Merge remote-tracking branch 'origin/dev' into dev-sge

IconsAuthors.txt

@@ -0,0 +1,16 @@
+Icons authors :
+
+https://www.flaticon.com/authors/alfredo-hernandez
+https://www.flaticon.com/authors/Becris
+https://www.flaticon.com/authors/dinosoftlabs
+https://www.flaticon.com/authors/freepik
+https://www.flaticon.com/authors/good-ware
+https://www.flaticon.com/authors/google
+https://www.flaticon.com/authors/itim2101
+https://www.flaticon.com/authors/kiranshastry
+https://www.flaticon.com/authors/mavadee
+https://www.flaticon.com/authors/pixel-perfect
+https://www.flaticon.com/authors/roundicons
+https://www.flaticon.com/authors/tanah-basah
+https://www.flaticon.com/authors/tempo-doloe
+https://www.flaticon.com/authors/vectors-market

lib/app/include/app/component/scene/destroyed.hpp

@@ -1,14 +1,14 @@
-#ifndef __VTX_APP_COMPONENT_SCENE_TRANSFORM__
-#define __VTX_APP_COMPONENT_SCENE_TRANSFORM__
-
-#include "app/ecs/core/base_component.hpp"
-
-namespace VTX::App::Component::Scene
-{
-	class Transform : public ECS::Core::BaseComponent
-	{
-	  public:
-		Transform() = default;
-	};
-} // namespace VTX::App::Component::Scene
-#endif
+// #ifndef __VTX_APP_COMPONENT_SCENE_TRANSFORM__
+// #define __VTX_APP_COMPONENT_SCENE_TRANSFORM__
+//
+// #include "app/ecs/core/base_component.hpp"
+//
+// namespace VTX::App::Component::Scene
+//{
+//	class Transform : public ECS::Core::BaseComponent
+//	{
+//	  public:
+//		Transform() = default;
+//	};
+// } // namespace VTX::App::Component::Scene
+// #endif

lib/app/include/app/component/scene/enable_component.hpp

@@ -2,11 +2,11 @@
 #define __VTX_APP_COMPONENT_SCENE_ENABLE__
 
 #include "app/application/system/ecs_system.hpp"
-#include "app/ecs/core/base_component.hpp"
+#include "app/core/ecs/base_component.hpp"
 
 namespace VTX::App::Component::Scene
 {
-	class EnableComponent : public ECS::Core::BaseComponent
+	class EnableComponent : public Core::ECS::BaseComponent
 	{
 	  private:
 		inline static Application::System::ECSSystem::ComponentStaticIDRegistration<EnableComponent> registration {

lib/app/include/app/core/ecs/registry.hpp

@@ -24,6 +24,7 @@ namespace VTX::App::Core::ECS
 		Registry() = default;
 
 		BaseEntity createEntity() { return BaseEntity( _enttRegistry.create() ); }
+		void	   destroyEntity( const BaseEntity p_entity ) { _enttRegistry.destroy( p_entity ); }
 
 		template<ECS_Component C>
 		inline BaseEntity getEntity( const C & p_component ) const

lib/app/include/app/vtx_app.hpp

@@ -28,7 +28,6 @@ namespace VTX::App
 
 		void start( const std::vector<std::string> & );
 		void update( const float p_elapsedTime = 0 );
-		void goToState( const std::string &, void * const = nullptr );
 		void stop();
 
 		inline const Core::System::SystemHandler & getSystemHandler() const { return *_systemHandlerPtr; };

lib/app/src/app/vtx_app.cpp

@@ -57,40 +57,11 @@ namespace VTX::App
 
 		// Regsiter loop events
 		onUpdate += []( const float p_elapsedTime ) { SCENE().update( p_elapsedTime ); };
-
 		onPostUpdate += []( const float p_elapsedTime ) { THREADING().lateUpdate(); };
 
