Merge pull request GUDHI#1108 from hschreiber/matrix_spelling

[Persistence matrix] fix spelling errors

src/Persistence_matrix/concept/PersistenceMatrixColumn.h

@@ -47,7 +47,7 @@ using Chain_column_option = Chain_column_extra_properties;
 /** 
  * @ingroup persistence_matrix
  *
- * @brief Concept of the column classes used by the @ref Matrix class. The classes the columns inheritates from
+ * @brief Concept of the column classes used by the @ref Matrix class. The classes the columns inherit from
  * are either real or dummy classes, see @ref Row_access_option, @ref Column_dimension_option, @ref Chain_column_option.
  * If used with column compression, the column type has to have its `std::hash` method.
  *
@@ -81,7 +81,7 @@ class PersistenceMatrixColumn :
    * @param colSettings Pointer to a setting structure or `nullptr`. The structure should contain all the necessary
    * classes specific to the column type, such as custom allocators. The specificities are this way hidden behind
    * a commun interface for all column types. If @p colSettings is not specified or is equal to `nullptr`, the column
-   * should still be constructable eventhough not necessarily "usable".
+   * should still be constructable even though not necessarily "usable".
    */
   PersistenceMatrixColumn(Column_settings* colSettings = nullptr);
   /**
@@ -291,7 +291,7 @@ class PersistenceMatrixColumn :
    * @brief Returns a begin @ref Cell iterator to iterate over all cells contained in the underlying container.
    *
    * @warning The iterators really just iterate over the underlying container. Depending of the column type,
-   * neither the content nor the order is garanteed. See description of the actual Column class for more details.
+   * neither the content nor the order is guaranteed. See description of the actual Column class for more details.
    * 
    * @return @ref Cell iterator.
    */
@@ -300,7 +300,7 @@ class PersistenceMatrixColumn :
    * @brief Returns a begin @ref Cell const iterator to iterate over all cells contained in the underlying container.
    *
    * @warning The iterators really just iterate over the underlying container. Depending of the column type,
-   * neither the content nor the order is garanteed. See description of the actual Column class for more details.
+   * neither the content nor the order is guaranteed. See description of the actual Column class for more details.
    * 
    * @return @ref Cell const iterator.
    */
@@ -309,7 +309,7 @@ class PersistenceMatrixColumn :
    * @brief Returns a end @ref Cell iterator, iterating over all cells contained in the underlying container.
    *
    * @warning The iterators really just iterate over the underlying container. Depending of the column type,
-   * neither the content nor the order is garanteed. See description of the actual Column class for more details.
+   * neither the content nor the order is guaranteed. See description of the actual Column class for more details.
    * 
    * @return @ref Cell iterator.
    */
@@ -318,7 +318,7 @@ class PersistenceMatrixColumn :
    * @brief Returns a end @ref Cell const iterator, iterating over all cells contained in the underlying container.
    *
    * @warning The iterators really just iterate over the underlying container. Depending of the column type,
-   * neither the content nor the order is garanteed. See description of the actual Column class for more details.
+   * neither the content nor the order is guaranteed. See description of the actual Column class for more details.
    * 
    * @return @ref Cell const iterator.
    */
@@ -327,7 +327,7 @@ class PersistenceMatrixColumn :
    * @brief Returns a begin @ref Cell reverse iterator to iterate over all cells contained in the underlying container.
    *
    * @warning The iterators really just iterate over the underlying container. Depending of the column type,
-   * neither the content nor the order is garanteed. See description of the actual Column class for more details.
+   * neither the content nor the order is guaranteed. See description of the actual Column class for more details.
    * 
    * @return @ref Cell reverse iterator.
    */
@@ -337,7 +337,7 @@ class PersistenceMatrixColumn :
    * container.
    *
    * @warning The iterators really just iterate over the underlying container. Depending of the column type,
-   * neither the content nor the order is garanteed. See description of the actual Column class for more details.
+   * neither the content nor the order is guaranteed. See description of the actual Column class for more details.
    * 
    * @return @ref Cell const reverse iterator.
    */
@@ -346,7 +346,7 @@ class PersistenceMatrixColumn :
    * @brief Returns a end @ref Cell reverse iterator, iterating over all cells contained in the underlying container.
    *
    * @warning The iterators really just iterate over the underlying container. Depending of the column type,
-   * neither the content nor the order is garanteed. See description of the actual Column class for more details.
+   * neither the content nor the order is guaranteed. See description of the actual Column class for more details.
    * 
    * @return @ref Cell reverse iterator.
    */
@@ -356,7 +356,7 @@ class PersistenceMatrixColumn :
    * container.
    *
    * @warning The iterators really just iterate over the underlying container. Depending of the column type,
-   * neither the content nor the order is garanteed. See description of the actual Column class for more details.
+   * neither the content nor the order is guaranteed. See description of the actual Column class for more details.
    * 
    * @return @ref Cell const reverse iterator.
    */
@@ -420,8 +420,8 @@ class PersistenceMatrixColumn :
 
