Fix cpplint on examples.

Bug fix on persistence_from_simple_simplex_tree.
Add persistence examples tests.



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@843 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9b7b73abb4a5d6bb110376deb689247bfdae035c

5 files changed, 169 insertions, 174 deletions

diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt
index d1228526..de0c7bba 100644
--- a/src/Skeleton_blocker/example/CMakeLists.txt
+++ b/src/Skeleton_blocker/example/CMakeLists.txt
@@ -1,10 +1,12 @@
 cmake_minimum_required(VERSION 2.6)
 project(GUDHIskbl)
 
-
 add_executable(SkeletonBlockerFromSimplices Skeleton_blocker_from_simplices.cpp)
 add_executable(SkeletonBlockerIteration Skeleton_blocker_iteration.cpp)
 add_executable(SkeletonBlockerLink Skeleton_blocker_link.cpp)
 
+target_link_libraries(SkeletonBlockerIteration ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY})
 
-target_link_libraries(SkeletonBlockerIteration ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY})	
+add_test(SkeletonBlockerFromSimplices ${CMAKE_CURRENT_BINARY_DIR}/SkeletonBlockerFromSimplices)
+add_test(SkeletonBlockerIteration ${CMAKE_CURRENT_BINARY_DIR}/SkeletonBlockerIteration)
+add_test(SkeletonBlockerLink ${CMAKE_CURRENT_BINARY_DIR}/SkeletonBlockerLink)
diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp
index 9f9b3d52..2738c01c 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp
@@ -1,34 +1,33 @@
- /*    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):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    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/>.
-  */
-
+/*    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):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    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/>.
+ */
+
+#include <gudhi/Skeleton_blocker.h>
 
 #include <stdio.h>
 #include <stdlib.h>
 #include <string>
 #include <fstream>
 #include <sstream>
-
-
-#include "gudhi/Skeleton_blocker.h"
+#include <vector>
 
 using namespace std;
 using namespace Gudhi;
@@ -39,45 +38,44 @@ typedef Complex::Vertex_handle Vertex_handle;
 typedef Complex::Simplex_handle Simplex_handle;
 typedef Complex::Simplex_handle Simplex;
 
-int main (int argc, char *argv[]){
-	std::vector<Simplex_handle> simplices;
+int main(int argc, char *argv[]) {
+  std::vector<Simplex_handle> simplices;
 
-	//add 4 triangles of a tetrahedron 0123
-	simplices.push_back(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3)));
-	simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(0),Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(0),Vertex_handle(1)));
+  // add 4 triangles of a tetrahedron 0123
+  simplices.push_back(Simplex_handle(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2)));
+  simplices.push_back(Simplex_handle(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)));
+  simplices.push_back(Simplex_handle(Vertex_handle(3), Vertex_handle(0), Vertex_handle(2)));
+  simplices.push_back(Simplex_handle(Vertex_handle(3), Vertex_handle(0), Vertex_handle(1)));
 
-	//get complex from top faces
-	Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(),simplices.end()));
+  // get complex from top faces
+  Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(), simplices.end()));
 
 
-	std::cout << "Simplices:"<<std::endl;
-	for(const Simplex & s : complex.simplex_range())
-		std::cout << s << " ";
-	std::cout << std::endl;
+  std::cout << "Simplices:" << std::endl;
+  for (const Simplex & s : complex.simplex_range())
+    std::cout << s << " ";
+  std::cout << std::endl;
 
-	//One blocker as simplex 0123 is not in the complex but all its proper faces are.
-	std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl;
+  // One blocker as simplex 0123 is not in the complex but all its proper faces are.
+  std::cout << "Blockers: " << complex.blockers_to_string() << std::endl;
 
-	//now build a complex from its full list of simplices
-	simplices.clear();
-	simplices.push_back(Simplex_handle(Vertex_handle(0)));
-	simplices.push_back(Simplex_handle(Vertex_handle(1)));
-	simplices.push_back(Simplex_handle(Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(0),Vertex_handle(1)));
-	simplices.push_back(Simplex_handle(Vertex_handle(1),Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(2),Vertex_handle(0)));
-	complex = Complex(simplices.begin(),simplices.end());
+  // now build a complex from its full list of simplices
+  simplices.clear();
+  simplices.push_back(Simplex_handle(Vertex_handle(0)));
+  simplices.push_back(Simplex_handle(Vertex_handle(1)));
+  simplices.push_back(Simplex_handle(Vertex_handle(2)));
+  simplices.push_back(Simplex_handle(Vertex_handle(0), Vertex_handle(1)));
+  simplices.push_back(Simplex_handle(Vertex_handle(1), Vertex_handle(2)));
+  simplices.push_back(Simplex_handle(Vertex_handle(2), Vertex_handle(0)));
+  complex = Complex(simplices.begin(), simplices.end());
 
