset
       uses: svenstaro/upload-release-action@v2
       with:
         repo_token: ${{ secrets.GITHUB_TOKEN }}
         tag: ${{ github.ref }}
-        file: ttk-macos-12.tar.gz/ttk.tar.gz
-        asset_name: ttk-$tag-macos-12.tar.gz
+        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:
         repo_token: ${{ secrets.GITHUB_TOKEN }}
         tag: ${{ github.ref }}
         file: ttk-macos-14.tar.gz/ttk.tar.gz
-        asset_name: ttk-$tag-macos-14-arm64.tar.gz
+        asset_name: ttk-$tag-macos-14.tar.gz
+
+    - name: Upload MacOS 15 binary archives as Release Asset
+      uses: svenstaro/upload-release-action@v2
+      with:
+        repo_token: ${{ secrets.GITHUB_TOKEN }}
+        tag: ${{ github.ref }}
+        file: ttk-macos-15.tar.gz/ttk.tar.gz
+        asset_name: ttk-$tag-macos-15.tar.gz
 
     - name: Upload Windows .exe as Release Asset
       uses: svenstaro/upload-release-action@v2

.github/workflows/test.yml

@@ -271,7 +271,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-12, macos-14]
+        os: [macos-13, macos-14, macos-15]
     if: ${{ github.repository_owner == 'topology-tool-kit' || !contains(github.ref, 'heads') }}
     env:
       DYLD_LIBRARY_PATH: /usr/local/lib
@@ -280,14 +280,13 @@ jobs:
     - uses: actions/checkout@v4
       name: Checkout TTK source code
 
-    - name: Remove hosted Python
-      run: |
-        sudo rm -rf /Library/Frameworks/Python.framework/
-        sudo rm -rf /usr/local/Frameworks/Python.framework/
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+
     - name: Install macOS dependencies
       run: |
         # ParaView dependencies
-        brew reinstall python
         brew install --cask xquartz
         brew install llvm ninja open-mpi
         # TTK dependencies
@@ -303,20 +302,18 @@ jobs:
 
     - name: Fetch TTK-ParaView headless macOS binary archive
       run: |
-        if [[ "${{ matrix.os }}" == "macos-12" ]]; then
           wget -O ttk-paraview-headless.tar.gz \
             https://github.com/${{ env.PV_REPO }}/releases/download/${{ env.PV_TAG }}/ttk-paraview-headless-${{ matrix.os }}.tar.gz
-        fi
-        if [[ "${{ matrix.os }}" == "macos-14" ]]; then
-          wget -O ttk-paraview-headless.tar.gz \
-            https://github.com/${{ env.PV_REPO }}/releases/download/${{ env.PV_TAG }}/ttk-paraview-headless-${{ matrix.os }}-arm64.tar.gz
-        fi
 
     - name: Install ParaView
       run: |
         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
         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: |
@@ -355,11 +352,6 @@ jobs:
       shell: bash
       run: sccache --show-stats
 
-    - name: Set PYTHONPATH for macOS pvpython
-      run: |
-        # pvpython does not embed the correct PYTHONPATH
-        echo "PYTHONPATH=/usr/local/lib/python3.12/site-packages:$PYTHONPATH" >> $GITHUB_ENV
-
     - name: Run TTK tests
       uses: ./.github/actions/test-ttk-unix
 
@@ -371,7 +363,6 @@ jobs:
       name: Checkout ttk-data
 
     - name: Run ttk-data states [NOT ENFORCED]
-      if: false
       id: validate
       continue-on-error: true
       run: |
@@ -380,6 +371,8 @@ jobs:
         rm ttk-data/states/nestedTrackingFromOverlap.py
         # remove examples which fill up the memory
         rm ttk-data/states/topologicalOptimization_darkSky.pvsm
+        # remove examples that take too long to render under mac
+        rm ttk-data/states/persistentGenerators_householdAnalysis.pvsm
         cd ttk-data/tests
         mkdir output_screenshots
         pvpython -u validate.py || (tar zcf screenshots.tar.gz output_screenshots && false)
@@ -390,7 +383,7 @@ jobs:
       if: steps.validate.outcome == 'failure'
       uses: actions/upload-artifact@v4
       with:
-        name: screenshots-macOS.tar.gz
+        name: screenshots-${{ matrix.os }}.tar.gz
         path: ttk-data/tests/screenshots.tar.gz
         retention-days: 10
 

