Redesign holder types

.github/workflows/macos.yml

@@ -69,6 +69,7 @@ jobs:
           -DCMAKE_C_COMPILER_LAUNCHER=ccache
           -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
           -DCMAKE_PREFIX_PATH=$SOFA_ROOT/lib/cmake
+          -DCMAKE_BUILD_TYPE=Release
           .
           && ninja && ninja install
           && echo ${CCACHE_BASEDIR}
@@ -125,24 +126,22 @@ jobs:
       - name: Binding.Sofa.Tests
         if: ${{ always() }}
         run: |
-          export DYLD_LIBRARY_PATH=$GITHUB_WORKSPACE/SofaPython3/lib:$SOFA_ROOT/lib:$DYLD_LIBRARY_PATH
-          export PYTHONPATH=$GITHUB_WORKSPACE/SofaPython3/lib/python3/site-packages:$PYTHONPATH
-          export SOFA_PLUGIN_PATH=$SOFA_ROOT/plugins
+          export DYLD_LIBRARY_PATH=$GITHUB_WORKSPACE/SofaPython3/lib:$SOFA_ROOT/lib
+          export PYTHONPATH=$GITHUB_WORKSPACE/SofaPython3/lib/python3/site-packages
           chmod +x SofaPython3/bin/Bindings.Sofa.Tests
           ./SofaPython3/bin/Bindings.Sofa.Tests
       - name: Bindings.SofaRuntime.Tests
         if: ${{ always() }}
         run: |
-          export DYLD_LIBRARY_PATH=$GITHUB_WORKSPACE/SofaPython3/lib:$SOFA_ROOT/lib:$DYLD_LIBRARY_PATH
-          export PYTHONPATH=$GITHUB_WORKSPACE/SofaPython3/lib/python3/site-packages:$PYTHONPATH
-          export SOFA_PLUGIN_PATH=$SOFA_ROOT/plugins
+          export DYLD_LIBRARY_PATH=$GITHUB_WORKSPACE/SofaPython3/lib:$SOFA_ROOT/lib
+          export PYTHONPATH=$GITHUB_WORKSPACE/SofaPython3/lib/python3/site-packages
           chmod +x SofaPython3/bin/Bindings.SofaRuntime.Tests
           ./SofaPython3/bin/Bindings.SofaRuntime.Tests
       - name: Bindings.SofaTypes.Tests
         if: ${{ always() }}
         run: |
-          export DYLD_LIBRARY_PATH=$GITHUB_WORKSPACE/SofaPython3/lib:$SOFA_ROOT/lib:$DYLD_LIBRARY_PATH
-          export PYTHONPATH=$GITHUB_WORKSPACE/SofaPython3/lib/python3/site-packages:$PYTHONPATH
+          export DYLD_LIBRARY_PATH=$GITHUB_WORKSPACE/SofaPython3/lib:$SOFA_ROOT/lib
+          export PYTHONPATH=$GITHUB_WORKSPACE/SofaPython3/lib/python3/site-packages
           chmod +x SofaPython3/bin/Bindings.SofaTypes.Tests
           ./SofaPython3/bin/Bindings.SofaTypes.Tests
 

.github/workflows/ubuntu.yml

@@ -85,6 +85,7 @@ jobs:
           -DCMAKE_C_COMPILER_LAUNCHER=ccache
           -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
           -DCMAKE_PREFIX_PATH=$SOFA_ROOT/lib/cmake
+          -DCMAKE_BUILD_TYPE=Release
           .
           && ninja && ninja install
           && echo ${CCACHE_BASEDIR}
@@ -143,23 +144,20 @@ jobs:
         run: |
           export LD_LIBRARY_PATH=$GITHUB_WORKSPACE/SofaPython3/lib:$SOFA_ROOT/lib:$LD_LIBRARY_PATH
           export PYTHONPATH=$GITHUB_WORKSPACE/SofaPython3/lib/python3/site-packages:$PYTHONPATH
-          export SOFA_PLUGIN_PATH=$SOFA_ROOT/plugins
           chmod +x SofaPython3/bin/Bindings.Sofa.Tests
           ./SofaPython3/bin/Bindings.Sofa.Tests
       - name: Bindings.SofaRuntime.Tests
         if: ${{ always() }}
         run: |
           export LD_LIBRARY_PATH=$GITHUB_WORKSPACE/SofaPython3/lib:$SOFA_ROOT/lib:$LD_LIBRARY_PATH
           export PYTHONPATH=$GITHUB_WORKSPACE/SofaPython3/lib/python3/site-packages:$PYTHONPATH
-          export SOFA_PLUGIN_PATH=$SOFA_ROOT/plugins
           chmod +x SofaPython3/bin/Bindings.SofaRuntime.Tests
           ./SofaPython3/bin/Bindings.SofaRuntime.Tests
       - name: Bindings.SofaTypes.Tests
         if: ${{ always() }}
         run: |
           export LD_LIBRARY_PATH=$GITHUB_WORKSPACE/SofaPython3/lib:$SOFA_ROOT/lib:$LD_LIBRARY_PATH
           export PYTHONPATH=$GITHUB_WORKSPACE/SofaPython3/lib/python3/site-packages:$PYTHONPATH
-          export SOFA_PLUGIN_PATH=$SOFA_ROOT/plugins
           chmod +x SofaPython3/bin/Bindings.SofaTypes.Tests
           ./SofaPython3/bin/Bindings.SofaTypes.Tests
 

