Fix cpplint on cython interfaces

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2229 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 41a958b1be51ac938b45b384cde7940a85e9dea0

14 files changed, 68 insertions, 81 deletions

diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
index 5223678d..3998fe8d 100644
--- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
+++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
@@ -35,9 +35,9 @@ namespace persistence_diagram {
  * 
  * \section bottleneckdefinition Definition
  * 
- * The bottleneck distance measures the similarity between two persistence diagrams. It is the shortest distance b for which there exists a perfect matching between
- * the points of the two diagrams (completed with all the points on the diagonal in order to ignore cardinality mismatchs) such that
- * any couple of matched points are at distance at most b.
+ * The bottleneck distance measures the similarity between two persistence diagrams. It is the shortest distance b for
+ * which there exists a perfect matching between the points of the two diagrams (completed with all the points on the
+ * diagonal in order to ignore cardinality mismatchs) such that any couple of matched points are at distance at most b.
  *
  * \image html perturb_pd.png On this picture, the red edges represent the matching. The bottleneck distance is the length of the longest edge.
  *
diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h
index d74ff304..d47db71f 100644
--- a/src/cython/include/Alpha_complex_interface.h
+++ b/src/cython/include/Alpha_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef ALPHA_COMPLEX_INTERFACE_H
-#define	ALPHA_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_ALPHA_COMPLEX_INTERFACE_H_
+#define INCLUDE_ALPHA_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Alpha_complex.h>
@@ -79,4 +79,4 @@ class Alpha_complex_interface {
 
 }  // namespace Gudhi
 
-#endif  // ALPHA_COMPLEX_INTERFACE_H
+#endif  // INCLUDE_ALPHA_COMPLEX_INTERFACE_H_
diff --git a/src/cython/include/Bottleneck_distance_interface.h b/src/cython/include/Bottleneck_distance_interface.h
index 6819734b..d5fbf6ea 100644
--- a/src/cython/include/Bottleneck_distance_interface.h
+++ b/src/cython/include/Bottleneck_distance_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef BOTTLENECK_DISTANCE_INTERFACE_H
-#define	BOTTLENECK_DISTANCE_INTERFACE_H
+#ifndef INCLUDE_BOTTLENECK_DISTANCE_INTERFACE_H_
+#define INCLUDE_BOTTLENECK_DISTANCE_INTERFACE_H_
 
 #include <gudhi/Bottleneck.h>
 
@@ -45,9 +45,9 @@ namespace persistence_diagram {
     return bottleneck_distance(diag1, diag2);
   }
 
-}  // namespace alpha_complex
+}  // namespace persistence_diagram
 
 }  // namespace Gudhi
 
 
-#endif  // BOTTLENECK_DISTANCE_INTERFACE_H
+#endif  // INCLUDE_BOTTLENECK_DISTANCE_INTERFACE_H_
diff --git a/src/cython/include/Cubical_complex_interface.h b/src/cython/include/Cubical_complex_interface.h
index 4c53523b..7c0148f1 100644
--- a/src/cython/include/Cubical_complex_interface.h
+++ b/src/cython/include/Cubical_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef CUBICAL_COMPLEX_INTERFACE_H
-#define	CUBICAL_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_CUBICAL_COMPLEX_INTERFACE_H_
+#define INCLUDE_CUBICAL_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Bitmap_cubical_complex.h>
 #include <gudhi/Bitmap_cubical_complex_base.h>
@@ -38,7 +38,6 @@ namespace cubical_complex {
 template<typename CubicalComplexOptions = Bitmap_cubical_complex_base<double>>
 class Cubical_complex_interface : public Bitmap_cubical_complex<CubicalComplexOptions> {
  public:
-
   Cubical_complex_interface(const std::vector<unsigned>& dimensions,
                             const std::vector<double>& top_dimensional_cells)
   : Bitmap_cubical_complex<CubicalComplexOptions>(dimensions, top_dimensional_cells) {
@@ -47,12 +46,11 @@ class Cubical_complex_interface : public Bitmap_cubical_complex<CubicalComplexOp
   Cubical_complex_interface(const std::string& perseus_file)
   : Bitmap_cubical_complex<CubicalComplexOptions>(perseus_file.c_str()) {
   }
-
 };
 
 }  // namespace cubical_complex
 
 }  // namespace Gudhi
 
-#endif  // CUBICAL_COMPLEX_INTERFACE_H
+#endif  // INCLUDE_CUBICAL_COMPLEX_INTERFACE_H_
 
diff --git a/src/cython/include/Euclidean_strong_witness_complex_interface.h b/src/cython/include/Euclidean_strong_witness_complex_interface.h
index 67d85e18..b9dd8177 100644
--- a/src/cython/include/Euclidean_strong_witness_complex_interface.h
+++ b/src/cython/include/Euclidean_strong_witness_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H
-#define	EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H_
+#define INCLUDE_EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Euclidean_strong_witness_complex.h>
@@ -50,7 +50,7 @@ class Euclidean_strong_witness_complex_interface {
   Euclidean_strong_witness_complex_interface(const std::vector<std::vector<double>>& landmarks,
                                              const std::vector<std::vector<double>>& witnesses) {
     landmarks_.reserve(landmarks.size());
-    for(auto& landmark : landmarks)
+    for (auto& landmark : landmarks)
       landmarks_.emplace_back(landmark.begin(), landmark.end());
     witness_complex_ = new Euclidean_strong_witness_complex<Dynamic_kernel>(landmarks_, witnesses);
   }
@@ -87,7 +87,7 @@ class Euclidean_strong_witness_complex_interface {
 
 }  // namespace witness_complex
 
-} // namespace Gudhi
+}  // namespace Gudhi
 
-#endif  // EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H
+#endif  // INCLUDE_EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H_
 
diff --git a/src/cython/include/Euclidean_witness_complex_interface.h b/src/cython/include/Euclidean_witness_complex_interface.h
index a2db6a2d..2a09b3b5 100644
--- a/src/cython/include/Euclidean_witness_complex_interface.h
+++ b/src/cython/include/Euclidean_witness_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H
-#define	EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H_
+#define INCLUDE_EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Euclidean_witness_complex.h>
@@ -50,7 +50,7 @@ class Euclidean_witness_complex_interface {
   Euclidean_witness_complex_interface(const std::vector<std::vector<double>>& landmarks,
                                       const std::vector<std::vector<double>>& witnesses) {
     landmarks_.reserve(landmarks.size());
-    for(auto& landmark : landmarks)
+    for (auto& landmark : landmarks)
       landmarks_.emplace_back(landmark.begin(), landmark.end());
     witness_complex_ = new Euclidean_witness_complex<Dynamic_kernel>(landmarks_, witnesses);
   }
@@ -86,7 +86,7 @@ class Euclidean_witness_complex_interface {
 
 }  // namespace witness_complex
 
-} // namespace Gudhi
+}  // namespace Gudhi
 
-#endif  // EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H
+#endif  // INCLUDE_EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H_
 
diff --git a/src/cython/include/Off_reader_interface.h b/src/cython/include/Off_reader_interface.h
index 97d64d3e..0ca55500 100644
--- a/src/cython/include/Off_reader_interface.h
+++ b/src/cython/include/Off_reader_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef OFF_READER_INTERFACE_H
-#define	OFF_READER_INTERFACE_H
+#ifndef INCLUDE_OFF_READER_INTERFACE_H_
+#define INCLUDE_OFF_READER_INTERFACE_H_
 
 #include <gudhi/Points_off_io.h>
 
@@ -38,5 +38,5 @@ std::vector<std::vector<double>> read_points_from_OFF_file(const std::string& of
 
 }  // namespace Gudhi
 
-#endif  // OFF_READER_INTERFACE_H
+#endif  // INCLUDE_OFF_READER_INTERFACE_H_
 
diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h
index 1ff0e09b..25c458d2 100644
--- a/src/cython/include/Persistent_cohomology_interface.h
+++ b/src/cython/include/Persistent_cohomology_interface.h
@@ -20,13 +20,14 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef PERSISTENT_COHOMOLOGY_INTERFACE_H
-#define	PERSISTENT_COHOMOLOGY_INTERFACE_H
+#ifndef INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_
+#define INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_
 
 #include <gudhi/Persistent_cohomology.h>
 
 #include <vector>
 #include <utility>  // for std::pair
+#include <algorithm>  // for sort
 
 namespace Gudhi {
 
@@ -34,12 +35,10 @@ template<class FilteredComplex>
 class Persistent_cohomology_interface : public
 persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp> {
  private:
-
   /*
    * Compare two intervals by dimension, then by length.
    */
   struct cmp_intervals_by_dim_then_length {
-
     explicit cmp_intervals_by_dim_then_length(FilteredComplex * sc)
         : sc_(sc) { }
 
