#1211 Add tests folder to Doxygen scope and fix warnings. ModelInstances not...

#1211 Add tests folder to Doxygen scope and fix warnings. ModelInstances not yet added but some of the warnings have nonetheless been fixed in the same time as their test counterpart (for instance NumberingSubsetIndex legend has been added for both tests and ModelInstances folder).

Documentation/Doxygen/morefem.dox

@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "MoReFEM
+PROJECT_NAME           = "MoReFEM"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -777,7 +777,8 @@ INPUT                  = ../../Sources/Utilities \
                          ../../Sources/OperatorInstances \
                          ../../Sources/FormulationSolver \
                          ../../Sources/Model \
-                         ../../Sources/PostProcessing
+                         ../../Sources/PostProcessing \
+                         ../../Sources/Test                         
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -834,8 +835,7 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       = *ThirdParty/Source* \
-                         *ModelInstances*
+EXCLUDE_PATTERNS       = *ThirdParty/Source* 
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the

MoReFEM.xcodeproj/project.pbxproj

@@ -5163,6 +5163,7 @@
 		BE7DE82A19CC541D00D24C7D /* Comm.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = Comm.cpp; sourceTree = "<group>"; };
 		BE7DE82B19CC541D00D24C7D /* Comm.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = Comm.hpp; sourceTree = "<group>"; };
 		BE80308718E43CAE00B4CA03 /* Interface.hxx */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.cpp.h; path = Interface.hxx; sourceTree = "<group>"; };
+		BE8058C91FF7DA5C008E97D2 /* Test.doxygen */ = {isa = PBXFileReference; lastKnownFileType = text; path = Test.doxygen; sourceTree = "<group>"; };
 		BE80EE571DE72A88005502B4 /* ScalarTransientSource.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; name = ScalarTransientSource.hpp; path = Parameter/Source/ScalarTransientSource.hpp; sourceTree = "<group>"; };
 		BE80EE581DE72A88005502B4 /* ScalarTransientSource.hxx */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; name = ScalarTransientSource.hxx; path = Parameter/Source/ScalarTransientSource.hxx; sourceTree = "<group>"; };
 		BE8553A31BBD77BF00DB109E /* DofSource.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = DofSource.cpp; sourceTree = "<group>"; };
@@ -8428,6 +8429,7 @@
 		BE372DCD18C47F0500127212 /* Test */ = {
 			isa = PBXGroup;
 			children = (
+				BE8058C91FF7DA5C008E97D2 /* Test.doxygen */,
 				BE6C215D19AF26AE00CC674B /* SConscript */,
 				BE372DDB18C4802900127212 /* main_test.cpp */,
 				BE436A151F694FBE003CE8E3 /* Tools */,

Sources/Core/Core.doxygen

@@ -26,3 +26,119 @@
 
 /// \namespace MoReFEM::TimeManagerNS::Policy
 /// \brief Namespace that enclose time step policies related to TimeManager.
+
+
+
+/*!
+ *
+ * \class doxygen_hide_input_parameter_data_arg
+ *
+ * \param[in] input_parameter_data Object which hold the values of all the parameters defined in
+ * the input file.
+ */
+
+
+/*!
+ *
+ * \class doxygen_hide_morefem_data_param
+ *
+ * \param[in] morefem_data Object which hold few objects (mpi, input parameter file, Petsc helper and directory into
+ * which results are stored) that are almost global variables.
+ */
+
+
+/*!
+ * \class doxygen_hide_mesh_enum
+ *
+ * \brief Enum used to index the available meshes.
+ */
+
+
+/*!
+ * \class doxygen_hide_domain_enum
+ *
+ * \brief Enum used to index the available domains.
+ */
+
+
+/*!
+ * \class doxygen_hide_felt_space_enum
+ *
+ * \brief Enum used to index the available finite element spaces.
+ */
+
+
+/*!
+ * \class doxygen_hide_unknown_enum
+ *
+ * \brief Enum used to index the available unknowns.
+ */
+
+
+/*!
+ * \class doxygen_hide_solver_enum
+ *
+ * \brief Enum used to index the available solvers.
+ */
+
+
+/*!
+ * \class doxygen_hide_numbering_subset_enum
+ *
+ * \brief Enum used to index the available numbering subsets.
+ */
+
+/*!
+ * \class doxygen_hide_source_enum
+ *
+ * \brief Enum used to index the available sources.
+ */
+
+/*!
+ * \class doxygen_hide_boundary_condition_enum
+ *
+ * \brief Enum used to index the available boundary conditions.
+ */
+
+
+/*!
+ * \class doxygen_hide_input_parameter_tuple
+ *
+ * \brief Tuple which enumerates all the quantities that are addressed in the input file.
+ *
+ */
+
+
+/*!
+ * \class doxygen_hide_initial_condition_enum
+ *
+ * \brief Enum used to index the available initial conditions.
+ *
+ */
+
+
+/*!
+ * \class doxygen_hide_model_specific_input_parameter_list
+ *
+ * \brief The input parameter list object required for the current test or model.
+ *
+ */
+
+
+
+/*!
+ * \class doxygen_hide_fiber_enum
+ *
+ * \brief Enum used to index the available fibers.
+ *
+ */
+
+/*!
+ * \class doxygen_hide_morefem_data_type
+ *
+ * \brief The MoReFEMDataType object required for the current test or model.
+ *
+ */
+
+
+

