Fix some doxygen warnings in Persistence_matrix

src/Doxyfile.in

@@ -314,7 +314,7 @@ AUTOLINK_SUPPORT       = YES
 # diagrams that involve STL classes more complete and accurate.
 # The default value is: NO.
 
-BUILTIN_STL_SUPPORT    = NO
+BUILTIN_STL_SUPPORT    = YES
 
 # If you use Microsoft's C++/CLI language, you should set this option to YES to
 # enable parsing support.

src/Persistence_matrix/concept/PersistenceMatrixColumn.h

@@ -143,7 +143,7 @@ class PersistenceMatrixColumn :
    * @tparam Row_container_type Either std::map if @ref PersistenceMatrixOptions::has_removable_rows is true or
    * std::vector<Row_type>.
    * @param columnIndex @ref MatIdx column index that should be specified to the cells.
-   * @param nonZeroRowIndices Range of @ref Matrix::cell_rep_type representing all rows with non zero values.
+   * @param nonZeroChainRowIndices Range of @ref Matrix::cell_rep_type representing all rows with non zero values.
    * @param dimension Dimension of the column. Is ignored if the dimension is not stored.
    * @param rowContainer Pointer to the row container that will be forwarded to @ref Row_access at construction.
    * @param colSettings Pointer to an existing setting structure. The structure should contain all the necessary

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

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

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

@@ -292,8 +292,7 @@ class Base_matrix_with_column_compression : protected Master_matrix::Matrix_row_
   /**
    * @brief Resets the matrix to an empty matrix.
    * 
-   * @param operators Pointer to the field operators.
-   * @param cellConstructor Pointer to the cell factory.
+   * @param colSettings Pointer to the cell factory.
    */
   void reset(Column_settings* colSettings) {
     columnToRep_.clear_and_dispose(delete_disposer(this));

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

@@ -66,7 +66,7 @@ class Base_swap {
    * 
    * @param matrixToCopy Matrix to copy.
    */
-  Base_swap(const Base_swap& matrixToCopy);
+  Base_swap(const Base_swap& matrixToCopy) = default;
   /**
    * @brief Move constructor.
    * 
@@ -132,13 +132,7 @@ inline Base_swap<Master_matrix, Base_matrix>::Base_swap(unsigned int numberOfCol
 }
 
 template <class Master_matrix, class Base_matrix>
-inline Base_swap<Master_matrix, Base_matrix>::Base_swap(const Base_swap<Master_matrix, Base_matrix>& matrixToCopy)
-    : indexToRow_(matrixToCopy.indexToRow_),
-      rowToIndex_(matrixToCopy.rowToIndex_),
-      rowSwapped_(matrixToCopy.rowSwapped_) {}
-
-template <class Master_matrix, class Base_matrix>
-inline Base_swap<Master_matrix, Base_matrix>::Base_swap(Base_swap<Master_matrix, Base_matrix>&& other) noexcept
+inline Base_swap<Master_matrix, Base_matrix>::Base_swap(Base_swap&& other) noexcept
     : indexToRow_(std::move(other.indexToRow_)),
       rowToIndex_(std::move(other.rowToIndex_)),
       rowSwapped_(std::exchange(other.rowSwapped_, 0)) {}

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

@@ -128,7 +128,7 @@ class Cell_field_element
   /**
    * @brief Stores the given element.
    * 
-   * @param columnIndex Value to store.
+   * @param element Value to store.
    */
   Cell_field_element(Field_element_type element) : element_(element){};
   /**

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

@@ -232,7 +232,7 @@ class Heap_column : public Master_matrix::Column_dimension_option, public Master
   using dim_opt = typename Master_matrix::Column_dimension_option;
   using chain_opt = typename Master_matrix::Chain_column_option;
 
-  struct {
+  struct CellPointerComp {
     bool operator()(const Cell* c1, const Cell* c2) const { return *c1 < *c2; }
   } cellPointerComp_;
 

src/Persistence_matrix/include/gudhi/Persistence_matrix/overlay_ididx_to_matidx.h

@@ -43,6 +43,7 @@ class Id_to_index_overlay
  public:
   using index = typename Master_matrix_type::index;                       /**< @ref MatIdx index type. */
   using id_index = typename Master_matrix_type::id_index;                 /**< @ref IDIdx index type. */
+  using pos_index = typename Master_matrix_type::pos_index;               /**< @ref PosIdx index type. */
   using dimension_type = typename Master_matrix_type::dimension_type;     /**< Dimension value type. */
   /**
    * @brief Field operators class. Necessary only if @ref PersistenceMatrixOptions::is_z2 is false.

src/Persistence_matrix/include/gudhi/Persistence_matrix/overlay_posidx_to_matidx.h

@@ -242,7 +242,7 @@ class Position_to_index_overlay
    * the faces are inserted by order of filtration), it is sufficient to indicate the ID of the face being inserted.
    * 
    * @tparam Boundary_type Range of @ref Matrix::cell_rep_type. Assumed to have a begin(), end() and size() method.
-   * @param faceID @ref IDIdx index to use to indentify the new face.
+   * @param faceIndex @ref IDIdx index to use to indentify the new face.
    * @param boundary Boundary generating the new column. The indices of the boundary have to correspond to the 
    * @p faceID values of precedent calls of the method for the corresponding faces and should be ordered in 
    * increasing order.

src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_vine_swap.h

@@ -89,7 +89,7 @@ class RU_vine_swap : public std::conditional<Master_matrix::Option_list::has_col
    * @brief Does the same than @ref vine_swap, but assumes that the swap is non trivial and
    * therefore skips a part of the case study.
    * 
-   * @param position @ref PosIdx index of the first face to swap. The second one has to be at `position + 1`.
+   * @param index @ref PosIdx index of the first face to swap. The second one has to be at `position + 1`.
    * @return true If the barcode changed from the swap.
    * @return false Otherwise.
    */
@@ -102,7 +102,7 @@ class RU_vine_swap : public std::conditional<Master_matrix::Option_list::has_col
    * not have a face/coface relation which each other ; \f$ F' \f$ has to be a valid filtration.
    * See @cite vineyards for more information about vine and vineyards.
    * 
-   * @param position @ref PosIdx index of the first face to swap. The second one has to be at `position + 1`.
+   * @param index @ref PosIdx index of the first face to swap. The second one has to be at `position + 1`.
    * @return true If the barcode changed from the swap.
    * @return false Otherwise.
    */

src/Persistence_matrix/include/gudhi/matrix.h

@@ -71,7 +71,7 @@ namespace Gudhi {
 namespace persistence_matrix {
 
 /**
- * @class Matrix persistence_matrix.h gudhi/persistence_matrix.h
+ * @class Matrix matrix.h gudhi/matrix.h
  * @ingroup persistence_matrix
  *
  * @brief Data structure for matrices, and in particular thought for matrices representing filtered complexes