Fix cppcheck issues

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3601 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 44cc04b1609d3b3d40382fd02d4fe15e5ba0159f

11 files changed, 54 insertions, 50 deletions

diff --git a/src/Cech_complex/include/gudhi/Cech_complex.h b/src/Cech_complex/include/gudhi/Cech_complex.h
index f4fb4288..f9b8a269 100644
--- a/src/Cech_complex/include/gudhi/Cech_complex.h
+++ b/src/Cech_complex/include/gudhi/Cech_complex.h
@@ -30,6 +30,7 @@
 
 #include <iostream>
 #include <stdexcept>  // for exception management
+#include <vector>
 
 namespace Gudhi {
 
diff --git a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
index e0fc7107..4a2b9d68 100644
--- a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
+++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
@@ -57,7 +57,7 @@ std::vector<std::pair<double, double> > read_persistence_intervals_in_one_dimens
 
   std::string line;
   std::vector<std::pair<double, double> > barcode_initial =
-      read_persistence_intervals_in_dimension(filename, (int)dimension);
+      read_persistence_intervals_in_dimension(filename, static_cast<int>(dimension));
   std::vector<std::pair<double, double> > final_barcode;
   final_barcode.reserve(barcode_initial.size());
 
@@ -92,8 +92,8 @@ std::vector<std::pair<double, double> > read_persistence_intervals_in_one_dimens
 
     if ((barcode_initial[i].second == std::numeric_limits<double>::infinity()) &&
         (what_to_substitute_for_infinite_bar != -1)) {
-      if (barcode_initial[i].first < what_to_substitute_for_infinite_bar)  // if only birth < death.
-      {
+      if (barcode_initial[i].first < what_to_substitute_for_infinite_bar) {
+        // if only birth < death.
         final_barcode.push_back(
             std::pair<double, double>(barcode_initial[i].first, what_to_substitute_for_infinite_bar));
       }
diff --git a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h
index 19a44b28..4dcc08ed 100644
--- a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h
+++ b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h
@@ -54,7 +54,7 @@ namespace rips_complex {
 template <typename Filtration_value>
 class Sparse_rips_complex {
  private:
-  // TODO: use a different graph where we know we can safely insert in parallel.
+  // TODO(MG): use a different graph where we know we can safely insert in parallel.
   typedef typename boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
                                          boost::property<vertex_filtration_t, Filtration_value>,
                                          boost::property<edge_filtration_t, Filtration_value>>
@@ -140,7 +140,7 @@ class Sparse_rips_complex {
       put(vertex_filtration_t(), graph_, v, 0);
     }
 
-    // TODO:
+    // TODO(MG):
     // - make it parallel
     // - only test near-enough neighbors
     for (int i = 0; i < n; ++i)
diff --git a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
index d4671b45..c78677d2 100644
--- a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
@@ -31,6 +31,7 @@
 #include <string>
 #include <vector>
 #include <limits>  // infinity
+#include <algorithm>  // for sort
 
 // Types definition
 using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h
index 81566824..4b755daa 100644
--- a/src/Witness_complex/example/generators.h
+++ b/src/Witness_complex/example/generators.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
-#define EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
+#ifndef GENERATORS_H_
+#define GENERATORS_H_
 
 #include <CGAL/Epick_d.h>
 #include <CGAL/point_generators_d.h>
@@ -163,4 +163,4 @@ void generate_points_torus(Point_Vector& W, int nbP, int dim) {
   }
 }
 
