Move Euclidean_distance in Gudhi namespace

Fix cpplints


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2331 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: bc5609c2df490db50e82b56a5e6d899dc6370182

15 files changed, 28 insertions, 20 deletions

diff --git a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
index fd9f0858..fd164b22 100644
--- a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
+++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
@@ -74,7 +74,7 @@ int main(int argc, char * argv[]) {
   // --------------------------------------------
   // Rips persistence
   // --------------------------------------------
-  Rips_complex rips_complex(off_reader.get_point_cloud(), threshold, Euclidean_distance());
+  Rips_complex rips_complex(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
 
   // Construct the Rips complex in a Simplex Tree
   Simplex_tree rips_stree;
diff --git a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
index ba752999..252e8aef 100644
--- a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
+++ b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
@@ -83,7 +83,7 @@ int main(int argc, char * argv[]) {
 
   // Compute the proximity graph of the points
   start = std::chrono::system_clock::now();
-  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
   end = std::chrono::system_clock::now();
   elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
   std::cout << "Compute Rips graph in " << elapsed_sec << " ms.\n";
diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index 7674b5a5..dae36ed2 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -62,7 +62,7 @@ int main(int argc, char * argv[]) {
   program_options(argc, argv, off_file_points, filediag, threshold, dim_max, min_p, max_p, min_persistence);
 
   Points_off_reader off_reader(off_file_points);
-  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
 
   // Construct the Rips complex in a Simplex Tree
   Simplex_tree simplex_tree;
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index c6378de7..d504798b 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -60,7 +60,7 @@ int main(int argc, char * argv[]) {
   program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
 
   Points_off_reader off_reader(off_file_points);
-  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
 
   // Construct the Rips complex in a Simplex Tree
   Simplex_tree simplex_tree;
diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
index b159c62e..554eeba6 100644
--- a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
@@ -82,7 +82,7 @@ int main(int argc, char * argv[]) {
 
   // Compute the proximity graph of the points
   Graph_t prox_graph = compute_proximity_graph(off_reader.get_point_cloud(), threshold
-                                               , Euclidean_distance());
+                                               , Gudhi::Euclidean_distance());
 
   // Construct the Rips complex in a Simplex Tree
   Simplex_tree st;
diff --git a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
index 63da9847..9618f278 100644
--- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
@@ -70,7 +70,7 @@ int main(int argc, char * argv[]) {
   program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
 
   Points_off_reader off_reader(off_file_points);
-  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
 
   // Construct the Rips complex in a Simplex Tree
   Simplex_tree& st = *new Simplex_tree;
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
index 3fd69ebc..a1db8910 100644
--- a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
@@ -27,7 +27,7 @@ int main() {
   // Init of a Rips complex from points
   // ----------------------------------------------------------------------------
   double threshold = 12.0;
-  Rips_complex rips_complex_from_points(points, threshold, Euclidean_distance());
+  Rips_complex rips_complex_from_points(points, threshold, Gudhi::Euclidean_distance());
 
   Simplex_tree stree;
   rips_complex_from_points.create_complex(stree, 1);
diff --git a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
index a1e4e255..de2e4ea4 100644
--- a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
+++ b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
@@ -32,7 +32,7 @@ int main(int argc, char **argv) {
   // Init of a Rips complex from an OFF file
   // ----------------------------------------------------------------------------
   Gudhi::Points_off_reader<Point> off_reader(off_file_name);
-  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
 
   std::streambuf* streambufffer;
   std::ofstream ouput_file_stream;
diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp
index ae68ba0d..fc2179f2 100644
--- a/src/Rips_complex/test/test_rips_complex.cpp
+++ b/src/Rips_complex/test/test_rips_complex.cpp
@@ -60,7 +60,7 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
       rips_threshold << "==========" << std::endl;
 
   Gudhi::Points_off_reader<Point> off_reader(off_file_name);
-  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold, Euclidean_distance());
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold, Gudhi::Euclidean_distance());
 
   const int DIMENSION_1 = 1;
   Simplex_tree st;
@@ -89,10 +89,10 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
         std::cout << vertex << ",";
         vp.push_back(off_reader.get_point_cloud().at(vertex));
       }
-      std::cout << ") - distance =" << Euclidean_distance()(vp.at(0), vp.at(1)) <<
+      std::cout << ") - distance =" << Gudhi::Euclidean_distance()(vp.at(0), vp.at(1)) <<
           " - filtration =" << st.filtration(f_simplex) << std::endl;
       BOOST_CHECK(vp.size() == 2);
-      BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), Euclidean_distance()(vp.at(0), vp.at(1))));
+      BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), Gudhi::Euclidean_distance()(vp.at(0), vp.at(1))));
     }
   }
 
@@ -341,7 +341,7 @@ BOOST_AUTO_TEST_CASE(Rips_create_complex_throw) {
       rips_threshold << "==========" << std::endl;
 
   Gudhi::Points_off_reader<Point> off_reader(off_file_name);
-  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold, Euclidean_distance());
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold, Gudhi::Euclidean_distance());
 
