Merged latest trunk changes to Nerve_GIC

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@2431 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 866ddfadee8160dfaa46b8d703fd8d8d4476892a

66 files changed, 634 insertions, 681 deletions

diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index 3ffdae7f..cf1a946a 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -71,7 +71,7 @@ namespace alpha_complex {
  * 
  * When launching:
  * 
- * \code $> ./alphapoints
+ * \code $> ./Alpha_complex_example_from_points
  * \endcode
  *
  * the program output is:
@@ -89,31 +89,64 @@ namespace alpha_complex {
  * \image html "alpha_complex_doc.png" "Simplicial complex structure construction example"
  *
  * \subsection filtrationcomputation Filtration value computation algorithm
- * 
- * \f{algorithm}{ 
- * \caption{Filtration value computation algorithm}\label{alpha}
- * \begin{algorithmic}
- * \For{i : dimension $\rightarrow$ 0}
- *   \ForAll{$\sigma$ of dimension i}
- *     \If {filtration($\sigma$) is NaN}
- *       \State filtration($\sigma$) = $\alpha^2(\sigma)$
- *     \EndIf
- *     \ForAll{$\tau$ face of $\sigma$} \Comment{propagate alpha filtration value}
- *       \If {filtration($\tau$) is not NaN} 
- *         \State filtration($\tau$) = min (filtration($\tau$), filtration($\sigma$))
- *       \Else
- *         \If {$\tau$ is not Gabriel for $\sigma$} 
- *           \State filtration($\tau$) = filtration($\sigma$)
- *         \EndIf
- *       \EndIf
- *     \EndFor
- *   \EndFor
- * \EndFor
- * \State make\_filtration\_non\_decreasing()
- * \State prune\_above\_filtration()
- * \end{algorithmic}
- * \f}
- * 
+ *
+ *
+ *
+ * <ul>
+ *   <li style="list-style-type: none;">\f$ \textbf{for } i : dimension \rightarrow 0 \textbf{ do} \f$
+ *     <ul>
+ *       <li style="list-style-type: none;">\f$\textbf{for all } \sigma of dimension i \f$
+ *         <ul>
+ *           <li style="list-style-type: none;">\f$\textbf{if } filtration( \sigma ) is NaN \textbf{ then} \f$
+ *             <ul>
+ *               <li style="list-style-type: none;">\f$ filtration( \sigma ) = \alpha^2( \sigma ) \f$
+ *               </li>
+ *             </ul>
+ *           </li>
+ *           <li style="list-style-type: none;">\f$\textbf{end if}\f$
+ *           </li>
+ *           <li style="list-style-type: none;">\f$\textbf{for all } \tau face of \sigma \textbf{ do} \f$
+ *             &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;// propagate alpha filtration value
+ *             <ul>
+ *               <li style="list-style-type: none;">\f$\textbf{if } filtration( \tau ) is not NaN \textbf{ then} \f$
+ *                 <ul>
+ *                   <li style="list-style-type: none;">\f$ filtration( \tau ) = min ( filtration( \tau ), filtration( \sigma ) ) \f$
+ *                   </li>
+ *                 </ul>
+ *               </li>
+ *               <li style="list-style-type: none;">\f$\textbf{else}\f$
+ *                 <ul>
+ *                   <li style="list-style-type: none;">\f$\textbf{if } \tau is not Gabriel for \sigma \textbf{ then} \f$
+ *                     <ul>
+ *                       <li style="list-style-type: none;">\f$ filtration( \tau ) = filtration( \sigma ) \f$
+ *                       </li>
+ *                     </ul>
+ *                   </li>
+ *                   <li style="list-style-type: none;">\f$\textbf{end if}\f$
+ *                   </li>
+ *                 </ul>
+ *               </li>
+ *               <li style="list-style-type: none;">\f$\textbf{end if}\f$
+ *               </li>
+ *             </ul>
+ *           </li>
+ *           <li style="list-style-type: none;">\f$\textbf{end for}\f$
+ *           </li>
+ *         </ul>
+ *       </li>
+ *       <li style="list-style-type: none;">\f$\textbf{end for}\f$
+ *       </li>
+ *     </ul>
+ *   </li>
+ *   <li style="list-style-type: none;">\f$\textbf{end for}\f$
+ *   </li>
+ *   <li style="list-style-type: none;">\f$make\_filtration\_non\_decreasing()\f$
+ *   </li>
+ *   <li style="list-style-type: none;">\f$prune\_above\_filtration()\f$
+ *   </li>
+ * </ul>
+ *
+ *
  * \subsubsection dimension2 Dimension 2
  * 
  * From the example above, it means the algorithm looks into each triangle ([0,1,2], [0,2,4], [1,2,3], ...),
@@ -155,7 +188,7 @@ namespace alpha_complex {
  * 
  * When launching:
  * 
- * \code $> ./alphaoffreader ../../data/points/alphacomplexdoc.off 32.0
+ * \code $> ./Alpha_complex_example_from_off ../../data/points/alphacomplexdoc.off 32.0
  * \endcode
  *
  * the program output is:
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index b9bcdb55..a4853d78 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -4,26 +4,29 @@ project(Alpha_complex_examples)
 # need CGAL 4.7
 # cmake -DCGAL_DIR=~/workspace/CGAL-4.7 ..
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-  add_executable ( alphapoints Alpha_complex_from_points.cpp )
-  target_link_libraries(alphapoints  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
-  add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
-  target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
+  add_executable ( Alpha_complex_example_from_points Alpha_complex_from_points.cpp )
+  target_link_libraries(Alpha_complex_example_from_points  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
+  add_executable ( Alpha_complex_example_from_off Alpha_complex_from_off.cpp )
+  target_link_libraries(Alpha_complex_example_from_off  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
   if (TBB_FOUND)
-    target_link_libraries(alphapoints ${TBB_LIBRARIES})
-    target_link_libraries(alphaoffreader ${TBB_LIBRARIES})
+    target_link_libraries(Alpha_complex_example_from_points ${TBB_LIBRARIES})
+    target_link_libraries(Alpha_complex_example_from_off ${TBB_LIBRARIES})
   endif()
 
-  add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints)
-  # Do not forget to copy test files in current binary dir
-  file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-  add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt)
-  add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt)
+  add_test(NAME Alpha_complex_example_from_points COMMAND $<TARGET_FILE:Alpha_complex_example_from_points>)
+
+  add_test(NAME Alpha_complex_example_from_off_60 COMMAND $<TARGET_FILE:Alpha_complex_example_from_off>
+      "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "60.0" "${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt")
+  add_test(NAME Alpha_complex_example_from_off_32 COMMAND $<TARGET_FILE:Alpha_complex_example_from_off>
+      "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt")
   if (DIFF_PATH)
     # Do not forget to copy test results files in current binary dir
     file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
     file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-    add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
-    add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
+    add_test(Alpha_complex_example_from_off_60_diff_files ${DIFF_PATH}
+        ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
+    add_test(Alpha_complex_example_from_off_32_diff_files ${DIFF_PATH}
+        ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
   endif()
 endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index 32091196..d7f49b53 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -1,28 +1,19 @@
 cmake_minimum_required(VERSION 2.6)
 project(Alpha_complex_tests)
 
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
-
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-  add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp )
-  target_link_libraries(AlphaComplexUT  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  include(GUDHI_test_coverage)
+
+  add_executable ( Alpha_complex_test_unit Alpha_complex_unit_test.cpp )
+  target_link_libraries(Alpha_complex_test_unit  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
   if (TBB_FOUND)
-    target_link_libraries(AlphaComplexUT ${TBB_LIBRARIES})
+    target_link_libraries(Alpha_complex_test_unit ${TBB_LIBRARIES})
   endif()
 
   # Do not forget to copy test files in current binary dir
   file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-  add_test(AlphaComplexUT ${CMAKE_CURRENT_BINARY_DIR}/AlphaComplexUT
-  # XML format for Jenkins xUnit plugin
-  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaComplexUT.xml --log_level=test_suite --report_level=no)
+  gudhi_add_coverage_test(Alpha_complex_test_unit)
 
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 
diff --git a/src/Alpha_complex/test/README b/src/Alpha_complex/test/README
index 45b87d91..0e5b9eb1 100644
--- a/src/Alpha_complex/test/README
+++ b/src/Alpha_complex/test/README
@@ -7,6 +7,6 @@ make
 To launch with details:
 ***********************
 
-./AlphaComplexUnitTest --report_level=detailed --log_level=all 
+./Alpha_complex_unit_test --report_level=detailed --log_level=all
 
    ==> echo $? returns 0 in case of success (non-zero otherwise)
diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
index e6bc6648..67735ba1 100644
--- a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
+++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
@@ -27,8 +27,9 @@
 
 // standard stuff
 #include <iostream>
-#include <sstream>
+#include <string>
 #include <vector>
+#include <cstddef>
 
 int main(int argc, char** argv) {
   std::cout << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical " <<
@@ -38,9 +39,6 @@ int main(int argc, char** argv) {
       "filtrations of top dimensional cells. We assume that the cells are in the lexicographical order. See " <<
       "CubicalOneSphere.txt or CubicalTwoSphere.txt for example.\n" << std::endl;
 
-  int p = 2;
-  double min_persistence = 0;
-
   if (argc != 2) {
     std::cerr << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at " <<
         "the input. The program will now terminate.\n";
@@ -56,16 +54,26 @@ int main(int argc, char** argv) {
 
   // Compute the persistence diagram of the complex
   Persistent_cohomology pcoh(b);
+  int p = 2;
+  double min_persistence = 0;
+
   pcoh.init_coefficients(p);  // initializes the coefficient field for homology
   pcoh.compute_persistent_cohomology(min_persistence);
 
-  std::stringstream ss;
-  ss << argv[1] << "_persistence";
-  std::ofstream out(ss.str().c_str());
+  std::string output_file_name(argv[1]);
+  output_file_name += "_persistence";
+
+  std::size_t last_in_path = output_file_name.find_last_of("/\\");
+
+  if (last_in_path != std::string::npos) {
+    output_file_name = output_file_name.substr(last_in_path+1);
+  }
+
+  std::ofstream out(output_file_name.c_str());
   pcoh.output_diagram(out);
   out.close();
 
-  std::cout << "Result in file: " << ss.str().c_str() << "\n";
+  std::cout << "Result in file: " << output_file_name << "\n";
 
   return 0;
 }
diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
index 839a4c89..f8754345 100644
--- a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
+++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
@@ -40,9 +40,6 @@ int main(int argc, char** argv) {
       "assume that the cells are in the lexicographical order. See CubicalOneSphere.txt or CubicalTwoSphere.txt for" <<
       " example.\n" << std::endl;
 
-  int p = 2;
-  double min_persistence = 0;
-
   if (argc != 2) {
     std::cerr << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at " <<
         "the input. The program will now terminate.\n";
@@ -58,16 +55,26 @@ int main(int argc, char** argv) {
   typedef Gudhi::persistent_cohomology::Persistent_cohomology<Bitmap_cubical_complex, Field_Zp> Persistent_cohomology;
   // Compute the persistence diagram of the complex
   Persistent_cohomology pcoh(b, true);
+
+  int p = 2;
+  double min_persistence = 0;
   pcoh.init_coefficients(p);  // initializes the coefficient field for homology
   pcoh.compute_persistent_cohomology(min_persistence);
 
-  std::stringstream ss;
-  ss << argv[1] << "_persistence";
-  std::ofstream out(ss.str().c_str());
+  std::string output_file_name(argv[1]);
+  output_file_name += "_persistence";
+
+  std::size_t last_in_path = output_file_name.find_last_of("/\\");
+
+  if (last_in_path != std::string::npos) {
+    output_file_name = output_file_name.substr(last_in_path+1);
+  }
+
+  std::ofstream out(output_file_name.c_str());
   pcoh.output_diagram(out);
   out.close();
 