-#endif  // EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
+#endif  // GENERATORS_H_
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
index 4661dbbe..56833d39 100644
--- a/src/common/doc/header.html
+++ b/src/common/doc/header.html
@@ -27,7 +27,7 @@ $extrastylesheet
     <nav class="top-bar" role="navigation" data-topbar>
         <ul class="title-area">
             <li class="name">
-                <h1 class="show-for-small-only"><a href="" class="icon-tree"> GUDHI C++ library</a></h1>
+                <h1 class="show-for-small-only"><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1/" class="icon-tree"> GUDHI C++ library</a></h1>
             </li>
             <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone -->
             <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li>
@@ -35,26 +35,26 @@ $extrastylesheet
         <section class="top-bar-section">
             <ul class="right">
                 <li class="divider"></li>
-                <li><a href="/contact/">Contact</a></li>
+                <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//contact/">Contact</a></li>
             </ul>
             <ul class="left">
-                <li><a href="/"> <img src="/assets/img/home.png" alt="&nbsp;&nbsp;GUDHI">&nbsp;&nbsp;GUDHI </a></li>
+                <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//"> <img src="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//assets/img/home.png" alt="&nbsp;&nbsp;GUDHI">&nbsp;&nbsp;GUDHI </a></li>
                 <li class="divider"></li>
                 <li class="has-dropdown">
                     <a href="#">Project</a>
                     <ul class="dropdown">
-                        <li><a href="/people/">People</a></li>
-                        <li><a href="/keepintouch/">Keep in touch</a></li>
-                        <li><a href="/partners/">Partners and Funding</a></li>
-                        <li><a href="/relatedprojects/">Related projects</a></li>
-                        <li><a href="/theyaretalkingaboutus/">They are talking about us</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//people/">People</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//keepintouch/">Keep in touch</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//partners/">Partners and Funding</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//relatedprojects/">Related projects</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//theyaretalkingaboutus/">They are talking about us</a></li>
                     </ul>
                 </li>
                 <li class="divider"></li>
                 <li class="has-dropdown">
                     <a href="#">Download</a>
                     <ul class="dropdown">
-                        <li><a href="/licensing/">Licensing</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//licensing/">Licensing</a></li>
                         <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li>
                         <li><a href="https://gforge.inria.fr/frs/download.php/file/37365/2018-02-01-16-59-31_GUDHI_2.1.0_OSX_UTILS.tar.gz" target="_blank">Utils for Mac OSx</a></li>
                         <li><a href="https://gforge.inria.fr/frs/download.php/file/37366/2018-01-31-09-25-53_GUDHI_2.1.0_WIN64_UTILS.zip" target="_blank">Utils for Win x64</a></li>
@@ -64,17 +64,17 @@ $extrastylesheet
                 <li class="has-dropdown">
                     <a href="#">Documentation</a>
                     <ul class="dropdown">
-                        <li><a href="/doc/latest/">C++ documentation</a></li>
-                        <li><a href="/doc/latest/installation.html">C++ installation manual</a></li>
-                        <li><a href="/python/latest/">Python documentation</a></li>
-                        <li><a href="/python/latest/installation.html">Python installation manual</a></li>
-                        <li><a href="/utils/">Utilities</a></li>
-                        <li><a href="/tutorials/">Tutorials</a></li>
-                        <li><a href="/dockerfile/">Dockerfile</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//doc/latest/">C++ documentation</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//doc/latest/installation.html">C++ installation manual</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//python/latest/">Python documentation</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//python/latest/installation.html">Python installation manual</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//utils/">Utilities</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//tutorials/">Tutorials</a></li>
+                        <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//dockerfile/">Dockerfile</a></li>
                     </ul>
                 </li>
                 <li class="divider"></li>
-                <li><a href="/interfaces/">Interfaces</a></li>
+                <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//interfaces/">Interfaces</a></li>
                 <li class="divider"></li>
             </ul>
         </section>
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index 024f0568..05a1e145 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.h
@@ -137,7 +137,7 @@ class Off_reader {
       if (!std::ifstream::sentry(stream_)) return false;
       std::getline(stream_, uncomment_line);
     } while (uncomment_line[0] == '#');
-    return (bool)stream_;
+    return static_cast<bool>(stream_);
   }
 
   template<typename OffVisitor>
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index 4dfba1bf..5ef12f2e 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -100,14 +100,14 @@ class Minimal_enclosing_ball_radius {
    */
   template< typename Point_cloud,
             typename Point_iterator = typename boost::range_const_iterator<Point_cloud>::type,
-            typename Point= typename std::iterator_traits<Point_iterator>::value_type,
+            typename Point = typename std::iterator_traits<Point_iterator>::value_type,
             typename Coordinate_iterator = typename boost::range_const_iterator<Point>::type,
             typename Coordinate = typename std::iterator_traits<Coordinate_iterator>::value_type>
   Coordinate
   operator()(const Point_cloud& point_cloud) const {
     using Min_sphere = Miniball::Miniball<Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>;
 
-    Min_sphere ms(boost::size(*point_cloud.begin()), point_cloud.begin(),point_cloud.end());
+    Min_sphere ms(boost::size(*point_cloud.begin()), point_cloud.begin(), point_cloud.end());
 #ifdef DEBUG_TRACES
     std::cout << "Minimal_enclosing_ball_radius = " << std::sqrt(ms.squared_radius()) << " | nb points = "
               << boost::size(point_cloud) << " | dimension = "
diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h
index 1f8f2cd8..f8107c8b 100644
--- a/src/common/include/gudhi/random_point_generators.h
+++ b/src/common/include/gudhi/random_point_generators.h
@@ -190,7 +190,8 @@ template <typename Kernel, typename OutputIterator>
 static void generate_uniform_points_on_torus_d(const Kernel &k, int dim, std::size_t num_slices,
                                                OutputIterator out,
                                                double radius_noise_percentage = 0.,
-                                               std::vector<typename Kernel::FT> current_point = std::vector<typename Kernel::FT>()) {
+                                               std::vector<typename Kernel::FT> current_point =
+                                                       std::vector<typename Kernel::FT>()) {
   CGAL::Random rng;
   int point_size = static_cast<int>(current_point.size());
   if (point_size == 2 * dim) {
diff --git a/src/common/include/gudhi/writing_persistence_to_file.h b/src/common/include/gudhi/writing_persistence_to_file.h
index 4c5ce918..34448576 100644
--- a/src/common/include/gudhi/writing_persistence_to_file.h
+++ b/src/common/include/gudhi/writing_persistence_to_file.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef WRITING_PERSISTENCE_TO_FILE_H
-#define WRITING_PERSISTENCE_TO_FILE_H
+#ifndef WRITING_PERSISTENCE_TO_FILE_H_
+#define WRITING_PERSISTENCE_TO_FILE_H_
 
