Support VTK 9

.github/workflows/test-vtk.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        vtk-version: ["8.2", "9.2"]
+        vtk-version: ["7.1", "8.2", "9.2"]
 
     steps:
       - name: checkout chaste
@@ -56,12 +56,12 @@ jobs:
             notebook
             numpy
             parmetis
-            petsc
-            petsc4py
+            petsc<3.19
+            petsc4py<3.19
             pip
             setuptools
             six
-            sundials
+            sundials<7.0
             tbb-devel
             vtk=${{ matrix.vtk-version }}
             wheel

CMakeLists.txt

@@ -30,10 +30,30 @@
 # OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 # 
 
+#========================================
+# Setup PyChaste project
+#========================================
+
+# PyChaste needs the cell_based component (and its dependencies)
 find_package(Chaste COMPONENTS cell_based)
 
+# Do Chaste project preprocessing, which does something like:
+#   add_custom_target(project_PyChaste)
+#   set(Chaste_project_PyChaste_SOURCE_DIR ...)
+#   set(Chaste_project_PyChaste_INCLUDE_DIRS ...)
+#   include_directories("${Chaste_THIRD_PARTY_INCLUDE_DIRS}")
+#   include_directories("${Chaste_project_PyChaste_INCLUDE_DIRS}")
+#   include_directories("${Chaste_INCLUDE_DIRS}")
+#   add_library(chaste_project_PyChaste ...)
+#   target_link_libraries(chaste_project_PyChaste ...)
+chaste_do_project(PyChaste)
+
+# PyChaste needs the Python3 development libraries
+find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
+target_link_libraries(Chaste_COMMON_DEPS INTERFACE Python3::Module Python3::Python)
+
 # PyChaste needs some additional VTK libraries
-if(VTK_MAJOR_VERSION LESS_EQUAL 6)
+if(VTK_MAJOR_VERSION LESS 7)
     find_package(VTK REQUIRED COMPONENTS
         vtkInteractionStyle
         vtkIOImage
@@ -44,7 +64,7 @@ if(VTK_MAJOR_VERSION LESS_EQUAL 6)
         vtkRenderingOpenGL
         vtkWrappingPythonCore
     )
-else()
+elseif(VTK_MAJOR_VERSION LESS 9)
     find_package(VTK REQUIRED COMPONENTS
         vtkFiltersProgrammable
         vtkFiltersVerdict
@@ -57,12 +77,156 @@ else()
         vtkRenderingOpenGL2
         vtkWrappingPythonCore
     )
+else()
+    find_package(VTK REQUIRED COMPONENTS
+        FiltersProgrammable
+        FiltersVerdict
+        InteractionStyle
+        IOImage
+        IOMovie
+        IOOggTheora
+        RenderingAnnotation
+        RenderingCore
+        RenderingFreeType # needs Freetype::Freetype
+        RenderingOpenGL2 # needs X11::X11 and GLEW::GLEW
+        WrappingPythonCore # needs Python3::Module
+    )
 endif()
 