-  std::cout << "Result in file: " << ss.str().c_str() << "\n";
+  std::cout << "Result in file: " << output_file_name << "\n";
 
   return 0;
 }
diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt
index 2fddc514..241a11e5 100644
--- a/src/Bitmap_cubical_complex/example/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt
@@ -6,21 +6,31 @@ target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
 if (TBB_FOUND)
   target_link_libraries(Bitmap_cubical_complex ${TBB_LIBRARIES})
 endif()
-add_test(Bitmap_cubical_complex_one_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt)
-add_test(Bitmap_cubical_complex_two_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
+
+add_test(NAME Bitmap_cubical_complex_example_persistence_one_sphere COMMAND $<TARGET_FILE:Bitmap_cubical_complex>
+    "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt")
+
+add_test(NAME Bitmap_cubical_complex_example_persistence_two_sphere COMMAND $<TARGET_FILE:Bitmap_cubical_complex>
+    "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt")
 
 add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp )
 target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
 if (TBB_FOUND)
   target_link_libraries(Random_bitmap_cubical_complex ${TBB_LIBRARIES})
 endif()
-add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap_cubical_complex 2 100 100)
+add_test(NAME Bitmap_cubical_complex_example_random COMMAND $<TARGET_FILE:Random_bitmap_cubical_complex>
+    "2" "100" "100")
 
 add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp )
 target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY})
 if (TBB_FOUND)
   target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_LIBRARIES})
 endif()
-add_test(Bitmap_cubical_complex_periodic_2d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt)
-add_test(Bitmap_cubical_complex_periodic_3d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt)
 
+add_test(NAME Bitmap_cubical_complex_example_periodic_boundary_conditions_2d_torus
+    COMMAND $<TARGET_FILE:Bitmap_cubical_complex_periodic_boundary_conditions>
+    "${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt")
+
+add_test(NAME Bitmap_cubical_complex_example_periodic_boundary_conditions_3d_torus
+    COMMAND $<TARGET_FILE:Bitmap_cubical_complex_periodic_boundary_conditions>
+    "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt")
diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt
index daf0e14f..b2895f85 100644
--- a/src/Bitmap_cubical_complex/test/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt
@@ -1,24 +1,12 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bitmap_cubical_complex_tests)
 
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
+include(GUDHI_test_coverage)
 
-add_executable ( BitmapCCUT Bitmap_test.cpp )
-target_link_libraries(BitmapCCUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( Bitmap_cubical_complex_test_unit Bitmap_test.cpp )
+target_link_libraries(Bitmap_cubical_complex_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(BitmapCCUT ${TBB_LIBRARIES})
+  target_link_libraries(Bitmap_cubical_complex_test_unit ${TBB_LIBRARIES})
 endif()
 
-# Unitary tests
-add_test(NAME BitmapCCUT
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/BitmapCCUT 
-    # XML format for Jenkins xUnit plugin 
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BitmapCCUT.xml --log_level=test_suite --report_level=no)
-
+gudhi_add_coverage_test(Bitmap_cubical_complex_test_unit)
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index b0a19f8b..0d0bff45 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -5,8 +5,6 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
   add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
 
-  add_test(bottleneck_basic_example ${CMAKE_CURRENT_BINARY_DIR}/bottleneck_basic_example)
-
   add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
   target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
   if (TBB_FOUND)
@@ -14,7 +12,11 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES})
     target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
   endif(TBB_FOUND)
-  add_test(alpha_rips_persistence_bottleneck_distance ${CMAKE_CURRENT_BINARY_DIR}/alpha_rips_persistence_bottleneck_distance
-      ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.15 -m 0.12 -d 3 -p 3)
+
+  add_test(NAME Bottleneck_distance_example_basic COMMAND $<TARGET_FILE:bottleneck_basic_example>)
+
+  add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck
+      COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
 
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h
index b90a0ee0..8c97dce9 100644
--- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h
+++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h
@@ -101,11 +101,11 @@ double bottleneck_distance_exact(Persistence_graph& g) {
  */
 template<typename Persistence_diagram1, typename Persistence_diagram2>
 double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2,
-                           double e = std::numeric_limits<double>::min()) {
+                           double e = (std::numeric_limits<double>::min)()) {
   Persistence_graph g(diag1, diag2, e);
   if (g.bottleneck_alive() == std::numeric_limits<double>::infinity())
     return std::numeric_limits<double>::infinity();
-  return std::max(g.bottleneck_alive(), e == 0. ? bottleneck_distance_exact(g) : bottleneck_distance_approx(g, e));
+  return (std::max)(g.bottleneck_alive(), e == 0. ? bottleneck_distance_exact(g) : bottleneck_distance_approx(g, e));
 }
 
 }  // namespace persistence_diagram
diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
index 44f4b827..622b0691 100644
--- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
+++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
@@ -102,7 +102,7 @@ Persistence_graph::Persistence_graph(const Persistence_diagram1 &diag1,
     b_alive = std::numeric_limits<double>::infinity();
   } else {
     for (auto it_u = u_alive.cbegin(), it_v = v_alive.cbegin(); it_u != u_alive.cend(); ++it_u, ++it_v)
-      b_alive = std::max(b_alive, std::fabs(*it_u - *it_v));
+      b_alive = (std::max)(b_alive, std::fabs(*it_u - *it_v));
   }
 }
 
@@ -129,7 +129,7 @@ inline double Persistence_graph::distance(int u_point_index, int v_point_index)
     return 0.;
   Internal_point p_u = get_u_point(u_point_index);
   Internal_point p_v = get_v_point(v_point_index);
-  return std::max(std::fabs(p_u.x() - p_v.x()), std::fabs(p_u.y() - p_v.y()));
+  return (std::max)(std::fabs(p_u.x() - p_v.x()), std::fabs(p_u.y() - p_v.y()));
 }
 
 inline int Persistence_graph::size() const {
@@ -175,9 +175,9 @@ inline Internal_point Persistence_graph::get_v_point(int v_point_index) const {
 inline double Persistence_graph::diameter_bound() const {
   double max = 0.;
   for (auto it = u.cbegin(); it != u.cend(); it++)
-    max = std::max(max, it->y());
+    max = (std::max)(max, it->y());
   for (auto it = v.cbegin(); it != v.cend(); it++)
-    max = std::max(max, it->y());
+    max = (std::max)(max, it->y());
   return max;
 }
 
diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt
index 3d8e1f95..e1bbbbec 100644
--- a/src/Bottleneck_distance/test/CMakeLists.txt
+++ b/src/Bottleneck_distance/test/CMakeLists.txt
@@ -1,25 +1,15 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_tests)
 
-
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
-
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-  add_executable ( bottleneckUT bottleneck_unit_test.cpp )
-  target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  include(GUDHI_test_coverage)
+
+  add_executable ( Bottleneck_distance_test_unit bottleneck_unit_test.cpp )
+  target_link_libraries(Bottleneck_distance_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
   if (TBB_FOUND)
-    target_link_libraries(bottleneckUT ${TBB_LIBRARIES})
+    target_link_libraries(Bottleneck_distance_test_unit ${TBB_LIBRARIES})
   endif(TBB_FOUND)
 
-  # Unitary tests
-  add_test(NAME bottleneckUT COMMAND ${CMAKE_CURRENT_BINARY_DIR}/bottleneckUT
-    # XML format for Jenkins xUnit plugin
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/bottleneckUT.xml --log_level=test_suite --report_level=no)
+  gudhi_add_coverage_test(Bottleneck_distance_test_unit)
+
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/test/README b/src/Bottleneck_distance/test/README
index 0e7b8673..00bd9a91 100644
--- a/src/Bottleneck_distance/test/README
+++ b/src/Bottleneck_distance/test/README
@@ -7,6 +7,6 @@ make
 To launch with details:
 ***********************
 
-./BottleneckUnitTest --report_level=detailed --log_level=all 
+./Bottleneck_distance_unit_test --report_level=detailed --log_level=all
 
    ==> echo $? returns 0 in case of success (non-zero otherwise)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index a4e6eb50..545a606b 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -2,8 +2,6 @@ cmake_minimum_required(VERSION 2.6)
 project(GUDHI)
 
 include("CMakeGUDHIVersion.txt")
-# Generate GUDHI official version file
-configure_file(GUDHIVersion.cmake.in "${CMAKE_SOURCE_DIR}/GUDHIVersion.cmake" @ONLY)
 
 enable_testing()
 
@@ -11,12 +9,12 @@ list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
 
 # For "make doxygen"
 set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
-include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt)
+include(GUDHI_doxygen_target)
 
 # This variable is used by Cython CMakeLists.txt to know its path
 set(GUDHI_CYTHON_PATH "cython")
 # For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
-include("${CMAKE_MODULE_PATH}/GUDHI_third_party_libraries.txt")
+include(GUDHI_third_party_libraries)
 
 if(MSVC)
   # Turn off some VC++ warnings
diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt
index 4c09a0a7..51a6832d 100644
--- a/src/Contraction/example/CMakeLists.txt
+++ b/src/Contraction/example/CMakeLists.txt
@@ -9,7 +9,10 @@ target_link_libraries(RipsContraction ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBR
 target_link_libraries(GarlandHeckbert ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY})	
 
 
-add_test(RipsContraction.tore3D.0.2 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 0.2)
+add_test(NAME Contraction_example_tore3D_0.2 COMMAND $<TARGET_FILE:RipsContraction>
+    "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "0.2")
 # TODO(DS) : These tests are too long under Windows
-#add_test(RipsContraction.sphere.0.2 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/sphere3D_2646.off 0.2)
-#add_test(RipsContraction.S0310000 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off 0.3)
+#add_test(NAME Contraction_example_sphere_0.2 COMMAND $<TARGET_FILE:RipsContraction>
+#    "${CMAKE_SOURCE_DIR}/data/points/sphere3D_2646.off" "0.2")
+#add_test(NAME Contraction_example_SO3_0.3 COMMAND $<TARGET_FILE:RipsContraction>
+#    "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off" "0.3")
diff --git a/src/Doxyfile b/src/Doxyfile
index 60959235..904a9a99 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -1428,7 +1428,7 @@ FORMULA_TRANSPARENT    = YES
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. See the MathJax site (see:
@@ -1451,14 +1451,14 @@ MATHJAX_FORMAT         = HTML-CSS
 # The default value is: http://cdn.mathjax.org/mathjax/latest.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
+MATHJAX_RELPATH        = http://gudhi.gforge.inria.fr/doc
 
 # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
 # extension names that should be enabled during MathJax rendering. For example
 # MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_EXTENSIONS     =
+MATHJAX_EXTENSIONS     = TeX/AMSmath TeX/AMSsymbols TeX/algorithm TeX/algpseudocode
 
 # The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
 # of code that will be used on startup of the MathJax code. See the MathJax site
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index a6b698c3..3c45e79b 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -32,20 +32,21 @@ if (TBB_FOUND)
   target_link_libraries(persistence_from_file ${TBB_LIBRARIES})
 endif()
 
-add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
-add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
-add_test(rips_distance_matrix ${CMAKE_CURRENT_BINARY_DIR}/rips_distance_matrix_persistence
-    ${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv -r 1.0 -d 3 -p 3 -m 0)
-add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence
-    ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3)
-add_test(rips_persistence_step_by_step_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_step_by_step
-    ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3)
-add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix
-    ${CMAKE_SOURCE_DIR}/data/points/Kl.off -r 0.16 -d 3 -p 3 -m 100)
-add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file
-    ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 2 -m 0)
-add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file
-    ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 3 -m 100)
+add_test(NAME Persistent_cohomology_example_plain_homology COMMAND $<TARGET_FILE:plain_homology>)
+add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $<TARGET_FILE:persistence_from_simple_simplex_tree>
+    "1" "0")
+add_test(NAME Persistent_cohomology_example_from_rips_distance_matrix COMMAND $<TARGET_FILE:rips_distance_matrix_persistence>
+    "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0")
+add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence>
+    "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3")
+add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence_step_by_step>
+    "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3")
+add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $<TARGET_FILE:rips_persistence_via_boundary_matrix>
+    "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100")
+add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $<TARGET_FILE:persistence_from_file>
+    "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "2" "-m" "0")
+add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $<TARGET_FILE:persistence_from_file>
+    "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100")
    
 if(GMP_FOUND)
    if(GMPXX_FOUND)
@@ -55,8 +56,8 @@ if(GMP_FOUND)
       if (TBB_FOUND)
         target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
       endif(TBB_FOUND)
-   add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence
-       ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 -q 71)
+   add_test(NAME Persistent_cohomology_example_multifield_2_71 COMMAND $<TARGET_FILE:rips_multifield_persistence>
+       "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "2" "-q" "71")
    endif(GMPXX_FOUND)
 endif(GMP_FOUND)
 
