Fix naming conventions and cpplint

Add Bottleneck_distance to GUDHI_MODULES in GUDHI_user_version_target.txt


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1569 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b96a2be25477ddf227e43d9941989f93a0f626bb

12 files changed, 74 insertions, 43 deletions

diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h
index bd90cc11..4c69343c 100644
--- a/src/Bottleneck_distance/concept/Persistence_diagram.h
+++ b/src/Bottleneck_distance/concept/Persistence_diagram.h
@@ -1,6 +1,31 @@
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       François Godi
+ *
+ *    Copyright (C) 2016  INRIA
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef CONCEPT_BOTTLENECK_DISTANCE_PERSISTENCE_DIAGRAM_H_
+#define CONCEPT_BOTTLENECK_DISTANCE_PERSISTENCE_DIAGRAM_H_
+
 namespace Gudhi {
-namespace Bottleneck_distance {
-namespace Concept {
+
+namespace bottleneck_distance {
 
 /** \brief Concept of persistence diagram point. The double first is the birth of the component and the double second is the death of the component.
  *
@@ -21,6 +46,8 @@ struct Persistence_Diagram
     const_iterator<Diagram_point> cend() const;
 };
 
-} //namespace Concept
-} //namespace Bottleneck_distance
-} //namespace Gudhi
+}  // namespace bottleneck_distance
+
+}  // namespace Gudhi
+
+#endif  // CONCEPT_BOTTLENECK_DISTANCE_PERSISTENCE_DIAGRAM_H_
diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
index 2cf10975..9a792048 100644
--- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
+++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
@@ -26,15 +26,20 @@
 // needs namespace for Doxygen to link on classes
 namespace Gudhi {
 // needs namespace for Doxygen to link on classes
-namespace Bottleneck_distance {
+namespace bottleneck_distance {
 
 /**  \defgroup bottleneck_distance Bottleneck distance
  * 
  * \author    François Godi
+ * @{
  * 
+ * \section bottleneckdefinition Definition
+ * 
+ * Bottleneck distance is blablabla...
  */
+/** @} */  // end defgroup bottleneck_distance
 
-}  // namespace Bottleneck_distance
+}  // namespace bottleneck_distance
 
 }  // namespace Gudhi
 
diff --git a/src/Bottleneck_distance/example/bottleneck_example.cpp b/src/Bottleneck_distance/example/bottleneck_example.cpp
index 472c5c84..0bec9746 100644
--- a/src/Bottleneck_distance/example/bottleneck_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_example.cpp
@@ -28,12 +28,9 @@
 #include <sstream>
 #include <string>
 
-using namespace std;
-
-//PD: I am using this type of procedures a lot in Gudhi stat. We should make one for all at some point.
 std::vector< std::pair<double, double> > read_diagram_from_file( const char* filename )
 {
-    ifstream in;
+    std::ifstream in;
     in.open( filename );
     std::vector< std::pair<double, double> > result;
     if ( !in.is_open() )
@@ -58,13 +55,15 @@ std::vector< std::pair<double, double> > read_diagram_from_file( const char* fil
     }
     in.close();
     return result;
-}//read_diagram_from_file
+}  //read_diagram_from_file
 
 int main( int argc , char** argv )
 {
   if ( argc < 3 )
   {
-      std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck distance (set by default to zero). The program will now terminate \n";
+      std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
+          "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
+          " distance (set by default to zero). The program will now terminate \n";
   }
   std::vector< std::pair< double , double > > diag1 = read_diagram_from_file( argv[1] );
   std::vector< std::pair< double , double > > diag2 = read_diagram_from_file( argv[2] );
@@ -73,6 +72,6 @@ int main( int argc , char** argv )
   {
       tolerance = atof( argv[3] );
   }
-  double b = Gudhi::Bottleneck_distance::compute(diag1, diag2, tolerance);
+  double b = Gudhi::bottleneck_distance::compute(diag1, diag2, tolerance);
   std::cout << "The distance between the diagrams is : " << b << ". The tolerace is : " << tolerance << std::endl;
 }
diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h b/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h
index 21be0bc7..91632149 100644
--- a/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h
+++ b/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h
@@ -27,7 +27,7 @@
 
 namespace CGAL {
 
-typedef Gudhi::Bottleneck_distance::Internal_point Internal_point;
+typedef Gudhi::bottleneck_distance::Internal_point Internal_point;
 
 template <>
 struct Kernel_traits<Internal_point> {
diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h
index 7a8c8ee0..5f579a0c 100644
--- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h
+++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_
-#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_
+#ifndef GRAPH_MATCHING_H_
+#define GRAPH_MATCHING_H_
 
 #include <deque>
 
@@ -29,7 +29,7 @@
 
 namespace Gudhi {
 
-namespace Bottleneck_distance {
+namespace bottleneck_distance {
 
 /** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. You get an additive e-approximation.
  *
@@ -238,11 +238,11 @@ double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &di
 
 
 
-}  // namespace Bottleneck_distance
+}  // namespace bottleneck_distance
 
 }  // namespace Gudhi
 
-#endif  // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_
+#endif  // GRAPH_MATCHING_H_
 