-list(APPEND Chaste_INCLUDES ${VTK_INCLUDE_DIRS})
-list(APPEND Chaste_project_PyChaste_INCLUDE_DIRS ${VTK_INCLUDE_DIRS})
-list(APPEND Chaste_THIRD_PARTY_LIBRARIES ${VTK_LIBRARIES})
-chaste_do_project(PyChaste)
+if (VTK_MAJOR_VERSION LESS 9)
+    list(APPEND Chaste_INCLUDES "${VTK_INCLUDE_DIRS}")
+    list(APPEND Chaste_project_PyChaste_INCLUDE_DIRS "${VTK_INCLUDE_DIRS}")
+    list(APPEND Chaste_THIRD_PARTY_LIBRARIES "${VTK_LIBRARIES}")
+else()
+    target_link_libraries(Chaste_COMMON_DEPS INTERFACE ${VTK_LIBRARIES})
+endif ()
+
+#========================================
+# Compiler options
+#========================================
+add_compile_options(-Wno-unused-local-typedefs)
+
+if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+    # https://stackoverflow.com/questions/25365160/boostmultiprecisionfloat128-and-c11
+    add_compile_options(-fext-numeric-literals)
+endif()
+
+#========================================
+# PyChaste non-wrapper C++ code
+#========================================
+
+# Non-wrapper code locations
+set(PYCHASTE_INCLUDE_DIRS
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/cell_based/
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/ode/
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/tutorial/
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/visualization/)
+
+# Non-wrapper code needs to be put in a separate shared library
+set(PYCHASTE_SHARED_LIB
+    "${CMAKE_CURRENT_BINARY_DIR}/libchaste_project_PyChaste${CMAKE_SHARED_LIBRARY_SUFFIX}")
+
+#========================================
+# Target for wrapper auto-generation
+#========================================
+add_custom_target(project_PyChaste_Python_Bindings)
+add_custom_command(TARGET project_PyChaste_Python_Bindings
+    COMMAND cppwg ${CMAKE_SOURCE_DIR}
+        -w ${CMAKE_CURRENT_SOURCE_DIR}/dynamic/wrappers
+        -p ${CMAKE_CURRENT_SOURCE_DIR}/dynamic/wrapper_generators/package_info.yaml
+        -i ${PYCHASTE_INCLUDE_DIRS} ${Chaste_INCLUDE_DIRS} ${Chaste_THIRD_PARTY_INCLUDE_DIRS}
+        --std c++17
+)
+
+#========================================
+# Build python modules from wrappers
+#========================================
+include_directories(${PYCHASTE_INCLUDE_DIRS})
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/dynamic/wrappers)
+include_directories(${PYTHON3_INCLUDE_DIRS})
+
+add_subdirectory(dynamic/pybind11)
+
+# Copy python package structure to build directory, ignoring existing shared libraries
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/src/python/
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/python/
+     PATTERN "*${CMAKE_SHARED_LIBRARY_SUFFIX}" EXCLUDE)
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/test/python/
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/python/test/)
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/doc/
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/python/doc/)
+
+# List of modules to build into shared libraries
+set (PYCHASTE_PYTHON_MODULES
+        # Modules with auto-generated wrappers
+        core
+        ode
+        pde
+        mesh
+        cell_based
+        visualization
+        tutorial
+        # Modules with manual wrappers
+        preload
+        tutorial_manual)
+
+# Locations to put each module library
+set (PYCHASTE_PYTHON_MODULE_LOCATIONS
+        # Modules with auto-generated wrappers
+        ${CMAKE_CURRENT_BINARY_DIR}/python/chaste/core/
+        ${CMAKE_CURRENT_BINARY_DIR}/python/chaste/ode/
+        ${CMAKE_CURRENT_BINARY_DIR}/python/chaste/pde/
+        ${CMAKE_CURRENT_BINARY_DIR}/python/chaste/mesh/
+        ${CMAKE_CURRENT_BINARY_DIR}/python/chaste/cell_based/
+        ${CMAKE_CURRENT_BINARY_DIR}/python/chaste/visualization/
+        ${CMAKE_CURRENT_BINARY_DIR}/python/chaste/tutorial/
+        # Modules with manual wrappers
+        ${CMAKE_CURRENT_BINARY_DIR}/python/chaste/
+        ${CMAKE_CURRENT_BINARY_DIR}/python/chaste/tutorial/)
+
+# The module library name must be the same as the pybind11 module name
+# defined in the main wrapper e.g. `dynamic/wrappers/ode/ode.main.cpp`
+# defines a pybind11 module `_chaste_project_PyChaste_ode`. By convention,
+# the name starts with an underscore. The usual 'lib' prefix is disabled.
+set(PYCHASTE_PYTHON_MODULE_PREFIX "_chaste_project_PyChaste_")
+
+# Create a shared library target for each module
+list(LENGTH PYCHASTE_PYTHON_MODULES max_idx)
+math(EXPR max_idx "${max_idx} - 1")
+
+foreach(idx RANGE ${max_idx})
+    list(GET PYCHASTE_PYTHON_MODULES ${idx} module)
+    list(GET PYCHASTE_PYTHON_MODULE_LOCATIONS ${idx} module_dir)
+
+    # Glob the module's wrapper code from the `dynamic` directory
+    file(GLOB module_sources ${CMAKE_CURRENT_SOURCE_DIR}/dynamic/wrappers/${module}/*.cpp)
+
+    set(module_library_name ${PYCHASTE_PYTHON_MODULE_PREFIX}${module})
+    add_library(${module_library_name} SHARED ${module_sources})
+
+    set_target_properties(${module_library_name}
+        PROPERTIES
+            LIBRARY_OUTPUT_DIRECTORY ${module_dir}
+            PREFIX "${PYTHON_MODULE_PREFIX}"
+            SUFFIX "${CMAKE_SHARED_LIBRARY_SUFFIX}")
+
+    # The order here is important - pybind11 and python come first
+    target_link_libraries(${module_library_name} 
+        pybind11::module
+        ${Python3_LIBRARIES}
+        ${Chaste_THIRD_PARTY_LIBRARIES}
+        Chaste_COMMON_DEPS
+        ${Chaste_LIBRARIES}
+        ${PYCHASTE_SHARED_LIB})
+
+    add_dependencies(${module_library_name} chaste_project_PyChaste)
+endforeach()
 
-# Include the Python wrapping build logic
-include(${CMAKE_CURRENT_SOURCE_DIR}/WrapPython.cmake)
+# Target for building all module shared libraries
+add_custom_target(project_PyChaste_Python)
+foreach(module IN LISTS PYCHASTE_PYTHON_MODULES)
+    add_dependencies(project_PyChaste_Python ${PYCHASTE_PYTHON_MODULE_PREFIX}${module})
+endforeach()