Add persistent unit test - warning fix - cpplint fix

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cpplint_test@346 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9ef774de762c68a449b2a9791085f58c39a0705e

7 files changed, 58 insertions, 72 deletions

diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 6430c300..9b3de20a 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -20,20 +20,22 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef GUDHI_SIMPLEX_TREE_H
-#define GUDHI_SIMPLEX_TREE_H
+#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_H_
+#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_H_
+
+#include <gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h>
+#include <gudhi/Simplex_tree/Simplex_tree_siblings.h>
+#include <gudhi/Simplex_tree/Simplex_tree_iterators.h>
+#include <gudhi/Simplex_tree/indexing_tag.h>
 
-#include <algorithm>
-#include <utility>
-#include <vector>
-#include "gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h"
-#include "gudhi/Simplex_tree/Simplex_tree_siblings.h"
-#include "gudhi/Simplex_tree/Simplex_tree_iterators.h"
-#include "gudhi/Simplex_tree/indexing_tag.h"
 #include <boost/container/flat_map.hpp>
 #include <boost/iterator/transform_iterator.hpp>
 #include <boost/graph/adjacency_list.hpp>
 
+#include <algorithm>
+#include <utility>
+#include <vector>
+
 namespace Gudhi {
 
 /** \defgroup simplex_tree Filtered Complexes Package
@@ -107,18 +109,12 @@ class Simplex_tree {
   /* Type of dictionary Vertex_handle -> Node for traversing the simplex tree. */
   typedef typename boost::container::flat_map<Vertex_handle, Node> Dictionary;
 
-  friend class Simplex_tree_node_explicit_storage<
-      Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> > ;
-  friend class Simplex_tree_siblings<
-      Simplex_tree<FiltrationValue, SimplexKey, VertexHandle>, Dictionary> ;
-  friend class Simplex_tree_simplex_vertex_iterator<
-      Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> > ;
-  friend class Simplex_tree_boundary_simplex_iterator<
-      Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> > ;
-  friend class Simplex_tree_complex_simplex_iterator<
-      Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> > ;
-  friend class Simplex_tree_skeleton_simplex_iterator<
-      Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> > ;
+  friend class Simplex_tree_node_explicit_storage< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
+  friend class Simplex_tree_siblings< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle>, Dictionary>;
+  friend class Simplex_tree_simplex_vertex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
+  friend class Simplex_tree_boundary_simplex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
+  friend class Simplex_tree_complex_simplex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
+  friend class Simplex_tree_skeleton_simplex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
   template<class T1, class T2> friend class Persistent_cohomology;
 
   /* \brief Set of nodes sharing a same parent in the simplex tree. */
@@ -400,7 +396,7 @@ class Simplex_tree {
    * <CODE>Vertex_handle</CODE>.
    */
   template<class RandomAccessVertexRange>
-  Simplex_handle find(RandomAccessVertexRange & s) {
+  Simplex_handle find(const RandomAccessVertexRange & s) {
     if (s.begin() == s.end())
       std::cerr << "Empty simplex \n";
 
@@ -597,7 +593,7 @@ class Simplex_tree {
    * Reverse lexicographic order has the property to always consider the subsimplex of a simplex
    * to be smaller. The filtration function must be monotonic. */
   struct is_before_in_filtration {
-    is_before_in_filtration(Simplex_tree * st)
+    explicit is_before_in_filtration(Simplex_tree * st)
         : st_(st) {
     }
 
@@ -632,7 +628,7 @@ class Simplex_tree {
    * boost::graph_traits<OneSkeletonGraph>::directed_category
    *                                    must be undirected_tag. */
   template<class OneSkeletonGraph>
-  void insert_graph(OneSkeletonGraph & skel_graph) {
+  void insert_graph(const OneSkeletonGraph& skel_graph) {
     assert(num_simplices() == 0);  // the simplex tree must be empty
 
