Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into dev

Author: julien-tierny

.github/workflows/test.yml

@@ -22,7 +22,7 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  PV_TAG: v5.12.0-headless
+  PV_TAG: v5.13.0-headless
   PV_REPO: topology-tool-kit/ttk-paraview
 
 
@@ -39,7 +39,7 @@ jobs:
     if: ${{ github.repository_owner == 'topology-tool-kit' || !contains(github.ref, 'heads') }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, ubuntu-22.04]
+        os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04]
 
     steps:
     - uses: actions/checkout@v4
@@ -59,11 +59,11 @@ jobs:
           libsqlite3-dev \
           libwebsocketpp-dev \
           graphviz \
+          python3-sklearn \
           ninja-build \
           zlib1g-dev \
           libqhull-dev \
           dpkg-dev
-        sudo python3 -m pip install scikit-learn
         cargo install sccache --version 0.4.2 --locked
         echo "PATH=/root/.cargo/bin:$PATH" >> $GITHUB_ENV
 
@@ -92,6 +92,7 @@ jobs:
       run: |
         sudo apt install ./ttk-paraview-headless.deb
 
+    # TODO: more aggressive warnings? (ubuntu-24.04)
     - name: Create & configure TTK build directory
       run: |
         mkdir build
@@ -143,13 +144,12 @@ jobs:
     needs: test-build-ubuntu
     strategy:
       matrix:
-        os: [ubuntu-20.04, ubuntu-22.04]
+        os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04]
         testSet: [pyTests, screenshotTests]
     steps:
     - name: Install Ubuntu dependencies
       run: |
         sudo apt update
-        sudo python3 -m pip install scikit-learn
 
     - name: Install Torch
       shell: bash
@@ -201,18 +201,21 @@ jobs:
       run: |
         VERS=$(hostnamectl | grep "Operating System")
         # Ubuntu 22.04 OOM killer also kills the parent process...
-        if [[ "$VERS" == *"22.04"* ]]; then
+        if [[ "$VERS" == *"22.04"* ]] || [[ "$VERS" == *"24.04"* ]]; then
           rm ttk-data/states/mergeTreeClustering.pvsm
           rm ttk-data/states/mergeTreePGA.pvsm
           rm ttk-data/states/mergeTreeTemporalReduction.pvsm
           rm ttk-data/states/persistentGenerators_darkSky.pvsm
         fi
+        # remove buggy example
+        # related issue: https://github.com/topology-tool-kit/ttk/issues/1055
+        rm ttk-data/states/nestedTrackingFromOverlap.py
 
         cd ttk-data/tests
         mkdir output_screenshots
         if ! python3 -u validate.py; then
 
-          if [[ "$VERS" == *"22.04"* ]]; then
+          if [[ "$VERS" == *"22.04"* ]] || [[ "$VERS" == *"24.04"* ]]; then
             # weird opacity difference between the two Ubuntus
             rm -f output_screenshots/clusteringKelvinHelmholtzInstabilities_1.png
             rm -f output_screenshots/clusteringKelvinHelmholtzInstabilities_2.png
@@ -235,6 +238,9 @@ jobs:
       if: matrix.testSet == 'pyTests'
       run: |
         cd ttk-data
+        # remove buggy example
+        # related issue: https://github.com/topology-tool-kit/ttk/issues/1055
+        rm python/nestedTrackingFromOverlap.py
         python3 -u python/run.py
 
     - name: Test ttk-data Python scripts results [NOT ENFORCED]
@@ -257,8 +263,13 @@ jobs:
   # Test macOS build #
   # -----------------#
   test-build-macos:
-    runs-on: macos-12
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-12, macos-14]
     if: ${{ github.repository_owner == 'topology-tool-kit' || !contains(github.ref, 'heads') }}
+    env:
+      DYLD_LIBRARY_PATH: /usr/local/lib
 
     steps:
     - uses: actions/checkout@v4
@@ -275,7 +286,7 @@ jobs:
         brew install --cask xquartz
         brew install llvm ninja open-mpi
         # TTK dependencies
-        brew install boost eigen graphviz numpy qhull
+        brew install boost eigen graphviz spectra sqlite zlib numpy qhull
 
     - name: Install and setup sccache
       uses: f3d-app/sccache-setup-action@v1
@@ -287,11 +298,18 @@ jobs:
 
