Support VTK8

.github/workflows/test-vtk.yml

@@ -15,10 +15,6 @@ jobs:
       matrix:
         vtk-version: ["8.2", "9.2"]
 
-    defaults:
-      run:
-        shell: bash -el {0}
-
     steps:
       - name: checkout chaste
         uses: actions/checkout@v4
@@ -39,34 +35,50 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y cmake g++ xvfb
 
-      - name: setup conda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: setup conda environment
+        uses: mamba-org/setup-micromamba@v1
         with:
-          auto-update-conda: true
-          use-mamba: true
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          channels: pychaste,conda-forge
+          micromamba-version: latest
+          generate-run-shell: false
+          init-shell: bash
+          condarc: |
+            channels:
+              - conda-forge
+              - pychaste
+          environment-name: test-env
+          create-args: >-
+            boost-cpp
+            fftw
+            hdf5=[build=*mpi_mpich*]
+            matplotlib
+            metis
+            mpich
+            notebook
+            numpy
+            parmetis
+            petsc
+            petsc4py
+            pip
+            setuptools
+            six
+            sundials
+            tbb-devel
+            vtk=${{ matrix.vtk-version }}
+            wheel
+            xerces-c
+            xsd
+            xvfbwrapper
+            xorg-libxext
+          cache-environment: true
+          post-cleanup: 'all'
 
-      - name: install pychaste conda dependencies
+      - name: fix cmake paths
         run: |
-          mamba install -n test \
-            boost-cpp \
-            hdf5="*=*mpi_mpich*" \
-            metis \
-            mpich \
-            notebook \
-            parmetis \
-            petsc \
-            petsc4py \
-            six \
-            sundials \
-            vtk=${{ matrix.vtk-version }} \
-            tbb-devel \
-            xerces-c \
-            xsd \
-            xvfbwrapper \
-            xorg-libxext
+          find $CONDA_PREFIX \
+            -type f \
+            -name '*.cmake' \
+            -exec sed -i.bak 's|/usr/lib64/libXext.so|libXext.so|g' {} \;
+        shell: bash -el {0}
 
       - name: make build directory
         run: |
@@ -79,7 +91,7 @@ jobs:
 
           cmake \
             -DCMAKE_BUILD_TYPE=Release \
-            -DPython3_EXECUTABLE=$(which python) \
+            -DPython3_EXECUTABLE=$(which python3) \
             -DCMAKE_LIBRARY_PATH="${CONDA_PREFIX}/lib" \
             -DCMAKE_PREFIX_PATH="${CONDA_PREFIX}" \
             -DCMAKE_INSTALL_PREFIX="${CONDA_PREFIX}" \
@@ -92,25 +104,30 @@ jobs:
             -DXSD_EXECUTABLE="${CONDA_PREFIX}/bin/xsd" \
             ../Chaste/
         working-directory: build
+        shell: bash -el {0}
 
       - name: build pychaste
         run: |
           cmake --build . --parallel $(nproc) --target project_PyChaste
         working-directory: build
+        shell: bash -el {0}
 
       - name: build pychaste python module
         run: |
           cmake --build . --parallel $(nproc) --target project_PyChaste_Python
         working-directory: build
+        shell: bash -el {0}
 
       - name: install pychaste
         run: |
           pip install .
         working-directory: build/projects/PyChaste/python
+        shell: bash -el {0}
 
       - name: run tests
         run: |
           xvfb-run \
             --server-args="-screen 0 1024x768x24" \
             ctest -j $(nproc) -L PyChaste --output-on-failure
         working-directory: build
+        shell: bash -el {0}

CMakeLists.txt

@@ -34,12 +34,29 @@ find_package(Chaste COMPONENTS cell_based)
 
 # PyChaste needs some additional VTK libraries
 if(VTK_MAJOR_VERSION LESS_EQUAL 6)
-    find_package(VTK COMPONENTS vtkWrappingPythonCore vtkIOImage vtkIOMovie vtkRenderingAnnotation vtkRenderingFreeType 
-                vtkRenderingFreeTypeOpenGL vtkRenderingCore 
-                vtkRenderingOpenGL vtkInteractionStyle  REQUIRED)
+    find_package(VTK REQUIRED COMPONENTS
+        vtkInteractionStyle
+        vtkIOImage
+        vtkIOMovie
+        vtkRenderingAnnotation
+        vtkRenderingCore
+        vtkRenderingFreeType
+        vtkRenderingOpenGL
+        vtkWrappingPythonCore
+    )
 else()
-    find_package(VTK COMPONENTS vtkWrappingPythonCore vtkParallelCore vtkParallelMPI vtkIOImage vtkIOMovie vtkRenderingAnnotation
-            vtkRenderingFreeType vtkRenderingOpenGL2 vtkRenderingCore vtkFiltersProgrammable vtkFiltersVerdict vtkInteractionStyle REQUIRED)
+    find_package(VTK REQUIRED COMPONENTS
+        vtkFiltersProgrammable
+        vtkFiltersVerdict
+        vtkInteractionStyle
+        vtkIOImage
+        vtkIOMovie
+        vtkRenderingAnnotation
+        vtkRenderingCore
+        vtkRenderingFreeType
+        vtkRenderingOpenGL2
+        vtkWrappingPythonCore
+    )
 endif()
 
