Merge branch 'master' of https://github.com/GUDHI/gudhi-devel into Ex…

…act_SW

CMakeLists.txt

@@ -71,6 +71,7 @@ endif()
 
 # For "make user_version" - Requires GUDHI_modules to be performed
 include(GUDHI_user_version_target)
+set(GUDHI_BIBLIO_DIR ${CMAKE_CURRENT_BINARY_DIR})
 # For "make doxygen" - Requires GUDHI_USER_VERSION_DIR to be set - Done in GUDHI_user_version_target for dev version
 include(GUDHI_doxygen_target)
 

src/CMakeLists.txt

@@ -46,6 +46,7 @@ add_gudhi_module(Witness_complex)
 add_gudhi_module(Nerve_GIC)
 add_gudhi_module(Persistence_matrix)
 
+set(GUDHI_BIBLIO_DIR ${CMAKE_SOURCE_DIR})
 # For "make doxygen" - Requires GUDHI_USER_VERSION_DIR to be set
 set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
 include(GUDHI_doxygen_target)

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.
@@ -699,8 +699,8 @@ LAYOUT_FILE            =
 # LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
 # search path. See also \cite for info how to create references.
 
-CITE_BIB_FILES         = @CMAKE_SOURCE_DIR@/biblio/bibliography.bib \
-                         @CMAKE_SOURCE_DIR@/biblio/how_to_cite_gudhi.bib
+CITE_BIB_FILES         = @GUDHI_BIBLIO_DIR@/biblio/bibliography.bib \
+                         @GUDHI_BIBLIO_DIR@/biblio/how_to_cite_gudhi.bib
 
 #---------------------------------------------------------------------------
 # Configuration options related to warning and progress messages

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;
 /**
@@ -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/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_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 class.
  */
 
 #ifndef MATRIX_FIELD_MULTI_OPERATORS_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 +11,7 @@
 /**
  * @file cell_constructors.h
  * @author Hannah Schreiber
- * @brief Contains the @ref New_cell_constructor and @ref Pool_cell_constructor structures.
+ * @brief Contains different versions of @ref Gudhi::persistence_matrix::Cell factories.
  */
 
 #ifndef PM_COLUMN_CELL_CONSTRUCTORS_H
@@ -25,6 +25,7 @@ namespace Gudhi {
 namespace persistence_matrix {
 
 /**
+ * @private
  * @ingroup persistence_matrix
  *
  * @brief @ref Cell factory. Constructs and destroyes cell pointers with new and delete.
@@ -64,6 +65,7 @@ struct New_cell_constructor
 };
 
 /**
+ * @private
  * @ingroup persistence_matrix
  *
  * @brief @ref Cell factory. Uses @ref Gudhi::Simple_object_pool, which is based on boost::object_pool,

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
@@ -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_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
@@ -66,7 +67,7 @@ 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 +133,7 @@ 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/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
@@ -128,7 +130,7 @@ 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/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
@@ -232,7 +233,7 @@ 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/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