@@ -73,13 +74,12 @@ if(CGAL_FOUND)
     target_link_libraries(exact_alpha_complex_3d_persistence ${TBB_LIBRARIES})
     target_link_libraries(weighted_alpha_complex_3d_persistence ${TBB_LIBRARIES})
   endif(TBB_FOUND)
-  add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence
-      ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45)
-  add_test(exact_alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/exact_alpha_complex_3d_persistence
-      ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45)
-  add_test(weighted_alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/weighted_alpha_complex_3d_persistence
-      ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights 2 0.45)
-
+  add_test(NAME Persistent_cohomology_example_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45")
+  add_test(NAME Persistent_cohomology_example_exact_alpha_complex_3d COMMAND $<TARGET_FILE:exact_alpha_complex_3d_persistence>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45")
+  add_test(NAME Persistent_cohomology_example_weighted_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_alpha_complex_3d_persistence>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights" "2" "0.45")
 
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
@@ -97,10 +97,10 @@ if(CGAL_FOUND)
       target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES})
       target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES})
     endif(TBB_FOUND)
-    add_test(alpha_complex_persistence_2_0_45 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_persistence
-        ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -m 0.45 -p 2)
-    add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence
-        ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off ${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt 2 0)
-    add_test(custom_persistence_sort ${CMAKE_CURRENT_BINARY_DIR}/custom_persistence_sort)
+    add_test(NAME Persistent_cohomology_example_alpha_complex COMMAND $<TARGET_FILE:alpha_complex_persistence>
+        "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45")
+    add_test(NAME Persistent_cohomology_example_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:periodic_alpha_complex_3d_persistence>
+        "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "2" "0")
+    add_test(NAME Persistent_cohomology_example_custom_persistence_sort COMMAND $<TARGET_FILE:custom_persistence_sort>)
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 endif(CGAL_FOUND)
diff --git a/src/Persistent_cohomology/example/README b/src/Persistent_cohomology/example/README
index 2ac79398..794b94ae 100644
--- a/src/Persistent_cohomology/example/README
+++ b/src/Persistent_cohomology/example/README
@@ -121,7 +121,7 @@ N.B.: - alpha_complex_persistence accepts OFF files in d-Dimension.
 
 3) 3D periodic special case
 ---------------------------
-./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 3 1.0
+./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off ../../data/points/iso_cuboid_3_in_0_1.txt 3 1.0
 
 output:
 Periodic Delaunay computed.
diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt
index a21f39c4..11e9a951 100644
--- a/src/Persistent_cohomology/test/CMakeLists.txt
+++ b/src/Persistent_cohomology/test/CMakeLists.txt
@@ -1,49 +1,37 @@
 cmake_minimum_required(VERSION 2.6)
 project(Persistent_cohomology_tests)
 
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif(GCOVR_PATH)
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif(GPROF_PATH)
-
-add_executable ( PersistentCohomologyUT persistent_cohomology_unit_test.cpp )
-target_link_libraries(PersistentCohomologyUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-add_executable ( BettiNumbersUT betti_numbers_unit_test.cpp )
-target_link_libraries(BettiNumbersUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+include(GUDHI_test_coverage)
+
+add_executable ( Persistent_cohomology_test_unit persistent_cohomology_unit_test.cpp )
+target_link_libraries(Persistent_cohomology_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( Persistent_cohomology_test_betti_numbers betti_numbers_unit_test.cpp )
+target_link_libraries(Persistent_cohomology_test_betti_numbers ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(PersistentCohomologyUT ${TBB_LIBRARIES})
-  target_link_libraries(BettiNumbersUT ${TBB_LIBRARIES})
+  target_link_libraries(Persistent_cohomology_test_unit ${TBB_LIBRARIES})
+  target_link_libraries(Persistent_cohomology_test_betti_numbers ${TBB_LIBRARIES})
 endif(TBB_FOUND)
 
-# Unitary tests
-add_test(NAME PersistentCohomologyUT 
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/PersistentCohomologyUT
-    ${CMAKE_SOURCE_DIR}/src/Persistent_cohomology/test/simplex_tree_file_for_unit_test.txt
-    # XML format for Jenkins xUnit plugin 
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/PersistentCohomologyUT.xml --log_level=test_suite --report_level=no)
+# Do not forget to copy test results files in current binary dir
+file(COPY "${CMAKE_SOURCE_DIR}/src/Persistent_cohomology/test/simplex_tree_file_for_unit_test.txt"
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-add_test(NAME BettiNumbersUT 
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/BettiNumbersUT
-    # XML format for Jenkins xUnit plugin 
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BettiNumbersUT.xml --log_level=test_suite --report_level=no)
+# Unitary tests
+gudhi_add_coverage_test(Persistent_cohomology_test_unit)
+gudhi_add_coverage_test(Persistent_cohomology_test_betti_numbers)
 
 if(GMPXX_FOUND AND GMP_FOUND)
-  add_executable ( PersistentCohomologyMultiFieldUT persistent_cohomology_unit_test_multi_field.cpp )
-  target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+  add_executable ( Persistent_cohomology_test_unit_multi_field persistent_cohomology_unit_test_multi_field.cpp )
+  target_link_libraries(Persistent_cohomology_test_unit_multi_field ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
   if (TBB_FOUND)
-    target_link_libraries(PersistentCohomologyMultiFieldUT ${TBB_LIBRARIES})
+    target_link_libraries(Persistent_cohomology_test_unit_multi_field ${TBB_LIBRARIES})
   endif(TBB_FOUND)
 
+  # Do not forget to copy test results files in current binary dir
+  file(COPY "${CMAKE_SOURCE_DIR}/src/Persistent_cohomology/test/simplex_tree_file_for_multi_field_unit_test.txt"
+       DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
   # Unitary tests
-  add_test(NAME PersistentCohomologyMultiFieldUT
-    COMMAND ${CMAKE_CURRENT_BINARY_DIR}/PersistentCohomologyMultiFieldUT
-      ${CMAKE_SOURCE_DIR}/src/Persistent_cohomology/test/simplex_tree_file_for_multi_field_unit_test.txt
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/PersistentCohomologyMultiFieldUT.xml --log_level=test_suite --report_level=no)
+  gudhi_add_coverage_test(Persistent_cohomology_test_unit_multi_field)
 
 endif(GMPXX_FOUND AND GMP_FOUND)
 
diff --git a/src/Persistent_cohomology/test/README b/src/Persistent_cohomology/test/README
index 6c64b5fe..0c41feed 100644
--- a/src/Persistent_cohomology/test/README
+++ b/src/Persistent_cohomology/test/README
@@ -11,13 +11,19 @@ To launch with details:
 
 SINGLE FIELD
 ------------
-./PersistentCohomologyUT simplex_tree_file_for_unit_test.txt --report_level=detailed --log_level=all 
+./Persistent_cohomology_test_unit --report_level=detailed --log_level=all
 
    ==> echo $? returns 0 in case of success (non-zero otherwise)
 
 MULTI FIELD
 -----------
-./PersistentCohomologyMultiFieldUT simplex_tree_file_for_multi_field_unit_test.txt --report_level=detailed --log_level=all
+./Persistent_cohomology_test_unit_multi_field --report_level=detailed --log_level=all
+
+   ==> echo $? returns 0 in case of success (non-zero otherwise)
+
+BETTI NUMBERS
+-------------
+./Persistent_cohomology_test_betti_numbers --report_level=detailed --log_level=all
 
    ==> echo $? returns 0 in case of success (non-zero otherwise)
 
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
index e2e0bc71..f8174020 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
@@ -22,11 +22,9 @@ using namespace boost::unit_test;
 typedef Simplex_tree<> typeST;
 
 std::string test_rips_persistence(int coefficient, int min_persistence) {
-  // file name is given as parameter from CMakeLists.txt
-  const std::string inputFile(framework::master_test_suite().argv[1]);
-
+  // file is copied in CMakeLists.txt
   std::ifstream simplex_tree_stream;
-  simplex_tree_stream.open(inputFile.c_str());
+  simplex_tree_stream.open("simplex_tree_file_for_unit_test.txt");
   typeST st;
   simplex_tree_stream >> st;
   simplex_tree_stream.close();
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
index 6a7ecbec..3537cfa4 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
@@ -22,11 +22,9 @@ using namespace boost::unit_test;
 typedef Simplex_tree<> typeST;
 
 std::string test_rips_persistence(int min_coefficient, int max_coefficient, double min_persistence) {
-  // file name is given as parameter from CMakeLists.txt
-  const std::string inputFile(framework::master_test_suite().argv[1]);
-
+  // file is copied in CMakeLists.txt
   std::ifstream simplex_tree_stream;
-  simplex_tree_stream.open(inputFile.c_str());
+  simplex_tree_stream.open("simplex_tree_file_for_multi_field_unit_test.txt");
   typeST st;
   simplex_tree_stream >> st;
   simplex_tree_stream.close();
diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
index 8e374c09..124dfec9 100644
--- a/src/Rips_complex/doc/Intro_rips_complex.h
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -77,7 +77,7 @@ namespace rips_complex {
  * When launching (Rips maximal distance between 2 points is 12.0, is expanded until dimension 1 - one skeleton graph
  * in other words):
  * 
- * \code $> ./oneskeletonripspoints
+ * \code $> ./Rips_complex_example_one_skeleton_from_points
  * \endcode
  *
  * the program output is:
@@ -97,7 +97,7 @@ namespace rips_complex {
  * 
  * When launching:
  * 
- * \code $> ./ripsoffreader ../../data/points/alphacomplexdoc.off 12.0 3
+ * \code $> ./Rips_complex_example_from_off ../../data/points/alphacomplexdoc.off 12.0 3
  * \endcode
  *
  * the program output is:
@@ -120,7 +120,7 @@ namespace rips_complex {
  * When launching (Rips maximal distance between 2 points is 1.0, is expanded until dimension 1 - one skeleton graph
  * with other words):
  * 
- * \code $> ./oneskeletonripsdistance
+ * \code $> ./Rips_complex_example_one_skeleton_from_distance_matrix
  * \endcode
  *
  * the program output is:
@@ -139,7 +139,7 @@ namespace rips_complex {
  * 
  * When launching:
  * 
- * \code $> ./ripscsvdistancereader ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3
+ * \code $> ./Rips_complex_example_from_csv_distance_matrix ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3
  * \endcode
  *
  * the program output is:
diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt
index 070ac710..8aee79e2 100644
--- a/src/Rips_complex/example/CMakeLists.txt
+++ b/src/Rips_complex/example/CMakeLists.txt
@@ -2,37 +2,40 @@ cmake_minimum_required(VERSION 2.6)
 project(Rips_complex_examples)
 
 # Point cloud
-add_executable ( ripsoffreader example_rips_complex_from_off_file.cpp )
-target_link_libraries(ripsoffreader  ${Boost_SYSTEM_LIBRARY})
+add_executable ( Rips_complex_example_from_off example_rips_complex_from_off_file.cpp )
+target_link_libraries(Rips_complex_example_from_off  ${Boost_SYSTEM_LIBRARY})
 
-add_executable ( oneskeletonripspoints example_one_skeleton_rips_from_points.cpp )
-target_link_libraries(oneskeletonripspoints  ${Boost_SYSTEM_LIBRARY})
+add_executable ( Rips_complex_example_one_skeleton_from_points example_one_skeleton_rips_from_points.cpp )
+target_link_libraries(Rips_complex_example_one_skeleton_from_points  ${Boost_SYSTEM_LIBRARY})
 
 # Distance matrix
-add_executable ( oneskeletonripsdistance example_one_skeleton_rips_from_distance_matrix.cpp )
-target_link_libraries(oneskeletonripsdistance  ${Boost_SYSTEM_LIBRARY})
+add_executable ( Rips_complex_example_one_skeleton_from_distance_matrix example_one_skeleton_rips_from_distance_matrix.cpp )
+target_link_libraries(Rips_complex_example_one_skeleton_from_distance_matrix  ${Boost_SYSTEM_LIBRARY})
 