   Simplex_tree stree;
   std::vector<int> simplex = {0, 1, 2};
diff --git a/src/Subsampling/example/example_choose_n_farthest_points.cpp b/src/Subsampling/example/example_choose_n_farthest_points.cpp
index fc9ea7a6..ebf631fc 100644
--- a/src/Subsampling/example/example_choose_n_farthest_points.cpp
+++ b/src/Subsampling/example/example_choose_n_farthest_points.cpp
@@ -19,7 +19,9 @@ int main(void) {
 
   K k;
   std::vector<Point_d> results;
-  Gudhi::subsampling::choose_n_farthest_points(k, points, 100, Gudhi::subsampling::random_starting_point, std::back_inserter(results));
+  Gudhi::subsampling::choose_n_farthest_points(k, points, 100,
+                                               Gudhi::subsampling::random_starting_point,
+                                               std::back_inserter(results));
   std::cout << "Before sparsification: " << points.size() << " points.\n";
   std::cout << "After  sparsification: " << results.size() << " points.\n";
 
diff --git a/src/Subsampling/example/example_custom_kernel.cpp b/src/Subsampling/example/example_custom_kernel.cpp
index 2719ee90..2d42bdde 100644
--- a/src/Subsampling/example/example_custom_kernel.cpp
+++ b/src/Subsampling/example/example_custom_kernel.cpp
@@ -54,7 +54,9 @@ int main(void) {
   std::vector<Point_d> points = {0, 1, 2, 3};
   std::vector<Point_d> results;
 
-  Gudhi::subsampling::choose_n_farthest_points(k, points, 2, Gudhi::subsampling::random_starting_point, std::back_inserter(results));
+  Gudhi::subsampling::choose_n_farthest_points(k, points, 2,
+                                               Gudhi::subsampling::random_starting_point,
+                                               std::back_inserter(results));
   std::cout << "Before sparsification: " << points.size() << " points.\n";
   std::cout << "After  sparsification: " << results.size() << " points.\n";
   std::cout << "Result table: {" << results[0] << "," << results[1] << "}\n";
diff --git a/src/Subsampling/include/gudhi/choose_n_farthest_points.h b/src/Subsampling/include/gudhi/choose_n_farthest_points.h
index 50d3cf80..86500b28 100644
--- a/src/Subsampling/include/gudhi/choose_n_farthest_points.h
+++ b/src/Subsampling/include/gudhi/choose_n_farthest_points.h
@@ -74,13 +74,13 @@ enum : std::size_t {
 template < typename Kernel,
 typename Point_range,
 typename PointOutputIterator,
-typename DistanceOutputIterator=Null_output_iterator>
+typename DistanceOutputIterator = Null_output_iterator>
 void choose_n_farthest_points(Kernel const &k,
                               Point_range const &input_pts,
                               std::size_t final_size,
                               std::size_t starting_point,
                               PointOutputIterator output_it,
-                              DistanceOutputIterator dist_it={}) {
+                              DistanceOutputIterator dist_it = {}) {
   std::size_t nb_points = boost::size(input_pts);
   if (final_size > nb_points)
     final_size = nb_points;
diff --git a/src/common/include/gudhi/Null_output_iterator.h b/src/common/include/gudhi/Null_output_iterator.h
index 0cf043cd..42e6e449 100644
--- a/src/common/include/gudhi/Null_output_iterator.h
+++ b/src/common/include/gudhi/Null_output_iterator.h
@@ -35,8 +35,8 @@ struct Null_output_iterator {
   typedef void                     pointer;
   typedef void                     reference;
 
-  Null_output_iterator& operator++(){return *this;}
-  Null_output_iterator operator++(int){return *this;}
+  Null_output_iterator& operator++() {return *this;}
+  Null_output_iterator operator++(int) {return *this;}
   struct proxy {
     template<class T>
     proxy& operator=(T&&){return *this;}
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index 22747637..f6e2ab5a 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -27,6 +27,8 @@
 #include <type_traits>  // for std::decay
 #include <iterator>  // for std::begin, std::end
 
+namespace Gudhi {
+
 /** @file
  * @brief Global distance functions
  */
@@ -48,4 +50,6 @@ class Euclidean_distance {
   }
 };
 
+}  // namespace Gudhi
+
 #endif  // DISTANCE_FUNCTIONS_H_
diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
index 1879bd74..fc9548fd 100644
--- a/src/cython/include/Rips_complex_interface.h
+++ b/src/cython/include/Rips_complex_interface.h
@@ -49,7 +49,7 @@ class Rips_complex_interface {
     if (euclidean) {
       // Rips construction where values is a vector of points
       rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(values, threshold,
-                                                                                   Euclidean_distance());
+                                                                                   Gudhi::Euclidean_distance());
     } else {
       // Rips construction where values is a distance matrix
       rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(values, threshold);
@@ -61,7 +61,7 @@ class Rips_complex_interface {
       // Rips construction where file_name is an OFF file
       Gudhi::Points_off_reader<Point_d> off_reader(file_name);
       rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(off_reader.get_point_cloud(),
-                                                                                   threshold, Euclidean_distance());
+                                                                                   threshold, Gudhi::Euclidean_distance());
     } else {
       // Rips construction where values is a distance matrix
       Distance_matrix distances =