Add PyChaste Support for VTK 9

[kwabenantim]

Description API changes from VTK 8 to 9: https://vtk.org/Wiki/VTK/API_Changes_8_2_0_to_9_0_0

[kwabenantim]

CMake Error at cmake/Modules/ChasteMacros.cmake:321 (add_library):
  Target "chaste_project_PyChaste" links to target "Freetype::Freetype" but
  the target was not found.  Perhaps a find_package() call is missing for an
  IMPORTED target, or an ALIAS target is missing?
Call Stack (most recent call first):
  cmake/Modules/ChasteMacros.cmake:411 (Chaste_DO_COMMON)
  projects/PyChaste/CMakeLists.txt:65 (chaste_do_project)

CMake Error at cmake/Modules/ChasteMacros.cmake:321 (add_library):
  Target "chaste_project_PyChaste" links to target "X11::X11" but the target
  was not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  cmake/Modules/ChasteMacros.cmake:411 (Chaste_DO_COMMON)
  projects/PyChaste/CMakeLists.txt:65 (chaste_do_project)

CMake Error at cmake/Modules/ChasteMacros.cmake:321 (add_library):
  Target "chaste_project_PyChaste" links to target "GLEW::GLEW" but the
  target was not found.  Perhaps a find_package() call is missing for an
  IMPORTED target, or an ALIAS target is missing?
Call Stack (most recent call first):
  cmake/Modules/ChasteMacros.cmake:411 (Chaste_DO_COMMON)
  projects/PyChaste/CMakeLists.txt:65 (chaste_do_project)

CMake Error at cmake/Modules/ChasteMacros.cmake:321 (add_library):
  Target "chaste_project_PyChaste" links to target "X11::X11" but the target
  was not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  cmake/Modules/ChasteMacros.cmake:411 (Chaste_DO_COMMON)
  projects/PyChaste/CMakeLists.txt:65 (chaste_do_project)

CMake Error at cmake/Modules/ChasteMacros.cmake:321 (add_library):
  Target "chaste_project_PyChaste" links to target "Python3::Module" but the
  target was not found.  Perhaps a find_package() call is missing for an
  IMPORTED target, or an ALIAS target is missing?
Call Stack (most recent call first):
  cmake/Modules/ChasteMacros.cmake:411 (Chaste_DO_COMMON)
  projects/PyChaste/CMakeLists.txt:65 (chaste_do_project)

[kwabenantim]

Steps to reproduce the CMake configuration errors:

git clone https://github.com/Chaste/Chaste.git

cd Chaste/projects
git clone --recursive https://github.com/PyChaste/PyChaste.git
cd ..

conda create -n vtk9-env
conda activate vtk9-env
mamba install -c conda-forge -c pychaste boost-cpp hdf5="*=*mpi_mpich*" metis mpich parmetis petsc petsc4py sundials vtk=9 tbb-devel xerces-c xsd xvfbwrapper xorg-libxext six notebook

mkdir build
cd build
export PETSC_DIR=$CONDA_PREFIX
export HDF5_ROOT=$CONDA_PREFIX

cmake \
  -DCMAKE_BUILD_TYPE=Release \
  -DPython3_EXECUTABLE=$(which python) \
  -DCMAKE_LIBRARY_PATH="${CONDA_PREFIX}/lib" \
  -DCMAKE_PREFIX_PATH="${CONDA_PREFIX}" \
  -DCMAKE_INSTALL_PREFIX="${CONDA_PREFIX}" \
  -DBUILD_SHARED_LIBS=ON \
  -DBOOST_ROOT="${CONDA_PREFIX}" \
  -DHDF5_C_COMPILER_EXECUTABLE="${CONDA_PREFIX}/bin/h5pcc" \
  -DVTK_DIR=${CONDA_PREFIX} \
  -DXERCESC_INCLUDE="${CONDA_PREFIX}/include" \
  -DXERCESC_LIBRARY="${CONDA_PREFIX}/lib/libxerces-c.so" \
  -DXSD_EXECUTABLE="${CONDA_PREFIX}/bin/xsd" \
  ..

[kwabenantim]

@fcooper8472 suggests investigating fixes like those done in https://github.com/Chaste/Chaste/pull/152/files

[kwabenantim]

There's now a github action testing this: https://github.com/Chaste/PyChaste/actions/runs/9082771049/job/24959931938

[kwabenantim]

CMake errors are from additional VTK components:

RenderingFreeType # needs Freetype::Freetype
RenderingOpenGL2 # needs X11::X11 and GLEW::GLEW
WrappingPythonCore # needs Python3::Module

[kwabenantim]

The errors seem to go away when the extra package modules are searched for directly in Chaste. Possibly subsequent calls to find_package() don't (can't?) add the extra targets correctly?

---find_package(Python3 3.5 )
+++find_package(Python3 3.5 REQUIRED COMPONENTS Interpreter Development)

find_package(
    VTK COMPONENTS CommonCore CommonDataModel FiltersCore FiltersGeneral FiltersGeneric FiltersGeometry
---    FiltersModeling FiltersSources IOCore IOGeometry IOLegacy IOParallelXML IOXML REQUIRED
+++    FiltersModeling FiltersSources IOCore IOGeometry IOLegacy IOParallelXML IOXML
+++    FiltersProgrammable FiltersVerdict InteractionStyle IOImage IOMovie RenderingAnnotation RenderingCore
+++    RenderingFreeType RenderingOpenGL2 WrappingPythonCore  REQUIRED
        )

[kwabenantim]

It still works when find_package() is called twice from Chaste to add extra components. Possibly a scope issue? The targets from the first find_package() call seem to disappear after the second call, however.

[kwabenantim]

PyChaste works with VTK9 but needs the cmake find package call to be done above the project scope. This will be done directly in the PyChaste merge into Chaste trunk: https://github.com/Chaste/Chaste/issues/273