core/base/approximateTopology/ApproximateTopology.h

@@ -1067,12 +1067,10 @@ bool ttk::ApproximateTopology::printPolarity(
   std::stringstream mymsg;
   std::vector<std::pair<polarity, polarity>> &vlp
     = vertexLinkPolarity[vertexId];
-  mymsg << "POLARITY PRINT"
-        << "\n";
+  mymsg << "POLARITY PRINT" << "\n";
   mymsg << "vertex " << vertexId << " has "
         << multiresTriangulation_.getVertexNeighborNumber(vertexId)
-        << " neighbors"
-        << "\n";
+        << " neighbors" << "\n";
   mymsg << "\tself  f:" << fakeScalars[vertexId] << " s:" << scalars[vertexId]
         << " o:" << offsets[vertexId] << " m:" << monotonyOffsets[vertexId]
         << "  isnew: " << (int)isNew[vertexId] << "\n";
@@ -1115,13 +1113,12 @@ bool ttk::ApproximateTopology::printPolarity(
     mymsg << " " << i << "th: " << nId << " f:" << fakeScalars[nId]
           << " s:" << scalars[nId] << " o:" << offsets[nId]
           << " m:" << monotonyOffsets[nId] << "  , pol:" << (bool)vlp[i].first
-          << "(" << (bool)vlp[i].second << ")"
-          << " rpol:" << (bool)rpol << "  true pol:" << (bool)isUpper
-          << " init " << init << "  isnew: " << (int)isNew[nId] << "\n";
+          << "(" << (bool)vlp[i].second << ")" << " rpol:" << (bool)rpol
+          << "  true pol:" << (bool)isUpper << " init " << init
+          << "  isnew: " << (int)isNew[nId] << "\n";
     if((rpol == isUpper and !vlp2.empty())
        or (isUpper != vlp[i].first and !vlp[i].second)) {
-      mymsg << "POLARITY ERROR "
-            << "\n";
+      mymsg << "POLARITY ERROR " << "\n";
       error = true;
     }
   }

core/base/arrayPreconditioning/ArrayPreconditioning.h

@@ -293,7 +293,9 @@ namespace ttk {
         std::vector<globalOrder::vertexToSort<DT>> verticesToSort;
         verticesToSort.reserve(nVerts);
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp declare reduction (merge : std::vector<globalOrder::vertexToSort<DT>> : omp_out.insert(omp_out.end(), omp_in.begin(), omp_in.end()))
+#pragma omp declare reduction(                                           \
+    merge : std::vector<globalOrder::vertexToSort<DT>> : omp_out.insert( \
+        omp_out.end(), omp_in.begin(), omp_in.end()))
 #pragma omp parallel for reduction(merge : verticesToSort) schedule(static)
 #endif
         for(size_t i = 0; i < nVerts; i++) {

core/base/assignmentSolver/AssignmentAuction.h

@@ -275,6 +275,7 @@ namespace ttk {
     initFirstRound();
     while(not stoppingCriterion(this->costMatrix)) {
       initBiddersAndGoods();
+
       runAuctionRound(this->costMatrix);
 
       dataType cost = getMatchingDistance(this->costMatrix);

core/base/clusteringMetrics/ClusteringMetrics.cpp

@@ -114,7 +114,8 @@ int ttk::ClusteringMetrics::computeARI(
 
   double sumNChooseContingency = 0;
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for num_threads(this->threadNumber_) reduction(+:sumNChooseContingency)
+#pragma omp parallel for num_threads(this->threadNumber_) \
+  reduction(+ : sumNChooseContingency)
 #endif // TTK_ENABLE_OPENMP
   for(size_t i1 = 0; i1 < nCluster1; i1++) {
     for(size_t i2 = 0; i2 < nCluster2; i2++)
@@ -165,7 +166,8 @@ int ttk::ClusteringMetrics::computeNMI(
   double mutualInfo = 0;
   bool invalidCell = false;
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for num_threads(this->threadNumber_) reduction(+:mutualInfo)
+#pragma omp parallel for num_threads(this->threadNumber_) \
+  reduction(+ : mutualInfo)
 #endif // TTK_ENABLE_OPENMP
   for(size_t i1 = 0; i1 < nCluster1; i1++) {
     for(size_t i2 = 0; i2 < nCluster2; i2++) {

core/base/common/Os.h

@@ -25,7 +25,7 @@
 #include <string>
 #include <vector>
 
-//#define SINGLE_PRECISION
+// #define SINGLE_PRECISION
 
 #ifdef SINGLE_PRECISION
 #define REAL_TYPE float