CMake/SofaPython3Tools.cmake

@@ -125,12 +125,13 @@ function(SP3_add_python_module)
         PUBLIC $<INSTALL_INTERFACE:include>
     )
 
-    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+    if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang") # Clang or AppleCLang
         target_compile_options(${A_TARGET} PUBLIC -fsized-deallocation)
     endif()
 
     if (NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
         target_compile_options(${A_TARGET} PRIVATE -Dregister=)
+        target_compile_options(${A_TARGET} PRIVATE -fvisibility=hidden)
     endif()
 
     target_link_libraries(${A_TARGET} PUBLIC pybind11::module)

CMakeLists.txt

@@ -64,6 +64,9 @@ if(MSVC)
     # With C++17 (/std:c++17), to get MSVC to behave, you need /permissive-
     # see https://github.com/pybind/pybind11/issues/1616
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /permissive-")
+
+    # use M_PI in cmath.h
+    add_definitions("-D_USE_MATH_DEFINES")
 endif()
 
 set(CMAKE_CXX_STANDARD 17)
@@ -172,13 +175,23 @@ if (SP3_LINK_TO_USER_SITE AND SP3_PYTHON_PACKAGES_LINK_DIRECTORY)
     install(DIRECTORY DESTINATION ${SP3_PYTHON_PACKAGES_LINK_DIRECTORY})
     foreach(directory ${directories})
         if(IS_DIRECTORY ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${SP3_PYTHON_PACKAGES_DIRECTORY}/${directory})
-            install(CODE "\
+            if(WIN32)
+                install(CODE "\
                 execute_process( \
-                    COMMAND ${CMAKE_COMMAND} -E create_symlink \
+                    COMMAND ${CMAKE_COMMAND} -E copy_directory \
                     ${CMAKE_INSTALL_PREFIX}/${LIBRARY_OUTPUT_DIRECTORY}/${SP3_PYTHON_PACKAGES_DIRECTORY}/${directory}/ \
                     ${SP3_PYTHON_PACKAGES_LINK_DIRECTORY}/${directory}   \
                 )"
             )
+            else()
+                install(CODE "\
+                    execute_process( \
+                        COMMAND ${CMAKE_COMMAND} -E create_symlink \
+                        ${CMAKE_INSTALL_PREFIX}/${LIBRARY_OUTPUT_DIRECTORY}/${SP3_PYTHON_PACKAGES_DIRECTORY}/${directory}/ \
+                        ${SP3_PYTHON_PACKAGES_LINK_DIRECTORY}/${directory}   \
+                    )"
+                )
+            endif()
         endif()
     endforeach()
 endif()

Plugin/CMakeLists.txt

@@ -37,7 +37,6 @@ endif(SP3_BUILD_TEST)
 find_package(pybind11 CONFIG REQUIRED)
 find_package(SofaFramework REQUIRED)
 find_package(SofaSimulation REQUIRED)
-find_package(SofaGeneral REQUIRED)
 
 add_library(${PROJECT_NAME} SHARED ${HEADER_FILES} ${SOURCE_FILES})
 add_library(SofaPython3::${PROJECT_NAME} ALIAS ${PROJECT_NAME})

Plugin/src/SofaPython3/DataHelper.cpp

@@ -66,21 +66,6 @@ void fillBaseObjectdescription(sofa::core::objectmodel::BaseObjectDescription& d
     }
 }
 
