cpplint fixes

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2232 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ac02d5dd3b2aedd4795f775c228fe5ef7e1b3320

12 files changed, 30 insertions, 32 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 6e9be97b..fd9f0858 100644
--- a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
+++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
@@ -56,7 +56,7 @@ void program_options(int argc, char * argv[]
                      , int & p
                      , Filtration_value & min_persistence);
 
-static inline std::pair<double, double> compute_root_square (std::pair<double, double> input) {
+static inline std::pair<double, double> compute_root_square(std::pair<double, double> input) {
   return std::make_pair(std::sqrt(input.first), std::sqrt(input.second));
 }
 
diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h
index 076f1be0..e7dafaa0 100644
--- a/src/Contraction/example/Garland_heckbert/Error_quadric.h
+++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h
@@ -21,8 +21,8 @@
  * 
  */
 
-#ifndef ERROR_QUADRIC_H_
-#define ERROR_QUADRIC_H_
+#ifndef GARLAND_HECKBERT_ERROR_QUADRIC_H_
+#define GARLAND_HECKBERT_ERROR_QUADRIC_H_
 
 #include <boost/optional/optional.hpp>
 
@@ -179,4 +179,4 @@ template <typename Point> class Error_quadric {
   }
 };
 
-#endif  // ERROR_QUADRIC_H_
+#endif  // GARLAND_HECKBERT_ERROR_QUADRIC_H_
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h
index ceefd2ba..7865e4ec 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef EXAMPLE_PERSISTENT_COHOMOLOGY_ALPHA_COMPLEX_3D_HELPER_H_
-#define EXAMPLE_PERSISTENT_COHOMOLOGY_ALPHA_COMPLEX_3D_HELPER_H_
+#ifndef ALPHA_COMPLEX_3D_HELPER_H_
+#define ALPHA_COMPLEX_3D_HELPER_H_
 
 template<class Vertex_list, class Cell_handle>
 Vertex_list from_cell(const Cell_handle& ch) {
@@ -73,4 +73,4 @@ Vertex_list from_vertex(const Vertex_handle& vh) {
   return the_list;
 }
 
-#endif  // EXAMPLE_PERSISTENT_COHOMOLOGY_ALPHA_COMPLEX_3D_HELPER_H_
+#endif  // ALPHA_COMPLEX_3D_HELPER_H_
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index ffb98283..40f4aff9 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -20,6 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#include "alpha_complex_3d_helper.h"
+
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/Points_3D_off_io.h>
@@ -30,8 +32,6 @@
 #include <CGAL/Alpha_shape_3.h>
 #include <CGAL/iterator.h>
 
-#include "alpha_complex_3d_helper.h"
-
 #include <fstream>
 #include <cmath>
 #include <string>
diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
index c016a596..70054601 100644
--- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
@@ -20,6 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#include "alpha_complex_3d_helper.h"
+
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/Points_3D_off_io.h>
@@ -30,8 +32,6 @@
 #include <CGAL/Alpha_shape_3.h>
 #include <CGAL/iterator.h>
 
-#include "alpha_complex_3d_helper.h"
-
 #include <fstream>
 #include <cmath>
 #include <string>
diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
index 4f6ea40e..28f563aa 100644
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -20,6 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#include "alpha_complex_3d_helper.h"
+
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/Points_3D_off_io.h>
@@ -31,8 +33,6 @@
 #include <CGAL/Alpha_shape_3.h>
 #include <CGAL/iterator.h>
 
-#include "alpha_complex_3d_helper.h"
-
 #include <fstream>
 #include <cmath>
 #include <string>
diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp
index ae82c817..50f692f2 100644
--- a/src/Persistent_cohomology/example/plain_homology.cpp
+++ b/src/Persistent_cohomology/example/plain_homology.cpp
@@ -27,13 +27,11 @@
 #include <vector>
 #include <cstdint>  // for std::uint8_t
 
-using namespace Gudhi;
-
 /* We could perfectly well use the default Simplex_tree<> (which uses
  * Simplex_tree_options_full_featured), the following simply demonstrates
  * how to save on storage by not storing a filtration value.  */
 
-struct MyOptions : Simplex_tree_options_full_featured {
+struct MyOptions : Gudhi::Simplex_tree_options_full_featured {
   // Implicitly use 0 as filtration value for all simplices
   static const bool store_filtration = false;
   // The persistence algorithm needs this
@@ -43,7 +41,10 @@ struct MyOptions : Simplex_tree_options_full_featured {
   // Maximum number of simplices to compute persistence is 2^8 - 1 = 255. One is reserved for null_key
   typedef std::uint8_t Simplex_key;
 };
-typedef Simplex_tree<MyOptions> ST;
+
+using ST = Gudhi::Simplex_tree<MyOptions>;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<ST, Field_Zp>;
 
 int main() {
   ST st;
@@ -70,7 +71,7 @@ int main() {
   st.initialize_filtration();
 