 list(APPEND Chaste_INCLUDES ${VTK_INCLUDE_DIRS})

WrapPython.cmake

@@ -60,7 +60,7 @@ endif()
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}/dynamic/pybind11/include)
 
 add_subdirectory(dynamic/pybind11)
-include_directories(${PYTHON_INCLUDE_DIRS})
+include_directories(${PYTHON3_INCLUDE_DIRS})
 
 ######### Build the Python modules ###################### 
 set (PYCHASTE_PYTHON_AUTO_MODULES "")
@@ -124,7 +124,7 @@ foreach(val RANGE ${len2})
         PREFIX "${PYTHON_MODULE_PREFIX}" SUFFIX ".so")
     target_compile_features(_chaste_project_PyChaste_${python_module} PRIVATE cxx_range_for)
     # order is important, pybind and python come first
-    target_link_libraries(_chaste_project_PyChaste_${python_module} pybind11::module ${PYTHON_LIBRARIES} ${Chaste_THIRD_PARTY_LIBRARIES} ${Chaste_LIBRARIES} ${PYCHASTE_SHARED_LIB})
+    target_link_libraries(_chaste_project_PyChaste_${python_module} pybind11::module ${PYTHON3_LIBRARIES} ${Chaste_THIRD_PARTY_LIBRARIES} ${Chaste_LIBRARIES} ${PYCHASTE_SHARED_LIB})
     add_dependencies(_chaste_project_PyChaste_${python_module} chaste_project_PyChaste)
 endforeach()
 

src/visualization/CellPopulationPyChasteActorGenerator.cpp

@@ -33,41 +33,6 @@ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 */
 
-/*
-
-Copyright (c) 2005-2024, University of Oxford.
- All rights reserved.
-
- University of Oxford means the Chancellor, Masters and Scholars of the
- University of Oxford, having an administrative office at Wellington
- Square, Oxford OX1 2JD, UK.
-
- This file is CellPopulation of Chaste.
-
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- * Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
- * Neither the name of the University of Oxford nor the names of its
- contributors may be used to endorse or promote products derived from this
- software without specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A CellPopulationICULAR PURPOSE
- ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
- LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
- GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
- OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
- */
-
 #include <algorithm>
 #include <boost/lexical_cast.hpp>
 #include <vtkPoints.h>
@@ -145,7 +110,7 @@ void CellPopulationPyChasteActorGenerator<DIM>::AddCaBasedCellPopulationActor(vt
     vtkSmartPointer<vtkGeometryFilter> p_geom_filter = vtkSmartPointer<vtkGeometryFilter>::New();
 
     boost::shared_ptr<CaBasedCellPopulation<DIM> > p_ca_population =
-            boost::dynamic_pointer_cast<CaBasedCellPopulation<DIM> >(mpCellPopulation);
+        boost::dynamic_pointer_cast<CaBasedCellPopulation<DIM> >(mpCellPopulation);
 
     if(p_ca_population && mShowPottsMeshEdges)
     {

src/visualization/VtkScene.cpp

@@ -34,6 +34,7 @@ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */
 
 #include <boost/lexical_cast.hpp>
+#include <boost/smart_ptr/make_shared.hpp>
 #include <vtkWindowToImageFilter.h>
 #include <vtkPNGWriter.h>
 #include <vtkPoints.h>
@@ -115,14 +116,14 @@ VtkScene<DIM>::VtkScene()
       mHasStarted(false),
       mAddAnnotations(false),
       mOutputFrequency(1),
-      mpCellPopulationGenerator(boost::shared_ptr<CellPopulationPyChasteActorGenerator<DIM> >(new CellPopulationPyChasteActorGenerator<DIM>()))
+      mpCellPopulationGenerator(boost::make_shared<CellPopulationPyChasteActorGenerator<DIM> >())
 {
     mpRenderer->SetBackground(1.0, 1.0, 1.0);
     mpRenderWindow->AddRenderer(mpRenderer);
     mpRenderWindow->SetSize(800.0, 600.0);
     mpRenderWindowInteractor->SetRenderWindow(mpRenderWindow);
 