-PythonTrampoline::~PythonTrampoline(){}
-void PythonTrampoline::setInstance(py::object s)
-{
-    s.inc_ref();
-
-    // TODO(bruno-marques) ici ça crash dans SOFA.
-    //--ref_counter;
-
-    pyobject = std::shared_ptr<PyObject>( s.ptr(), [](PyObject* ob)
-    {
-            // runSofa Sofa/tests/pyfiles/ScriptController.py => CRASH
-            // Py_DECREF(ob);
-});
-}
-
 std::ostream& operator<<(std::ostream& out, const py::buffer_info& p)
 {
     out << "buffer{"<< p.format << ", " << p.ndim << ", " << p.shape[0];

Plugin/src/SofaPython3/DataHelper.h

@@ -37,8 +37,7 @@ along with sofaqtquick. If not, see <http://www.gnu.org/licenses/>.
 #include <sofa/core/objectmodel/Base.h>
 #include <sofa/core/objectmodel/BaseObject.h>
 #include <sofa/core/objectmodel/BaseNode.h>
-
-#include "config.h"
+#include <SofaPython3/config.h>
 
 ////////////////////////// FORWARD DECLARATION ///////////////////////////
 namespace sofa {
@@ -183,7 +182,6 @@ namespace sofa {
 /////////////////////////////// DECLARATION //////////////////////////////
 namespace sofapython3
 {
-namespace py { using namespace pybind11; }
 
 using sofa::core::objectmodel::Base;
 using sofa::core::objectmodel::BaseData;
@@ -192,61 +190,40 @@ using sofa::core::objectmodel::BaseNode;
 using sofa::core::objectmodel::BaseObject;
 using sofa::defaulttype::AbstractTypeInfo;
 
+SOFAPYTHON3_API void setItem2D(pybind11::array a, pybind11::slice slice, pybind11::object o);
+SOFAPYTHON3_API void setItem2D(pybind11::array a, const pybind11::slice& slice,
+               const pybind11::slice& slice1, pybind11::object o);
+SOFAPYTHON3_API void setItem1D(pybind11::array a, pybind11::slice slice, pybind11::object o);
+SOFAPYTHON3_API void setItem(pybind11::array a, pybind11::slice slice, pybind11::object value);
 
-class SOFAPYTHON3_API PythonTrampoline
-{
-protected:
-    std::shared_ptr<PyObject> pyobject;
-public:
-    virtual ~PythonTrampoline();
-    virtual void  setInstance(py::object s);
-};
-
-template <typename T> class py_shared_ptr : public sofa::core::sptr<T>
-{
-public:
-    py_shared_ptr(T *ptr) : sofa::core::sptr<T>(ptr)
-    {
-        auto nptr = dynamic_cast<PythonTrampoline*>(ptr);
-        if(nptr)
-            nptr->setInstance( py::cast(ptr) ) ;
-    }
-};
-
-SOFAPYTHON3_API void setItem2D(py::array a, py::slice slice, py::object o);
-SOFAPYTHON3_API void setItem2D(py::array a, const py::slice& slice,
-               const py::slice& slice1, py::object o);
-SOFAPYTHON3_API void setItem1D(py::array a, py::slice slice, py::object o);
-SOFAPYTHON3_API void setItem(py::array a, py::slice slice, py::object value);
-
-SOFAPYTHON3_API py::slice toSlice(const py::object& o);
+SOFAPYTHON3_API pybind11::slice toSlice(const pybind11::object& o);
 SOFAPYTHON3_API std::string getPathTo(Base* b);
 SOFAPYTHON3_API const char* getFormat(const AbstractTypeInfo& nfo);
 
-SOFAPYTHON3_API std::map<void*, py::array>& getObjectCache();
+SOFAPYTHON3_API std::map<void*, pybind11::array>& getObjectCache();
 SOFAPYTHON3_API void trimCache();
 
 SOFAPYTHON3_API bool hasArrayFor(BaseData* d);
-SOFAPYTHON3_API py::array resetArrayFor(BaseData* d);
-SOFAPYTHON3_API py::array getPythonArrayFor(BaseData* d);
+SOFAPYTHON3_API pybind11::array resetArrayFor(BaseData* d);
+SOFAPYTHON3_API pybind11::array getPythonArrayFor(BaseData* d);
 
 
 
-py::buffer_info SOFAPYTHON3_API toBufferInfo(BaseData& m);
-py::object SOFAPYTHON3_API convertToPython(BaseData* d);
+pybind11::buffer_info SOFAPYTHON3_API toBufferInfo(BaseData& m);
+pybind11::object SOFAPYTHON3_API convertToPython(BaseData* d);
 
-void SOFAPYTHON3_API copyFromListScalar(BaseData& d, const AbstractTypeInfo& nfo, const py::list& l);
+void SOFAPYTHON3_API copyFromListScalar(BaseData& d, const AbstractTypeInfo& nfo, const pybind11::list& l);
 
-std::string SOFAPYTHON3_API toSofaParsableString(const py::handle& p);
+std::string SOFAPYTHON3_API toSofaParsableString(const pybind11::handle& p);
 
-//py::object SOFAPYTHON3_API dataToPython(BaseData* d);
+//pybind11::object SOFAPYTHON3_API dataToPython(BaseData* d);
 
 /// RVO optimized function. Don't care about copy on the return code.
 void SOFAPYTHON3_API fillBaseObjectdescription(sofa::core::objectmodel::BaseObjectDescription& desc,
-                               const py::dict& dict);
+                               const pybind11::dict& dict);
 
 template<typename T>
-void copyScalar(BaseData* a, const AbstractTypeInfo& nfo, py::array_t<T, py::array::c_style> src)
+void copyScalar(BaseData* a, const AbstractTypeInfo& nfo, pybind11::array_t<T, pybind11::array::c_style> src)
 {
     void* ptr = a->beginEditVoidPtr();
 
@@ -271,7 +248,7 @@ size_t SOFAPYTHON3_API getNDim(BaseData* self);
 /// https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.size.html#numpy.ndarray.size
 size_t SOFAPYTHON3_API getSize(BaseData* self);
 
-SOFAPYTHON3_API std::ostream& operator<<(std::ostream& out, const py::buffer_info& p);
+SOFAPYTHON3_API std::ostream& operator<<(std::ostream& out, const pybind11::buffer_info& p);
 
 // TODO: move this somewhere else as we will probably need it in several other places.
 template <class T> class raw_ptr
@@ -317,8 +294,8 @@ class scoped_writeonly_access
     ~scoped_writeonly_access(){ data->endEditVoidPtr(); }
 };
 
-SOFAPYTHON3_API BaseData* addData(py::object py_self, const std::string& name, py::object value = py::none(), py::object defaultValue = py::none(), const std::string& help = "", const std::string& group = "Property", std::string type = "");
-SOFAPYTHON3_API BaseLink* addLink(py::object py_self, const std::string& name, py::object value, const std::string& help);
+SOFAPYTHON3_API BaseData* addData(pybind11::object py_self, const std::string& name, pybind11::object value = pybind11::none(), pybind11::object defaultValue = pybind11::none(), const std::string& help = "", const std::string& group = "Property", std::string type = "");
+SOFAPYTHON3_API BaseLink* addLink(pybind11::object py_self, const std::string& name, pybind11::object value, const std::string& help);
 SOFAPYTHON3_API bool isProtectedKeyword(const std::string& name);
 
 }  // namespace sofapython3

Plugin/src/SofaPython3/Prefab.cpp

@@ -1,5 +1,4 @@
-#include "Prefab.h"
-
+#include <SofaPython3/Prefab.h>
 #include <SofaPython3/DataHelper.h>
 #include <SofaPython3/PythonFactory.h>
 #include <SofaPython3/PythonEnvironment.h>
@@ -15,6 +14,9 @@ using sofa::simulation::VisualInitVisitor;
 #include <sofa/simulation/Simulation.h>
 using sofa::simulation::Simulation;
 
+/// Makes an alias for the pybind11 namespace to increase readability.
+namespace py { using namespace pybind11; }
+
 namespace sofapython3
 {
 using sofa::core::objectmodel::Event;

Plugin/src/SofaPython3/Prefab.h

@@ -39,7 +39,7 @@ class SOFAPYTHON3_API Prefab : public BasePrefab
     void reinit();
     virtual void doReInit() ;
 
-    void addPrefabParameter(const std::string& name, const std::string& help, const std::string& type, pybind11::object defaultValue = py::none());
+    void addPrefabParameter(const std::string& name, const std::string& help, const std::string& type, pybind11::object defaultValue = pybind11::none());
     void setSourceTracking(const std::string& filename);
     void breakPrefab();
 

Plugin/src/SofaPython3/PythonEnvironment.cpp

@@ -76,7 +76,9 @@ using sofa::simulation::SceneLoaderFactory;
 
 #include <pybind11/embed.h>
 #include <pybind11/eval.h>
-namespace py = pybind11;
+
+/// Makes an alias for the pybind11 namespace to increase readability.
+namespace py { using namespace pybind11; }
 
 #include "SceneLoaderPY3.h"
 using sofapython3::SceneLoaderPY3;

Plugin/src/SofaPython3/PythonEnvironment.h

@@ -70,7 +70,6 @@ along with sofaqtquick. If not, see <http://www.gnu.org/licenses/>.
 