 #include <iostream>
 #include <string>
@@ -112,6 +112,6 @@ void write_persistence_intervals_to_stream(const Persistence_interval_range& int
   }
 }
 
-}
+}  // namespace Gudhi
 
-#endif  // WRITING_PERSISTENCE_TO_FILE_H
+#endif  // WRITING_PERSISTENCE_TO_FILE_H_
diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html
index 081d2dda..494d2738 100644
--- a/src/cython/doc/_templates/layout.html
+++ b/src/cython/doc/_templates/layout.html
@@ -168,7 +168,7 @@
       <nav class="top-bar" role="navigation" data-topbar>
           <ul class="title-area">
               <li class="name">
-                  <h1 class="show-for-small-only"><a href="" class="icon-tree"> GUDHI C++ library</a></h1>
+                  <h1 class="show-for-small-only"><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1/" class="icon-tree"> GUDHI C++ library</a></h1>
               </li>
               <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone -->
               <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li>
@@ -176,26 +176,26 @@
           <section class="top-bar-section">
               <ul class="right">
                   <li class="divider"></li>
-                  <li><a href="/contact/">Contact</a></li>
+                  <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//contact/">Contact</a></li>
               </ul>
               <ul class="left">
-                  <li><a href="/"> <img src="/assets/img/home.png" alt="&nbsp;&nbsp;GUDHI">&nbsp;&nbsp;GUDHI </a></li>
+                  <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//"> <img src="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//assets/img/home.png" alt="&nbsp;&nbsp;GUDHI">&nbsp;&nbsp;GUDHI </a></li>
                   <li class="divider"></li>
                   <li class="has-dropdown">
                       <a href="#">Project</a>
                       <ul class="dropdown">
-                          <li><a href="/people/">People</a></li>
-                          <li><a href="/keepintouch/">Keep in touch</a></li>
-                          <li><a href="/partners/">Partners and Funding</a></li>
-                          <li><a href="/relatedprojects/">Related projects</a></li>
-                          <li><a href="/theyaretalkingaboutus/">They are talking about us</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//people/">People</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//keepintouch/">Keep in touch</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//partners/">Partners and Funding</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//relatedprojects/">Related projects</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//theyaretalkingaboutus/">They are talking about us</a></li>
                       </ul>
                   </li>
                   <li class="divider"></li>
                   <li class="has-dropdown">
                       <a href="#">Download</a>
                       <ul class="dropdown">
-                          <li><a href="/licensing/">Licensing</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//licensing/">Licensing</a></li>
                           <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li>
                           <li><a href="https://gforge.inria.fr/frs/download.php/file/37365/2018-02-01-16-59-31_GUDHI_2.1.0_OSX_UTILS.tar.gz" target="_blank">Utils for Mac OSx</a></li>
                           <li><a href="https://gforge.inria.fr/frs/download.php/file/37366/2018-01-31-09-25-53_GUDHI_2.1.0_WIN64_UTILS.zip" target="_blank">Utils for Win x64</a></li>
@@ -205,22 +205,23 @@
                   <li class="has-dropdown">
                       <a href="#">Documentation</a>
                       <ul class="dropdown">
-                          <li><a href="/doc/latest/">C++ documentation</a></li>
-                          <li><a href="/doc/latest/installation.html">C++ installation manual</a></li>
-                          <li><a href="/python/latest/">Python documentation</a></li>
-                          <li><a href="/python/latest/installation.html">Python installation manual</a></li>
-                          <li><a href="/utils/">Utilities</a></li>
-                          <li><a href="/tutorials/">Tutorials</a></li>
-                          <li><a href="/dockerfile/">Dockerfile</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//doc/latest/">C++ documentation</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//doc/latest/installation.html">C++ installation manual</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//python/latest/">Python documentation</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//python/latest/installation.html">Python installation manual</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//utils/">Utilities</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//tutorials/">Tutorials</a></li>
+                          <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//dockerfile/">Dockerfile</a></li>
                       </ul>
                   </li>
                   <li class="divider"></li>
-                  <li><a href="/interfaces/">Interfaces</a></li>
+                  <li><a href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/2.2.0.rc1//interfaces/">Interfaces</a></li>
                   <li class="divider"></li>
               </ul>
           </section>
       </nav>
   </div><!-- /#navigation -->
+
   <!-- GUDHI website header BEGIN -->