-- 
cgit v1.2.3

From b06c5d015ba1524fe63997eefe7b461e06dd9966 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 13 Apr 2017 09:31:33 +0000
Subject: Add radius search

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Spatial_searching-Add_radius_search@2341 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c30c32b27b8c3c1c8dd65e45d2bdd49738794062
---
 .../doc/Intro_spatial_searching.h                  |  2 +-
 .../example/example_spatial_searching.cpp          |  8 +++
 .../include/gudhi/Kd_tree_search.h                 | 57 +++++++++++++++-------
 src/Spatial_searching/test/test_Kd_tree_search.cpp |  8 +++
 4 files changed, 56 insertions(+), 19 deletions(-)

diff --git a/src/Spatial_searching/doc/Intro_spatial_searching.h b/src/Spatial_searching/doc/Intro_spatial_searching.h
index 23705378..9a3c1b65 100644
--- a/src/Spatial_searching/doc/Intro_spatial_searching.h
+++ b/src/Spatial_searching/doc/Intro_spatial_searching.h
@@ -46,7 +46,7 @@ namespace spatial_searching {
  * 
  * \section spatial_searching_examples Example
  * 
- * This example generates 500 random points, then performs queries for nearest and farthest points using different methods.
+ * This example generates 500 random points, then performs radius search, and queries for nearest and farthest points using different methods.
  * 
  * \include Spatial_searching/example_spatial_searching.cpp
  * 
diff --git a/src/Spatial_searching/example/example_spatial_searching.cpp b/src/Spatial_searching/example/example_spatial_searching.cpp
index 14b324ae..9e6a8f32 100644
--- a/src/Spatial_searching/example/example_spatial_searching.cpp
+++ b/src/Spatial_searching/example/example_spatial_searching.cpp
@@ -48,5 +48,13 @@ int main(void) {
   for (auto ifs_iterator = ifn_range.begin(); ifs_iterator->first != 0; ++ifs_iterator)
     std::cout << ifs_iterator->first << " (sq. dist. = " << ifs_iterator->second << ")\n";
 
+  // Radius search
+  std::cout << "Radius search:\n";
+  std::vector<std::size_t> rs_result;
+  points_ds.radius_search(points[45], 0.5, std::back_inserter(rs_result));
+  K k;
+  for (auto const& p_idx : rs_result)
+    std::cout << p_idx << " (sq. dist. = " << k.squared_distance_d_object()(points[p_idx], points[45]) << ")\n";
+
   return 0;
 }
diff --git a/src/Spatial_searching/include/gudhi/Kd_tree_search.h b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
index 6728d56e..374ebed6 100644
--- a/src/Spatial_searching/include/gudhi/Kd_tree_search.h
+++ b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
@@ -27,6 +27,7 @@
 #include <CGAL/Orthogonal_incremental_neighbor_search.h>
 #include <CGAL/Search_traits.h>
 #include <CGAL/Search_traits_adapter.h>
+#include <CGAL/Fuzzy_sphere.h>
 #include <CGAL/property_map.h>
 
 #include <boost/property_map/property_map.hpp>
@@ -104,6 +105,7 @@ class Kd_tree_search {
   /// of a point P and `second` is the squared distance between P and the query point.
   typedef Incremental_neighbor_search                       INS_range;
 
+  typedef CGAL::Fuzzy_sphere<STraits>                       Fuzzy_sphere;
   /// \brief Constructor
   /// @param[in] points Const reference to the point range. This range
   /// is not copied, so it should not be destroyed or modified afterwards.
@@ -164,9 +166,9 @@ class Kd_tree_search {
   /// @param[in] k Number of nearest points to search.
   /// @param[in] sorted Indicates if the computed sequence of k-nearest neighbors needs to be sorted.
   /// @param[in] eps Approximation factor.
-  /// @return A range containing the k-nearest neighbors.
-  KNS_range query_k_nearest_neighbors(const
-    Point &p,
+  /// @return A range (whose `value_type` is `std::size_t`) containing the k-nearest neighbors.
+  KNS_range query_k_nearest_neighbors(
+    Point const& p,
     unsigned int k,
     bool sorted = true,
     FT eps = FT(0)) const {
@@ -179,8 +181,7 @@ class Kd_tree_search {
       k,
       eps,
       true,
-      CGAL::Distance_adapter<std::ptrdiff_t, Point_property_map, CGAL::Euclidean_distance<Traits_base> >(
-        std::begin(m_points)), sorted);
+      Orthogonal_distance(std::begin(m_points)), sorted);
 
