#20 Build cells example correctly

cppwg/info/class_info.py

@@ -305,7 +305,7 @@ class instantiation. For example, class "Foo" with template arguments
                     arg_str = arg_str.replace(name, replacement)
 
                 # Remove special characters
-                arg_str = arg_str.translate(rm_table)
+                arg_str = arg_str.replace("<", "_").replace(",", "_").translate(rm_table)
 
                 # Capitalize the first letter
                 if len(arg_str) > 1:

examples/cells/CMakeLists.txt

@@ -1,11 +1,41 @@
 cmake_minimum_required(VERSION 3.16...3.22)
-project(shapes LANGUAGES CXX)
+project(cells LANGUAGES CXX)
 
 set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 # Find Python
 find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
 
+# Find VTK
+find_package(VTK 7.1
+    REQUIRED
+    COMPONENTS
+        vtkCommonCore
+        vtkCommonDataModel
+        vtkFiltersCore
+        vtkFiltersGeneral
+        vtkFiltersGeneric
+        vtkFiltersGeometry
+        vtkFiltersModeling
+        vtkFiltersProgrammable
+        vtkFiltersSources
+        vtkFiltersVerdict
+        vtkInteractionStyle
+        vtkIOCore
+        vtkIOGeometry
+        vtkIOImage
+        vtkIOLegacy
+        vtkIOMovie
+        vtkIOParallelXML
+        vtkIOXML
+        vtkRenderingAnnotation
+        vtkRenderingCore
+        vtkRenderingFreeType
+        vtkRenderingOpenGL2
+        vtkWrappingPythonCore
+)
+
 # Fetch pybind11
 include(FetchContent)
 FetchContent_Declare(
@@ -20,61 +50,35 @@ FetchContent_MakeAvailable(pybind11)
 add_subdirectory(extern/meshgen meshgen_build)
 
 # Add a shared library for the main C++ source
-file(GLOB_RECURSE SHAPES_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/src/cpp/*.cpp)
-add_library(shapes SHARED ${SHAPES_SOURCES})
+file(GLOB_RECURSE CELLS_SOURCES
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/cpp/*.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/cpp/*.hpp
+)
+add_library(cells SHARED ${CELLS_SOURCES})
 target_include_directories(
-    shapes
+    cells
     PUBLIC
     ${CMAKE_CURRENT_SOURCE_DIR}/src/cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/cpp/geometry
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/cpp/math_funcs
     ${CMAKE_CURRENT_SOURCE_DIR}/src/cpp/mesh
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/cpp/primitives
 )
-target_link_libraries(shapes PUBLIC meshgen::meshgen)
+target_link_libraries(cells PUBLIC meshgen::meshgen)
 
-# Copy the Python source and test trees to the build location
-file(
-    COPY ${CMAKE_CURRENT_SOURCE_DIR}/src/py/pyshapes
-    DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/
+# Set up Pybind11 module
+file(GLOB PYCELLS_SOURCES 
+    ${CMAKE_CURRENT_SOURCE_DIR}/dynamic/wrappers/lib/*.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/dynamic/wrappers/lib/*.hpp
 )
-file(
-    COPY ${CMAKE_CURRENT_SOURCE_DIR}/src/py/test/
-    DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/
+pybind11_add_module(_pycells_lib MODULE ${PYCELLS_SOURCES})
+target_link_libraries(
+    _pycells_lib
+    PRIVATE
+    cells
+)
+target_include_directories(
+    _pycells_lib
+    PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}/wrappers/lib
 )
 
-# Create a shared library for each wrapper module
-foreach(MODULE geometry math_funcs mesh primitives)
-    # Add the autogenerated wrappers to the module target
-    file(GLOB MODULE_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/wrapper/${MODULE}/*.cpp)
-
-    set(MODULE_LIB _pyshapes_${MODULE})
-    add_library(${MODULE_LIB} SHARED ${MODULE_SOURCES})
-    target_link_libraries(
-        ${MODULE_LIB}
-        PRIVATE
-        Python3::Python
-        pybind11::module
-        shapes
-    )
-    target_include_directories(
-        ${MODULE_LIB}
-        PRIVATE
-        ${CMAKE_CURRENT_SOURCE_DIR}/wrapper
-        ${CMAKE_CURRENT_SOURCE_DIR}/wrapper/geometry
-        ${CMAKE_CURRENT_SOURCE_DIR}/wrapper/math_funcs
-        ${CMAKE_CURRENT_SOURCE_DIR}/wrapper/mesh
-        ${CMAKE_CURRENT_SOURCE_DIR}/wrapper/primitives
-    )
-
-    # Set suitable extensions for the module and place the compiled
-    # shared library in a suitable location inside the python package
-    set_target_properties(
-        ${MODULE_LIB}
-        PROPERTIES
-            PREFIX "${PYTHON_MODULE_PREFIX}"
-            SUFFIX "${PYTHON_MODULE_EXTENSION}"
-            LIBRARY_OUTPUT_DIRECTORY
-            ${CMAKE_CURRENT_BINARY_DIR}/pyshapes/${MODULE}/
-    )
-endforeach()
+# Add install target for scikit-build
+install(TARGETS cells DESTINATION .)

examples/cells/dynamic/config.yaml

@@ -29,19 +29,24 @@ modules:
 
     classes:
       # cell
-      - name: Cell
+      # - name: Cell
 
       # mesh
       - name: AbstractMesh
       - name: MeshFactory
+        source_includes:
+          - PottsMesh.hpp
+        template_substitutions:
+          - signature: <class MESH>
+            replacement: [['PottsMesh<2>'], ['PottsMesh<3>']]
       - name: PottsMesh
 