   /**
    * @brief Equality comparator. Equal in the sense that what is "supposed" to be contained in the columns is equal,
-   * not what is actually stored in the underlying container. For exemple, the underlying container of 
-   * @ref Vector_column can contain cells which were erased explicitely by @ref clear(index). Those cells should not
+   * not what is actually stored in the underlying container. For example, the underlying container of 
+   * @ref Vector_column can contain cells which were erased explicitly by @ref clear(index). Those cells should not
    * be taken into account while comparing.
    * 
    * @param c1 First column to compare.
@@ -433,8 +433,8 @@ class PersistenceMatrixColumn :
   /**
    * @brief "Strictly smaller than" comparator. Usually a lexicographical order, but what matters is that the
    * order is total. The order should apply on what is "supposed" to be contained in the columns,
-   * not what is actually stored in the underlying container. For exemple, the underlying container of 
-   * @ref Vector_column can contain cells which were erased explicitely by @ref clear(index). Those cells should not
+   * not what is actually stored in the underlying container. For example, the underlying container of 
+   * @ref Vector_column can contain cells which were erased explicitly by @ref clear(index). Those cells should not
    * be taken into account while comparing.
    * 
    * @param c1 First column to compare.

src/Persistence_matrix/concept/PersistenceMatrixOptions.h

@@ -68,7 +68,7 @@ struct PersistenceMatrixOptions
   /**
    * @brief Only enabled for @ref basematrix "base matrices" (i.e., none of the following is true:
    * @ref has_column_pairings, @ref has_vine_update, @ref can_retrieve_representative_cycles), is ignored otherwise.
-   * If set to true, two identical columns in the matrix are not explicitely stored separately but are represented 
+   * If set to true, two identical columns in the matrix are not explicitly stored separately but are represented 
    * by a same column.
    *
    * Note that some methods of the @ref basematrix "base matrix" are not available when true:
@@ -166,7 +166,7 @@ struct PersistenceMatrixOptions
   //  * the following is true: @ref has_column_pairings, @ref has_vine_update or
   //  * @ref can_retrieve_representative_cycles.
   //  * Is ignored otherwise
-  //  * If set to true, the matrix is decomposed in several submatrices containing each all the
+  //  * If set to true, the matrix is decomposed in several sub-matrices containing each all the
   //  * columns of same dimension.
   //  */
   //  static const bool is_separated_by_dimension;

src/Persistence_matrix/doc/Intro_field_elements_and_operators.h

@@ -26,11 +26,11 @@ namespace persistence_fields {
  *
  * There are two types of classes:
  * - those defining directly a field element, allowing to use them as any integer: the operators are overwritten such
- *   that the calculation is done in the field. For example, if \f$ e = 2 \f$ is an instanciation of an
- *   \f$ \mathbb{F}_3 \f$ element class, then `e + 3` returns an element instanciation of value `2`,
+ *   that the calculation is done in the field. For example, if \f$ e = 2 \f$ is an instantiation of an
+ *   \f$ \mathbb{F}_3 \f$ element class, then `e + 3` returns an element instantiation of value `2`,
  * - those only defining the operators of a field or multi-field. They represent a collection of methods taking
  *   one or two integers as input and treating them as elements of the field. For example, if \f$ op \f$ is an
- *   instanciation of a \f$ \mathbb{F}_3 \f$ operator class, `op.add(2, 3)` returns `2`.
+ *   instantiation of a \f$ \mathbb{F}_3 \f$ operator class, `op.add(2, 3)` returns `2`.
  *
  * The field operator classes all respect the @ref persistence_matrix::FieldOperators concept.
  * 

src/Persistence_matrix/doc/Intro_persistence_matrix.h

@@ -25,9 +25,9 @@ namespace persistence_matrix {
  * and used as backend for persistence algorithms, such at persistent homology, @ref persistent_cohomology,
  * or zigzag @cite zigzag.
  *
- * The structure is entirely accessed via the class @ref Matrix and it provides several functionnalities which can
+ * The structure is entirely accessed via the class @ref Matrix and it provides several functionalities which can
  * be enabled or disabled through a template argument following the @ref PersistenceMatrixOptions concept.
- * The main functionnalities are:
+ * The main functionalities are:
  * @li column and row access,
  * @li column addition and scalar multiplication,
  * @li removal of maximal faces while maintaining a valid reduced boundary matrix or compatible chain complex base

