Updating include paths from python package

lib/python_binding/include/python_binding/api/selection/helper.hpp

@@ -1,7 +1,7 @@
 #ifndef __VTX_PYTHON_API_SELECTION_HELPER__
 #define __VTX_PYTHON_API_SELECTION_HELPER__
 
-#include <app/application/selection/selection.hpp>
+#include <app/selection/selection.hpp>
 #include <functional>
 #include <optional>
 #include <pybind11/pybind11.h>
@@ -13,7 +13,7 @@
 
 namespace VTX::PythonBinding::API::Selection
 {
-	using SelectionObj = App::Application::Selection::Selection;
+	using SelectionObj = App::Selection::Selection;
 
 	// Function that manage a param that can be a single T1 or a list of T1 and convert it into a vector of str
 	template<typename T1, typename T2>

lib/python_binding/include/python_binding/api/selection/selection_interpretor.hpp

@@ -2,13 +2,13 @@
 #define __VTX_PYTHON_API_SELECTION_SELECTION_INTERPRETOR__
 
 #include "_fwd.hpp"
-#include <app/application/selection/selection.hpp>
 #include <app/component/chemistry/_fwd.hpp>
+#include <app/selection/selection.hpp>
 #include <pybind11/pybind11.h>
 
 namespace VTX::PythonBinding::API::Selection
 {
-	using Selection = App::Application::Selection::Selection;
+	using Selection = App::Selection::Selection;
 
 	class SelectionInterpretor
 	{

lib/python_binding/include/python_binding/api/selection/selection_wrapper.hpp

@@ -3,15 +3,15 @@
 
 #include "_fwd.hpp"
 #include "python_binding/api/selection/helper.hpp"
-#include <app/application/selection/selection.hpp>
+#include <app/selection/selection.hpp>
 #include <app/component/chemistry/_fwd.hpp>
 #include <pybind11/pybind11.h>
 #include <string>
 #include <vector>
 
 namespace VTX::PythonBinding::API::Selection
 {
-	using Selection = App::Application::Selection::Selection;
+	using Selection = App::Selection::Selection;
 
 	class SelectionWrapper
 	{

lib/python_binding/include/python_binding/api/selection/system_interpretor.hpp

@@ -1,8 +1,8 @@
 #ifndef __VTX_PYTHON_API_SELECTION_MOLECULE_INTERPRETOR__
 #define __VTX_PYTHON_API_SELECTION_MOLECULE_INTERPRETOR__
 
-#include <app/application/selection/selection.hpp>
-#include <app/application/selection/system_data.hpp>
+#include <app/selection/selection.hpp>
+#include <app/selection/system_data.hpp>
 #include <core/chemdb/atom.hpp>
 #include <pybind11/pybind11.h>
 #include <set>
@@ -49,31 +49,31 @@ namespace VTX::PythonBinding::API::Selection
 		};
 
 	  public:
-		static void interpretSystems( App::Application::Selection::Selection &, const pybind11::kwargs & );
+		static void interpretSystems( App::Selection::Selection &, const pybind11::kwargs & );
 
 	  private:
 		static std::set<App::Component::Chemistry::System *> _getSystems( const InterpretedKwargs & p_kwargs );
 
 		static void _selectChains(
 			const InterpretedKwargs &				  p_kwargs,
-			App::Application::Selection::SystemData & p_systemSelectionData
+			App::Selection::SystemData & p_systemSelectionData
 		);
 
 		static void _selectResidues(
 			const InterpretedKwargs &				  p_kwargs,
-			App::Application::Selection::SystemData & p_systemSelectionData
+			App::Selection::SystemData & p_systemSelectionData
 		);
 
 		static void _selectAtoms(
 			const InterpretedKwargs &				  p_kwargs,
-			App::Application::Selection::SystemData & p_systemSelectionData
+			App::Selection::SystemData & p_systemSelectionData
 		);
 
 		static void _addAtomsFollowingKwargs(
 			const atom_index_t						  p_firstAtom,
 			const atom_index_t						  p_lastAtom,
 			App::Component::Chemistry::System &		  p_system,
-			App::Application::Selection::SystemData & p_systemSelectionData,
+			App::Selection::SystemData & p_systemSelectionData,
 			const InterpretedKwargs &				  p_kwargs
 		);
 	};