-add_executable ( ripscsvdistancereader example_rips_complex_from_csv_distance_matrix_file.cpp )
-target_link_libraries(ripscsvdistancereader  ${Boost_SYSTEM_LIBRARY})
+add_executable ( Rips_complex_example_from_csv_distance_matrix example_rips_complex_from_csv_distance_matrix_file.cpp )
+target_link_libraries(Rips_complex_example_from_csv_distance_matrix  ${Boost_SYSTEM_LIBRARY})
 
 if (TBB_FOUND)
-  target_link_libraries(ripsoffreader ${TBB_LIBRARIES})
-  target_link_libraries(oneskeletonripspoints ${TBB_LIBRARIES})
-  target_link_libraries(oneskeletonripsdistance ${TBB_LIBRARIES})
-  target_link_libraries(ripscsvdistancereader ${TBB_LIBRARIES})
+  target_link_libraries(Rips_complex_example_from_off ${TBB_LIBRARIES})
+  target_link_libraries(Rips_complex_example_one_skeleton_from_points ${TBB_LIBRARIES})
+  target_link_libraries(Rips_complex_example_one_skeleton_from_distance_matrix ${TBB_LIBRARIES})
+  target_link_libraries(Rips_complex_example_from_csv_distance_matrix ${TBB_LIBRARIES})
 endif()
 
-add_test(oneskeletonripspoints ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints)
-add_test(oneskeletonripsdistance ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripsdistance)
+add_test(NAME Rips_complex_example_one_skeleton_from_points
+    COMMAND $<TARGET_FILE:Rips_complex_example_one_skeleton_from_points>)
+add_test(NAME Rips_complex_example_one_skeleton_from_distance_matrix
+    COMMAND $<TARGET_FILE:Rips_complex_example_one_skeleton_from_distance_matrix>)
 
-# Do not forget to copy test files in current binary dir
-file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-add_test(ripsoffreader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt)
-add_test(ripsoffreader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt)
+add_test(NAME Rips_complex_example_from_off_doc_12_1 COMMAND $<TARGET_FILE:Rips_complex_example_from_off>
+    "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "12.0" "1" "${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt")
+add_test(NAME Rips_complex_example_from_off_doc_12_3 COMMAND $<TARGET_FILE:Rips_complex_example_from_off>
+    "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "12.0" "3" "${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt")
 
-file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-add_test(ripscsvdistancereader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt)
-add_test(ripscsvdistancereader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt)
+add_test(NAME Rips_complex_example_from_csv_distance_matrix_doc_12_1 COMMAND $<TARGET_FILE:Rips_complex_example_from_csv_distance_matrix>
+    "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "12.0" "1" "${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt")
+add_test(NAME Rips_complex_example_from_csv_distance_matrix_doc_12_3 COMMAND $<TARGET_FILE:Rips_complex_example_from_csv_distance_matrix>
+    "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "12.0" "3" "${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt")
 
 
 if (DIFF_PATH)
@@ -40,8 +43,16 @@ if (DIFF_PATH)
   file(COPY "one_skeleton_rips_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
   file(COPY "full_skeleton_rips_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-  add_test(ripsoffreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt)
-  add_test(ripsoffreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt)
-  add_test(ripscsvreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt)
-  add_test(ripscsvreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt)
+  add_test(Rips_complex_example_from_off_doc_12_1_diff_files ${DIFF_PATH}
+      ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt
+      ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt)
+  add_test(Rips_complex_example_from_off_doc_12_3_diff_files ${DIFF_PATH}
+      ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt
+      ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt)
+  add_test(Rips_complex_example_from_csv_distance_matrix_doc_12_1_diff_files ${DIFF_PATH}
+      ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt
+      ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt)
+  add_test(Rips_complex_example_from_csv_distance_matrix_doc_12_3_diff_files ${DIFF_PATH}
+      ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt
+      ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt)
 endif()
diff --git a/src/Rips_complex/test/CMakeLists.txt b/src/Rips_complex/test/CMakeLists.txt
index 87bad2ed..57f780f1 100644
--- a/src/Rips_complex/test/CMakeLists.txt
+++ b/src/Rips_complex/test/CMakeLists.txt
@@ -1,25 +1,16 @@
 cmake_minimum_required(VERSION 2.6)
 project(Rips_complex_tests)
 
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
+include(GUDHI_test_coverage)
 
-add_executable ( rips_complex_UT test_rips_complex.cpp )
-target_link_libraries(rips_complex_UT  ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( Rips_complex_test_unit test_rips_complex.cpp )
+target_link_libraries(Rips_complex_test_unit  ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(rips_complex_UT ${TBB_LIBRARIES})
+  target_link_libraries(Rips_complex_test_unit ${TBB_LIBRARIES})
 endif()
 
 # Do not forget to copy test files in current binary dir
 file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-add_test(rips_complex_UT ${CMAKE_CURRENT_BINARY_DIR}/rips_complex_UT
-         # XML format for Jenkins xUnit plugin 
-         --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/rips_complex_UT.xml --log_level=test_suite --report_level=no)
+gudhi_add_coverage_test(Rips_complex_test_unit)
diff --git a/src/Simplex_tree/doc/Intro_simplex_tree.h b/src/Simplex_tree/doc/Intro_simplex_tree.h
index 940dd694..f5b72ff6 100644
--- a/src/Simplex_tree/doc/Intro_simplex_tree.h
+++ b/src/Simplex_tree/doc/Intro_simplex_tree.h
@@ -32,7 +32,7 @@ namespace Gudhi {
  * \author    Cl&eacute;ment Maria
  *
  * A simplicial complex \f$\mathbf{K}\f$ on a set of vertices \f$V = \{1, \cdots ,|V|\}\f$ is a collection of
- * implices \f$\{\sigma\}\f$, \f$\sigma \subseteq V\f$ such that
+ * simplices \f$\{\sigma\}\f$, \f$\sigma \subseteq V\f$ such that
  * \f$\tau \subseteq \sigma \in \mathbf{K} \rightarrow \tau \in \mathbf{K}\f$. The dimension \f$n=|\sigma|-1\f$ of
  * \f$\sigma\f$ is its number of elements minus \f$1\f$.
  *
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index e5285591..b1ea98d4 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -1,33 +1,32 @@
 cmake_minimum_required(VERSION 2.6)
 project(Simplex_tree_examples)
 
-add_executable ( simplex_tree_from_cliques_of_graph simplex_tree_from_cliques_of_graph.cpp )
+add_executable ( Simplex_tree_example_from_cliques_of_graph simplex_tree_from_cliques_of_graph.cpp )
 if (TBB_FOUND)
-  target_link_libraries(simplex_tree_from_cliques_of_graph ${TBB_LIBRARIES})
+  target_link_libraries(Simplex_tree_example_from_cliques_of_graph ${TBB_LIBRARIES})
 endif()
-add_test(simplex_tree_from_cliques_of_graph_2 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph
-         ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/Klein_bottle_complex.fsc 2)
-add_test(simplex_tree_from_cliques_of_graph_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph
-         ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/Klein_bottle_complex.fsc 3)
+add_test(NAME Simplex_tree_example_from_cliques_of_graph_2 COMMAND $<TARGET_FILE:Simplex_tree_example_from_cliques_of_graph>
+    "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/Klein_bottle_complex.fsc" "2")
+add_test(NAME Simplex_tree_example_from_cliques_of_graph_3 COMMAND $<TARGET_FILE:Simplex_tree_example_from_cliques_of_graph>
+    "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/Klein_bottle_complex.fsc" "3")
 
-add_executable ( simple_simplex_tree simple_simplex_tree.cpp )
+add_executable ( Simplex_tree_example_simple_simplex_tree simple_simplex_tree.cpp )
 if (TBB_FOUND)
-  target_link_libraries(simple_simplex_tree ${TBB_LIBRARIES})
+  target_link_libraries(Simplex_tree_example_simple_simplex_tree ${TBB_LIBRARIES})
 endif()
-add_test(simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/simple_simplex_tree)
+add_test(NAME Simplex_tree_example_simple_simplex_tree COMMAND $<TARGET_FILE:Simplex_tree_example_simple_simplex_tree>)
 
-add_executable ( mini_simplex_tree mini_simplex_tree.cpp )
-add_test(mini_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/mini_simplex_tree)
+add_executable ( Simplex_tree_example_mini_simplex_tree mini_simplex_tree.cpp )
+add_test(NAME Simplex_tree_example_mini_simplex_tree COMMAND $<TARGET_FILE:Simplex_tree_example_mini_simplex_tree>)
 
 
 # An example with Simplex-tree using CGAL alpha_shapes_3
 if(GMP_FOUND AND CGAL_FOUND)
-  add_executable ( alpha_shapes_3_simplex_tree_from_off_file example_alpha_shapes_3_simplex_tree_from_off_file.cpp )
-  target_link_libraries(alpha_shapes_3_simplex_tree_from_off_file ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY})
+  add_executable ( Simplex_tree_example_alpha_shapes_3_from_off example_alpha_shapes_3_simplex_tree_from_off_file.cpp )
+  target_link_libraries(Simplex_tree_example_alpha_shapes_3_from_off ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY})
   if (TBB_FOUND)
-    target_link_libraries(alpha_shapes_3_simplex_tree_from_off_file ${TBB_LIBRARIES})
+    target_link_libraries(Simplex_tree_example_alpha_shapes_3_from_off ${TBB_LIBRARIES})
   endif()
-  add_test(alpha_shapes_3_simplex_tree_from_off_file
-           ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_3_simplex_tree_from_off_file
-           ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off)
+  add_test(NAME Simplex_tree_example_alpha_shapes_3_from_off COMMAND $<TARGET_FILE:Simplex_tree_example_alpha_shapes_3_from_off>
+      "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off")
 endif()
diff --git a/src/Simplex_tree/example/README b/src/Simplex_tree/example/README
index e37af790..a9498173 100644
--- a/src/Simplex_tree/example/README
+++ b/src/Simplex_tree/example/README
@@ -10,7 +10,7 @@ Example of use :
 
 *** Simple simplex tree construction
 
-./simple_simplex_tree
+./Simplex_tree_example_simple_simplex_tree
 
 ********************************************************************
 EXAMPLE OF SIMPLE INSERTION
@@ -52,7 +52,7 @@ EXAMPLE OF SIMPLE INSERTION
 
 *** Simplex tree construction with Z/2Z coefficients on weighted graph Klein bottle file:
 
-./simplex_tree_from_cliques_of_graph ../../../data/points/Klein_bottle_complex.txt 2
+./Simplex_tree_example_from_cliques_of_graph ../../../data/points/Klein_bottle_complex.txt 2
 Insert the 1-skeleton in the simplex tree in 0 s. 
 Expand the simplex tree in 0 s. 
 Information of the Simplex Tree: 
@@ -60,7 +60,7 @@ Information of the Simplex Tree:
 
 with Z/3Z coefficients:
 
-./simplex_tree_from_cliques_of_graph ../../../data/points/Klein_bottle_complex.txt 3
+./Simplex_tree_example_from_cliques_of_graph ../../../data/points/Klein_bottle_complex.txt 3
 
 Insert the 1-skeleton in the simplex tree in 0 s.
 Expand the simplex tree in 0 s.
@@ -70,4 +70,4 @@ Information of the Simplex Tree:
 *** Simplex_tree computed and displayed from a 3D alpha complex:
     [ Requires CGAL, GMP and GMPXX to be installed]
 
-./simplex_tree_from_alpha_shapes_3 ../../../data/points/bunny_5000
+./Simplex_tree_example_alpha_shapes_3_from_off ../../../data/points/bunny_5000
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index e95d0782..17b0f2c2 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -1,27 +1,15 @@
 cmake_minimum_required(VERSION 2.6)
 project(Simplex_tree_tests)
 
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
+include(GUDHI_test_coverage)
 
-add_executable ( SimplexTreeUT simplex_tree_unit_test.cpp )
-target_link_libraries(SimplexTreeUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( Simplex_tree_test_unit simplex_tree_unit_test.cpp )
+target_link_libraries(Simplex_tree_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(SimplexTreeUT ${TBB_LIBRARIES})
+  target_link_libraries(Simplex_tree_test_unit ${TBB_LIBRARIES})
 endif()
 
 # Do not forget to copy test files in current binary dir
 file(COPY "simplex_tree_for_unit_test.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-# Unitary tests
-add_test(NAME SimplexTreeUT
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/SimplexTreeUT 
-    # XML format for Jenkins xUnit plugin 
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/SimplexTreeUT.xml --log_level=test_suite --report_level=no)
-
+gudhi_add_coverage_test(Simplex_tree_test_unit)
diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt
index cc7f37f3..c887e408 100644
--- a/src/Skeleton_blocker/example/CMakeLists.txt
+++ b/src/Skeleton_blocker/example/CMakeLists.txt
@@ -1,12 +1,12 @@
 cmake_minimum_required(VERSION 2.6)
 project(Skeleton_blocker_examples)
 