src/Persistence_matrix/example/example_field_operations.cpp

@@ -41,7 +41,7 @@ void field_element_example(int ini){
   std::cout << "e -= 4: " << e << "\n";
   t = 4;
   t -= e;   //standard integer addition
-  std::cout << "4 -= e: " << t << "    //standard integer substraction\n";
+  std::cout << "4 -= e: " << t << "    //standard integer subtraction\n";
   std::cout << "e * 6: " << (e * 6) << "\n";
   std::cout << "6 * e: " << (6 * e) << "\n";
   e *= 6;
@@ -57,8 +57,8 @@ void field_operator_example(const Field_operator& op){
   std::cout << "Characteristic: " << op.get_characteristic() << "\n";
   std::cout << "2 + 3: " << op.add(2u, 3u) << "\n";
   std::cout << "3 + 2: " << op.add(3u, 2u) << "\n";
-  std::cout << "10 - 4: " << op.substract(10u, 4u) << "\n";
-  std::cout << "4 - 10: " << op.substract(4u, 10u) << "\n";
+  std::cout << "10 - 4: " << op.subtract(10u, 4u) << "\n";
+  std::cout << "4 - 10: " << op.subtract(4u, 10u) << "\n";
   std::cout << "3 * 6: " << op.multiply(3u, 6u) << "\n";
   std::cout << "6 * 3: " << op.multiply(6u, 3u) << "\n";
   std::cout << "Value of 7: " << op.get_value(7u) << "\n";

src/Persistence_matrix/example/representative_cycles_from_matrix.cpp

@@ -58,14 +58,14 @@ void print_representative_cycles_example()
   auto rc = mp.get_representative_cycles();
   for (auto cycle : rc) {
     // cycle[0] gives the row index of a simplex in the cycle
-    // because the simplices where indexed from 0 continously, the simplex represented by the row index cycle[0] is
+    // because the simplices where indexed from 0 continuously, the simplex represented by the row index cycle[0] is
     // the same simplex represented by the column at position cycle[0] in RU
     // that is why `mp.get_column_dimension(cycle[0])` gives us the dimension of the simplex for RU_matrix
     //
     // for the chain matrix, the row index will always represent a simplex ID. So,
     // `mp.get_column_dimension(mp.get_column_with_pivot(cycle[0]))` will always work to get the dimension
-    // of the simplex. But in this particlar case, because of the simplex indexation and the fact that no swap
-    // occured, mp.get_column_with_pivot(cycle[0]) == cycle[0] and so `mp.get_column_dimension(cycle[0])` also works.
+    // of the simplex. But in this particular case, because of the simplex indexation and the fact that no swap
+    // occurred, mp.get_column_with_pivot(cycle[0]) == cycle[0] and so `mp.get_column_dimension(cycle[0])` also works.
     std::cout << mp.get_column_dimension(cycle[0]);
     std::cout << "-cycle: ";
     for (auto index : cycle) {

src/Persistence_matrix/example/simplex_tree_to_matrix.cpp

@@ -87,7 +87,7 @@ void print_matrix(Base_matrix& bm, unsigned int size){
 
 void print_matrix(const Chain_matrix& cm, unsigned int size){
   std::cout << "Chain_matrix:\n";
-  // just note that if some vine swaps or removals occured, this would
+  // just note that if some vine swaps or removals occurred, this would
   // not give us the columns in the order of filtration anymore, but just
   // in the order they are stored in the matrix
   for (unsigned int i = 0; i < size; ++i) {

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

@@ -29,7 +29,7 @@ namespace persistence_fields {
  * @class Multi_field_operators Multi_field_operators.h gudhi/Fields/Multi_field_operators.h
  * @ingroup persistence_fields
  *
- * @brief Class defining operators for a multi-field with "consecutive" charateristic range.
+ * @brief Class defining operators for a multi-field with "consecutive" characteristic range.
  */
 class Multi_field_operators
 {
@@ -46,7 +46,7 @@ class Multi_field_operators
    * @brief Constructor setting the characteristics to all prime numbers between the two given integers.
    * 
    * @param minCharacteristic Smallest value of a prime.
-   * @param maxCharacteristic Heighest value of a prime.
+   * @param maxCharacteristic Highest value of a prime.
    */
   Multi_field_operators(int minCharacteristic, int maxCharacteristic)
       : productOfAllCharacteristics_(0)  //, multiplicativeID_(1)
@@ -81,7 +81,7 @@ class Multi_field_operators
    * The characteristics will be all prime numbers in the given interval.
    * 
    * @param minimum Smallest value of a prime.
-   * @param maximum Heighest value of a prime.
+   * @param maximum Highest value of a prime.
    */
   void set_characteristic(int minimum, int maximum) {
     if (maximum < 2) throw std::invalid_argument("Characteristic must be strictly positive");
@@ -184,36 +184,36 @@ class Multi_field_operators
   }
 