-	std::cout << "Simplices:"<<std::endl;
-	for(const Simplex & s : complex.simplex_range())
-		std::cout << s << " ";
-	std::cout << std::endl;
+  std::cout << "Simplices:" << std::endl;
+  for (const Simplex & s : complex.simplex_range())
+    std::cout << s << " ";
+  std::cout << std::endl;
 
-	//One blocker as simplex 012 is not in the complex but all its proper faces are.
-	std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl;
+  // One blocker as simplex 012 is not in the complex but all its proper faces are.
+  std::cout << "Blockers: " << complex.blockers_to_string() << std::endl;
 
-	return EXIT_SUCCESS;
+  return EXIT_SUCCESS;
 }
-
diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
index 126e32ec..69557694 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
@@ -1,24 +1,26 @@
- /*    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):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    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/>.
-  */
+/*    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):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    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/>.
+ */
+
+#include <gudhi/Skeleton_blocker.h>
 
 #include <boost/timer/timer.hpp>
 
@@ -29,8 +31,6 @@
 #include <sstream>
 
 
-#include "gudhi/Skeleton_blocker.h"
-
 using namespace std;
 using namespace Gudhi;
 using namespace skbl;
@@ -39,54 +39,53 @@ typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
 typedef Complex::Vertex_handle Vertex_handle;
 typedef Complex::Simplex_handle Simplex;
 
-
-Complex build_complete_complex(int n){
-	// build a full complex with n vertices and 2^n-1 simplices
-		Complex complex;
-		for(int i=0;i<n;i++)
-			complex.add_vertex();
-		for(int i=0;i<n;i++)
-			for(int j=0;j<i;j++)
-				//note that add_edge, add the edge and all its cofaces
-				complex.add_edge(Vertex_handle(i),Vertex_handle(j));
-		return complex;
+Complex build_complete_complex(int n) {
+  // build a full complex with n vertices and 2^n-1 simplices
+  Complex complex;
+  for (int i = 0; i < n; i++)
+    complex.add_vertex();
+  for (int i = 0; i < n; i++)
+    for (int j = 0; j < i; j++)
+      // note that add_edge, add the edge and all its cofaces
+      complex.add_edge(Vertex_handle(i), Vertex_handle(j));
+  return complex;
 }
 
-int main (int argc, char *argv[]){
-	boost::timer::auto_cpu_timer t;
+int main(int argc, char *argv[]) {
+  boost::timer::auto_cpu_timer t;
 
-	const int n = 15;
+  const int n = 15;
 
-	// build a full complex with n vertices and 2^n-1 simplices
-	Complex complex(build_complete_complex(n));
+  // build a full complex with n vertices and 2^n-1 simplices
+  Complex complex(build_complete_complex(n));
 
-	// this is just to illustrate iterators, to count number of vertices
-	// or edges, complex.num_vertices() and complex.num_edges() are
-	// more appropriated!
-	unsigned num_vertices = 0;
-	for(auto v : complex.vertex_range()) {
-	  std::cout << "Vertex " << v <<std::endl;
-	  ++num_vertices;
-        }
+  // this is just to illustrate iterators, to count number of vertices
+  // or edges, complex.num_vertices() and complex.num_edges() are
+  // more appropriated!
+  unsigned num_vertices = 0;
+  for (auto v : complex.vertex_range()) {
+    std::cout << "Vertex " << v << std::endl;
+    ++num_vertices;
+  }
 
-	// such loop can also be done directly with distance as iterators are STL compliant
-	auto edges = complex.edge_range();
-	unsigned num_edges = std::distance(edges.begin(), edges.end());
+  // such loop can also be done directly with distance as iterators are STL compliant
+  auto edges = complex.edge_range();
+  unsigned num_edges = std::distance(edges.begin(), edges.end());
 