-add_executable(SkeletonBlockerFromSimplices Skeleton_blocker_from_simplices.cpp)
-add_executable(SkeletonBlockerIteration Skeleton_blocker_iteration.cpp)
-add_executable(SkeletonBlockerLink Skeleton_blocker_link.cpp)
+add_executable(Skeleton_blocker_example_from_simplices Skeleton_blocker_from_simplices.cpp)
+add_executable(Skeleton_blocker_example_iteration Skeleton_blocker_iteration.cpp)
+add_executable(Skeleton_blocker_example_link Skeleton_blocker_link.cpp)
 
-target_link_libraries(SkeletonBlockerIteration ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY})
+target_link_libraries(Skeleton_blocker_example_iteration ${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)
+add_test(NAME Skeleton_blocker_example_from_simplices COMMAND $<TARGET_FILE:Skeleton_blocker_example_from_simplices>)
+add_test(NAME Skeleton_blocker_example_iteration COMMAND $<TARGET_FILE:Skeleton_blocker_example_iteration>)
+add_test(NAME Skeleton_blocker_example_link COMMAND $<TARGET_FILE:Skeleton_blocker_example_link>)
diff --git a/src/Skeleton_blocker/test/CMakeLists.txt b/src/Skeleton_blocker/test/CMakeLists.txt
index f98517f0..0887fcff 100644
--- a/src/Skeleton_blocker/test/CMakeLists.txt
+++ b/src/Skeleton_blocker/test/CMakeLists.txt
@@ -1,35 +1,18 @@
 cmake_minimum_required(VERSION 2.6)
 project(Skeleton_blocker_tests)
 
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
+include(GUDHI_test_coverage)
 
-add_executable ( test_skeleton_blocker_complex test_skeleton_blocker_complex.cpp )
-target_link_libraries(test_skeleton_blocker_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-add_executable ( test_skeleton_blocker_geometric_complex test_skeleton_blocker_geometric_complex.cpp )
-target_link_libraries(test_skeleton_blocker_geometric_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-add_executable ( test_skeleton_blocker_simplifiable test_skeleton_blocker_simplifiable.cpp )
-target_link_libraries(test_skeleton_blocker_simplifiable ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( Skeleton_blocker_test_unit test_skeleton_blocker_complex.cpp )
+target_link_libraries(Skeleton_blocker_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( Skeleton_blocker_test_geometric_complex test_skeleton_blocker_geometric_complex.cpp )
+target_link_libraries(Skeleton_blocker_test_geometric_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( Skeleton_blocker_test_simplifiable test_skeleton_blocker_simplifiable.cpp )
+target_link_libraries(Skeleton_blocker_test_simplifiable ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
 # Do not forget to copy test files in current binary dir
 file(COPY "test2.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-# Unitary tests
-add_test(NAME test_skeleton_blocker_complex
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/test_skeleton_blocker_complex
-    # XML format for Jenkins xUnit plugin 
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/skbl_complexUT.xml --log_level=test_suite --report_level=no)
-add_test(NAME test_skeleton_blocker_geometric_complex
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/test_skeleton_blocker_geometric_complex
-    # XML format for Jenkins xUnit plugin 
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/skbl_geometric_complexUT.xml --log_level=test_suite --report_level=no)
-add_test(NAME test_skeleton_blocker_simplifiable
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/test_skeleton_blocker_simplifiable
-    # XML format for Jenkins xUnit plugin 
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/skbl_simplifiableUT.xml --log_level=test_suite --report_level=no)
+gudhi_add_coverage_test(Skeleton_blocker_test_unit)
+gudhi_add_coverage_test(Skeleton_blocker_test_geometric_complex)
+gudhi_add_coverage_test(Skeleton_blocker_test_simplifiable)
diff --git a/src/Spatial_searching/example/CMakeLists.txt b/src/Spatial_searching/example/CMakeLists.txt
index 6238a0ec..f4b9f3cb 100644
--- a/src/Spatial_searching/example/CMakeLists.txt
+++ b/src/Spatial_searching/example/CMakeLists.txt
@@ -1,13 +1,9 @@
 cmake_minimum_required(VERSION 2.6)
 project(Spatial_searching_examples)
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    if (EIGEN3_FOUND)
-      add_executable( Spatial_searching_example_spatial_searching example_spatial_searching.cpp )
-      target_link_libraries(Spatial_searching_example_spatial_searching ${CGAL_LIBRARY})
-      add_test(Spatial_searching_example_spatial_searching
-               ${CMAKE_CURRENT_BINARY_DIR}/Spatial_searching_example_spatial_searching)
-    endif()
-  endif()
-endif()
+if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable( Spatial_searching_example_spatial_searching example_spatial_searching.cpp )
+  target_link_libraries(Spatial_searching_example_spatial_searching ${CGAL_LIBRARY})
+  add_test(NAME Spatial_searching_example_spatial_searching
+      COMMAND $<TARGET_FILE:Spatial_searching_example_spatial_searching>)
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Spatial_searching/test/CMakeLists.txt b/src/Spatial_searching/test/CMakeLists.txt
index bdc95e4a..2502ea5e 100644
--- a/src/Spatial_searching/test/CMakeLists.txt
+++ b/src/Spatial_searching/test/CMakeLists.txt
@@ -1,21 +1,12 @@
 cmake_minimum_required(VERSION 2.6)
 project(Spatial_searching_tests)
 
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
-
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  include(GUDHI_test_coverage)
+
   add_executable( Spatial_searching_test_Kd_tree_search test_Kd_tree_search.cpp )
   target_link_libraries(Spatial_searching_test_Kd_tree_search
     ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-  add_test(Spatial_searching_test_Kd_tree_search ${CMAKE_CURRENT_BINARY_DIR}/Spatial_searching_test_Kd_tree_search
-  # XML format for Jenkins xUnit plugin
-  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Spatial_searching_UT.xml --log_level=test_suite --report_level=no)
+  gudhi_add_coverage_test(Spatial_searching_test_Kd_tree_search)
 endif ()
diff --git a/src/Subsampling/example/CMakeLists.txt b/src/Subsampling/example/CMakeLists.txt
index bb043297..71b8d2e8 100644
--- a/src/Subsampling/example/CMakeLists.txt
+++ b/src/Subsampling/example/CMakeLists.txt
@@ -8,10 +8,10 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   add_executable(Subsampling_example_sparsify_point_set example_sparsify_point_set.cpp)
   target_link_libraries(Subsampling_example_sparsify_point_set ${CGAL_LIBRARY})
 
-  add_test(Subsampling_example_pick_n_random_points
-           ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_pick_n_random_points)
-  add_test(Subsampling_example_choose_n_farthest_points
-           ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_choose_n_farthest_points)
-  add_test(Subsampling_example_sparsify_point_set
-           ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_sparsify_point_set)
+  add_test(NAME Subsampling_example_pick_n_random_points
+      COMMAND $<TARGET_FILE:Subsampling_example_pick_n_random_points>)
+  add_test(NAME Subsampling_example_choose_n_farthest_points
+      COMMAND $<TARGET_FILE:Subsampling_example_choose_n_farthest_points>)
+  add_test(NAME Subsampling_example_sparsify_point_set
+      COMMAND $<TARGET_FILE:Subsampling_example_sparsify_point_set>)
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Subsampling/test/CMakeLists.txt b/src/Subsampling/test/CMakeLists.txt
index 5517fe9d..dbf97db3 100644
--- a/src/Subsampling/test/CMakeLists.txt
+++ b/src/Subsampling/test/CMakeLists.txt
@@ -1,16 +1,9 @@
 cmake_minimum_required(VERSION 2.6)
 project(Subsampling_tests)
 
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
-
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  include(GUDHI_test_coverage)
+
   add_executable( Subsampling_test_pick_n_random_points test_pick_n_random_points.cpp )
   target_link_libraries(Subsampling_test_pick_n_random_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
@@ -20,15 +13,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   add_executable(Subsampling_test_sparsify_point_set test_sparsify_point_set.cpp)
   target_link_libraries(Subsampling_test_sparsify_point_set ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-  add_test(Subsampling_test_pick_n_random_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_pick_n_random_points
-  # XML format for Jenkins xUnit plugin
-  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_pick_n_random_points_UT.xml --log_level=test_suite --report_level=no)
-
-  add_test(Subsampling_test_choose_n_farthest_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_choose_n_farthest_points
-  # XML format for Jenkins xUnit plugin
-  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_choose_n_farthest_points_UT.xml --log_level=test_suite --report_level=no)
-
-  add_test(Subsampling_test_sparsify_point_set ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_sparsify_point_set
-  # XML format for Jenkins xUnit plugin
-  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_sparsify_point_set_UT.xml --log_level=test_suite --report_level=no)
+  gudhi_add_coverage_test(Subsampling_test_pick_n_random_points)
+  gudhi_add_coverage_test(Subsampling_test_choose_n_farthest_points)
+  gudhi_add_coverage_test(Subsampling_test_sparsify_point_set)
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt
index 47a56e3b..339d0581 100644
--- a/src/Tangential_complex/example/CMakeLists.txt
+++ b/src/Tangential_complex/example/CMakeLists.txt
@@ -11,9 +11,8 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES})
   endif(TBB_FOUND)
 
-  add_test(Tangential_complex_example_basic
-           ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_basic)
-
-  add_test(Tangential_complex_example_with_perturb
-           ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_with_perturb)
+  add_test(NAME Tangential_complex_example_basic
+      COMMAND $<TARGET_FILE:Tangential_complex_example_basic>)
+  add_test(NAME Tangential_complex_example_with_perturb
+      COMMAND $<TARGET_FILE:Tangential_complex_example_with_perturb>)
 endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h
index cfc82eb1..9fa7c825 100644
--- a/src/Tangential_complex/include/gudhi/Tangential_complex.h
+++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h
@@ -1059,7 +1059,6 @@ class Tangential_complex {
                                 Triangulation &triangulation, bool verbose = false) {
     int tangent_space_dim = tsb.dimension();
     const Tr_traits &local_tr_traits = triangulation.geom_traits();
-    Tr_vertex_handle center_vertex;
 
     // Kernel functor & objects
     typename K::Squared_distance_d k_sqdist = m_k.squared_distance_d_object();
@@ -1084,7 +1083,7 @@ class Tangential_complex {
       proj_wp = project_point_and_compute_weight(wp, tsb, local_tr_traits);
     }
 
-    center_vertex = triangulation.insert(proj_wp);
+    Tr_vertex_handle center_vertex = triangulation.insert(proj_wp);
     center_vertex->data() = i;
     if (verbose)
       std::cerr << "* Inserted point #" << i << "\n";
@@ -1823,7 +1822,6 @@ class Tangential_complex {
     bool is_inconsistent = false;
 
     Star const& star = m_stars[tr_index];
-    Tr_vertex_handle center_vh = m_triangulations[tr_index].center_vertex();
 
     // For each incident simplex
     Star::const_iterator it_inc_simplex = star.begin();
@@ -1950,7 +1948,6 @@ class Tangential_complex {
       bool is_star_inconsistent = false;
 
       Triangulation const& tr = it_tr->tr();
-      Tr_vertex_handle center_vh = it_tr->center_vertex();
 
       if (tr.current_dimension() < m_intrinsic_dim)
         continue;
diff --git a/src/Tangential_complex/test/CMakeLists.txt b/src/Tangential_complex/test/CMakeLists.txt
index b2bf5dd7..fc710676 100644
--- a/src/Tangential_complex/test/CMakeLists.txt
+++ b/src/Tangential_complex/test/CMakeLists.txt
@@ -1,23 +1,14 @@
 cmake_minimum_required(VERSION 2.6)
 project(Tangential_complex_tests)
 
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
-
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  include(GUDHI_test_coverage)
+
   add_executable( Tangential_complex_test_TC test_tangential_complex.cpp )
   target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Tangential_complex_test_TC ${TBB_LIBRARIES})
   endif()
-  add_test(Tangential_complex_test_TC ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_test_TC
-  # XML format for Jenkins xUnit plugin
-  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Tangential_complex_UT.xml --log_level=test_suite --report_level=no)
 