   // Class for homology computation
-  persistent_cohomology::Persistent_cohomology<ST, persistent_cohomology::Field_Zp> pcoh(st);
+  Persistent_cohomology pcoh(st);
 
   // Initialize the coefficient field Z/2Z for homology
   pcoh.init_coefficients(2);
diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
index 5203548a..0b137535 100644
--- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
@@ -20,6 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#include "alpha_complex_3d_helper.h"
+
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/Points_3D_off_io.h>
@@ -31,8 +33,6 @@
 #include <CGAL/Alpha_shape_3.h>
 #include <CGAL/iterator.h>
 
-#include "alpha_complex_3d_helper.h"
-
 #include <fstream>
 #include <cmath>
 #include <string>
@@ -49,7 +49,7 @@ using Gt = CGAL::Regular_triangulation_euclidean_traits_3<Kernel>;
 using Vb = CGAL::Alpha_shape_vertex_base_3<Gt>;
 using Fb = CGAL::Alpha_shape_cell_base_3<Gt>;
 using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>;
-using Triangulation_3 = CGAL::Regular_triangulation_3<Gt,Tds>;
+using Triangulation_3 = CGAL::Regular_triangulation_3<Gt, Tds>;
 using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>;
 
 // From file type definition
@@ -115,8 +115,7 @@ int main(int argc, char * const argv[]) {
     double weight = 0.0;
     std::size_t index = 0;
     // Attempt read the weight in a double format, return false if it fails
-    while((weights_ifstr >> weight) && (index < lp.size()))
-    {
+    while ((weights_ifstr >> weight) && (index < lp.size())) {
       wp.push_back(Weighted_point_3(lp[index], weight));
       index++;
     }
diff --git a/src/Simplex_tree/example/mini_simplex_tree.cpp b/src/Simplex_tree/example/mini_simplex_tree.cpp
index 7e48aaaf..ad99df23 100644
--- a/src/Simplex_tree/example/mini_simplex_tree.cpp
+++ b/src/Simplex_tree/example/mini_simplex_tree.cpp
@@ -24,19 +24,18 @@
 #include <iostream>
 #include <initializer_list>
 
-using namespace Gudhi;
-
-struct MyOptions : Simplex_tree_options_full_featured {
+struct MyOptions : Gudhi::Simplex_tree_options_full_featured {
   // Not doing persistence, so we don't need those
   static const bool store_key = false;
   static const bool store_filtration = false;
   // I have few vertices
   typedef short Vertex_handle;
 };
-typedef Simplex_tree<MyOptions> ST;
+
+using ST = Gudhi::Simplex_tree<MyOptions>;
 
 // Dictionary should be private, but for now this is the easiest way.
-static_assert(sizeof(ST::Dictionary::value_type) < sizeof(Simplex_tree<>::Dictionary::value_type),
+static_assert(sizeof(ST::Dictionary::value_type) < sizeof(Gudhi::Simplex_tree<>::Dictionary::value_type),
     "Not storing the filtration and key should save some space");
 
 int main() {
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index e2791f76..63f03687 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -178,7 +178,7 @@ class Witness_complex {
           norelax_dist2 = l_it->second;
       }
     } else if (dim == 0) {
-      for (;l_it != end && l_it->second - alpha2 <= norelax_dist2; ++l_it) {
+      for (; l_it != end && l_it->second - alpha2 <= norelax_dist2; ++l_it) {
         simplex.push_back(l_it->first);
         double filtration_value = 0;
         // if norelax_dist is infinite, relaxation is 0.
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index 7bf97c23..22747637 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -24,8 +24,8 @@
 #define DISTANCE_FUNCTIONS_H_
 
 #include <cmath>  // for std::sqrt
-#include <type_traits> // for std::decay
-#include <iterator> // for std::begin, std::end
+#include <type_traits>  // for std::decay
+#include <iterator>  // for std::begin, std::end
 
 /** @file
  * @brief Global distance functions
diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h
index 25c458d2..55028fd0 100644
--- a/src/cython/include/Persistent_cohomology_interface.h
+++ b/src/cython/include/Persistent_cohomology_interface.h
@@ -88,7 +88,6 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
  private:
   // A copy
   FilteredComplex* stptr_;
-
 };
 
 }  // namespace Gudhi