Sources/Core/InputParameterData/InputParameterList.hpp

@@ -33,17 +33,6 @@ namespace MoReFEM
     /// \addtogroup CoreGroup
     ///@{
 
-
-    /*!
-     *
-     * \class doxygen_hide_input_parameter_data_arg
-     *
-     * \param[in] input_parameter_data Object which hold the values of all the parameters defined in
-     * the input file.
-     */
-    
-    
- 
     /*!
      * \brief This class read the input parameters and then is in charge of holding the values read.
      *

Sources/Core/TimeManager/TimeManager.doxygen

 /*!
  * \class doxygen_hide_time_manager_arg
  *
- * \param[in] time_manager Object in charge of keeping track of the time-related informations.
+ * \param[in,out] time_manager Object in charge of keeping track of the time-related informations.
  */
 
 
@@ -11,4 +11,4 @@
  * \brief Object in charge of keeping track of the time-related informations.
  *
  * \return Reference to the \a TimeManager.
- */
\ No newline at end of file
+ */

Sources/FormulationSolver/VariationalFormulation.doxygen

@@ -21,4 +21,26 @@
 ///@}
 
 
+/*!
+ * \class doxygen_hide_varf_constructor
+ *
+ * \copydoc doxygen_hide_morefem_data_param
+ * \copydoc doxygen_hide_time_manager_arg
+ * \param[in] god_of_dof \a GodOfDof upon which the variational formulation is defined.
+ * \param[in] boundary_condition_list List of Dirichlet boundary conditions to consider (please notice it is also
+ * possible to handle them directly; it is for conveniency it might be given here).
+ */
+
+
+/*!
+ * \class doxygen_hide_varf_suppl_init
+ *
+ * \brief Specific initialisation for derived class attributes.
+ *
+ * \internal <b><tt>[internal]</tt></b> This method is called by base class method VariationalFormulation::Init().
+ *
+ * \copydoc doxygen_hide_input_parameter_data_arg
+ */
+
+
 

Sources/Model/Model.doxygen

@@ -18,5 +18,27 @@
 
 ///@}
 
+/*!
+ * \class doxygen_hide_model_SupplHasFinishedConditions_common
+ *
+ * \brief Whether the model wants to add additional cases in which the Model stops (besides the reach of
+ * maximum time).
+ *
+ */
+
+/*!
+* \class doxygen_hide_model_SupplHasFinishedConditions
+*
+* \copydoc doxygen_hide_model_SupplHasFinishedConditions_common
+*
+* \return True if one of the additional finish condition defined specifically in current \a Model is reached.
+*/
 
+/*!
+ * \class doxygen_hide_model_SupplHasFinishedConditions_always_true
+ *
+ * \copydoc doxygen_hide_model_SupplHasFinishedConditions_common
+ *
+ * \return Always true (no such additional condition in this Model).
+ */
 

Sources/ModelInstances/Elasticity/ElasticityModel.hpp

@@ -52,7 +52,7 @@ namespace MoReFEM
             /*!
              * \brief Constructor.
              *
-             * \copydetails doxygen_hide_mpi_param
+             * \copydoc doxygen_hide_morefem_data_param
              */
             ElasticityModel(const morefem_data_type& morefem_data);
 
@@ -82,6 +82,7 @@ namespace MoReFEM
              * \brief Initialise the problem.
              *
              * This initialisation includes the resolution of the static problem.
+             * \copydoc doxygen_hide_morefem_data_param
              */
             void SupplInitialize(const morefem_data_type& morefem_data);
 
@@ -113,12 +114,7 @@ namespace MoReFEM
 
 
 