 /* Dichotomic version
 template<typename Persistence_diagram1, typename Persistence_diagram2>
diff --git a/src/Bottleneck_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h
index 2080900d..f05d5fc9 100644
--- a/src/Bottleneck_distance/include/gudhi/Internal_point.h
+++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h
@@ -20,12 +20,12 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_
-#define SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_
+#ifndef INTERNAL_POINT_H_
+#define INTERNAL_POINT_H_
 
 namespace Gudhi {
 
-namespace Bottleneck_distance {
+namespace bottleneck_distance {
 
 /** \internal \brief Returns the used index for encoding none of the points */
 int null_point_index();
@@ -67,8 +67,8 @@ inline int null_point_index() {
     return -1;
 }
 
-}  // namespace Bottleneck_distance
+}  // namespace bottleneck_distance
 
 }  // namespace Gudhi
 
-#endif  // SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_
+#endif  // INTERNAL_POINT_H_
diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
index 7ad79126..1bd5879c 100644
--- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
+++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
@@ -20,15 +20,15 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_
-#define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_
+#ifndef NEIGHBORS_FINDER_H_
+#define NEIGHBORS_FINDER_H_
 
 #include <unordered_set>
 #include <gudhi/Planar_neighbors_finder.h>
 
 namespace Gudhi {
 
-namespace Bottleneck_distance {
+namespace bottleneck_distance {
 
 /** \internal \brief data structure used to find any point (including projections) in V near to a query point from U
  * (which can be a projection).
@@ -147,8 +147,8 @@ inline int Layered_neighbors_finder::vlayers_number() const {
     return static_cast<int>(neighbors_finder.size());
 }
 
-}  // namespace Bottleneck_distance
+}  // namespace bottleneck_distance
 
 }  // namespace Gudhi
 
-#endif  // SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_
+#endif  // NEIGHBORS_FINDER_H_
diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h
index e31b2dae..1f6d6683 100644
--- a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h
+++ b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_
-#define SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_
+#ifndef PERSISTENCE_DIAGRAMS_GRAPH_H_
+#define PERSISTENCE_DIAGRAMS_GRAPH_H_
 
 #include <vector>
 #include <set>
@@ -34,7 +34,7 @@
 
 namespace Gudhi {
 
-namespace Bottleneck_distance {
+namespace bottleneck_distance {
 
 
 /** \internal \brief Structure representing an euclidean bipartite graph containing
@@ -162,8 +162,8 @@ inline double G::diameter() {
     return max;
 }
 
-}  // namespace Bottleneck_distance
+}  // namespace bottleneck_distance
 
 }  // namespace Gudhi
 
-#endif  // SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_
+#endif  // PERSISTENCE_DIAGRAMS_GRAPH_H_
diff --git a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h
index 30f7dc3c..bf70ed0b 100644
--- a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h
+++ b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_
-#define SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_
+#ifndef PLANAR_NEIGHBORS_FINDER_H_
+#define PLANAR_NEIGHBORS_FINDER_H_
 
 #include <list>
 #include <map>
@@ -40,7 +40,7 @@
 
 namespace Gudhi {
 
-namespace Bottleneck_distance {
+namespace bottleneck_distance {
 
 /** \internal \brief Structure used to find any point in V near (according to the planar distance) to a query point from U.
  *
@@ -217,8 +217,8 @@ inline std::shared_ptr< std::list<int> > Cgal_pnf::pull_all_near(int u_point_ind
 }
 
 
-}  // namespace Bottleneck_distance
+}  // namespace bottleneck_distance
 
 }  // namespace Gudhi
 
-#endif  // SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_
+#endif  // PLANAR_NEIGHBORS_FINDER_H_
diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp
index 8b49b6be..8b143b18 100644
--- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp
+++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp
@@ -24,7 +24,7 @@
 #include <chrono>
 #include <fstream>
 
-using namespace Gudhi::Bottleneck_distance;
+using namespace Gudhi::bottleneck_distance;
 
 
 double upper_bound = 400.; // any real >0
diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp
index d5b71156..d2331c5d 100644
--- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp
+++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp
@@ -27,7 +27,7 @@
 #include <random>
 #include <gudhi/Graph_matching.h>
 
-using namespace Gudhi::Bottleneck_distance;
+using namespace Gudhi::bottleneck_distance;
 
 int n1 = 81; // a natural number >0
 int n2 = 180; // a natural number >0
diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt
index 805f0a83..de16ef4c 100644
--- a/src/cmake/modules/GUDHI_user_version_target.txt
+++ b/src/cmake/modules/GUDHI_user_version_target.txt
@@ -48,7 +48,7 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
   
-  set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Contraction;Hasse_complex;Persistent_cohomology;Simplex_tree;Skeleton_blocker;Witness_complex")
+  set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Hasse_complex;Persistent_cohomology;Simplex_tree;Skeleton_blocker;Witness_complex")
   
   foreach(GUDHI_MODULE ${GUDHI_MODULES})
     # doc files