     if (boost::num_vertices(skel_graph) == 0) {
@@ -738,25 +734,22 @@ class Simplex_tree {
   }
   /** \brief Intersects Dictionary 1 [begin1;end1) with Dictionary 2 [begin2,end2)
    * and assigns the maximal possible Filtration_value to the Nodes. */
-  void intersection(std::vector<std::pair<Vertex_handle, Node> > & intersection,
+  void intersection(std::vector<std::pair<Vertex_handle, Node> >& intersection,
                     Dictionary_it begin1, Dictionary_it end1,
                     Dictionary_it begin2, Dictionary_it end2,
                     Filtration_value filtration) {
     if (begin1 == end1 || begin2 == end2)
-      return;  // 0;
+      return;  // ----->>
     while (true) {
       if (begin1->first == begin2->first) {
         intersection.push_back(
             std::pair<Vertex_handle, Node>(
                 begin1->first,
-                Node(
-                    NULL,
-                    maximum(begin1->second.filtration(),
-                            begin2->second.filtration(), filtration))));
+                Node(NULL, maximum(begin1->second.filtration(), begin2->second.filtration(), filtration))));
         ++begin1;
         ++begin2;
         if (begin1 == end1 || begin2 == end2)
-          return;
+          return;  // ----->>
       } else {
         if (begin1->first < begin2->first) {
           ++begin1;
@@ -765,7 +758,7 @@ class Simplex_tree {
         } else {
           ++begin2;
           if (begin2 == end2)
-            return;
+            return;  // ----->>
         }
       }
     }
@@ -784,7 +777,7 @@ class Simplex_tree {
    * dim idx_1 ... idx_k fil   where dim is the dimension of the simplex,
    * idx_1 ... idx_k are the row index (starting from 0) of the simplices of the boundary
    * of the simplex, and fil is its filtration value. */
-  void print_hasse(std::ostream & os) {
+  void print_hasse(std::ostream& os) {
     os << num_simplices() << " " << std::endl;
     for (auto sh : filtration_simplex_range(Indexing_tag())) {
       os << dimension(sh) << " ";
@@ -832,7 +825,7 @@ std::istream& operator>>(std::istream & is, Simplex_tree<T1, T2, T3> & st) {
   size_t num_simplices = 0;
   while (read_simplex(is, simplex, fil)) {  // read all simplices in the file as a list of vertices
     ++num_simplices;
-    int dim = (int) simplex.size() - 1;  // Warning : simplex_size needs to be casted in int - Can be 0
+    int dim = static_cast<int>(simplex.size() - 1);  // Warning : simplex_size needs to be casted in int - Can be 0
     if (max_dim < dim) {
       max_dim = dim;
     }
@@ -852,4 +845,4 @@ std::istream& operator>>(std::istream & is, Simplex_tree<T1, T2, T3> & st) {
 /** @} */  // end defgroup simplex_tree
 }  // namespace Gudhi
 
-#endif  // GUDHI_SIMPLEX_TREE_H
+#endif  // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_H_
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 54d4d296..06462c88 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
@@ -20,12 +20,13 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SIMPLEX_TREE_ITERATORS_H
-#define SIMPLEX_TREE_ITERATORS_H
+#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
+#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
 
-#include <vector>
 #include <boost/iterator/iterator_facade.hpp>
 
+#include <vector>
+
 namespace Gudhi {
 
 /* \addtogroup simplex_tree
@@ -47,7 +48,7 @@ class Simplex_tree_simplex_vertex_iterator : public boost::iterator_facade<
   typedef typename SimplexTree::Siblings Siblings;
   typedef typename SimplexTree::Vertex_handle Vertex_handle;
 
-  Simplex_tree_simplex_vertex_iterator(SimplexTree * st)
+  explicit Simplex_tree_simplex_vertex_iterator(SimplexTree * st)
       :  // any end() iterator
         sib_(NULL),
         v_(st->null_vertex()) {
@@ -93,7 +94,7 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
   typedef typename SimplexTree::Siblings Siblings;
 
 // any end() iterator
-  Simplex_tree_boundary_simplex_iterator(SimplexTree * st)
+  explicit Simplex_tree_boundary_simplex_iterator(SimplexTree * st)
       : last_(st->null_vertex()),
         sib_(NULL) {
   }
@@ -166,7 +167,7 @@ class Simplex_tree_complex_simplex_iterator : public boost::iterator_facade<
       : st_(NULL) {
   }
 
-  Simplex_tree_complex_simplex_iterator(SimplexTree * st)
+  explicit Simplex_tree_complex_simplex_iterator(SimplexTree * st)
       : st_(st) {
     if (st == NULL || st->root() == NULL || st->root()->members().empty()) {
       st_ = NULL;
@@ -302,4 +303,4 @@ class Simplex_tree_skeleton_simplex_iterator : public boost::iterator_facade<
 /* @} */  // end addtogroup simplex_tree
 }  // namespace Gudhi
 
-#endif  // SIMPLEX_TREE_ITERATORS_H
+#endif  // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_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 27120f00..1f1a34cc 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
@@ -20,11 +20,10 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef GUDHI_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H
-#define GUDHI_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H
+#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_
+#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_
 
 #include <vector>
-#include <iostream>
 
 namespace Gudhi {
 
@@ -42,14 +41,10 @@ namespace Gudhi {
 template<class SimplexTree>
 class Simplex_tree_node_explicit_storage {
  public:
-//  friend SimplexTree;
-
   typedef typename SimplexTree::Siblings Siblings;
   typedef typename SimplexTree::Filtration_value Filtration_value;
   typedef typename SimplexTree::Simplex_key Simplex_key;
 
-  //private:
-  //friend class Simplex_tree; 
   // Default constructor.
   Simplex_tree_node_explicit_storage()
       : children_(NULL),
@@ -69,13 +64,6 @@ class Simplex_tree_node_explicit_storage {
   }
 