-            /*!
-             * \brief Whether the model wants to add additional cases in which the Model stops (besides the reach of
-             * maximum time).
-             *
-             * Returns always true (no such additional condition in this Model).
-             */
+            //! \copydoc doxygen_hide_model_SupplHasFinishedConditions_always_true
             bool SupplHasFinishedConditions() const;
 
 

Sources/ModelInstances/Elasticity/InputParameterList.hpp

@@ -32,12 +32,14 @@ namespace MoReFEM
     {
 
 
+        //! \copydoc doxygen_hide_mesh_enum
         enum class MeshIndex
         {
             mesh = 1 // only one mesh considered in current model!
         };
 
 
+        //! \copydoc doxygen_hide_domain_enum
         enum class DomainIndex
         {
             highest_dimension = 1,
@@ -47,6 +49,7 @@ namespace MoReFEM
         };
 
 
+        //! \copydoc doxygen_hide_felt_space_enum
         enum class FEltSpaceIndex
         {
             highest_dimension = 1,
@@ -54,24 +57,28 @@ namespace MoReFEM
         };
 
 
+        //! \copydoc doxygen_hide_unknown_enum
         enum class UnknownIndex
         {
             solid_displacement = 1
         };
 
 
+        //! \copydoc doxygen_hide_solver_enum
         enum class SolverIndex
         {
             solver = 1
         };
 
 
+        //! \copydoc doxygen_hide_numbering_subset_enum
         enum class NumberingSubsetIndex
         {
             monolithic = 1
         };
 
 
+        //! \copydoc doxygen_hide_source_enum
         enum class SourceIndex
         {
             volumic = 1,
@@ -79,12 +86,14 @@ namespace MoReFEM
         };
 
 
+        //! \copydoc doxygen_hide_boundary_condition_enum
         enum class BoundaryConditionIndex
         {
             sole = 1
         };
 
 
+        //! \copydoc doxygen_hide_input_parameter_tuple
         using InputParameterTuple = std::tuple
         <
             InputParameter::TimeManager,
@@ -119,8 +128,10 @@ namespace MoReFEM
         >;
 
 
+        //! \copydoc doxygen_hide_model_specific_input_parameter_list
         using InputParameterList = InputParameterList<InputParameterTuple>;
 
+        //! \copydoc doxygen_hide_morefem_data_type
         using morefem_data_type = MoReFEMData<InputParameterList>;
 
 

Sources/ModelInstances/Elasticity/VariationalFormulationElasticity.hpp

@@ -76,11 +76,7 @@ namespace MoReFEM
             /// \name Special members.
             ///@{
 
-            /*!
-             * \brief Constructor.
-             *
-             * \copydetails doxygen_hide_mpi_param
-             */
+            //! copydoc doxygen_hide_varf_constructor
             explicit VariationalFormulationElasticity(const morefem_data_type& morefem_data,
                                                       const FEltSpace& main_felt_space,
                                                       const FEltSpace& neumann_felt_space,

Sources/ModelInstances/Elasticity/main.cpp

@@ -21,7 +21,8 @@ using namespace MoReFEM;
 int main(int argc, char** argv)
 {
     
-    using InputParameterList = ElasticityNS::InputParameterList;
+    //! \copydoc doxygen_hide_model_specific_input_parameter_list
+        using InputParameterList = ElasticityNS::InputParameterList;
     
     try
     {

Sources/ModelInstances/Elasticity/main_ensight_output.cpp

@@ -29,6 +29,7 @@ int main(int argc, char** argv)
     
     try
     {
+        //! \copydoc doxygen_hide_model_specific_input_parameter_list
         using InputParameterList = ElasticityNS::InputParameterList;
         
         MoReFEMData<InputParameterList, Utilities::InputParameterListNS::DoTrackUnusedFields::no> morefem_data(argc, argv);

Sources/ModelInstances/Heat/HeatModel.hpp

@@ -54,7 +54,7 @@ namespace MoReFEM
             /*!
              * \brief Constructor.
              *
-             * \copydetails doxygen_hide_mpi_param
+             * \copydoc doxygen_hide_morefem_data_param
              */
             explicit HeatModel(const morefem_data_type& morefem_data);
 
@@ -84,6 +84,7 @@ namespace MoReFEM
              * \brief Initialise the problem.
              *
              * This initialisation includes the resolution of the static problem.
+             * \copydoc doxygen_hide_morefem_data_param
              */
             void SupplInitialize(const morefem_data_type& morefem_data);
 
@@ -119,12 +120,7 @@ namespace MoReFEM
         private:
 
 
-            /*!
-             * \brief Whether the model wants to add additional cases in which the Model stops (besides the reach of
-             * maximum time).
-             *
-             * Returns always true (no such additional condition in this Model).
-             */
+            //! \copydoc doxygen_hide_model_SupplHasFinishedConditions_always_true
             bool SupplHasFinishedConditions() const;
 
 

Sources/ModelInstances/Heat/HeatVariationalFormulation.hpp

@@ -73,11 +73,7 @@ namespace MoReFEM
             /// \name Special members.
             ///@{
 
-            /*!
-             * \brief Constructor.
-             *
-             * \copydetails doxygen_hide_mpi_param
-             */
+            //! copydoc doxygen_hide_varf_constructor
             explicit HeatVariationalFormulation(const morefem_data_type& morefem_data,
                                                 const NumberingSubset& numbering_subset,
                                                 TimeManager& time_manager,
@@ -175,11 +171,7 @@ namespace MoReFEM
             /// \name CRTP-required methods.
             ///@{
 
-            /*!
-             * \brief Specific initialisation for derived class attributes.
-             *
-             * \internal <b><tt>[internal]</tt></b> This method is called by base class method VariationalFormulation::Init().
-             */
+            //! \copydoc doxygen_hide_varf_suppl_init
             void SupplInit(const InputParameterList& input_parameter_data);
 
             /*!

Sources/ModelInstances/Heat/InputParameterList.hpp

@@ -29,6 +29,7 @@ namespace MoReFEM
     {
 
 
+        //! \copydoc doxygen_hide_source_enum
         enum class ForceIndexList : unsigned int
         {
             volumic_source = 1,
@@ -37,13 +38,15 @@ namespace MoReFEM
         };
 
 
-        enum class MeshIndex
+        //! \copydoc doxygen_hide_mesh_enum
+            enum class MeshIndex
         {
             mesh = 1 // only one mesh considered in current model!
         };
 
 
-        enum class DomainIndex
+        //! \copydoc doxygen_hide_domain_enum
+            enum class DomainIndex
         {
             highest_dimension = 1,
             neumann = 2,
@@ -54,6 +57,7 @@ namespace MoReFEM
         };
 
 
+        //! \copydoc doxygen_hide_boundary_condition_enum
         enum class BoundaryConditionIndex
         {
             first = 1,
@@ -61,7 +65,8 @@ namespace MoReFEM
         };
 
 
-        enum class FEltSpaceIndex
+        //! \copydoc doxygen_hide_felt_space_enum
+            enum class FEltSpaceIndex
         {
             highest_dimension = 1,
             neumann = 2,
@@ -69,19 +74,23 @@ namespace MoReFEM
         };
 
 
-        enum class UnknownIndex
+        //! \copydoc doxygen_hide_unknown_enum
+            enum class UnknownIndex
         {
             temperature = 1
         };
 
 
-        enum class SolverIndex
+        //! \copydoc doxygen_hide_solver_enum
+            enum class SolverIndex
+
         {
             solver = 1
         };
 
 
-        enum class NumberingSubsetIndex
+        //! \copydoc doxygen_hide_numbering_subset_enum
+            enum class NumberingSubsetIndex
         {
             monolithic = 1
         };
@@ -92,11 +101,14 @@ namespace MoReFEM
         };
 
 
+        //! \copydoc doxygen_hide_initial_condition_enum
         enum class InitialConditionIndex
         {
             temperature_initial_condition = 1
         };
+            
 
+        //! \copydoc doxygen_hide_input_parameter_tuple
         using InputParameterTuple = std::tuple
         <
             InputParameter::TimeManager,
@@ -138,8 +150,10 @@ namespace MoReFEM
         >;
 
 
+        //! \copydoc doxygen_hide_model_specific_input_parameter_list
         using InputParameterList = InputParameterList<InputParameterTuple>;
 
+        //! \copydoc doxygen_hide_morefem_data_type
         using morefem_data_type = MoReFEMData<InputParameterList>;
 
 

Sources/ModelInstances/Heat/main.cpp

@@ -21,7 +21,8 @@ using namespace MoReFEM;
 int main(int argc, char** argv)
 {
     
-    using InputParameterList = HeatNS::InputParameterList;
+    //! \copydoc doxygen_hide_model_specific_input_parameter_list
+        using InputParameterList = HeatNS::InputParameterList;
     
     try
     {

Sources/ModelInstances/Heat/main_ensight_output.cpp

@@ -29,6 +29,7 @@ int main(int argc, char** argv)
     
     try
     {
+        //! \copydoc doxygen_hide_model_specific_input_parameter_list
         using InputParameterList = HeatNS::InputParameterList;
         
         MoReFEMData<InputParameterList, Utilities::InputParameterListNS::DoTrackUnusedFields::no> morefem_data(argc, argv);

Sources/ModelInstances/Hyperelasticity/InputParameterList.hpp

@@ -31,22 +31,26 @@ namespace MoReFEM
     {
 
 
-        enum class NumberingSubsetIndex
+        //! \copydoc doxygen_hide_numbering_subset_enum
+            enum class NumberingSubsetIndex
         {
             displacement = 1
         };
 
-        enum class UnknownIndex
+        //! \copydoc doxygen_hide_unknown_enum
+            enum class UnknownIndex
         {
             displacement = 1
         };
 
-        enum class MeshIndex
+        //! \copydoc doxygen_hide_mesh_enum
+            enum class MeshIndex
         {
             mesh = 1
         };
 
-        enum class DomainIndex
+        //! \copydoc doxygen_hide_domain_enum
+            enum class DomainIndex
         {
             full_mesh = 1,
             volume = 2,
@@ -54,28 +58,34 @@ namespace MoReFEM
             dirichlet = 4,
         };
 
+        //! \copydoc doxygen_hide_boundary_condition_enum
         enum class BoundaryConditionIndex
         {
             clamped = 1
         };
 
-        enum class FEltSpaceIndex
+        //! \copydoc doxygen_hide_felt_space_enum
+            enum class FEltSpaceIndex
         {
             volume = 1,
             force = 2
         };
 
 
-        enum class SolverIndex
+        //! \copydoc doxygen_hide_solver_enum
+            enum class SolverIndex
+
         {
             solver = 1
         };
 
+        //! \copydoc doxygen_hide_source_enum
         enum class ForceIndexList
         {
             surfacic = 1
         };
 
+        //! \copydoc doxygen_hide_input_parameter_tuple
         using InputParameterTuple = std::tuple
         <
             InputParameter::TimeManager,
@@ -109,8 +119,10 @@ namespace MoReFEM
         >;
 
 
+        //! \copydoc doxygen_hide_model_specific_input_parameter_list
         using InputParameterList = InputParameterList<InputParameterTuple>;
 
+        //! \copydoc doxygen_hide_morefem_data_type
         using morefem_data_type = MoReFEMData<InputParameterList>;
 
 

Sources/ModelInstances/Hyperelasticity/Model.hpp

@@ -57,7 +57,7 @@ namespace MoReFEM
             /*!
              * \brief Constructor.
              *
-             * \copydetails doxygen_hide_mpi_param
+             * \copydoc doxygen_hide_morefem_data_param
              */
             Model(const morefem_data_type& morefem_data);
 
@@ -87,6 +87,7 @@ namespace MoReFEM
             * \brief Initialise the problem.
             *
             * This initialisation includes the resolution of the static problem.
+            * \copydoc doxygen_hide_morefem_data_param
             */
            void SupplInitialize(const morefem_data_type& morefem_data);
 
@@ -112,12 +113,7 @@ namespace MoReFEM
        private:
 
 
-           /*!
-            * \brief Whether the model wants to add additional cases in which the Model stops (besides the reach of
-            * maximum time).
-            *
-            * Returns always true (no such additional condition in this Model).
-            */
+           //! \copydoc doxygen_hide_model_SupplHasFinishedConditions_always_true
            bool SupplHasFinishedConditions() const;
 
 

Sources/ModelInstances/Hyperelasticity/VariationalFormulation.hpp

@@ -117,11 +117,7 @@ namespace MoReFEM
             /// \name Special members.
             ///@{
 
-            /*!
-             * \brief Constructor.
-             *
-             * \copydetails doxygen_hide_mpi_param
-             */
+            //! copydoc doxygen_hide_varf_constructor
             explicit VariationalFormulation(const morefem_data_type& morefem_data,
                                             const NumberingSubset& displacement_numbering_subset,
                                             TimeManager& time_manager,
@@ -163,11 +159,7 @@ namespace MoReFEM
             /// \name CRTP-required methods.
             ///@{
 
-            /*!
-             * \brief Specific initialisation for derived class attributes.
-             *
-             * \internal <b><tt>[internal]</tt></b> This method is called by base class method VariationalFormulation::Init().
-             */
+            //! \copydoc doxygen_hide_varf_suppl_init
             void SupplInit(const InputParameterList& input_parameter_data);
 
             /*!

Sources/ModelInstances/Hyperelasticity/main.cpp

@@ -19,7 +19,8 @@ using namespace MoReFEM;