     - name: Fetch TTK-ParaView headless macOS binary archive
       run: |
-        wget https://github.com/${{ env.PV_REPO }}/releases/download/${{ env.PV_TAG }}/ttk-paraview-headless-macos-12.tar.gz
+        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-macos-12.tar.gz
+        tar xzf ttk-paraview-headless.tar.gz
         sudo cp -r ttk-paraview/* /usr/local
         pvpython -m pip install --break-system-packages scikit-learn
 
@@ -352,6 +370,9 @@ jobs:
       id: validate
       continue-on-error: true
       run: |
+        # remove buggy example
+        # related issue: https://github.com/topology-tool-kit/ttk/issues/1055
+        rm ttk-data/states/nestedTrackingFromOverlap.py
         cd ttk-data/tests
         mkdir output_screenshots
         pvpython -u validate.py || (tar zcf screenshots.tar.gz output_screenshots && false)
@@ -369,6 +390,9 @@ jobs:
     - name: Run ttk-data Python scripts
       run: |
         cd ttk-data
+        # remove buggy example
+        # related issue: https://github.com/topology-tool-kit/ttk/issues/1055
+        rm python/nestedTrackingFromOverlap.py
         pvpython -u python/run.py
       env:
         PV_PLUGIN_PATH: /usr/local/bin/plugins/TopologyToolKit
@@ -400,7 +424,8 @@ jobs:
       shell: bash
       run: |
         conda install -c conda-forge libboost-devel glew eigen spectralib zfp  \
-          scikit-learn graphviz ninja python=3.10 zlib qhull llvm-openmp clangxx
+          sqlite scikit-learn graphviz ninja python=3.10 zlib qhull \
+          llvm-openmp clangxx
         # add TTK & ParaView install folders to PATH
         echo "$PV_DIR/bin" >> $GITHUB_PATH
         echo "$TTK_DIR/bin" >> $GITHUB_PATH
@@ -549,6 +574,7 @@ jobs:
         set PYTHONPATH=%PV_DIR%\bin\Lib\site-packages;%TTK_DIR%\bin\Lib\site-packages;%CONDA_ROOT%\Lib;%CONDA_ROOT%\DLLs
         set PV_PLUGIN_PATH=%TTK_DIR%\bin\plugins
         cd ttk-data
+        rm python/nestedTrackingFromOverlap.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 (= 5.12.0), python3-sklearn, libboost-system-dev, python3-dev, libgraphviz-dev, libsqlite3-dev, libgl1-mesa-dev")
+  "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")
 # autogenerate dependency information
 set (CPACK_DEBIAN_PACKAGE_SHLIBDEPS ON)
 # package will be installed under %ProgramFiles%\${CPACK_PACKAGE_INSTALL_DIRECTORY} on Windows

ChangeLog.md

@@ -10,7 +10,7 @@
 - DMS performance improvements (allocation)
 - Saddle connector reversal performance improvements
 - Signed distance fields
-- Migration to ParaView 5.12
+- Migration to ParaView 5.12, 5.13
 - Switch to C++17
 - Bug fixes
 

core/base/cinemaQuery/CinemaQuery.cpp

@@ -1,7 +1,7 @@
 #include <CinemaQuery.h>
 #include <iostream>
 
-#if TTK_ENABLE_SQLITE3
+#ifdef TTK_ENABLE_SQLITE3
 #include <sqlite3.h>
 #endif
 
@@ -18,7 +18,7 @@ int ttk::CinemaQuery::execute(
   int &csvNColumns,
   int &csvNRows) const {
 
-#if TTK_ENABLE_SQLITE3
+#ifdef TTK_ENABLE_SQLITE3
   // print input
   {
     std::vector<std::string> sqlLines;