+  gudhi_add_coverage_test(Tangential_complex_test_TC)
 endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index 549a85be..670651ce 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -6,7 +6,8 @@ target_link_libraries(Witness_complex_example_nearest_landmark_table ${Boost_SYS
 if (TBB_FOUND)
   target_link_libraries(Witness_complex_example_nearest_landmark_table ${TBB_LIBRARIES})
 endif()
-add_test(Witness_complex_test_nearest_landmark_table Witness_complex_example_nearest_landmark_table)
+add_test(NAME Witness_complex_example_nearest_landmark_table
+    COMMAND $<TARGET_FILE:Witness_complex_example_nearest_landmark_table>)
 
 # CGAL and Eigen3 are required for Euclidean version of Witness
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
@@ -28,17 +29,18 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
     target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES})
   endif()
 
-  add_test(Witness_complex_off_test_torus
-           ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_off
-           ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 20 1.0 3)
-  add_test(Witness_complex_strong_off_test_torus
-           ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_strong_off
-           ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 20 1.0 3)
-  add_test(Witness_complex_test_sphere_10 Witness_complex_example_sphere 10)
-  add_test(Witness_complex_test_torus_persistence
-           ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_witness_persistence
-           ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -l 20 -a 0.5)
-  add_test(Witness_complex_strong_test_torus_persistence
-           ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_strong_witness_persistence
-           ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -l 20 -a 0.5)
+  add_test(NAME Witness_complex_example_off_test_torus
+      COMMAND $<TARGET_FILE:Witness_complex_example_off>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3")
+  add_test(NAME Witness_complex_example_strong_off_test_torus
+      COMMAND $<TARGET_FILE:Witness_complex_example_strong_off>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3")
+  add_test(NAME Witness_complex_example_test_sphere_10
+      COMMAND $<TARGET_FILE:Witness_complex_example_sphere> "10")
+  add_test(NAME Witness_complex_example_test_torus_persistence
+      COMMAND $<TARGET_FILE:Witness_complex_example_witness_persistence>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
+  add_test(NAME Witness_complex_example_strong_test_torus_persistence
+      COMMAND $<TARGET_FILE:Witness_complex_example_strong_witness_persistence>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
index a973ddb7..6f4bcf60 100644
--- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
@@ -105,10 +105,6 @@ class Strong_witness_complex {
                 << "non-negative.\n";
       return false;
     }
-    if (limit_dimension < 0) {
-      std::cerr << "Strong witness complex cannot create complex - limit dimension must be non-negative.\n";
-      return false;
-    }
     for (auto w : nearest_landmark_table_) {
       ActiveWitness aw(w);
       typeVectorVertex simplex;
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index 63f03687..bcfe8484 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -106,10 +106,6 @@ class Witness_complex {
       std::cerr << "Witness complex cannot create complex - squared relaxation parameter must be non-negative.\n";
       return false;
     }
-    if (limit_dimension < 0) {
-      std::cerr << "Witness complex cannot create complex - limit dimension must be non-negative.\n";
-      return false;
-    }
     ActiveWitnessList active_witnesses;
     Landmark_id k = 0; /* current dimension in iterative construction */
     for (auto w : nearest_landmark_table_)
diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt
index e73f9c3a..152e2f2c 100644
--- a/src/Witness_complex/test/CMakeLists.txt
+++ b/src/Witness_complex/test/CMakeLists.txt
@@ -1,14 +1,7 @@
 cmake_minimum_required(VERSION 2.6)
 project(Witness_complex_tests)
 
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
+include(GUDHI_test_coverage)
 
 add_executable ( Witness_complex_test_simple_witness_complex test_simple_witness_complex.cpp )
 target_link_libraries(Witness_complex_test_simple_witness_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
@@ -16,11 +9,7 @@ if (TBB_FOUND)
   target_link_libraries(Witness_complex_test_simple_witness_complex ${TBB_LIBRARIES})
 endif(TBB_FOUND)
 
-# Unitary tests definition and xml result file generation
-add_test(NAME simple_witness_complex
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_test_simple_witness_complex 
-    # XML format for Jenkins xUnit plugin 
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Witness_complex_test_simple_witness_complexUT.xml --log_level=test_suite --report_level=no)
+gudhi_add_coverage_test(Witness_complex_test_simple_witness_complex)
 
 # CGAL and Eigen3 are required for Euclidean version of Witness
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
@@ -30,9 +19,5 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
     target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${TBB_LIBRARIES})
   endif(TBB_FOUND)
 
-  # Unitary tests definition and xml result file generation
-  add_test(NAME euclidean_simple_witness_complex
-    COMMAND ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_test_euclidean_simple_witness_complex
-      # XML format for Jenkins xUnit plugin
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Witness_complex_test_euclidean_simple_witness_complexUT.xml --log_level=test_suite --report_level=no)
+  gudhi_add_coverage_test(Witness_complex_test_euclidean_simple_witness_complex)
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/cmake/modules/FindCython.cmake b/src/cmake/modules/FindCython.cmake
new file mode 100644
index 00000000..04aed1f8
--- /dev/null
+++ b/src/cmake/modules/FindCython.cmake
@@ -0,0 +1,44 @@
+# Find the Cython compiler.
+#
+# This code sets the following variables:
+#
+#  CYTHON_EXECUTABLE
+#
+# See also UseCython.cmake
+
+#=============================================================================
+# Copyright 2011 Kitware, Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#=============================================================================
+
+# Use the Cython executable that lives next to the Python executable
+# if it is a local installation.
+find_package( PythonInterp )
+if( PYTHONINTERP_FOUND )
+  get_filename_component( _python_path ${PYTHON_EXECUTABLE} PATH )
+  find_program( CYTHON_EXECUTABLE
+    NAMES cython cython.bat cython3
+    HINTS ${_python_path}
+    )
+else()
+  find_program( CYTHON_EXECUTABLE
+    NAMES cython cython.bat cython3
+    )
+endif()
+
+
+include( FindPackageHandleStandardArgs )
+FIND_PACKAGE_HANDLE_STANDARD_ARGS( Cython REQUIRED_VARS CYTHON_EXECUTABLE )
+
+mark_as_advanced( CYTHON_EXECUTABLE )
diff --git a/src/cmake/modules/GUDHI_doxygen_target.txt b/src/cmake/modules/GUDHI_doxygen_target.cmake
index d2cb952d..d2cb952d 100644
--- a/src/cmake/modules/GUDHI_doxygen_target.txt
+++ b/src/cmake/modules/GUDHI_doxygen_target.cmake
diff --git a/src/cmake/modules/GUDHI_test_coverage.cmake b/src/cmake/modules/GUDHI_test_coverage.cmake
new file mode 100644
index 00000000..ce171a0e
--- /dev/null
+++ b/src/cmake/modules/GUDHI_test_coverage.cmake
@@ -0,0 +1,14 @@
+
+if (GCOVR_PATH)
+  # for gcovr to make coverage reports - Corbera Jenkins plugin
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+  # for gprof to make coverage reports - Jenkins
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+endif()
+
+function(gudhi_add_coverage_test unitary_test)
+  add_test(NAME ${unitary_test} COMMAND $<TARGET_FILE:${unitary_test}>
+      "--log_format=XML" "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml" "--log_level=test_suite" "--report_level=no")
+endfunction()
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.txt b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 2ddc9f1f..5f84c602 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.txt
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -121,33 +121,24 @@ endmacro( find_the_lib )
 
 # Find the correct Python interpreter.
 # Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
-if(PYTHON_EXECUTABLE)
-  if(NOT EXISTS "${PYTHON_EXECUTABLE}")
-    message(FATAL_ERROR "ERROR: ${PYTHON_EXECUTABLE} does not exist.")
-  endif(NOT EXISTS "${PYTHON_EXECUTABLE}")
-endif(PYTHON_EXECUTABLE)
-find_package(PythonInterp)
+find_package(Cython)
 
 if(NOT GUDHI_CYTHON_PATH)
   message(FATAL_ERROR "ERROR: GUDHI_CYTHON_PATH is not valid.")
 endif(NOT GUDHI_CYTHON_PATH)
 
-if(PYTHONINTERP_FOUND)
+if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
+  # Unitary tests are available through py.test
+  find_program( PYTEST_PATH py.test )
   # Default found version 2
   if(PYTHON_VERSION_MAJOR EQUAL 2)
-    FIND_PROGRAM(CYTHON_PATH cython)
-    # Unitary tests are available through py.test
-    find_program( PYTEST_PATH py.test )
     # Documentation generation is available through sphinx
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
-    FIND_PROGRAM(CYTHON_PATH cython3)
-    # Unitary tests are available through py.test
-    find_program( PYTEST_PATH py.test )
     # Documentation generation is available through sphinx
     set(SPHINX_PATH "${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
   else()
     message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
   endif(PYTHON_VERSION_MAJOR EQUAL 2)
-endif(PYTHONINTERP_FOUND)
+endif(PYTHONINTERP_FOUND AND CYTHON_FOUND)
 
diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt
index e4c4ca93..0d409cc3 100644
--- a/src/cmake/modules/GUDHI_user_version_target.txt
+++ b/src/cmake/modules/GUDHI_user_version_target.txt
@@ -35,8 +35,6 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
                      copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfig.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfig.cmake.in)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy ${CMAKE_SOURCE_DIR}/CMakeGUDHIVersion.txt ${GUDHI_USER_VERSION_DIR}/CMakeGUDHIVersion.txt)
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy ${CMAKE_SOURCE_DIR}/GUDHIVersion.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIVersion.cmake.in)
   
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy_directory ${CMAKE_SOURCE_DIR}/biblio ${GUDHI_USER_VERSION_DIR}/biblio)
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
index 94e641b2..53b5c0a2 100644
--- a/src/common/doc/header.html
+++ b/src/common/doc/header.html
@@ -64,8 +64,8 @@ $extrastylesheet
                   <ul class="dropdown">
                       <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">C++ documentation</a></li>
                       <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li>
-                      <li><a href="http://gudhi.gforge.inria.fr/cython/latest/">Cython documentation</a></li>
-                      <li><a href="http://gudhi.gforge.inria.fr/cython/latest/installation.html">Cython installation manual</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/python/latest/">Python documentation</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/python/latest/installation.html">Python installation manual</a></li>
                   </ul>
               </li>
               <li class="divider"></li>
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index b1625e69..8d282fca 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -1,11 +1,10 @@
-/*! \mainpage
+/*! \mainpage The C++ library
  *  \tableofcontents
  * \image html "Gudhi_banner.png" "" width=20cm
  * 
  * \section Introduction Introduction
  * The GUDHI library (Geometry Understanding in Higher Dimensions) is a generic open source
- * <a class="el" target="_blank" href="http://gudhi.gforge.inria.fr/doc/latest/">C++ library</a>, with a
- * <a class="el" target="_blank" href="http://gudhi.gforge.inria.fr/cython/latest/">Cython interface</a>, for
+ * <a class="el" target="_blank" href="http://gudhi.gforge.inria.fr/doc/latest/">C++ library</a> for
  * Computational Topology and Topological Data Analysis
  * (<a class="el" target="_blank" href="https://en.wikipedia.org/wiki/Topological_data_analysis">TDA</a>).
  * The GUDHI library intends  to help the development of new algorithmic solutions in TDA and their transfer to
@@ -16,7 +15,7 @@
  * 
  * \li Data structures to represent, construct and manipulate simplicial complexes.
  * \li Simplification of simplicial complexes by edge contraction.
- * \li Algorithms to compute persistent homology persistent homology.
+ * \li Algorithms to compute persistent homology and bottleneck distance.
  * 
  * All data-structures are generic and several of their aspects can be parameterized via template classes.
  * We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library.
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
index 61c94391..d5311b18 100644
--- a/src/common/example/CMakeLists.txt
+++ b/src/common/example/CMakeLists.txt
@@ -3,17 +3,20 @@ project(Common_examples)
 
 add_executable ( vector_double_off_reader example_vector_double_points_off_reader.cpp )
 target_link_libraries(vector_double_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-add_test(vector_double_off_reader ${CMAKE_CURRENT_BINARY_DIR}/vector_double_off_reader ${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off)
+add_test(NAME Common_example_vector_double_off_reader COMMAND $<TARGET_FILE:vector_double_off_reader>
+    "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off")
 
 if(CGAL_FOUND)
   add_executable ( cgal_3D_off_reader example_CGAL_3D_points_off_reader.cpp )
   target_link_libraries(cgal_3D_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-  add_test(cgal_3D_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_3D_off_reader ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+  add_test(NAME Common_example_vector_cgal_3D_off_reader COMMAND $<TARGET_FILE:cgal_3D_off_reader>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off")
 