lib/python_binding/src/python_binding/api/selection/selection_wrapper.cpp

@@ -1,13 +1,13 @@
 #include "python_binding/api/selection/selection_wrapper.hpp"
 #include <app/application/scene.hpp>
-#include <app/application/selection/selection_manager.hpp>
-#include <app/application/selection/system_data.hpp>
 #include <app/component/chemistry/atom.hpp>
 #include <app/component/chemistry/chain.hpp>
 #include <app/component/chemistry/residue.hpp>
 #include <app/component/chemistry/system.hpp>
 #include <app/component/scene/selectable.hpp>
 #include <app/helper/chemistry.hpp>
+#include <app/selection/selection_manager.hpp>
+#include <app/selection/system_data.hpp>
 #include <app/vtx_app.hpp>
 #include <sstream>
 
@@ -84,9 +84,10 @@ namespace VTX::PythonBinding::API::Selection
 		{
 			App::Component::Chemistry::System & mol = *it;
 
-			const App::Application::Selection::SystemData & molSelection
-				//= PythonFixture::ECS_REGISTRY().getComponent<PythonFixture::Application::Selection::SystemData>( *it );
-				= _selection->getSelectionDataFromComponent<App::Application::Selection::SystemData>( mol
+			const App::Selection::SystemData & molSelection
+				//= PythonFixture::ECS_REGISTRY().getComponent<PythonFixture::Application::Selection::SystemData>( *it
+				//);
+				= _selection->getSelectionDataFromComponent<App::Selection::SystemData>( mol
 				); // TODO : is this working properly ?
 
 			for ( const size_t & chainID : molSelection.getChainIds() )
@@ -107,9 +108,10 @@ namespace VTX::PythonBinding::API::Selection
 		{
 			App::Component::Chemistry::System & mol = *it;
 
-			const App::Application::Selection::SystemData & molSelection
-				//= PythonFixture::ECS_REGISTRY().getComponent<PythonFixture::Application::Selection::SystemData>( *it );
-				= _selection->getSelectionDataFromComponent<App::Application::Selection::SystemData>( mol
+			const App::Selection::SystemData & molSelection
+				//= PythonFixture::ECS_REGISTRY().getComponent<PythonFixture::Application::Selection::SystemData>( *it
+				//);
+				= _selection->getSelectionDataFromComponent<App::Selection::SystemData>( mol
 				); // TODO : is this working properly ?
 
 			for ( const size_t & residueID : molSelection.getResidueIds() )
@@ -130,8 +132,8 @@ namespace VTX::PythonBinding::API::Selection
 		{
 			App::Component::Chemistry::System & mol = *it;
 
-			const App::Application::Selection::SystemData & molSelection
-				= _selection->getSelectionDataFromComponent<App::Application::Selection::SystemData>( mol );
+			const App::Selection::SystemData & molSelection
+				= _selection->getSelectionDataFromComponent<App::Selection::SystemData>( mol );
 
 			for ( const atom_index_t & atomID : molSelection.getAtomIds() )
 			{

lib/python_binding/src/python_binding/api/selection/system_interpretor.cpp

@@ -72,7 +72,7 @@ namespace VTX::PythonBinding::API::Selection
 	bool SystemInterpretor::InterpretedKwargs::hasSpecifyAtom() const { return _hasAtomParams; }
 
 	void SystemInterpretor::interpretSystems(
-		App::Application::Selection::Selection & p_selection,
+		App::Selection::Selection & p_selection,
 		const pybind11::kwargs &				 p_kwargs
 	)
 	{
@@ -92,9 +92,9 @@ namespace VTX::PythonBinding::API::Selection
 			App::Component::Scene::Selectable & selectableComponent
 				= App::ECS_REGISTRY().getComponent<App::Component::Scene::Selectable>( *system );
 