-    vtkSmartPointer<customMouseInteractorStyle> style = vtkSmartPointer<customMouseInteractorStyle>::New();
+    auto style = vtkSmartPointer<customMouseInteractorStyle>::New();
     mpRenderWindowInteractor->SetInteractorStyle( style );
 }
 
@@ -186,7 +187,6 @@ void VtkScene<DIM>::ResetRenderer(unsigned time_step)
     {
         mpRenderer->RemoveActor(p_actor);
     }
-    mpRenderer->Clear();
 
     if(mpCellPopulationGenerator)
     {
@@ -269,9 +269,10 @@ void VtkScene<DIM>::Start()
         mpRenderWindow->SetOffScreenRendering(1);
     }
 
-    if(mSaveAsImages or mSaveAsAnimation)
+    if(mSaveAsImages || mSaveAsAnimation)
     {
         mpRenderWindow->SetOffScreenRendering(1);
+        mpRenderWindow->Render();
         mWindowToImageFilter->SetInput(mpRenderWindow);
         mWindowToImageFilter->Update();
     }

src/visualization/VtkScene.hpp

@@ -41,8 +41,15 @@ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <vtkVersion.h>
 #include <vtkOggTheoraWriter.h>
 #include <vtkAutoInit.h>
-VTK_MODULE_INIT(vtkRenderingOpenGL2);
-VTK_MODULE_INIT(vtkRenderingFreeType);
+#if VTK_MAJOR_VERSION >= 6
+#   include <vtkAutoInit.h>
+#   if VTK_MAJOR_VERSION == 6
+        VTK_MODULE_INIT(vtkRenderingOpenGL);
+#   else
+        VTK_MODULE_INIT(vtkRenderingOpenGL2);
+#   endif
+    VTK_MODULE_INIT(vtkRenderingFreeType);
+#endif
 #include <vtkSmartPointer.h>
 #include <vtkRenderer.h>
 #include <vtkLookupTable.h>

test/python/cell_based/tutorials/TestImmersedBoundaryTutorial.py

@@ -99,11 +99,7 @@ def test_simple_immersed_boundary_simulation(self):
 
         ## Setup the simulation environment in the notebook
 
-        SetupNotebookTest()
-
-        ## Set the start time for the simulation
-
-        SimulationTime.Instance().SetStartTime(0.0)
+        # JUPYTER_SETUP
 
         ## Next, we define the necessary geometry by generating a mesh to 
         ## contain a single cell.
@@ -212,7 +208,7 @@ def test_simple_immersed_boundary_simulation(self):
 
         ## Reset the simulation environment in the notebook
 
-        TearDownNotebookTest()
+        # JUPYTER_TEARDOWN
 
     ## ### 2. Adding More Cells
 
@@ -222,11 +218,7 @@ def test_multicell_immersed_boundary_simulation(self):
 
         ## Setup the simulation environment in the notebook
 
-        SetupNotebookTest()
-
-        ## Set the start time for the simulation
-
-        SimulationTime.Instance().SetStartTime(0.0)
+        # JUPYTER_SETUP
 
         ## We can use the mesh generator to generate multiple cells. The first
         ## parameter of the mesh generator constructor controls the number of
@@ -335,7 +327,7 @@ def test_multicell_immersed_boundary_simulation(self):
 
         ## Reset the simulation environment in the notebook
 
-        TearDownNotebookTest()
+        # JUPYTER_TEARDOWN
 
     ## ### 3. Adding Fluid Sources
     ## Now that we are familiar with how to generate the cells, we will
@@ -347,11 +339,7 @@ def test_fluid_source_immersed_boundary_simulation(self):
 
         ## Setup the simulation environment in the notebook
 
-        SetupNotebookTest()
-
-        ## Set the start time for the simulation
-
-        SimulationTime.Instance().SetStartTime(0.0)
+        # JUPYTER_SETUP
 
         ## We begin by constructing a fluid source object:
 
@@ -457,8 +445,7 @@ def test_fluid_source_immersed_boundary_simulation(self):
         nb_manager.vtk_show(scene, height=300)
 
         ## Reset the simulation environment in the notebook
-
-        TearDownNotebookTest()
+        # JUPYTER_TEARDOWN
 
         ## #### Further Exercises
         ## * Try integrating a different cell cycle model to introduce cell