@@ -55,23 +54,26 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
   };
 
  public:
-
   Persistent_cohomology_interface(FilteredComplex* stptr)
       : persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>(*stptr),
       stptr_(stptr) { }
 
   Persistent_cohomology_interface(FilteredComplex* stptr, bool persistence_dim_max)
-      : persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>(*stptr,
-                                                                                                       persistence_dim_max),
-      stptr_(stptr) { }
+      : persistent_cohomology::Persistent_cohomology<FilteredComplex,
+          persistent_cohomology::Field_Zp>(*stptr, persistence_dim_max),
+        stptr_(stptr) { }
 
-  std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field, double min_persistence) {
-    persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>::init_coefficients(homology_coeff_field);
-    persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>::compute_persistent_cohomology(min_persistence);
+  std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field,
+                                                                         double min_persistence) {
+    persistent_cohomology::Persistent_cohomology<FilteredComplex,
+      persistent_cohomology::Field_Zp>::init_coefficients(homology_coeff_field);
+    persistent_cohomology::Persistent_cohomology<FilteredComplex,
+      persistent_cohomology::Field_Zp>::compute_persistent_cohomology(min_persistence);
 
     // Custom sort and output persistence
     cmp_intervals_by_dim_then_length cmp(stptr_);
-    auto persistent_pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>::get_persistent_pairs();
+    auto persistent_pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex,
+      persistent_cohomology::Field_Zp>::get_persistent_pairs();
     std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);
 
     std::vector<std::pair<int, std::pair<double, double>>> persistence;
@@ -81,7 +83,6 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
                                                           stptr_->filtration(get<1>(pair)))));
     }
     return persistence;
-
   }
 
  private:
@@ -90,7 +91,6 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
 
 };
 
-} // namespace Gudhi
-
-#endif  // PERSISTENT_COHOMOLOGY_INTERFACE_H
+}  // namespace Gudhi
 
+#endif  // INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_
diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
index 01df5366..1879bd74 100644
--- a/src/cython/include/Rips_complex_interface.h
+++ b/src/cython/include/Rips_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef RIPS_COMPLEX_INTERFACE_H
-#define	RIPS_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_RIPS_COMPLEX_INTERFACE_H_
+#define INCLUDE_RIPS_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Rips_complex.h>
@@ -53,7 +53,6 @@ class Rips_complex_interface {
     } else {
       // Rips construction where values is a distance matrix
       rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(values, threshold);
-
     }
   }
 
@@ -65,11 +64,10 @@ class Rips_complex_interface {
                                                                                    threshold, Euclidean_distance());
     } else {
       // Rips construction where values is a distance matrix
-      Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
+      Distance_matrix distances =
+          read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
       rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(distances, threshold);
-
     }
-
   }
 
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) {
@@ -85,4 +83,4 @@ class Rips_complex_interface {
 
 }  // namespace Gudhi
 
-#endif  // RIPS_COMPLEX_INTERFACE_H
+#endif  // INCLUDE_RIPS_COMPLEX_INTERFACE_H_
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
index c2783e22..4266b3ef 100644
--- a/src/cython/include/Simplex_tree_interface.h
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SIMPLEX_TREE_INTERFACE_H
-#define	SIMPLEX_TREE_INTERFACE_H
+#ifndef INCLUDE_SIMPLEX_TREE_INTERFACE_H_
+#define INCLUDE_SIMPLEX_TREE_INTERFACE_H_
 
 #include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/distance_functions.h>
@@ -48,7 +48,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   using Complex = std::vector<std::pair<Simplex, Filtration_value>>;
 
  public:
-
   bool find_simplex(const Simplex& vh) {
     return (Base::find(vh) != Base::null_simplex());
   }
@@ -98,7 +97,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
       filtered_tree.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
     }
     return filtered_tree;
-
   }
 
   Complex get_skeleton_tree(int dimension) {
@@ -144,10 +142,8 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   void create_persistence(Gudhi::Persistent_cohomology_interface<Base>* pcoh) {
     pcoh = new Gudhi::Persistent_cohomology_interface<Base>(*this);
   }
-
 };
 
-} // namespace Gudhi
-
-#endif  // SIMPLEX_TREE_INTERFACE_H
+}  // namespace Gudhi
 