-			App::Application::Selection::SystemData & systemSelectionData
-				= p_selection.select<App::Application::Selection::SystemData>(
-					selectableComponent, App::Application::Selection::AssignmentType::APPEND
+			App::Selection::SystemData & systemSelectionData
+				= p_selection.select<App::Selection::SystemData>(
+					selectableComponent, App::Selection::AssignmentType::APPEND
 				);
 
 			if ( !selectFullSystem )
@@ -158,7 +158,7 @@ namespace VTX::PythonBinding::API::Selection
 
 	void SystemInterpretor::_selectChains(
 		const InterpretedKwargs &				  p_kwargs,
-		App::Application::Selection::SystemData & p_systemSelectionData
+		App::Selection::SystemData & p_systemSelectionData
 	)
 	{
 		System &   system		   = p_systemSelectionData.getSystem();
@@ -203,11 +203,11 @@ namespace VTX::PythonBinding::API::Selection
 
 	void SystemInterpretor::_selectResidues(
 		const InterpretedKwargs &				  p_kwargs,
-		App::Application::Selection::SystemData & p_systemSelectionData
+		App::Selection::SystemData & p_systemSelectionData
 	)
 	{
 		const System &													system = p_systemSelectionData.getSystem();
-		const App::Application::Selection::SystemData::IndexRangeList & chainIDs
+		const App::Selection::SystemData::IndexRangeList & chainIDs
 			= p_systemSelectionData.getChainIds();
 
 		const bool selectFullResidue = !p_kwargs.hasSpecifyAtom();
@@ -303,17 +303,17 @@ namespace VTX::PythonBinding::API::Selection
 
 	void SystemInterpretor::_selectAtoms(
 		const InterpretedKwargs &				  p_kwargs,
-		App::Application::Selection::SystemData & p_systemSelectionData
+		App::Selection::SystemData & p_systemSelectionData
 	)
 	{
 		System & system = p_systemSelectionData.getSystem();
 
-		const App::Application::Selection::SystemData::IndexRangeList & residueIDs
+		const App::Selection::SystemData::IndexRangeList & residueIDs
 			= p_systemSelectionData.getResidueIds();
 
 		if ( residueIDs.isEmpty() )
 		{
-			const App::Application::Selection::SystemData::IndexRangeList & chainIDs
+			const App::Selection::SystemData::IndexRangeList & chainIDs
 				= p_systemSelectionData.getChainIds();
 
 			if ( chainIDs.isEmpty() )
@@ -343,7 +343,7 @@ namespace VTX::PythonBinding::API::Selection
 		}
 		else
 		{
-			const App::Application::Selection::SystemData::IndexRangeList & residueIDs
+			const App::Selection::SystemData::IndexRangeList & residueIDs
 				= p_systemSelectionData.getResidueIds();
 
 			for ( const size_t residueID : residueIDs )
@@ -368,7 +368,7 @@ namespace VTX::PythonBinding::API::Selection
 		const atom_index_t						  p_firstAtom,
 		const atom_index_t						  p_lastAtom,
 		System &								  p_system,
-		App::Application::Selection::SystemData & p_systemSelectionData,
+		App::Selection::SystemData & p_systemSelectionData,
 		const InterpretedKwargs &				  p_kwargs
 	)
 	{

lib/python_binding/src/python_binding/binding/binders/selection.cpp

@@ -2,7 +2,7 @@
 #include "python_binding/api/selection/selection_interpretor.hpp"
 #include "python_binding/api/selection/selection_wrapper.hpp"
 #include "python_binding/api/selection/system_interpretor.hpp"
-#include <app/application/selection/selection.hpp>
+#include <app/selection/selection.hpp>
 #include <app/component/chemistry/atom.hpp>
 #include <app/component/chemistry/chain.hpp>
 #include <app/component/chemistry/residue.hpp>
@@ -35,7 +35,7 @@ namespace VTX::PythonBinding::Binding::Binders
 		p_apiModule.def( "intersect", &API::Selection::SelectionWrapper::intersect );
 		p_apiModule.def( "exclusive", &API::Selection::SelectionWrapper::exclusive );
 
-		pybind11::class_<App::Application::Selection::Selection>(
+		pybind11::class_<App::Selection::Selection>(
 			p_apiModule, "_VTXSelection", pybind11::module_local()
 		);
 

lib/python_binding/test/src/util/selection.cpp

@@ -1,6 +1,6 @@
 #include "selection.hpp"
 #include <app/application/scene.hpp>
-#include <app/application/selection/selection_manager.hpp>
+#include <app/selection/selection_manager.hpp>
 #include <app/core/ecs/base_entity.hpp>
 #include <app/core/ecs/registry.hpp>
 #include <app/vtx_app.hpp>

lib/python_binding/test/src/util/selection.hpp

@@ -1,10 +1,10 @@
 #ifndef __VTX_APP_TEST_UTIL_SELECTION__
 #define __VTX_APP_TEST_UTIL_SELECTION__
 
