Merge branch 'master' into feature/bug_class_diagrams

5 files changed, 30 insertions, 26 deletions

diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 6dce947c..9059219c 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -42,6 +42,10 @@
 
 namespace Gudhi {
 
+/** \addtogroup simplex_tree 
+ *  @{
+ */
+
 /**
  * \class Extended_simplex_type Simplex_tree.h gudhi/Simplex_tree.h
  * \brief Extended simplex type data structure for representing the type of simplices in an extended filtration.
@@ -97,8 +101,7 @@ class Simplex_tree {
   // Simplex_key next to each other).
   typedef typename boost::container::flat_map<Vertex_handle, Node> Dictionary;
 
-  /* \brief Set of nodes sharing a same parent in the simplex tree. */
-  /* \brief Set of nodes sharing a same parent in the simplex tree. */
+  /** \brief Set of nodes sharing a same parent in the simplex tree. */
   typedef Simplex_tree_siblings<Simplex_tree, Dictionary> Siblings;
 
 
@@ -965,7 +968,7 @@ class Simplex_tree {
         // If we reached the end of the vertices, and the simplex has more vertices than the given simplex
         // => we found a coface
 
-        // Add a coface if we wan't the star or if the number of vertices of the current simplex matches with nbVertices
+        // Add a coface if we want the star or if the number of vertices of the current simplex matches with nbVertices
         bool addCoface = (star || curr_nbVertices == nbVertices);
         if (addCoface)
           cofaces.push_back(simplex);
@@ -1338,7 +1341,7 @@ class Simplex_tree {
     }
   }
 
-  /* \private Returns the Simplex_handle composed of the vertex list (from the Simplex_handle), plus the given
+  /** \private Returns the Simplex_handle composed of the vertex list (from the Simplex_handle), plus the given
    * Vertex_handle if the Vertex_handle is found in the Simplex_handle children list.
    * Returns null_simplex() if it does not exist
   */
@@ -1491,7 +1494,7 @@ class Simplex_tree {
 
       int sh_dimension = dimension(sh);
       if (sh_dimension >= dimension_)
-        // Stop browsing as soon as the dimension is reached, no need to go furter
+        // Stop browsing as soon as the dimension is reached, no need to go further
         return false;
       new_dimension = (std::max)(new_dimension, sh_dimension);
     }
@@ -1801,7 +1804,7 @@ struct Simplex_tree_options_fast_persistence {
   static const bool contiguous_vertices = true;
 };
 
-/** @} */  // end defgroup simplex_tree
+/** @}*/  // end addtogroup simplex_tree
 
 }  // namespace Gudhi
 
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
index 394c6ee1..b63a5595 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
@@ -22,12 +22,12 @@
 
 namespace Gudhi {
 
-/* \addtogroup simplex_tree
+/** \addtogroup simplex_tree 
  * Iterators and range types for the Simplex_tree.
- * @{
+ *  @{
  */
 
-/* \brief Iterator over the vertices of a simplex
+/** \brief Iterator over the vertices of a simplex
  * in a SimplexTree.
  *
  * Forward iterator, 'value_type' is SimplexTree::Vertex_handle.*/
@@ -73,7 +73,7 @@ class Simplex_tree_simplex_vertex_iterator : public boost::iterator_facade<
 };
 
 /*---------------------------------------------------------------------------*/
-/* \brief Iterator over the simplices of the boundary of a
+/** \brief Iterator over the simplices of the boundary of a
  *  simplex.
  *
  * Forward iterator, value_type is SimplexTree::Simplex_handle.*/
@@ -181,7 +181,7 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
   SimplexTree * st_;  // simplex containing the simplicial complex
 };
 
-/* \brief Iterator over the simplices of the boundary of a simplex and their opposite vertices.
+/** \brief Iterator over the simplices of the boundary of a simplex and their opposite vertices.
  *
  * Forward iterator, value_type is std::pair<SimplexTree::Simplex_handle, SimplexTree::Vertex_handle>.*/
 template<class SimplexTree>
@@ -291,7 +291,7 @@ class Simplex_tree_boundary_opposite_vertex_simplex_iterator : public boost::ite
 };
 