   # need CGAL 4.7and Eigen3
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     add_executable ( cgal_off_reader example_CGAL_points_off_reader.cpp )
     target_link_libraries(cgal_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-    add_test(cgal_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_off_reader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off)
+    add_test(NAME Common_example_vector_cgal_off_reader COMMAND $<TARGET_FILE:cgal_off_reader>
+        "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off")
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 endif()
diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt
index baa24539..c695fbf4 100644
--- a/src/common/test/CMakeLists.txt
+++ b/src/common/test/CMakeLists.txt
@@ -1,33 +1,18 @@
 cmake_minimum_required(VERSION 2.6)
 project(Common_tests)
 
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
+include(GUDHI_test_coverage)
 
-add_executable ( poffreader_UT test_points_off_reader.cpp )
-target_link_libraries(poffreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( Common_test_points_off_reader test_points_off_reader.cpp )
+target_link_libraries(Common_test_points_off_reader ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-add_executable ( distancematrixreader_UT test_distance_matrix_reader.cpp )
-target_link_libraries(distancematrixreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( Common_test_distance_matrix_reader test_distance_matrix_reader.cpp )
+target_link_libraries(Common_test_distance_matrix_reader ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
 # Do not forget to copy test files in current binary dir
 file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-# Unitary tests
-add_test(poffreader_UT ${CMAKE_CURRENT_BINARY_DIR}/poffreader_UT
-         # XML format for Jenkins xUnit plugin 
-         --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/poffreader_UT.xml --log_level=test_suite --report_level=no)
-
-add_test(distancematrixreader_UT ${CMAKE_CURRENT_BINARY_DIR}/distancematrixreader_UT
-         # XML format for Jenkins xUnit plugin 
-         --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/distancematrixreader_UT.xml --log_level=test_suite --report_level=no)
-
-
+gudhi_add_coverage_test(Common_test_points_off_reader)
+gudhi_add_coverage_test(Common_test_distance_matrix_reader)
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 51c208aa..96c2acb3 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -1,8 +1,8 @@
 cmake_minimum_required(VERSION 2.8)
 project(Cython)
 
-if(CYTHON_PATH)
-  message("${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_PATH} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}")
+if(CYTHON_FOUND)
+  message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}")
 
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
@@ -281,4 +281,4 @@ if(CYTHON_PATH)
           COMMAND make.bat html doctest)
     endif (UNIX)
   endif(SPHINX_PATH)
-endif(CYTHON_PATH)
+endif(CYTHON_FOUND)
diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html
index af0eef64..b11c1236 100644
--- a/src/cython/doc/_templates/layout.html
+++ b/src/cython/doc/_templates/layout.html
@@ -205,8 +205,8 @@
                     <ul class="dropdown">
                         <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">C++ documentation</a></li>
                         <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li>
-                        <li><a href="http://gudhi.gforge.inria.fr/cython/latest/">Cython documentation</a></li>
-                        <li><a href="http://gudhi.gforge.inria.fr/cython/latest/installation.html">Cython installation manual</a></li>
+                        <li><a href="http://gudhi.gforge.inria.fr/python/latest/">Python documentation</a></li>
+                        <li><a href="http://gudhi.gforge.inria.fr/python/latest/installation.html">Python installation manual</a></li>
                     </ul>
                 </li>
                 <li class="divider"></li>
diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst
index 8437e901..a5f6420a 100644
--- a/src/cython/doc/alpha_complex_sum.rst
+++ b/src/cython/doc/alpha_complex_sum.rst
@@ -16,7 +16,7 @@
 |                                                                | complex.                                                               |
 |                                                                |                                                                        |
 |                                                                | This package requires having CGAL version 4.7 or higher (4.8.1 is      |
-|                                                                | advised for better perfomances).                                       |
+|                                                                | advised for better performance).                                       |
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | :doc:`alpha_complex_user`                                      | :doc:`alpha_complex_ref`                                               |
 +----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst
index 2356944d..e8268ef1 100644
--- a/src/cython/doc/alpha_complex_user.rst
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -1,4 +1,3 @@
-=========================
 Alpha complex user manual
 =========================
 Definition
@@ -30,39 +29,40 @@ This example builds the Delaunay triangulation from the given points, and initia
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
+    fmt = '%s -> %.2f'
     for filtered_value in simplex_tree.get_filtration():
-        print(filtered_value)
+        print(fmt % tuple(filtered_value))
 
 The output is:
 
 .. testoutput::
 
    Alpha complex is of dimension 2 - 25 simplices - 7 vertices.
-   ([0], 0.0)
-   ([1], 0.0)
-   ([2], 0.0)
-   ([3], 0.0)
-   ([4], 0.0)
-   ([5], 0.0)
-   ([6], 0.0)
-   ([2, 3], 6.25)
-   ([4, 5], 7.25)
-   ([0, 2], 8.5)
-   ([0, 1], 9.25)
-   ([1, 3], 10.0)
-   ([1, 2], 11.25)
-   ([1, 2, 3], 12.5)
-   ([0, 1, 2], 12.995867768595042)
-   ([5, 6], 13.25)
-   ([2, 4], 20.0)
-   ([4, 6], 22.736686390532547)
-   ([4, 5, 6], 22.736686390532547)
-   ([3, 6], 30.25)
-   ([2, 6], 36.5)
-   ([2, 3, 6], 36.5)
-   ([2, 4, 6], 37.24489795918368)
-   ([0, 4], 59.710743801652896)
-   ([0, 2, 4], 59.710743801652896)
+   [0] -> 0.00
+   [1] -> 0.00
+   [2] -> 0.00
+   [3] -> 0.00
+   [4] -> 0.00
+   [5] -> 0.00
+   [6] -> 0.00
+   [2, 3] -> 6.25
+   [4, 5] -> 7.25
+   [0, 2] -> 8.50
+   [0, 1] -> 9.25
+   [1, 3] -> 10.00
+   [1, 2] -> 11.25
+   [1, 2, 3] -> 12.50
+   [0, 1, 2] -> 13.00
+   [5, 6] -> 13.25
+   [2, 4] -> 20.00
+   [4, 6] -> 22.74
+   [4, 5, 6] -> 22.74
+   [3, 6] -> 30.25
+   [2, 6] -> 36.50
+   [2, 3, 6] -> 36.50
+   [2, 4, 6] -> 37.24
+   [0, 4] -> 59.71
+   [0, 2, 4] -> 59.71
 
 
 Algorithm
@@ -164,39 +164,39 @@ Then, it is asked to display information about the alpha complex:
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
+    fmt = '%s -> %.2f'
     for filtered_value in simplex_tree.get_filtration():
-        print(filtered_value)
+        print(fmt % tuple(filtered_value))
 
 the program output is:
 
 .. testoutput::
 
    Alpha complex is of dimension 2 - 23 simplices - 7 vertices.
-   ([0], 0.0)
-   ([1], 0.0)
-   ([2], 0.0)
-   ([3], 0.0)
-   ([4], 0.0)
-   ([5], 0.0)
-   ([6], 0.0)
-   ([2, 3], 6.25)
-   ([4, 5], 7.25)
-   ([0, 2], 8.5)
-   ([0, 1], 9.25)
-   ([1, 3], 10.0)
-   ([1, 2], 11.25)
-   ([1, 2, 3], 12.5)
-   ([0, 1, 2], 12.995867768595042)
-   ([5, 6], 13.25)
-   ([2, 4], 20.0)
-   ([4, 6], 22.736686390532547)
-   ([4, 5, 6], 22.736686390532547)
-   ([3, 6], 30.25)
-   ([2, 6], 36.5)
-   ([2, 3, 6], 36.5)
-   ([2, 4, 6], 37.24489795918368)
+   [0] -> 0.00
+   [1] -> 0.00
+   [2] -> 0.00
+   [3] -> 0.00
+   [4] -> 0.00
+   [5] -> 0.00
+   [6] -> 0.00
+   [2, 3] -> 6.25
+   [4, 5] -> 7.25
+   [0, 2] -> 8.50
+   [0, 1] -> 9.25
+   [1, 3] -> 10.00
+   [1, 2] -> 11.25
+   [1, 2, 3] -> 12.50
+   [0, 1, 2] -> 13.00
+   [5, 6] -> 13.25
+   [2, 4] -> 20.00
+   [4, 6] -> 22.74
+   [4, 5, 6] -> 22.74
+   [3, 6] -> 30.25
+   [2, 6] -> 36.50
+   [2, 3, 6] -> 36.50
+   [2, 4, 6] -> 37.24
 
-==============
 CGAL citations
 ==============
 
diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst
index 8c29d069..0066992f 100644
--- a/src/cython/doc/bottleneck_distance_user.rst
+++ b/src/cython/doc/bottleneck_distance_user.rst
@@ -1,4 +1,3 @@
-===============================
 Bottleneck distance user manual
 ===============================
 Definition
@@ -23,15 +22,15 @@ This example computes the bottleneck distance from 2 persistence diagrams:
     diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]]
     diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]]
 
-    message = "Bottleneck distance approximation=" + repr(gudhi.bottleneck_distance(diag1, diag2, 0.1))
+    message = "Bottleneck distance approximation=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0.1)
     print(message)
 
-    message = "Bottleneck distance exact value=" + repr(gudhi.bottleneck_distance(diag1, diag2, 0))
+    message = "Bottleneck distance exact value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0)
     print(message)
 
 The output is:
 
 .. testoutput::
 
-    Bottleneck distance approximation=0.8081763781405569
+    Bottleneck distance approximation=0.81
     Bottleneck distance exact value=0.75
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
index 692acdd9..344b9554 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -1,4 +1,3 @@
-===========================
 Cubical complex user manual
 ===========================
 Definition
@@ -154,7 +153,7 @@ Examples.
 End user programs are available in cython/example/ folder.
 
 Bibliography
-************
+============
 
 .. bibliography:: bibliography.bib
    :filter: docnames
diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst
index fca63d65..f6d10567 100644
--- a/src/cython/doc/index.rst
+++ b/src/cython/doc/index.rst
@@ -1,5 +1,5 @@
-GUDHI documentation
-###################
+GUDHI Python module documentation
+#################################
 
 .. image:: img/Gudhi_banner.png
    :align: center
@@ -7,9 +7,9 @@ GUDHI documentation
 Introduction
 ************
 
-The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic
-open source `C++ library <http://gudhi.gforge.inria.fr/doc/latest/>`_, with a
-`Cython interface <http://gudhi.gforge.inria.fr/cython/latest/>`_, for
+The Python interface for the Gudhi library (Geometry Understanding in Higher
+Dimensions) is a generic open source
+`Python module <http://gudhi.gforge.inria.fr/python/latest/>`_, for
 Computational Topology and Topological Data Analysis
 (`TDA <https://en.wikipedia.org/wiki/Topological_data_analysis>`_).
 The GUDHI library intends to help the development of new algorithmic solutions
@@ -20,12 +20,11 @@ data structures.
 The current release of the GUDHI library includes:
 
 * Data structures to represent, construct and manipulate simplicial complexes.
-* Algorithms to compute persistent homology and multi-field persistent homology.
-* Simplication of simplicial complexes by edge contraction.
+* Simplification of simplicial complexes by edge contraction.
+* Algorithms to compute persistent homology and bottleneck distance.
 
-All data-structures are generic and several of their aspects can be
-parameterized via template classes. We refer to :cite:`gudhilibrary_ICMS14`
-for a detailed description of the design of the library.
+We refer to :cite:`gudhilibrary_ICMS14` for a detailed description of the
+design of the library.
 