-#include <app/application/selection/concepts.hpp>
-#include <app/application/selection/selection.hpp>
-#include <app/application/selection/selection_data.hpp>
-#include <app/application/selection/system_data.hpp>
+#include <app/selection/concepts.hpp>
+#include <app/selection/selection.hpp>
+#include <app/selection/selection_data.hpp>
+#include <app/selection/system_data.hpp>
 #include <string>
 #include <util/concepts.hpp>
 #include <util/math/range_list.hpp>
@@ -13,9 +13,9 @@ namespace VTX::App::Test::Util
 {
 	class Selection
 	{
-		using SystemData	= VTX::App::Application::Selection::SystemData;
-		using SelectionData = VTX::App::Application::Selection::SelectionData;
-		using SelectionObj	= VTX::App::Application::Selection::Selection;
+		using SystemData	= VTX::App::Selection::SystemData;
+		using SelectionData = VTX::App::Selection::SelectionData;
+		using SelectionObj	= VTX::App::Selection::Selection;
 
 	  public:
 		static bool checkSelection(
@@ -27,17 +27,15 @@ namespace VTX::App::Test::Util
 		static SelectionObj createSelection( const SelectionData & p_item );
 		static SelectionObj createSelection( const std::unique_ptr<SelectionData> & p_itemPtr );
 
-		template<Application::Selection::SelectionDataConcept T>
+		template<App::Selection::SelectionDataConcept T>
 		static SelectionObj createSelection( const std::initializer_list<T> & p_items )
 		{
 			SelectionObj res = SelectionObj();
 
 			for ( const T & sourceItemPtr : p_items )
 			{
 				res.select(
-					sourceItemPtr.getSelectionComponent(),
-					sourceItemPtr,
-					VTX::App::Application::Selection::AssignmentType::APPEND
+					sourceItemPtr.getSelectionComponent(), sourceItemPtr, VTX::App::Selection::AssignmentType::APPEND
 				);
 			}
 
@@ -52,9 +50,7 @@ namespace VTX::App::Test::Util
 			for ( const SelectionData * const sourceItemPtr : p_items )
 			{
 				res.select(
-					sourceItemPtr->getSelectionComponent(),
-					*sourceItemPtr,
-					VTX::App::Application::Selection::AssignmentType::APPEND
+					sourceItemPtr->getSelectionComponent(), *sourceItemPtr, VTX::App::Selection::AssignmentType::APPEND
 				);
 			}
 
@@ -68,5 +64,5 @@ namespace VTX::App::Test::Util
 			const std::vector<atom_index_t> & p_atoms	 = {}
 		);
 	};
-} // namespace VTX::PythonFixture::Test::Util
+} // namespace VTX::App::Test::Util
 #endif

lib/python_binding/test/src/vtx_api_selection.cpp

@@ -1,8 +1,8 @@
 #include "util/app.hpp"
 #include "util/selection.hpp"
 #include <app/application/scene.hpp>
-#include <app/application/selection/selection_manager.hpp>
-#include <app/application/selection/system_data.hpp>
+#include <app/selection/selection_manager.hpp>
+#include <app/selection/system_data.hpp>
 #include <app/fixture.hpp>
 #include <app/vtx_app.hpp>
 #include <catch2/benchmark/catch_benchmark.hpp>
@@ -60,7 +60,7 @@ TEST_CASE( "VTX_PYTHON_BINDING - VTX API Selection Tests", "[integration]" )
 										  *SelectionUtil::generateSystemData( "8QHQ", { 0, 6 } ) } )
 	) );
 
-	std::unique_ptr<App::Application::Selection::SelectionData> allHistidineOn4HHB = SelectionUtil::generateSystemData(
+	std::unique_ptr<App::Selection::SelectionData> allHistidineOn4HHB = SelectionUtil::generateSystemData(
 		"4HHB",
 		{},
 		{
@@ -172,7 +172,7 @@ TEST_CASE( "VTX_PYTHON_BINDING - VTX API Selection Tests", "[integration]" )
 	) );
 
 	CHECK( SelectionUtil::checkSelection(
-		"test_empty_1", "select( mol_n='Nimportequoi', chain_i=1 )", App::Application::Selection::Selection()
+		"test_empty_1", "select( mol_n='Nimportequoi', chain_i=1 )", App::Selection::Selection()
 	) );
 
 	CHECK( SelectionUtil::checkSelection(