+#endif  // INCLUDE_SIMPLEX_TREE_INTERFACE_H_
diff --git a/src/cython/include/Strong_witness_complex_interface.h b/src/cython/include/Strong_witness_complex_interface.h
index 83bf0f3c..d05eaac5 100644
--- a/src/cython/include/Strong_witness_complex_interface.h
+++ b/src/cython/include/Strong_witness_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef STRONG_WITNESS_COMPLEX_INTERFACE_H
-#define	STRONG_WITNESS_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_STRONG_WITNESS_COMPLEX_INTERFACE_H_
+#define INCLUDE_STRONG_WITNESS_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Strong_witness_complex.h>
@@ -64,12 +64,10 @@ class Strong_witness_complex_interface {
 
  private:
   Strong_witness_complex<Nearest_landmark_table>* witness_complex_;
-
 };
 
 }  // namespace witness_complex
 
-} // namespace Gudhi
-
-#endif  // STRONG_WITNESS_COMPLEX_INTERFACE_H
+}  // namespace Gudhi
 
+#endif  // INCLUDE_STRONG_WITNESS_COMPLEX_INTERFACE_H_
diff --git a/src/cython/include/Subsampling_interface.h b/src/cython/include/Subsampling_interface.h
index 5fc16767..1c6032c0 100644
--- a/src/cython/include/Subsampling_interface.h
+++ b/src/cython/include/Subsampling_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SUBSAMPLING_INTERFACE_H
-#define	SUBSAMPLING_INTERFACE_H
+#ifndef INCLUDE_SUBSAMPLING_INTERFACE_H_
+#define INCLUDE_SUBSAMPLING_INTERFACE_H_
 
 #include <gudhi/choose_n_farthest_points.h>
 #include <gudhi/pick_n_random_points.h>
@@ -112,10 +112,8 @@ std::vector<std::vector<double>> subsampling_sparsify_points_from_file(const std
   return subsampling_sparsify_points(points, min_squared_dist);
 }
 
-
 }  // namespace subsampling
 
 }  // namespace Gudhi
 
-#endif  // SUBSAMPLING_INTERFACE_H
-
+#endif  // INCLUDE_SUBSAMPLING_INTERFACE_H_
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index 2ca4c393..5e9dc0e4 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef TANGENTIAL_COMPLEX_INTERFACE_H
-#define	TANGENTIAL_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_TANGENTIAL_COMPLEX_INTERFACE_H_
+#define INCLUDE_TANGENTIAL_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Tangential_complex.h>
@@ -33,6 +33,7 @@
 #include <vector>
 #include <utility>  // std::pair
 #include <iostream>
+#include <string>
 
 namespace Gudhi {
 
@@ -49,7 +50,7 @@ class Tangential_complex_interface {
     unsigned intrisic_dim = 0;
     if (points.size() > 0)
       intrisic_dim = points[0].size() - 1;
-    
+
     tangential_complex_ = new TC(points, intrisic_dim, k);
     tangential_complex_->compute_tangential_complex();
     num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
@@ -117,7 +118,6 @@ class Tangential_complex_interface {
 
 }  // namespace tangential_complex
 
-} // namespace Gudhi
-
-#endif  // TANGENTIAL_COMPLEX_INTERFACE_H
+}  // namespace Gudhi
 
+#endif  // INCLUDE_TANGENTIAL_COMPLEX_INTERFACE_H_
diff --git a/src/cython/include/Witness_complex_interface.h b/src/cython/include/Witness_complex_interface.h
index 4f2a903b..6501cc35 100644
--- a/src/cython/include/Witness_complex_interface.h
+++ b/src/cython/include/Witness_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef WITNESS_COMPLEX_INTERFACE_H
-#define	WITNESS_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_WITNESS_COMPLEX_INTERFACE_H_
+#define INCLUDE_WITNESS_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Witness_complex.h>
@@ -64,12 +64,11 @@ class Witness_complex_interface {
 
  private:
   Witness_complex<Nearest_landmark_table>* witness_complex_;
-
 };
 
 }  // namespace witness_complex
 
-} // namespace Gudhi
+}  // namespace Gudhi
 
-#endif  // WITNESS_COMPLEX_INTERFACE_H
+#endif  // INCLUDE_WITNESS_COMPLEX_INTERFACE_H_