   /**
-   * @brief Returns the substraction in the field of the first element by the second element.
+   * @brief Returns the subtraction in the field of the first element by the second element.
    * 
    * @param e1 First element.
    * @param e2 Second element.
    * @return `(e1 - e2) % productOfAllCharacteristics`, such that the result is positive.
    */
-  element_type substract(element_type e1, const element_type& e2) const {
-    substract_inplace_front(e1, e2);
+  element_type subtract(element_type e1, const element_type& e2) const {
+    subtract_inplace_front(e1, e2);
     return e1;
   }
 
   /**
-   * @brief Stores in the first element the substraction in the field of the first element by the second element,
+   * @brief Stores in the first element the subtraction in the field of the first element by the second element,
    * that is `(e1 - e2) % productOfAllCharacteristics`, such that the result is positive.
    * 
    * @param e1 First element.
    * @param e2 Second element.
    */
-  void substract_inplace_front(element_type& e1, const element_type& e2) const {
+  void subtract_inplace_front(element_type& e1, const element_type& e2) const {
     e1 -= e2;
     get_value_inplace(e1);
   }
   /**
-   * @brief Stores in the second element the substraction in the field of the first element by the second element,
+   * @brief Stores in the second element the subtraction in the field of the first element by the second element,
    * that is `(e1 - e2) % productOfAllCharacteristics`, such that the result is positive.
    * 
    * @param e1 First element.
    * @param e2 Second element.
    */
-  void substract_inplace_back(const element_type& e1, element_type& e2) const {
+  void subtract_inplace_back(const element_type& e1, element_type& e2) const {
     mpz_sub(e2.get_mpz_t(), e1.get_mpz_t(), e2.get_mpz_t());
     get_value_inplace(e2);
   }

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

@@ -29,9 +29,9 @@ namespace persistence_fields {
  * @class Shared_multi_field_element Multi_field_shared.h gudhi/Fields/Multi_field_shared.h
  * @ingroup persistence_fields
  *
- * @brief Class representing an element of a multi-field. If each instanciation of the class can represent another
- * element, they all share the same characteritics. That is if the characteristics are set for one, they will be
- * set for all the others. The characteristics can be set before instianciating the elements with the static 
+ * @brief Class representing an element of a multi-field. If each instantiation of the class can represent another
+ * element, they all share the same characteristics. That is if the characteristics are set for one, they will be
+ * set for all the others. The characteristics can be set before instantiating the elements with the static 
  * @ref Shared_multi_field_element::initialize method.
  */
 class Shared_multi_field_element 

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

@@ -135,7 +135,7 @@ class Multi_field_element_with_small_characteristics {
    */
   friend void operator-=(Multi_field_element_with_small_characteristics& f1,
                          Multi_field_element_with_small_characteristics const& f2) {
-    f1.element_ = _substract(f1.element_, f2.element_);
+    f1.element_ = _subtract(f1.element_, f2.element_);
   }
   /**
    * @brief operator-
@@ -152,7 +152,7 @@ class Multi_field_element_with_small_characteristics {
    */
   template <typename Integer_type, class = isInteger<Integer_type> >
   friend void operator-=(Multi_field_element_with_small_characteristics& f, const Integer_type& v) {
-    f.element_ = _substract(f.element_, _get_value(v));
+    f.element_ = _subtract(f.element_, _get_value(v));
   }
   /**
    * @brief operator-
@@ -172,7 +172,7 @@ class Multi_field_element_with_small_characteristics {
    */
   template <typename Integer_type, class = isInteger<Integer_type> >
   friend Integer_type operator-(const Integer_type& v, const Multi_field_element_with_small_characteristics& f) {
-    return _substract(_get_value(v), f.element_);
+    return _subtract(_get_value(v), f.element_);
   }
 
   /**
@@ -431,7 +431,7 @@ class Multi_field_element_with_small_characteristics {
 
     return element;
   }
-  static constexpr element_type _substract(element_type element, element_type v) {
+  static constexpr element_type _subtract(element_type element, element_type v) {
     if (element < v) {
       element += productOfAllCharacteristics_;
     }
@@ -444,7 +444,7 @@ class Multi_field_element_with_small_characteristics {
     int M = mod;
     int A = element;
     int y = 0, x = 1;
-    // extended euclidien division
+    // extended euclidean division
     while (A > 1) {
       int quotient = A / M;
       int temp = M;