 /*---------------------------------------------------------------------------*/
-/* \brief Iterator over the simplices of a simplicial complex.
+/** \brief Iterator over the simplices of a simplicial complex.
  *
  * Forward iterator, value_type is SimplexTree::Simplex_handle.*/
 template<class SimplexTree>
@@ -364,7 +364,7 @@ class Simplex_tree_complex_simplex_iterator : public boost::iterator_facade<
   SimplexTree * st_;
 };
 
-/* \brief Iterator over the simplices of the skeleton of a given
+/** \brief Iterator over the simplices of the skeleton of a given
  * dimension of the simplicial complex.
  *
  * Forward iterator, value_type is SimplexTree::Simplex_handle.*/
@@ -447,7 +447,8 @@ class Simplex_tree_skeleton_simplex_iterator : public boost::iterator_facade<
   int curr_dim_;
 };
 
-/* @} */  // end addtogroup simplex_tree
+/** @}*/  // end addtogroup simplex_tree
+
 }  // namespace Gudhi
 
 #endif  // SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h
index ae140859..63023daa 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h
@@ -15,16 +15,15 @@
 
 namespace Gudhi {
 
-/* \addtogroup simplex_tree
+/** \addtogroup simplex_tree
  * Represents a node of a Simplex_tree.
  * @{
  */
 
-/*
- * \brief Node of a simplex tree with filtration value
+/** \brief Node of a simplex tree with filtration value
  * and simplex key.
  *
- * It stores explicitely its own filtration value and its own Simplex_key.
+ * It stores explicitly its own filtration value and its own Simplex_key.
  */
 template<class SimplexTree>
 struct Simplex_tree_node_explicit_storage : SimplexTree::Filtration_simplex_base, SimplexTree::Key_simplex_base {
@@ -54,7 +53,8 @@ struct Simplex_tree_node_explicit_storage : SimplexTree::Filtration_simplex_base
   Siblings * children_;
 };
 
-/* @} */  // end addtogroup simplex_tree
+/** @}*/  // end addtogroup simplex_tree
+
 }  // namespace Gudhi
 
 #endif  // SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
index ae25d290..d849eeba 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
@@ -20,12 +20,12 @@
 
 namespace Gudhi {
 
-/* \addtogroup simplex_tree
+/** \addtogroup simplex_tree
  * Represents a set of node of a Simplex_tree that share the same parent.
  * @{
  */
 
-/* \brief Data structure to store a set of nodes in a SimplexTree sharing
+/** \brief Data structure to store a set of nodes in a SimplexTree sharing
  * the same parent node.*/
 template<class SimplexTree, class MapContainer>
 class Simplex_tree_siblings {
@@ -58,7 +58,7 @@ class Simplex_tree_siblings {
         members_() {
   }
 
-  /* \brief Constructor with initialized set of members.
+  /** \brief Constructor with initialized set of members.
    *
    * 'members' must be sorted and unique.*/
   template<typename RandomAccessVertexRange>
@@ -72,8 +72,7 @@ class Simplex_tree_siblings {
     }
   }
 
-  /*
-   * \brief Inserts a Node in the set of siblings nodes.
+  /** \brief Inserts a Node in the set of siblings nodes.
    *
    * If already present, assigns the minimal filtration value 
    * between input filtration_value and the value already 
@@ -114,7 +113,8 @@ class Simplex_tree_siblings {
   Dictionary members_;
 };
 
-/* @} */  // end addtogroup simplex_tree
+/** @}*/  // end addtogroup simplex_tree
+
 }  // namespace Gudhi
 
 #endif  // SIMPLEX_TREE_SIMPLEX_TREE_SIBLINGS_H_
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h
index 3e395ae2..29c76e50 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h
@@ -20,7 +20,7 @@ namespace Gudhi {
 struct linear_indexing_tag {
 };
 
-/* \brief Tag for a zigzag ordering of simplices. */
+/** \brief Tag for a zigzag ordering of simplices. */
 //  struct zigzag_indexing_tag {};
 }  // namespace Gudhi