   /*
-   * Return true if the node has children,
-   * false otherwise.
-   */
-  //bool has_children(Vertex label)
-  //{ //if(children_ == NULL)             return false; //for root simplices
-  //  return (children_->parent() == label);}
-  /*
    * Assign a children to the node
    */
   void assign_children(Siblings * children) {
@@ -92,7 +80,7 @@ class Simplex_tree_node_explicit_storage {
     return filtration_;
   }
 
-  /* Careful -> has_children() must be true*/
+  /* Careful -> children_ can be NULL*/
   Siblings * children() {
     return children_;
   }
@@ -106,11 +94,10 @@ class Simplex_tree_node_explicit_storage {
 
   // Data attached to simplex, explicit storage
   Simplex_key simplex_key_;
-  Filtration_value filtration_;   //value in the filtration
-
+  Filtration_value filtration_;   // value in the filtration
 };
 
 /* @} */  // end addtogroup simplex_tree
-}// namespace Gudhi
+}  // namespace Gudhi
 
-#endif // GUDHI_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H
+#endif  // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_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 680458a5..69ffa44b 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h
@@ -20,6 +20,9 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_INDEXING_TAG_H_
+#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_INDEXING_TAG_H_
+
 namespace Gudhi {
 
 /** \brief Tag for a linear ordering of simplices. 
@@ -31,4 +34,6 @@ struct linear_indexing_tag {
 
 /* \brief Tag for a zigzag ordering of simplices. */
 //  struct zigzag_indexing_tag {};
-}// namespace Gudhi
+}  // namespace Gudhi
+
+#endif  // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_INDEXING_TAG_H_
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index eeb066d4..d7f968af 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -12,22 +12,22 @@ if(NOT MSVC)
 endif()
 
 include_directories(${Boost_INCLUDE_DIRS})
-add_executable ( TestSimplexTree UnitTestSimplexTree.cpp )
-target_link_libraries(TestSimplexTree ${Boost_LIBRARIES})
+add_executable ( simplex_tree_unit_test simplex_tree_unit_test.cpp )
+target_link_libraries(simplex_tree_unit_test ${Boost_LIBRARIES})
 
 # Unitary tests
-add_test(TestSimplexTree ${CMAKE_CURRENT_BINARY_DIR}/TestSimplexTree)
+add_test(simplex_tree_unit_test ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_unit_test)
 
 if (LCOV_PATH)
   # Lcov code coverage of unitary test
-  add_test(TestSimplexTreeCov ${CMAKE_SOURCE_DIR}/scripts/check_code_coverage.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree)
+  add_test(simplex_tree_unit_test_coverage.info ${CMAKE_SOURCE_DIR}/scripts/check_code_coverage.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree)
 endif()
 
 if (PYTHON_PATH)
   # Cpplint tests on coding style
-  add_test(CpplintSimplexTree ${CMAKE_SOURCE_DIR}/scripts/check_google_style.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi/Simplex_tree.h)
-  add_test(CpplintSimplexTreeIndexingTag ${CMAKE_SOURCE_DIR}/scripts/check_google_style.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h)
-  add_test(CpplintSimplexTreeIterator ${CMAKE_SOURCE_DIR}/scripts/check_google_style.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h)
-  add_test(CpplintSimplexTreeNode ${CMAKE_SOURCE_DIR}/scripts/check_google_style.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h)
-  add_test(CpplintSimplexTreeSiblings ${CMAKE_SOURCE_DIR}/scripts/check_google_style.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h)
+  add_test(Simplex_tree.h.cpplint ${CMAKE_SOURCE_DIR}/scripts/check_google_style.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi/Simplex_tree.h)
+  add_test(indexing_tag.h.cpplint ${CMAKE_SOURCE_DIR}/scripts/check_google_style.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h)
+  add_test(Simplex_tree_iterators.h.cpplint ${CMAKE_SOURCE_DIR}/scripts/check_google_style.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h)
+  add_test(Simplex_tree_node_explicit_storage.h.cpplint ${CMAKE_SOURCE_DIR}/scripts/check_google_style.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h)
+  add_test(Simplex_tree_siblings.h.cpplint ${CMAKE_SOURCE_DIR}/scripts/check_google_style.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h)
 endif()
\ No newline at end of file
diff --git a/src/Simplex_tree/test/README b/src/Simplex_tree/test/README
index 3d6981ff..620bcd5f 100644
--- a/src/Simplex_tree/test/README
+++ b/src/Simplex_tree/test/README
@@ -7,6 +7,6 @@ make
 To launch with details:
 ***********************
 
-./TestSimplexTree --report_level=detailed --log_level=all 
+./simplex_tree_unit_test --report_level=detailed --log_level=all 
 
    ==> echo $? returns 0 in case of success (non-zero otherwise)
diff --git a/src/Simplex_tree/test/UnitTestSimplexTree.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index a3671f56..a3671f56 100644
--- a/src/Simplex_tree/test/UnitTestSimplexTree.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp