fix most matrix related doxygen warnings

src/Persistence_matrix/concept/PersistenceMatrixColumn.h

@@ -23,7 +23,7 @@ namespace persistence_matrix {
  * @brief If PersistenceMatrixOptions::has_row_access is true, then @ref Row_access. Otherwise @ref Dummy_row_access.
  * Can eventually be removed if the structure of the column does not allow row access (as for @ref Heap_column), but
  * then it needs to be notified in the documentation of @ref Column_types and as static_assert in
- * @ref Matrix::_assert_options.
+ * Matrix::_assert_options.
  */
 using Row_access_option = Row_access;
 /**

src/Persistence_matrix/doc/Intro_field_elements_and_operators.h

@@ -19,6 +19,8 @@ namespace persistence_fields {
  * @{
  * \author    Hannah Schreiber, Clément Maria
  *
+ * \section fieldintro Persistence Fields
+ *
  * Set of classes allowing addition and multiplication, as well as inverse computation, in \f$ \mathbb{F}_p \f$ fields,
  * with \f$ p \f$ some prime number, or in multi-fields as defined in \cite boissonnat:hal-00922572.
  *

src/Persistence_matrix/doc/Intro_persistence_matrix.h

@@ -19,6 +19,8 @@ namespace persistence_matrix {
  * @{
  * \author    Hannah Schreiber
  *
+ * \section matrixintro Persistence Matrix
+ *
  * The module provides a data structure for matrices, in particular thought for matrices representing filtered complexes
  * and used as backend for persistence algorithms, such at persistent homology, @ref persistent_cohomology,
  * or zigzag @cite zigzag.

src/Persistence_matrix/include/gudhi/Fields/Multi_field.h

@@ -11,7 +11,7 @@
 /**
  * @file Multi_field.h
  * @author Hannah Schreiber, Clément Maria
- * @brief Contains the @ref Multi_field_element class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Multi_field_element class.
  */
 
 #ifndef MATRIX_FIELD_MULTI_H_

src/Persistence_matrix/include/gudhi/Fields/Multi_field_shared.h

@@ -11,7 +11,7 @@
 /**
  * @file Multi_field_shared.h
  * @author Hannah Schreiber, Clément Maria
- * @brief Contains the @ref Shared_multi_field_element class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Shared_multi_field_element class.
  */
 
 #ifndef MATRIX_FIELD_MULTI_SHARED_H_

src/Persistence_matrix/include/gudhi/Fields/Multi_field_small.h

@@ -11,7 +11,7 @@
 /**
  * @file Multi_field_small.h
  * @author Hannah Schreiber, Clément Maria
- * @brief Contains the @ref Multi_field_element_with_small_characteristics class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Multi_field_element_with_small_characteristics class.
  */
 
 #ifndef MATRIX_FIELD_MULTI_SMALL_H_

src/Persistence_matrix/include/gudhi/Fields/Multi_field_small_operators.h

@@ -11,7 +11,7 @@
 /**
  * @file Multi_field_small_operators.h
  * @author Hannah Schreiber, Clément Maria
- * @brief Contains the @ref Multi_field_operators_with_small_characteristics class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Multi_field_operators_with_small_characteristics class.
  */
 
 #ifndef MATRIX_FIELD_MULTI_SMALL_OPERATORS_H_

src/Persistence_matrix/include/gudhi/Fields/Multi_field_small_shared.h

@@ -11,7 +11,7 @@
 /**
  * @file Multi_field_small_shared.h
  * @author Hannah Schreiber, Clément Maria
- * @brief Contains the @ref Shared_multi_field_element_with_small_characteristics class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Shared_multi_field_element_with_small_characteristics class.
  */
 
 #ifndef MATRIX_FIELD_MULTI_SMALL_SHARED_H_

src/Persistence_matrix/include/gudhi/Fields/Z2_field.h

@@ -11,7 +11,7 @@
 /**
  * @file Z2_field.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Z2_field_element class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Z2_field_element class.
  */
 
 #ifndef MATRIX_FIELD_Z2_H_

src/Persistence_matrix/include/gudhi/Fields/Z2_field_operators.h

@@ -11,7 +11,7 @@
 /**
  * @file Z2_field_operators.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Z2_field_operators class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Z2_field_operators class.
  */
 
 #ifndef MATRIX_FIELD_Z2_OPERATORS_H_

src/Persistence_matrix/include/gudhi/Fields/Zp_field.h

@@ -11,7 +11,7 @@
 /**
  * @file Zp_field.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Zp_field_element class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Zp_field_element class.
  */
 