-		// Event manager - Useless: nothing is delayed.
-		//_updateCallback.addCallback(
-		//	this, []( const float p_elapsedTime ) { Event::EventManager::get().update( p_elapsedTime ); }
-		//);
-
-		// Useless while delayed actions are disabled
-		//_updateCallback.addCallback( this, []( const float p_elapsedTime ) { VTX_ACTION().update( p_elapsedTime );
-		//}
-		//);
-
-		// TODO: use camera callbacks.
-		//_preRenderCallback.addCallback( this, [ this ]( const float p_elapsedTime ) { _applyCameraUniforms(); } );
-		//_renderCallback.addCallback(
-		//	this, [ this ]( const float p_elapsedTime ) { _renderer->render( p_elapsedTime ); }
-		//);
-
 		_tickChrono.start();
 
 		_handleArgs( p_args );
-
-#ifndef VTX_PRODUCTION
-		if ( p_args.size() == 0 )
-		{
-			// VTX_ACTION(
-			//	 new Action::Main::Open( Internal::IO::Filesystem::getDataPath( FilePath( "4hhb.pdb" )
-			//).absolute() ) );
-			// VTX_ACTION( new Action::Main::OpenApi( "1aon" ) );
-			// VTX_ACTION( new Action::Main::OpenApi( "4hhb" ) );
-			// VTX_ACTION( new Action::Main::OpenApi( "1aga" ) );
-		}
-#endif
 	}
 
 	void VTXApp::update( const float p_elapsedTime )
@@ -185,27 +156,8 @@ namespace VTX::App
 		// VTX::MVC_MANAGER().deleteModel( _renderEffectLibrary );
 
 		// Old::Application::Selection::SelectionManager::get().deleteModel();
-
-		// if ( _scene != nullptr )
-		//{
-		//	delete _scene;
-		// }
 	}
 
-	void VTXApp::goToState( const std::string & p_name, void * const p_arg ) {}
-
-	// void VTXApp::deleteAtEndOfFrame( const Component::Generic::BaseAutoDelete * const p_object )
-	//{
-	//	_deleteAtEndOfFrameObjects.emplace_back( p_object );
-	// }
-	// void VTXApp::_applyEndOfFrameDeletes()
-	//{
-	//	for ( const Component::Generic::BaseAutoDelete * const p_object : _deleteAtEndOfFrameObjects )
-	//		p_object->autoDelete();
-
-	//	_deleteAtEndOfFrameObjects.clear();
-	//}
-
 	Application::Scene &	   VTXApp::getScene() { return _systemHandlerPtr->get<Application::Scene>( SCENE_KEY ); }
 	const Application::Scene & VTXApp::getScene() const
 	{

lib/core/src/core/chemdb/residue.cpp

@@ -1,22 +1,16 @@
 #include "core/chemdb/residue.hpp"
 #include <algorithm>
-#include <util/enum.hpp>
 #include <optional>
+#include <util/enum.hpp>
+#include <util/string.hpp>
 
 namespace VTX::Core::ChemDB::Residue
 {
 
 	const SYMBOL getSymbolFromShortName( const std::string & p_residueName )
 	{
-		std::string upcasedName = std::string( p_residueName.begin(), p_residueName.end() );
-
 		// Upcase residue name
-		std::transform(
-			p_residueName.begin(),
-			p_residueName.end(),
-			upcasedName.begin(),
-			[]( unsigned char c ) { return std::toupper( c ); }
-		);
+		std::string upcasedName = Util::String::toUpper( p_residueName );
 
 		for ( int i = 0; i < int( SYMBOL::COUNT ); i++ )
 		{
@@ -29,15 +23,7 @@ namespace VTX::Core::ChemDB::Residue
 
 	const SYMBOL getSymbolFromName( const std::string & p_residueName )
 	{
-		std::string upcasedName = std::string( p_residueName.begin(), p_residueName.end() );
-
-		// Upcase residue name
-		std::transform(
-			p_residueName.begin(),
-			p_residueName.end(),
-			upcasedName.begin(),
-			[]( unsigned char c ) { return std::toupper( c ); }
-		);
+		std::string upcasedName = Util::String::toUpper( p_residueName );
 
 		// Convert name
 		const std::optional symbol = magic_enum::enum_cast<ChemDB::Residue::SYMBOL>( upcasedName );
@@ -49,7 +35,7 @@ namespace VTX::Core::ChemDB::Residue
 		std::string formattedName = std::string( p_residueName.begin(), p_residueName.end() );
 		formattedName[ 0 ]		  = std::toupper( formattedName[ 0 ] );
 