 Data structures
 ***************
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index 373e0717..f98a5039 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -33,7 +33,7 @@ To build the GUDHI cython module, run the following commands in a terminal:
 Test suites
 ===========
 
-To test your build, `py.test <http://doc.pytest.org>`_ is required. Run the
+To test your build, `py.test <http://doc.pytest.org>`_ is optional. Run the
 following command in a terminal:
 
 .. code-block:: bash
@@ -41,7 +41,7 @@ following command in a terminal:
     cd /path-to-gudhi/build/cython
     # For windows, you have to set PYTHONPATH environment variable
     export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython'
-    py.test
+    ctest -R py_test
 
 Documentation
 =============
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index f713e971..cae18323 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -1,4 +1,3 @@
-=======================================
 Persistence graphical tools user manual
 =======================================
 Definition
diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst
index 69be3b86..72f1a7f7 100644
--- a/src/cython/doc/persistent_cohomology_user.rst
+++ b/src/cython/doc/persistent_cohomology_user.rst
@@ -1,4 +1,3 @@
-=================================
 Persistent cohomology user manual
 =================================
 Definition
@@ -108,7 +107,7 @@ We provide several example files: run these examples with -h for details on thei
     * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
 
 Bibliography
-************
+============
 
 .. bibliography:: bibliography.bib
    :filter: docnames
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
index c89409a0..f9760976 100644
--- a/src/cython/doc/rips_complex_user.rst
+++ b/src/cython/doc/rips_complex_user.rst
@@ -1,4 +1,3 @@
-=========================
 Rips complex user manual
 =========================
 Definition
@@ -60,8 +59,9 @@ Finally, it is asked to display information about the simplicial complex.
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
+    fmt = '%s -> %.2f'
     for filtered_value in simplex_tree.get_filtration():
-        print(filtered_value)
+        print(fmt % tuple(filtered_value))
 
 When launching (Rips maximal distance between 2 points is 12.0, is expanded
 until dimension 1 - one skeleton graph in other words), the output is:
@@ -69,24 +69,24 @@ until dimension 1 - one skeleton graph in other words), the output is:
 .. testoutput::
 
     Rips complex is of dimension 1 - 18 simplices - 7 vertices.
-    ([0], 0.0)
-    ([1], 0.0)
-    ([2], 0.0)
-    ([3], 0.0)
-    ([4], 0.0)
-    ([5], 0.0)
-    ([6], 0.0)
-    ([2, 3], 5.0)
-    ([4, 5], 5.385164807134504)
-    ([0, 2], 5.830951894845301)
-    ([0, 1], 6.082762530298219)
-    ([1, 3], 6.324555320336759)
-    ([1, 2], 6.708203932499369)
-    ([5, 6], 7.280109889280518)
-    ([2, 4], 8.94427190999916)
-    ([0, 3], 9.433981132056603)
-    ([4, 6], 9.486832980505138)
-    ([3, 6], 11.0)
+    [0] -> 0.00
+    [1] -> 0.00
+    [2] -> 0.00
+    [3] -> 0.00
+    [4] -> 0.00
+    [5] -> 0.00
+    [6] -> 0.00
+    [2, 3] -> 5.00
+    [4, 5] -> 5.39
+    [0, 2] -> 5.83
+    [0, 1] -> 6.08
+    [1, 3] -> 6.32
+    [1, 2] -> 6.71
+    [5, 6] -> 7.28
+    [2, 4] -> 8.94
+    [0, 3] -> 9.43
+    [4, 6] -> 9.49
+    [3, 6] -> 11.00
 
 Example from OFF file
 ^^^^^^^^^^^^^^^^^^^^^
@@ -107,32 +107,33 @@ Finally, it is asked to display information about the Rips complex.
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
+    fmt = '%s -> %.2f'
     for filtered_value in simplex_tree.get_filtration():
-        print(filtered_value)
+        print(fmt % tuple(filtered_value))
 
 the program output is:
 
 .. testoutput::
 
     Rips complex is of dimension 1 - 18 simplices - 7 vertices.
-    ([0], 0.0)
-    ([1], 0.0)
-    ([2], 0.0)
-    ([3], 0.0)
-    ([4], 0.0)
-    ([5], 0.0)
-    ([6], 0.0)
-    ([2, 3], 5.0)
-    ([4, 5], 5.385164807134504)
-    ([0, 2], 5.830951894845301)
-    ([0, 1], 6.082762530298219)
-    ([1, 3], 6.324555320336759)
-    ([1, 2], 6.708203932499369)
-    ([5, 6], 7.280109889280518)
-    ([2, 4], 8.94427190999916)
-    ([0, 3], 9.433981132056603)
-    ([4, 6], 9.486832980505138)
-    ([3, 6], 11.0)
+    [0] -> 0.00
+    [1] -> 0.00
+    [2] -> 0.00
+    [3] -> 0.00
+    [4] -> 0.00
+    [5] -> 0.00
+    [6] -> 0.00
+    [2, 3] -> 5.00
+    [4, 5] -> 5.39
+    [0, 2] -> 5.83
+    [0, 1] -> 6.08
+    [1, 3] -> 6.32
+    [1, 2] -> 6.71
+    [5, 6] -> 7.28
+    [2, 4] -> 8.94
+    [0, 3] -> 9.43
+    [4, 6] -> 9.49
+    [3, 6] -> 11.00
 
 Distance matrix
 ---------------
@@ -162,8 +163,9 @@ Finally, it is asked to display information about the simplicial complex.
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
+    fmt = '%s -> %.2f'
     for filtered_value in simplex_tree.get_filtration():
-        print(filtered_value)
+        print(fmt % tuple(filtered_value))
 
 When launching (Rips maximal distance between 2 points is 12.0, is expanded
 until dimension 1 - one skeleton graph in other words), the output is:
@@ -171,24 +173,24 @@ until dimension 1 - one skeleton graph in other words), the output is:
 .. testoutput::
 
     Rips complex is of dimension 1 - 18 simplices - 7 vertices.
-    ([0], 0.0)
-    ([1], 0.0)
-    ([2], 0.0)
-    ([3], 0.0)
-    ([4], 0.0)
-    ([5], 0.0)
-    ([6], 0.0)
-    ([2, 3], 5.0)
-    ([4, 5], 5.3851648071)
-    ([0, 2], 5.8309518948)
-    ([0, 1], 6.0827625303)
-    ([1, 3], 6.3245553203)
-    ([1, 2], 6.7082039325)
-    ([5, 6], 7.2801098893)
-    ([2, 4], 8.94427191)
-    ([0, 3], 9.4339811321)
-    ([4, 6], 9.4868329805)
-    ([3, 6], 11.0)
+    [0] -> 0.00
+    [1] -> 0.00
+    [2] -> 0.00
+    [3] -> 0.00
+    [4] -> 0.00
+    [5] -> 0.00
+    [6] -> 0.00
+    [2, 3] -> 5.00
+    [4, 5] -> 5.39
+    [0, 2] -> 5.83
+    [0, 1] -> 6.08
+    [1, 3] -> 6.32
+    [1, 2] -> 6.71
+    [5, 6] -> 7.28
+    [2, 4] -> 8.94
+    [0, 3] -> 9.43
+    [4, 6] -> 9.49
+    [3, 6] -> 11.00
 
 Example from csv file
 ^^^^^^^^^^^^^^^^^^^^^
@@ -209,29 +211,30 @@ Finally, it is asked to display information about the Rips complex.
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
+    fmt = '%s -> %.2f'
     for filtered_value in simplex_tree.get_filtration():
-        print(filtered_value)
+        print(fmt % tuple(filtered_value))
 
 the program output is:
 
 .. testoutput::
 
     Rips complex is of dimension 1 - 18 simplices - 7 vertices.
-    ([0], 0.0)
-    ([1], 0.0)
-    ([2], 0.0)
-    ([3], 0.0)
-    ([4], 0.0)
-    ([5], 0.0)
-    ([6], 0.0)
-    ([2, 3], 5.0)
-    ([4, 5], 5.3851648071)
-    ([0, 2], 5.8309518948)
-    ([0, 1], 6.0827625303)
-    ([1, 3], 6.3245553203)
-    ([1, 2], 6.7082039325)
-    ([5, 6], 7.2801098893)
-    ([2, 4], 8.94427191)
-    ([0, 3], 9.4339811321)
-    ([4, 6], 9.4868329805)
-    ([3, 6], 11.0)
+    [0] -> 0.00
+    [1] -> 0.00
+    [2] -> 0.00
+    [3] -> 0.00
+    [4] -> 0.00
+    [5] -> 0.00
+    [6] -> 0.00
+    [2, 3] -> 5.00
+    [4, 5] -> 5.39
+    [0, 2] -> 5.83
+    [0, 1] -> 6.08
+    [1, 3] -> 6.32
+    [1, 2] -> 6.71
+    [5, 6] -> 7.28
+    [2, 4] -> 8.94
+    [0, 3] -> 9.43
+    [4, 6] -> 9.49
+    [3, 6] -> 11.00
diff --git a/src/cython/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst
index b2efca8b..4b1dde19 100644
--- a/src/cython/doc/simplex_tree_user.rst
+++ b/src/cython/doc/simplex_tree_user.rst
@@ -1,4 +1,3 @@
-========================
 Simplex tree user manual
 ========================
 Definition
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
index 24f68f85..03f9fea6 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -1,4 +1,3 @@
-==============================
 Tangential complex user manual
 ==============================
 .. include:: tangential_complex_sum.rst
@@ -134,7 +133,7 @@ This example builds the Tangential complex of point set read in an OFF file.
         repr(st.num_vertices()) + ' vertices.'
     print(result_str)
     for filtered_value in st.get_filtration():
-        print(filtered_value)
+        print(filtered_value[0])
 
 The output is:
 
@@ -142,21 +141,21 @@ The output is:
 
     Tangential contains 12 simplices - 7 vertices.
     Simplex tree is of dimension 1 - 15 simplices - 7 vertices.
-    ([0], 0.0)
-    ([1], 0.0)
-    ([0, 1], 0.0)
-    ([2], 0.0)
-    ([0, 2], 0.0)
-    ([1, 2], 0.0)
-    ([3], 0.0)
-    ([1, 3], 0.0)
-    ([4], 0.0)
-    ([2, 4], 0.0)
-    ([5], 0.0)
-    ([4, 5], 0.0)
-    ([6], 0.0)
-    ([3, 6], 0.0)
-    ([5, 6], 0.0)
+    [0]
+    [1]
+    [0, 1]
+    [2]
+    [0, 2]
+    [1, 2]
+    [3]
+    [1, 3]
+    [4]
+    [2, 4]
+    [5]
+    [4, 5]
+    [6]
+    [3, 6]
+    [5, 6]
 
 
 Example with perturbation
@@ -187,8 +186,9 @@ The output is:
     Tangential contains 4 vertices.
     Inconsistencies has been fixed.
 
+
 Bibliography
-************
+============
 
 .. bibliography:: bibliography.bib
    :filter: docnames
diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst
index 07945361..aa9cbb2c 100644
--- a/src/cython/doc/witness_complex_user.rst
+++ b/src/cython/doc/witness_complex_user.rst
@@ -1,12 +1,8 @@
-===========================
 Witness complex user manual
 ===========================
-Definition
-----------
 
 .. include:: witness_complex_sum.rst
 
-
 Definitions
 -----------
 
@@ -128,7 +124,7 @@ Here is an example of constructing a strong witness complex filtration and compu
 * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
 
 Bibliography
-************
+============
 
 .. bibliography:: bibliography.bib
    :filter: docnames
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
index 664eb5c4..984dbf1b 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -43,29 +43,22 @@ parser.add_argument('--no-diagram', default=False, action='store_true' , help='F
 
 args = parser.parse_args()
 
-with open(args.file, 'r') as f:
-    first_line = f.readline()
-    if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
-        print("#####################################################################")
-        print("RipsComplex creation from distance matrix read in a csv file")
-        
-        message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
-        print(message)
-        
-        rips_complex = gudhi.RipsComplex(off_file=args.file, max_edge_length=args.max_edge_length)
-        simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
-    
-        message = "Number of simplices=" + repr(simplex_tree.num_simplices())
-        print(message)
-        
-        diag = simplex_tree.persistence()
-    
-        print("betti_numbers()=")
-        print(simplex_tree.betti_numbers())
-    
-        if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
-    else:
-        print(args.file, "is not a valid OFF file")
-
-    f.close()
+print("#####################################################################")
+print("RipsComplex creation from distance matrix read in a csv file")
+
+message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
+print(message)
+
+rips_complex = gudhi.RipsComplex(csv_file=args.file, max_edge_length=args.max_edge_length)
+simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
+
+message = "Number of simplices=" + repr(simplex_tree.num_simplices())
+print(message)
+
+diag = simplex_tree.persistence()
+
+print("betti_numbers()=")
+print(simplex_tree.betti_numbers())
+
+if args.no_diagram == False:
+    gudhi.plot_persistence_diagram(diag)