     return search;
   }
@@ -188,10 +189,11 @@ class Kd_tree_search {
   /// \brief Search incrementally for the nearest neighbors from a query point.
   /// @param[in] p The query point.
   /// @param[in] eps Approximation factor.
-  /// @return A range containing the neighbors sorted by their distance to p.
+  /// @return A range (whose `value_type` is `std::size_t`) containing the 
+  /// neighbors sorted by their distance to p.
   /// All the neighbors are not computed by this function, but they will be
   /// computed incrementally when the iterator on the range is incremented.
-  INS_range query_incremental_nearest_neighbors(const Point &p, FT eps = FT(0)) const {
+  INS_range query_incremental_nearest_neighbors(Point const& p, FT eps = FT(0)) const {
     // Initialize the search structure, and search all N points
     // Note that we need to pass the Distance explicitly since it needs to
     // know the property map
@@ -200,8 +202,7 @@ class Kd_tree_search {
       p,
       eps,
       true,
-      CGAL::Distance_adapter<std::ptrdiff_t, Point_property_map, CGAL::Euclidean_distance<Traits_base> >(
-        std::begin(m_points)) );
+      Orthogonal_distance(std::begin(m_points)) );
 
     return search;
   }
@@ -211,9 +212,9 @@ class Kd_tree_search {
   /// @param[in] k Number of farthest points to search.
   /// @param[in] sorted Indicates if the computed sequence of k-farthest neighbors needs to be sorted.
   /// @param[in] eps Approximation factor.
-  /// @return A range containing the k-farthest neighbors.
-  KNS_range query_k_farthest_neighbors(const
-    Point &p,
+  /// @return A range (whose `value_type` is `std::size_t`) containing the k-farthest neighbors.
+  KNS_range query_k_farthest_neighbors(
+    Point const& p,
     unsigned int k,
     bool sorted = true,
     FT eps = FT(0)) const {
@@ -226,8 +227,7 @@ class Kd_tree_search {
       k,
       eps,
       false,
-      CGAL::Distance_adapter<std::ptrdiff_t, Point_property_map, CGAL::Euclidean_distance<Traits_base> >(
-        std::begin(m_points)), sorted);
+      Orthogonal_distance(std::begin(m_points)), sorted);
 
     return search;
   }
@@ -235,10 +235,11 @@ class Kd_tree_search {
   /// \brief Search incrementally for the farthest neighbors from a query point.
   /// @param[in] p The query point.
   /// @param[in] eps Approximation factor.
-  /// @return A range containing the neighbors sorted by their distance to p.
+  /// @return A range (whose `value_type` is `std::size_t`) 
+  /// containing the neighbors sorted by their distance to p.
   /// All the neighbors are not computed by this function, but they will be
   /// computed incrementally when the iterator on the range is incremented.
-  INS_range query_incremental_farthest_neighbors(const Point &p, FT eps = FT(0)) const {
+  INS_range query_incremental_farthest_neighbors(Point const& p, FT eps = FT(0)) const {
     // Initialize the search structure, and search all N points
     // Note that we need to pass the Distance explicitly since it needs to
     // know the property map
@@ -247,12 +248,32 @@ class Kd_tree_search {
       p,
       eps,
       false,
-      CGAL::Distance_adapter<std::ptrdiff_t, Point_property_map, CGAL::Euclidean_distance<Traits_base> >(
-        std::begin(m_points)) );
+      Orthogonal_distance(std::begin(m_points)) );
 
     return search;
   }
 
+  /// \brief Search for all the neighbors in a ball.
+  /// @param[in] p The query point.
+  /// @param[in] radius The search radius
+  /// @param[out] it The points that lie inside the sphere of center `p` and radius `radius`.
+  ///                The `value_type` of the iterator must be `Point`.
+  /// @param[in] eps Approximation factor.
+  template <typename OutputIterator>
+  void radius_search(
+    Point const& p,
+    FT radius,
+    OutputIterator it,
+    FT eps = FT(0)) const {
+    
+    m_tree.search(it, Fuzzy_sphere(p, radius, eps, m_tree.traits()));
+  }
+
+  int tree_depth() const
+  {
+    return m_tree.root()->depth();
+  }
+
  private:
   Point_range const& m_points;
   Tree m_tree;
diff --git a/src/Spatial_searching/test/test_Kd_tree_search.cpp b/src/Spatial_searching/test/test_Kd_tree_search.cpp
index 0ef22023..f79114bc 100644
--- a/src/Spatial_searching/test/test_Kd_tree_search.cpp
+++ b/src/Spatial_searching/test/test_Kd_tree_search.cpp
@@ -109,4 +109,12 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) {
 