-		// Upcase residue name
+		// Downcase residue name
 		std::transform(
 			++p_residueName.begin(),
 			p_residueName.end(),
@@ -90,13 +76,7 @@ namespace VTX::Core::ChemDB::Residue
 
 	bool checkIfStandardFromName( const std::string & p_residueSymbol )
 	{
-		std::string residueSymbol = p_residueSymbol;
-		std::transform(
-			residueSymbol.begin(),
-			residueSymbol.end(),
-			residueSymbol.begin(),
-			[]( unsigned char c ) { return std::toupper( c ); }
-		);
+		const std::string residueSymbol = Util::String::toUpper( p_residueSymbol );
 
 		return std::find(
 				   std::begin( ChemDB::Residue::SYMBOL_STR ), std::end( ChemDB::Residue::SYMBOL_STR ), residueSymbol

lib/python_binding/include/python_binding/wrapper/pybind11_extra_convertor.hpp

@@ -5,6 +5,7 @@
 
 namespace VTX::PythonBinding::Wrapper
 {
+	// Manage Pybind11 "Extra" arguments
 	class Pybind11ExtraConvertor
 	{
 	  public:

lib/ui/include/ui/qt/application_qt.hpp

@@ -14,10 +14,6 @@
 
 namespace VTX::UI::QT
 {
-	namespace State
-	{
-		class StateMachine;
-	}
 	class MainWindow;
 
 	class ApplicationQt : public Core::BaseUIApplication, public QApplication

lib/ui/include/ui/qt/main_window.hpp

@@ -13,7 +13,6 @@
 #include <QDockWidget>
 #include <QKeySequence>
 #include <QMainWindow>
-#include <QShortcut>
 #include <unordered_set>
 #include <util/types.hpp>
 
@@ -47,20 +46,6 @@ namespace VTX::UI::QT
 		QT::Widget::MainMenu::MenuTooltabWidget &	getMainMenuToolTab( const Core::ToolLayoutData & layoutData );
 		QT::Widget::MainMenu::MenuToolBlockWidget & getMainMenuToolBlock( const Core::ToolLayoutData & layoutData );
 
-		void addShortcut( const std::string & p_shortcut, QAction * const p_action );
-
-		template<typename Obj, typename Func>
-		void addShortcut( const std::string & p_shortcut, Obj p_obj, Func p_func )
-		{
-			assert( _shortcuts.find( p_shortcut ) == _shortcuts.end() );
-
-			connect(
-				new QShortcut( QKeySequence( tr( p_shortcut.c_str() ) ), this ), &QShortcut::activated, p_obj, p_func
-			);
-
-			_shortcuts.emplace( p_shortcut );
-		}
-
 		Core::WindowMode getWindowMode();
 		void			 setWindowMode( const Core::WindowMode & p_mode );
 		void			 toggleWindowState();
@@ -101,8 +86,6 @@ namespace VTX::UI::QT
 	  private:
 		QT::Widget::MainMenu::MainMenuBar * _mainMenuBar = nullptr;
 
-		std::unordered_set<std::string> _shortcuts = std::unordered_set<std::string>();
-
 		// Actions.
 		void _onDockWindowVisibilityChange( bool p_visible );
 

lib/ui/src/ui/qt/main_window.cpp

@@ -46,22 +46,6 @@ namespace VTX::UI::QT
 		);
 	}
 
-	void MainWindow::addShortcut( const std::string & p_shortcut, QAction * const p_action )
-	{
-		assert( _shortcuts.find( p_shortcut ) == _shortcuts.end() );
-
-		p_action->setParent( this );
-
-		connect(
-			new QShortcut( QKeySequence( tr( p_shortcut.c_str() ) ), this ),
-			&QShortcut::activated,
-			p_action,
-			&QAction::trigger
-		);
-
-		_shortcuts.emplace( p_shortcut );
-	}
-
 	void MainWindow::_loadStyleSheet( const char * p_stylesheetPath )
 	{
 		QFile stylesheetFile( p_stylesheetPath );

lib/util/include/util/algorithm/range.hpp

@@ -13,6 +13,7 @@ namespace VTX::Util::Algorithm::Range
 	template<std::integral T>
 	using RangeList = Math::RangeList<T>;
 
