merge with upstream branch

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/FieldOperators.h

@@ -30,30 +30,30 @@ namespace persistence_matrix {
 class FieldOperators 
 {
  public:
-  using element_type = unspecified;         /**< Type for the elements in the field. */
-  using characteristic_type = unspecified;  /**< Type for the field characteristic. */
+  using Element = unspecified;         /**< Type for the elements in the field. */
+  using Characteristic = unspecified;  /**< Type for the field characteristic. */
 
   /**
    * @brief Default constructor. If a non-zero characteristic is given, initializes the field with it.
    * The characteristic can later be changed again or initialized with @ref set_characteristic.
    *
    * @param characteristic Prime number corresponding to the desired characteristic of the field.
    */
-  FieldOperators(characteristic_type characteristic = 0);
+  FieldOperators(Characteristic characteristic = 0);
 
   /**
    * @brief Sets the characteristic of the field. Can eventually be omitted if the characteristic of the class
    * is fixed.
    * 
    * @param characteristic Prime number corresponding to the desired characteristic of the field.
    */
-  void set_characteristic(const characteristic_type& characteristic);
+  void set_characteristic(const Characteristic& characteristic);
   /**
    * @brief Returns the current characteristic.
    * 
    * @return The value of the current characteristic.
    */
-  const characteristic_type& get_characteristic() const;
+  const Characteristic& get_characteristic() const;
 
   /**
    * @brief Returns the value of an integer in the field.
@@ -64,9 +64,9 @@ class FieldOperators
    * @return @p e modulo the current characteristic, such that the result is positive.
    */
   template <typename Integer_type>
-  element_type get_value(Integer_type e) const;
+  Element get_value(Integer_type e) const;
 
-  // void get_value(element_type& e) const;
+  // void get_value(Element& e) const;
 
   /**
    * @brief Stores in the first element the sum of two given elements in the field, that is
@@ -75,7 +75,7 @@ class FieldOperators
    * @param e1 First element.
    * @param e2 Second element.
    */
-  void add_inplace(element_type& e1, const element_type& e2) const;
+  void add_inplace(Element& e1, const Element& e2) const;
 
   /**
    * @brief Stores in the first element the multiplication of two given elements in the field,
@@ -84,7 +84,7 @@ class FieldOperators
    * @param e1 First element.
    * @param e2 Second element.
    */
-  void multiply_inplace(element_type& e1, const element_type& e2) const;
+  void multiply_inplace(Element& e1, const Element& e2) const;
 
   /**
    * @brief Multiplies the first element with the second one and adds the third one, that is
@@ -94,7 +94,7 @@ class FieldOperators
    * @param m Second element.
    * @param a Third element.
    */
-  void multiply_and_add_inplace_front(element_type& e, const element_type& m, const element_type& a) const;
+  void multiply_and_add_inplace_front(Element& e, const Element& m, const Element& a) const;
   /**
    * @brief Multiplies the first element with the second one and adds the third one, that is
    * `(e * m + a) % characteristic`, such that the result is positive. Stores the result in the third element.
@@ -103,28 +103,28 @@ class FieldOperators
    * @param m Second element.
    * @param a Third element.
    */
-  void multiply_and_add_inplace_back(const element_type& e, const element_type& m, element_type& a) const;
+  void multiply_and_add_inplace_back(const Element& e, const Element& m, Element& a) const;
 
   /**
    * @brief Returns the inverse of the given element in the field.
    * 
    * @param e Element to get the inverse from.
    * @return Inverse in the current field of `e % characteristic`.
    */
-  element_type get_inverse(const element_type& e) const;
+  Element get_inverse(const Element& e) const;
 
   /**
    * @brief Returns the additive identity of the field.
    * 
    * @return The additive identity of the field.
    */
-  static const element_type& get_additive_identity();
+  static const Element& get_additive_identity();
   /**
    * @brief Returns the multiplicative identity of the field.
    * 
    * @return The multiplicative identity of the field.
    */
-  static const element_type& get_multiplicative_identity();
+  static const Element& get_multiplicative_identity();
 
   /**
    * @brief Assign operator.