core/base/discreteMorseSandwich/DiscreteMorseSandwich.h

@@ -478,12 +478,28 @@ namespace ttk {
           this->pairedCritCells_[i].resize(
             this->dg_.getNumberOfCells(i, triangulation), false);
         }
-        for(int i = 1; i < dim + 1; ++i) {
+        // NOTE:
+        // a for loop used to stand here, but gcc 13 looks buggy with it...
+        if(dim >= 1) {
 #ifdef TTK_ENABLE_OPENMP
 #pragma omp task
 #endif
-          this->critCellsOrder_[i].resize(
-            this->dg_.getNumberOfCells(i, triangulation), -1);
+          this->critCellsOrder_[1].resize(
+            this->dg_.getNumberOfCells(1, triangulation), -1);
+        }
+        if(dim >= 2) {
+#ifdef TTK_ENABLE_OPENMP
+#pragma omp task
+#endif
+          this->critCellsOrder_[2].resize(
+            this->dg_.getNumberOfCells(2, triangulation), -1);
+        }
+        if(dim >= 3) {
+#ifdef TTK_ENABLE_OPENMP
+#pragma omp task
+#endif
+          this->critCellsOrder_[3].resize(
+            this->dg_.getNumberOfCells(3, triangulation), -1);
         }
       }
       this->printMsg("Memory allocations", 1.0, tm.getElapsedTime(), 1,

core/base/webSocketIO/CMakeLists.txt

@@ -8,5 +8,5 @@ ttk_add_base_library(webSocketIO
 
 if (TTK_ENABLE_WEBSOCKETPP)
   target_compile_definitions(webSocketIO PUBLIC TTK_ENABLE_WEBSOCKETPP)
-  target_include_directories(webSocketIO PUBLIC ${WEBSOCKETPP_INCLUDE_DIR})
+  target_include_directories(webSocketIO SYSTEM PRIVATE ${WEBSOCKETPP_INCLUDE_DIR})
 endif()

paraview/patch/headless.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, ubuntu-22.04]
+        os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04]
     steps:
     - uses: actions/checkout@v4
       name: Checkout TTK-ParaView source code
@@ -232,6 +232,15 @@ jobs:
         file: ttk-paraview-headless-ubuntu-22.04/ttk-paraview.deb
         asset_name: ttk-paraview-headless-ubuntu-22.04.deb
 
+    - name: Upload Ubuntu Noble Numbat .deb as Release Asset
+      uses: svenstaro/upload-release-action@v2
+      with:
+        repo_token: ${{ secrets.GITHUB_TOKEN }}
+        tag: ${{ github.ref }}
+        file: ttk-paraview-headless-ubuntu-24.04/ttk-paraview.deb
+        asset_name: ttk-paraview-headless-ubuntu-24.04.deb
+
+
     - name: Upload MacOS 14 (arm64) .tar.gz as Release Asset
       uses: svenstaro/upload-release-action@v2
       with:

paraview/patch/paraview-5.13.0-vtkPVFileInformation.cxx.patch

@@ -0,0 +1,13 @@
+--- a/Remoting/Core/vtkPVFileInformation.cxx	2018-04-06 22:03:33.000000000 +0200
++++ b/Remoting/Core/vtkPVFileInformation.cxx	2018-05-20 07:11:10.114020235 +0200
+@@ -1226,6 +1222,11 @@
+     resource_dir = vtksys::SystemTools::CollapseFullPath(resource_dir);
+   }
+
++  vtkProcessModule* pm = vtkProcessModule::GetProcessModule();
++
++  if((pm)&&(prefixes.size()))
++    resource_dir = pm->GetSelfDir() + "/../" + prefixes[0];
++
+   return resource_dir;
+ }

paraview/patch/patch-paraview-5.13.0.sh

@@ -74,9 +74,8 @@ mkdir -p TTK/Data/
 cp ${PATCH_DIR}/data/* TTK/Data/
 cp TTK/Data/*pvsm Qt/ApplicationComponents/Resources/ExampleVisualizations/
 cp TTK/Data/*png Qt/ApplicationComponents/Resources/Thumbnails/
-# the patch below makes the build fail under macos-14...
-#$PATCH_BIN Remoting/Core/vtkPVFileInformation.cxx \
-#  < "${PATCH_DIR}/paraview-5.8.0-vtkPVFileInformation.cxx.patch"
+$PATCH_BIN Remoting/Core/vtkPVFileInformation.cxx \
+  < "${PATCH_DIR}/paraview-5.13.0-vtkPVFileInformation.cxx.patch"
 $PATCH_BIN Qt/ApplicationComponents/Resources/UI/pqExampleVisualizationsDialog.ui \
   < "${PATCH_DIR}/paraview-5.13.0-ApplicationComponents.patch"
 $PATCH_BIN Qt/ApplicationComponents/pqExampleVisualizationsDialog.cxx \