       # population
-      - name: AbstractCellPopulation
-      - name: PottsCellPopulation
+      # - name: AbstractCellPopulation
+      # - name: PottsCellPopulation
 
       # visualization
-      - name: VtkScene
+      # - name: VtkScene
 
 prefix_text: |
   // This file is auto-generated by cppwg; manual changes will be overwritten.

examples/cells/dynamic/wrappers/wrapper_header_collection.cppwg.hpp

@@ -0,0 +1,30 @@
+// This file is auto-generated by cppwg; manual changes will be overwritten.
+
+#ifndef pycells_HEADERS_HPP_
+#define pycells_HEADERS_HPP_
+
+// Includes
+#include "AbstractMesh.hpp"
+#include "MeshFactory.hpp"
+#include "PottsMesh.hpp"
+
+// Instantiate Template Classes
+template class AbstractMesh<2, 2>;
+template class AbstractMesh<3, 3>;
+template class MeshFactory<PottsMesh<2>>;
+template class MeshFactory<PottsMesh<3>>;
+template class PottsMesh<2>;
+template class PottsMesh<3>;
+
+// Typedefs for nicer naming
+namespace cppwg
+{
+    typedef AbstractMesh<2, 2> AbstractMesh_2_2;
+    typedef AbstractMesh<3, 3> AbstractMesh_3_3;
+    typedef MeshFactory<PottsMesh<2>> MeshFactory_PottsMesh_2;
+    typedef MeshFactory<PottsMesh<3>> MeshFactory_PottsMesh_3;
+    typedef PottsMesh<2> PottsMesh_2;
+    typedef PottsMesh<3> PottsMesh_3;
+} // namespace cppwg
+
+#endif // pycells_HEADERS_HPP_

examples/cells/pyproject.toml

@@ -0,0 +1,10 @@
+[project]
+name = "pycells"
+version = "0.0.1"
+
+[build-system]
+requires = ["scikit-build-core"]
+build-backend = "scikit_build_core.build"
+
+[tool.scikit-build.cmake]
+build-type = "Release"

examples/cells/src/cpp/mesh/AbstractMesh.cpp

@@ -22,10 +22,10 @@ void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::SetIndex(unsigned index)
     mIndex = index;
 }
 
-template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
-void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::AddVertex(Point<SPACE_DIM> vertex)
-{
-}
+// template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
+// void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::AddVertex(Node<SPACE_DIM> vertex)
+// {
+// }
 
 template class AbstractMesh<2, 2>;
 template class AbstractMesh<3, 3>;

examples/cells/src/cpp/mesh/AbstractMesh.hpp

@@ -1,8 +1,6 @@
 #ifndef _ABSTRACT_MESH_HPP
 #define _ABSTRACT_MESH_HPP
 
-#include "Point.hpp"
-
 /**
  * A mesh in SPACE_DIM space with ELEMENT_DIM dimensional elements
  */
@@ -39,7 +37,7 @@ class AbstractMesh
     /**
      * Add a vertex to the mesh
      */
-    void AddVertex(Point<SPACE_DIM> vertex);
+    // void AddVertex(Node<SPACE_DIM> vertex);
 
     /**
      * Scale the mesh by a factor

examples/cells/src/cpp/mesh/MeshFactory.cpp

@@ -1,4 +1,4 @@
-#include "ConcreteMesh.hpp"
+#include "PottsMesh.hpp"
 
 #include "MeshFactory.hpp"
 
@@ -12,5 +12,5 @@ MeshFactory<MESH>::~MeshFactory()
 {
 }
 
-template class MeshFactory<ConcreteMesh<2> >;
-template class MeshFactory<ConcreteMesh<3> >;
+template class MeshFactory<PottsMesh<2> >;
+template class MeshFactory<PottsMesh<3> >;

examples/cells/src/cpp/mesh/PottsMesh.cpp

@@ -1,19 +1,19 @@
 #include "AbstractMesh.hpp"
-#include "ConcreteMesh.hpp"
+#include "PottsMesh.hpp"
 
 template <unsigned DIM>
-ConcreteMesh<DIM>::ConcreteMesh() : AbstractMesh<DIM, DIM>()
+PottsMesh<DIM>::PottsMesh() : AbstractMesh<DIM, DIM>()
 {
 }
 
 template <unsigned DIM>
-ConcreteMesh<DIM>::~ConcreteMesh()
+PottsMesh<DIM>::~PottsMesh()
 {
 }
 template <unsigned DIM>
-void ConcreteMesh<DIM>::Scale(const double factor){
+void PottsMesh<DIM>::Scale(const double factor){
     // Scale the mesh
 };
 
-template class ConcreteMesh<2>;
-template class ConcreteMesh<3>;
+template class PottsMesh<2>;
+template class PottsMesh<3>;

examples/cells/src/cpp/mesh/PottsMesh.hpp

@@ -1,29 +1,29 @@
-#ifndef _CONCRETE_MESH_HPP
-#define _CONCRETE_MESH_HPP
+#ifndef _POTTS_MESH_HPP
+#define _POTTS_MESH_HPP
 
 #include "AbstractMesh.hpp"
 
 /**
- * A concrete mesh implementation
+ * A Potts mesh implementation
  */
 template <unsigned DIM>
-class ConcreteMesh : public AbstractMesh<DIM, DIM>
+class PottsMesh : public AbstractMesh<DIM, DIM>
 {
 public:
     /**
      * Default Constructor
      */
-    ConcreteMesh();
+    PottsMesh();
 
     /**
      * Destructor
      */
-    ~ConcreteMesh();
+    ~PottsMesh();
 
     /**
      * Scale the mesh by a factor
      */
     void Scale(const double factor) override;
 };
 
-#endif // _CONCRETE_MESH_HPP
+#endif // _POTTS_MESH_HPP