+	// Merge two RangeList and return the result
 	template<std::integral T>
 	RangeList<T> merge( const RangeList<T> & p_lhs, const RangeList<T> & p_rhs )
 	{
@@ -26,6 +27,8 @@ namespace VTX::Util::Algorithm::Range
 
 		return res;
 	}
+
+	// Merge RangeList p_other directly in p_obj
 	template<std::integral T>
 	void mergeInSitu( RangeList<T> & p_obj, const RangeList<T> & p_other )
 	{
@@ -36,6 +39,7 @@ namespace VTX::Util::Algorithm::Range
 		}
 	}
 
+	// Substract RangeList p_rhs to p_lhs and return the result
 	template<std::integral T>
 	RangeList<T> substract( const RangeList<T> & p_lhs, const RangeList<T> & p_rhs )
 	{
@@ -49,6 +53,7 @@ namespace VTX::Util::Algorithm::Range
 
 		return res;
 	}
+	// Substract directly RangeList p_other from p_obj
 	template<std::integral T>
 	void substractInSitu( RangeList<T> & p_obj, const RangeList<T> & p_other )
 	{
@@ -59,6 +64,7 @@ namespace VTX::Util::Algorithm::Range
 		}
 	}
 
+	// Return intersection between two RangeList (items which are in p_lhs and in p_rhs )
 	template<std::integral T>
 	RangeList<T> intersect( const RangeList<T> & p_lhs, const RangeList<T> & p_rhs )
 	{
@@ -103,24 +109,29 @@ namespace VTX::Util::Algorithm::Range
 		return RangeList<T>( newRange );
 	}
 
+	// Set p_obj as the intersection between itself and p_other
 	template<std::integral T>
 	void intersectInSitu( RangeList<T> & p_obj, const RangeList<T> & p_other )
 	{
 		p_obj = intersect( p_obj, p_other );
 	}
 
+	// Return exclusive between two RangeList (items which are in p_lhs but not in p_rhs and items which are in p_rhs
+	// but not in p_lhs  )
 	template<std::integral T>
 	Math::RangeList<T> exclusive( const Math::RangeList<T> & p_lhs, const Math::RangeList<T> & p_rhs )
 	{
 		return Details::Range::Exclusive( p_lhs, p_rhs ).getRes();
 	}
 
+	// Set p_obj as the exclusive between itself and p_other
 	template<std::integral T>
 	void exclusiveInSitu( RangeList<T> & p_obj, const RangeList<T> & p_other )
 	{
 		p_obj = Details::Range::Exclusive( p_obj, p_other ).getRes();
 	}
 
+	// Generate a RangeList of index from any container following a predicate on its items
 	template<Container C, std::predicate<typename C::value_type> Predicate>
 	RangeList<typename C::size_type> generateIndexRangeList( const C & p_container, const Predicate & p_predicate )
 	{

lib/util/include/util/concepts.hpp

@@ -59,6 +59,7 @@ namespace VTX
 	// https://en.cppreference.com/w/cpp/container/vector_bool
 	|| std::same_as<ContainerType, std::vector<bool>>;
 
+	// Concept to template any container of ValueType
 	template<typename ContainerType, typename ValueType>
 	concept ContainerOfType = requires( ContainerType p_container ) {
 								  requires Container<ContainerType>;

lib/util/include/util/enum.hpp

@@ -12,12 +12,14 @@
 
 namespace VTX::Util::Enum
 {
+	// Get name of an enum
 	template<EnumConcept E>
 	inline constexpr std::string_view enumName( const E & p_enum )
 	{
 		return magic_enum::enum_name( p_enum );
 	}
 
+	// Get an enum from its name
 	template<EnumConcept E>
 	inline constexpr E enumCast( const std::string & p_name )
 	{
@@ -45,6 +47,7 @@ namespace VTX::Util::Enum
 		return magic_enum::enum_value<E>( p_index );
 	}
 
+	// Cast an enum to an other enum using it's name
 	template<EnumConcept E1, EnumConcept E2>
 	inline constexpr E2 enumToAnother( const E1 & p_enum )
 	{