-	unsigned euler = 0;
-	unsigned num_simplices = 0;
-	// we use a reference to a simplex instead of a copy
-	// value here because a simplex is a set of integers
-	// and copying it cost time
-	for(const Simplex & s : complex.simplex_range()){
-		++num_simplices;
-		if(s.dimension()%2 == 0) 
-			euler += 1;
-		else 
-			euler -= 1;
-	}
-	std::cout << "Saw "<<num_vertices<<" vertices, "<<num_edges<<" edges and "<<num_simplices<<" simplices"<<std::endl;
-	std::cout << "The Euler Characteristic is "<<euler<<std::endl;
-	return EXIT_SUCCESS;
+  unsigned euler = 0;
+  unsigned num_simplices = 0;
+  // we use a reference to a simplex instead of a copy
+  // value here because a simplex is a set of integers
+  // and copying it cost time
+  for (const Simplex & s : complex.simplex_range()) {
+    ++num_simplices;
+    if (s.dimension() % 2 == 0)
+      euler += 1;
+    else
+      euler -= 1;
+  }
+  std::cout << "Saw " << num_vertices << " vertices, " << num_edges << " edges and " << num_simplices << " simplices"
+      << std::endl;
+  std::cout << "The Euler Characteristic is " << euler << std::endl;
+  return EXIT_SUCCESS;
 }
-
diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp
index 0987cc89..002cbc49 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp
@@ -1,25 +1,26 @@
- /*    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):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    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/>.
-  */
+/*    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):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    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/>.
+ */
 
+#include <gudhi/Skeleton_blocker.h>
 
 #include <stdio.h>
 #include <stdlib.h>
@@ -27,9 +28,6 @@
 #include <fstream>
 #include <sstream>
 
-
-#include "gudhi/Skeleton_blocker.h"
-
 using namespace std;
 using namespace Gudhi;
 using namespace skbl;
@@ -39,33 +37,31 @@ typedef Complex::Vertex_handle Vertex_handle;
 typedef Complex::Root_vertex_handle Root_vertex_handle;
 typedef Complex::Simplex_handle Simplex;
 
+int main(int argc, char *argv[]) {
+  // build a full complex with 4 vertices and 2^4-1 simplices
+  // Initial vertices are (0,1,2,3,4)
+  Simplex tetrahedron(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
+  Complex complex;
+  complex.add_simplex(tetrahedron);
 
-int main (int argc, char *argv[]){
-	// build a full complex with 4 vertices and 2^4-1 simplices
-	// Initial vertices are (0,1,2,3,4)
-	Simplex tetrahedron(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2),Vertex_handle(3));
-	Complex complex;
-	complex.add_simplex(tetrahedron);
+  cout << "complex:" << complex.to_string() << endl;
 
-	cout<<"complex:"<<complex.to_string()<<endl;
+  // build the link of vertex 1, eg a triangle {0,2,3}
+  auto link = complex.link(Vertex_handle(1));
+  cout << "link:" << link.to_string() << endl;
 
-	//build the link of vertex 1, eg a triangle {0,2,3}
-	auto link = complex.link(Vertex_handle(1));
-	cout<<"link:"<<link.to_string()<<endl;
+  // Internally link is a subcomplex of 'complex' and its vertices are stored in a vector.
+  // They can be accessed via Vertex_handle(x) where x is an index of the vector.
+  // In that example, link has three vertices and thus it contains only
+  // Vertex_handle(0),Vertex_handle(1) and Vertex_handle(2) are).
+  for (int i = 0; i < 5; ++i)
+    cout << "link.contains_vertex(Vertex_handle(" << i << ")):" << link.contains_vertex(Vertex_handle(i)) << endl;
+  cout << endl;
 
-	//Internally link is a subcomplex of 'complex' and its vertices are stored in a vector.
-	//They can be accessed via Vertex_handle(x) where x is an index of the vector.
-	//In that example, link has three vertices and thus it contains only
-	// Vertex_handle(0),Vertex_handle(1) and Vertex_handle(2) are).
-	for(int i = 0; i<5; ++i)
-		cout << "link.contains_vertex(Vertex_handle("<<i<<")):"<<link.contains_vertex(Vertex_handle(i))<<endl;
-	cout<<endl;
+  // To access to the initial vertices eg (0,1,2,3,4),  Root_vertex_handle must be used.
+  // For instance, to test if the link contains the vertex that was labeled i:
+  for (int i = 0; i < 5; ++i)
+    cout << "link.contains_vertex(Root_vertex_handle(" << i << ")):" << link.contains_vertex(Root_vertex_handle(i)) << endl;
 
-	//To access to the initial vertices eg (0,1,2,3,4),  Root_vertex_handle must be used.
-	//For instance, to test if the link contains the vertex that was labeled i:
-	for(int i = 0; i<5; ++i)
-		cout << "link.contains_vertex(Root_vertex_handle("<<i<<")):"<<link.contains_vertex(Root_vertex_handle(i))<<endl;
-
-	return EXIT_SUCCESS;
+  return EXIT_SUCCESS;
 }
-
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h
index 10d552ec..0d2de767 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h
@@ -179,4 +179,4 @@ struct Skeleton_blocker_simple_traits {
 
 }  // namespace Gudhi
 
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_TRAITS_H_
+#endif  // SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_TRAITS_H_