#20 Add cells example

examples/cells/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.16...3.22)
+project(shapes LANGUAGES CXX)
+
+set(CMAKE_CXX_STANDARD 17)
+
+# Find Python
+find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
+
+# Fetch pybind11
+include(FetchContent)
+FetchContent_Declare(
+    pybind11
+    GIT_REPOSITORY https://github.com/pybind/pybind11
+    GIT_TAG v2.13.5
+    GIT_SHALLOW 1
+)
+FetchContent_MakeAvailable(pybind11)
+
+# Add external library
+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})
+target_include_directories(
+    shapes
+    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)
+
+# 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}/
+)
+file(
+    COPY ${CMAKE_CURRENT_SOURCE_DIR}/src/py/test/
+    DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/
+)
+
+# 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()

examples/cells/dynamic/config.yaml

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+# For docs on config options, see examples/shapes/wrapper/package_info.yaml
+name: pycells
+
+smart_ptr_type: std::shared_ptr
+pointer_call_policy: reference
+reference_call_policy: reference_internal
+
+common_include_file: False
+source_includes:
+  - <memory>
+
+exclude_default_args: False
+
+template_substitutions:
+  - signature: <unsigned DIM>
+    replacement: [[2], [3]]
+  - signature: <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
+    replacement: [[2, 2], [3, 3]]
+  - signature: <unsigned ELEMENT_DIM, unsigned SPACE_DIM=ELEMENT_DIM>
+    replacement: [[2, 2], [3, 3]]
+
+modules:
+  - name: lib
+    source_locations:
+      - cycle
+      - mesh
+      - ode
+      - pde
+      - population
+      - visualization
+
+    classes:
+      - name: AbstractCellPopulation
+      - name: MeshBasedCellPopulation
+
+prefix_text: |
+  // This file is auto-generated by cppwg; manual changes will be overwritten.

examples/cells/extern/meshgen/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.8)
+project(meshgen)
+
+add_library(meshgen MeshGen.cpp MeshGen.hpp)
+target_include_directories(meshgen PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+add_library(meshgen::meshgen ALIAS meshgen)

examples/cells/extern/meshgen/MeshGen.cpp

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+#include "MeshGen.hpp"
+
+MeshGen::MeshGen()
+{
+    // Constructor
+}
+
+MeshGen::~MeshGen()
+{
+    // Destructor
+}
+
+void MeshGen::generateMesh()
+{
+    // Generate a mesh
+}

examples/cells/extern/meshgen/MeshGen.hpp

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+#ifndef _MESHGEN_HPP
+#define _MESHGEN_HPP
+
+class MeshGen
+{
+
+public:
+    /**
+     * Default Constructor
+     */
+    MeshGen();
+
+    /**
+     * Destructor
+     */
+    ~MeshGen();
+
+    /**
+     * Generate a mesh
+     */
+    void generateMesh();
+};
+
+#endif // _MESHGEN_HPP

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

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+#include "AbstractMesh.hpp"
+
+template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
+AbstractMesh<ELEMENT_DIM, SPACE_DIM>::AbstractMesh() : mIndex(0)
+{
+}
+
+template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
+AbstractMesh<ELEMENT_DIM, SPACE_DIM>::~AbstractMesh()
+{
+}
+
+template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
+unsigned AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetIndex() const
+{
+    return mIndex;
+}
+
+template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
+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 class AbstractMesh<2, 2>;
+template class AbstractMesh<3, 3>;

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

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+#ifndef _ABSTRACT_MESH_HPP
+#define _ABSTRACT_MESH_HPP
+
+#include "Point.hpp"
+
+/**
+ * A mesh in SPACE_DIM space with ELEMENT_DIM dimensional elements
+ */
+template <unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
+class AbstractMesh
+{
+private:
+    /**
+     * AbstractMesh index
+     */
+    unsigned mIndex;
+
+public:
+    /**
+     * Default Constructor
+     */
+    AbstractMesh();
+
+    /**
+     * Destructor
+     */
+    ~AbstractMesh();
+
+    /**
+     * Return the index
+     */
+    unsigned GetIndex() const;
+
+    /**
+     * Set the index
+     */
+    void SetIndex(unsigned index);
+
+    /**
+     * Add a vertex to the mesh
+     */
+    void AddVertex(Point<SPACE_DIM> vertex);
+
+    /**
+     * Scale the mesh by a factor
+     */
+    virtual void Scale(const double factor) = 0;
+};
+
+#endif // _ABSTRACT_MESH_HPP

examples/cells/src/cpp/mesh/ConcreteMesh.cpp

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

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

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

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

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+#include "ConcreteMesh.hpp"
+
+#include "MeshFactory.hpp"
+
+template <class MESH>
+MeshFactory<MESH>::MeshFactory(): mMeshGen()
+{
+}
+
+template <class MESH>
+MeshFactory<MESH>::~MeshFactory()
+{
+}
+
+template class MeshFactory<ConcreteMesh<2> >;
+template class MeshFactory<ConcreteMesh<3> >;

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

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+#ifndef _MESH_FACTORY_HPP
+#define _MESH_FACTORY_HPP
+
+#include "MeshGen.hpp"
+
+/**
+ * A concrete mesh implementation
+ */
+template <class MESH>
+class MeshFactory
+{
+private:
+    MeshGen mMeshGen;
+
+public:
+    /**
+     * Default Constructor
+     */
+    MeshFactory();
+
+    /**
+     * Destructor
+     */
+    ~MeshFactory();
+};
+
+#endif // _MESH_FACTORY_HPP

examples/cells/src/py/cells/_syntax.py

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+import inspect
+from collections.abc import Iterable
+
+
+class TemplateClassDict:
+
+    def __init__(self, template_dict):
+        self._dict = {}
+        for arg_tuple, cls in template_dict.items():
+            if not inspect.isclass(cls):
+                raise TypeError("Expected class, got {}".format(type(cls)))
+            if not isinstance(arg_tuple, Iterable):
+                arg_tuple = (arg_tuple,)
+            key = tuple(
+                arg.__name__ if inspect.isclass(arg) else str(arg) for arg in arg_tuple
+            )
+            self._dict[key] = cls
+
+    def __getitem__(self, arg_tuple):
+        if not isinstance(arg_tuple, Iterable):
+            arg_tuple = (arg_tuple,)
+        key = tuple(
+            arg.__name__ if inspect.isclass(arg) else str(arg) for arg in arg_tuple
+        )
+        return self._dict[key]

examples/cells/src/py/cells/mesh/__init__.py

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+from pycells._pycells_lib import ConcreteMesh_2

examples/cells/src/py/test/test_cells.py

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+import unittest
+
+
+class TestCells(unittest.TestCase):
+
+    def testCells(self):
+        pass
+
+if __name__ == "__main__":
+    unittest.main()