 #ifndef MATRIX_FIELD_ZP_H_

src/Persistence_matrix/include/gudhi/Fields/Zp_field_operators.h

@@ -11,7 +11,7 @@
 /**
  * @file Zp_field_operators.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Zp_field_operators class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Zp_field_operators class.
  */
 
 #ifndef MATRIX_FIELD_ZP_OPERATOR_H_

src/Persistence_matrix/include/gudhi/Fields/Zp_field_shared.h

@@ -11,7 +11,7 @@
 /**
  * @file Zp_field_shared.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Shared_Zp_field_element class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Shared_Zp_field_element class.
  */
 
 #ifndef MATRIX_FIELD_ZP_VAR_H_

src/Persistence_matrix/include/gudhi/Persistence_matrix/allocators/cell_constructors.h

@@ -11,7 +11,8 @@
 /**
  * @file cell_constructors.h
  * @author Hannah Schreiber
- * @brief Contains the @ref New_cell_constructor and @ref Pool_cell_constructor structures.
+ * @brief Contains the @ref Gudhi::persistence_matrix::New_cell_constructor and
+ * @ref Gudhi::persistence_matrix::Pool_cell_constructor structures.
  */
 
 #ifndef PM_COLUMN_CELL_CONSTRUCTORS_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix.h

@@ -11,7 +11,7 @@
 /**
  * @file base_matrix.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Base_matrix class.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Base_matrix class.
  */
 
 #ifndef PM_BASE_MATRIX_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix_with_column_compression.h

@@ -11,7 +11,7 @@
 /**
  * @file base_matrix_with_column_compression.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Base_matrix_with_column_compression class.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Base_matrix_with_column_compression class.
  */
 
 #ifndef PM_BASE_MATRIX_COMPRESSION_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/base_pairing.h

@@ -11,7 +11,8 @@
 /**
  * @file base_pairing.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Base_pairing class and @ref Dummy_base_pairing structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Base_pairing class and
+ * @ref Gudhi::persistence_matrix::Dummy_base_pairing structure.
  */
 
 #ifndef PM_BASE_PAIRING_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/base_swap.h

@@ -11,7 +11,8 @@
 /**
  * @file base_swap.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Base_swap class and @ref Dummy_base_swap structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Base_swap class and
+ * @ref Gudhi::persistence_matrix::Dummy_base_swap structure.
  */
 
 #ifndef PM_BASE_SWAP_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/boundary_matrix.h

@@ -11,7 +11,7 @@
 /**
  * @file boundary_matrix.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Boundary_matrix class.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Boundary_matrix class.
  */
 
 #ifndef PM_BOUNDARY_MATRIX_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_matrix.h

@@ -11,7 +11,7 @@
 /**
  * @file chain_matrix.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Chain_matrix class.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_matrix class.
  */
 
 #ifndef PM_CHAIN_MATRIX_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_pairing.h

@@ -11,7 +11,8 @@
 /**
  * @file chain_pairing.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Chain_pairing class and @ref Dummy_chain_pairing structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_pairing class and
+ * @ref Gudhi::persistence_matrix::Dummy_chain_pairing structure.
  */
 
 #ifndef PM_CHAIN_PAIRING_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_rep_cycles.h

@@ -11,7 +11,8 @@
 /**
  * @file chain_rep_cycles.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Chain_representative_cycles class and @ref Dummy_chain_representative_cycles structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_representative_cycles class and
+ * @ref Gudhi::persistence_matrix::Dummy_chain_representative_cycles structure.
  */
 
 #ifndef PM_CHAIN_REP_CYCLES_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_vine_swap.h

@@ -11,8 +11,10 @@
 /**
  * @file chain_vine_swap.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Chain_barcode_swap and @ref Chain_vine_swap classes, as well as the
- * @ref Dummy_chain_vine_swap and @ref Dummy_chain_vine_pairing structures.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_barcode_swap and
+ * @ref Gudhi::persistence_matrix::Chain_vine_swap classes, as well as the
+ * @ref Gudhi::persistence_matrix::Dummy_chain_vine_swap and
+ * @ref Gudhi::persistence_matrix::Dummy_chain_vine_pairing structures.
  */
 
 #ifndef PM_CHAIN_VINE_SWAP_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/cell_types.h

@@ -11,9 +11,11 @@
 /**
  * @file cell_types.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Cell, @ref Cell_column_index and @ref Cell_field_element classes, as well as the
- * @ref Dummy_cell_column_index_mixin and @ref Dummy_cell_field_element_mixin structures. Also defines the
- * std::hash method for @ref Cell.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Cell, @ref Gudhi::persistence_matrix::Cell_column_index and
+ * @ref Gudhi::persistence_matrix::Cell_field_element classes, as well as the
+ * @ref Gudhi::persistence_matrix::Dummy_cell_column_index_mixin and
+ * @ref Gudhi::persistence_matrix::Dummy_cell_field_element_mixin structures.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Cell.
  */
 
 #ifndef PM_MATRIX_CELL_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h

@@ -11,7 +11,8 @@
 /**
  * @file chain_column_extra_properties.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Chain_column_extra_properties class and @ref Dummy_chain_properties structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_column_extra_properties class and
+ * @ref Gudhi::persistence_matrix::Dummy_chain_properties structure.
  */
 
 #ifndef PM_CHAIN_COLUMN_PROP_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/column_dimension_holder.h

@@ -11,7 +11,8 @@
 /**
  * @file column_dimension_holder.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Column_dimension_holder class and @ref Dummy_dimension_holder structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Column_dimension_holder class and
+ * @ref Gudhi::persistence_matrix::Dummy_dimension_holder structure.
  */
 
 #ifndef PM_COLUMN_DIM_HOLDER_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/heap_column.h

@@ -11,7 +11,8 @@
 /**
  * @file heap_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Heap_column class. Also defines the std::hash method for @ref Heap_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Heap_column class. Also defines the std::hash method
+ * for @ref Gudhi::persistence_matrix::Heap_column.
  */
 
 #ifndef PM_HEAP_COLUMN_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/intrusive_list_column.h

@@ -11,8 +11,8 @@
 /**
  * @file intrusive_list_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Intrusive_list_column class.
- * Also defines the std::hash method for @ref Intrusive_list_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Intrusive_list_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Intrusive_list_column.
  */
 
 #ifndef PM_INTRUSIVE_LIST_COLUMN_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/intrusive_set_column.h

@@ -11,8 +11,8 @@
 /**
  * @file intrusive_set_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Intrusive_set_column class.
- * Also defines the std::hash method for @ref Intrusive_set_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Intrusive_set_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Intrusive_set_column.
  */
 
 #ifndef PM_INTRUSIVE_SET_COLUMN_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/list_column.h

@@ -11,8 +11,8 @@
 /**
  * @file list_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref List_column class.
- * Also defines the std::hash method for @ref List_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::List_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::List_column.
  */
 
 #ifndef PM_LIST_COLUMN_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/naive_vector_column.h

@@ -11,8 +11,8 @@
 /**
  * @file naive_vector_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Naive_vector_column class.
- * Also defines the std::hash method for @ref Naive_vector_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Naive_vector_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Naive_vector_column.
  */
 
 #ifndef PM_NAIVE_VECTOR_COLUMN_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/row_access.h

@@ -11,7 +11,8 @@
 /**
  * @file row_access.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Row_access class and @ref Dummy_row_access structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Row_access class and
+ * @ref Gudhi::persistence_matrix::Dummy_row_access structure.
  */
 
 #ifndef PM_ROW_ACCESS_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/set_column.h

@@ -11,8 +11,8 @@
 /**
  * @file set_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Set_column class.
- * Also defines the std::hash method for @ref Set_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Set_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Set_column.
  */
 
 #ifndef PM_SET_COLUMN_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/unordered_set_column.h

@@ -11,8 +11,8 @@
 /**
  * @file unordered_set_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Unordered_set_column class.
- * Also defines the std::hash method for @ref Unordered_set_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Unordered_set_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Unordered_set_column.
  */
 
 #ifndef PM_UNORDERED_SET_COLUMN_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/vector_column.h

@@ -11,8 +11,8 @@
 /**
  * @file vector_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Vector_column class.
- * Also defines the std::hash method for @ref Vector_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Vector_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Vector_column.
  */
 
 #ifndef PM_VECTOR_COLUMN_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/matrix_dimension_holders.h

@@ -11,8 +11,9 @@
 /**
  * @file matrix_dimension_holders.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Matrix_max_dimension_holder @ref Matrix_all_dimension_holder classes
- * and the @ref Dummy_matrix_dimension_holder structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Matrix_max_dimension_holder
+ * @ref Gudhi::persistence_matrix::Matrix_all_dimension_holder classes
+ * and the @ref Gudhi::persistence_matrix::Dummy_matrix_dimension_holder structure.
  */
 
 #ifndef PM_MATRIX_DIM_HOLDER_H

src/Persistence_matrix/include/gudhi/Persistence_matrix/matrix_row_access.h

@@ -11,7 +11,8 @@
 /**
  * @file matrix_row_access.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Matrix_row_access class and @ref Dummy_matrix_row_access structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Matrix_row_access class and
+ * @ref Gudhi::persistence_matrix::Dummy_matrix_row_access structure.
  */
 
 #ifndef PM_BASE_MATRIX_RA_H