 namespace sofapython3
 {
-namespace py { using namespace pybind11; }
 using sofa::simulation::SceneLoader ;
 
 /// Forward definition
@@ -82,9 +81,9 @@ class SOFAPYTHON3_API PythonEnvironment
     static void Init();
     static void Release();
 
-    static py::module importFromFile(const std::string& module,
+    static pybind11::module importFromFile(const std::string& module,
                                      const std::string& path,
-                                     py::object* globals = nullptr);
+                                     pybind11::object* globals = nullptr);
 
     /// Add a path to sys.path, the list of search path for Python modules.
     static void addPythonModulePath(const std::string& path);

Plugin/src/SofaPython3/PythonFactory.cpp

@@ -26,8 +26,8 @@ along with sofaqtquick. If not, see <http://www.gnu.org/licenses/>.
 ********************************************************************/
 
 #include <functional>
-#include "PythonFactory.h"
-#include "DataHelper.h"
+#include <SofaPython3/PythonFactory.h>
+#include <SofaPython3/DataHelper.h>
 
 #include <SofaSimulationGraph/DAGNode.h>
 
@@ -60,6 +60,11 @@ using sofa::core::objectmodel::Event;
 
 #include <sofa/defaulttype/DataTypeInfo.h>
 
+/// Bind the python's attribute error
+namespace pybind11 { PYBIND11_RUNTIME_EXCEPTION(attribute_error, PyExc_AttributeError) }
+/// Makes an alias for the pybind11 namespace to increase readability.
+namespace py { using namespace pybind11; }
+
 namespace sofapython3
 {
 using namespace pybind11::literals;

Plugin/src/SofaPython3/PythonFactory.h

@@ -37,25 +37,22 @@ along with sofaqtquick. If not, see <http://www.gnu.org/licenses/>.
 /////////////////////////////// DECLARATION //////////////////////////////
 namespace sofapython3
 {
-    /// Makes an alias for the pybind11 namespace to increase readability.
-    namespace py { using namespace pybind11; }
-
-    typedef std::function<py::object(sofa::core::objectmodel::Base*)> componentDowncastingFunction;
-    typedef std::function<py::object(sofa::core::objectmodel::BaseData*)> dataDowncastingFunction;
-    typedef std::function<py::dict(sofa::core::objectmodel::Event*)> eventDowncastingFunction;
+    typedef std::function<pybind11::object(sofa::core::objectmodel::Base*)> componentDowncastingFunction;
+    typedef std::function<pybind11::object(sofa::core::objectmodel::BaseData*)> dataDowncastingFunction;
+    typedef std::function<pybind11::dict(sofa::core::objectmodel::Event*)> eventDowncastingFunction;
     typedef std::function<sofa::core::objectmodel::BaseData*()> dataCreatorFunction;
 
     typedef sofa::helper::Factory< std::string, sofa::core::objectmodel::BaseData> DataFactory;
 
     class SOFAPYTHON3_API PythonFactory
     {
     public:
-        static py::object toPython(sofa::core::objectmodel::Base* object);
-        static py::object toPython(const sofa::core::objectmodel::BaseData* data);
-        static py::object toPython(sofa::core::objectmodel::BaseData* data);
-        static py::object valueToPython_ro(sofa::core::objectmodel::BaseData* data);
-        static void fromPython(sofa::core::objectmodel::BaseData* data, const py::object& value);
-        static py::object toPython(sofa::core::objectmodel::Event* event);
+        static pybind11::object toPython(sofa::core::objectmodel::Base* object);
+        static pybind11::object toPython(const sofa::core::objectmodel::BaseData* data);
+        static pybind11::object toPython(sofa::core::objectmodel::BaseData* data);
+        static pybind11::object valueToPython_ro(sofa::core::objectmodel::BaseData* data);
+        static void fromPython(sofa::core::objectmodel::BaseData* data, const pybind11::object& value);
+        static pybind11::object toPython(sofa::core::objectmodel::Event* event);
         static sofa::core::objectmodel::BaseData* createInstance(const std::string& typeName);
 
         static void registerType(const std::string& typeName, componentDowncastingFunction fct);

Plugin/src/SofaPython3/PythonTest.h

@@ -28,7 +28,7 @@ along with sofaqtquick. If not, see <http://www.gnu.org/licenses/>.
 #pragma once
 
 #include <string>
-#include "config.h"
+#include <SofaPython3/config.h>
 #include <sofa/helper/testing/BaseTest.h>
 
 #include <boost/filesystem/path.hpp>