   // Same result for KFN and IFN?
   BOOST_CHECK(kfn_result == ifn_result);
+
+  // Test radius search
+  Point rs_q(rd.get_double(-1., 1), rd.get_double(-1., 1), rd.get_double(-1., 1), rd.get_double(-1., 1));
+  std::vector<std::size_t> rs_result;
+  points_ds.radius_search(rs_q, 0.5, std::back_inserter(rs_result));
+  K k;
+  for (auto const& p_idx : rs_result)
+    BOOST_CHECK(k.squared_distance_d_object()(points[p_idx], rs_q) <= 0.5);
 }
-- 
cgit v1.2.3


From 2efd0154ec5299a175ea2633db0dd739a620762d Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 24 Apr 2017 15:19:09 +0000
Subject: Fix doc of the output iterator

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Spatial_searching-Add_radius_search@2378 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: dda01f1c99debbf21ccd57cb961055dfe34036a8
---
 src/Spatial_searching/include/gudhi/Kd_tree_search.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Spatial_searching/include/gudhi/Kd_tree_search.h b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
index 374ebed6..c4a15876 100644
--- a/src/Spatial_searching/include/gudhi/Kd_tree_search.h
+++ b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
@@ -257,7 +257,7 @@ class Kd_tree_search {
   /// @param[in] p The query point.
   /// @param[in] radius The search radius
   /// @param[out] it The points that lie inside the sphere of center `p` and radius `radius`.
-  ///                The `value_type` of the iterator must be `Point`.
+  ///                Note: `it` is used this way: `*it++ = each_point`.
   /// @param[in] eps Approximation factor.
   template <typename OutputIterator>
   void radius_search(
-- 
cgit v1.2.3

-- 
cgit v1.2.3


From e7162cf121d5e1619ca4b7b54b9cef4d9ff1c9f7 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 16 May 2017 14:25:19 +0000
Subject: Add read_persistence_diagram_from_file

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2439 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 026fbb0528343a15a46935ded3aaf13297afeff5
---
 src/common/include/gudhi/reader_utils.h | 38 ++++++++++++++++++++++++++++++++-
 1 file changed, 37 insertions(+), 1 deletion(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 97a87edd..ceee8daf 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -2,7 +2,7 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
  *    library for computational topology.
  *
- *    Author(s):       Clement Maria, Pawel Dlotko
+ *    Author(s):       Clement Maria, Pawel Dlotko, Clement Jamin
  *
  *    Copyright (C) 2014  INRIA
  *
@@ -295,4 +295,40 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
   return result;
 }  // read_lower_triangular_matrix_from_csv_file
 
+/**
+Reads a file containing persistance intervals.
+Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+**/
+
+std::vector< std::pair<double, double> > read_persistence_diagram_from_file(std::string const& filename) {
+
+  std::vector< std::pair<double, double> > result;
+
+  std::ifstream in;
+  in.open(filename);
+  if (!in.is_open()) {
+#ifdef DEBUG_TRACES
+    std::cerr << "File \"" << filename << "\" does not exist.\n";
+#endif  // DEBUG_TRACES
+    return result;
+  }
+
+  std::string line;
+  while (!in.eof()) {
+    getline(in, line);
+    if (line.length() != 0 && line[0] != '#') {
+      double numbers[4];
+      int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
+      result.push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
+#ifdef DEBUG_TRACES
+      std::cerr << numbers[n - 2] << " - " << numbers[n - 1] << "\n";
+#endif  // DEBUG_TRACES
+    }
+  }
+
+  in.close();
+  return result;
+}  // read_diagram_from_file
+
+
 #endif  // READER_UTILS_H_
-- 
cgit v1.2.3


From 884d91ed81876af1a3d986843253acaaff443834 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 16 May 2017 14:26:11 +0000
Subject: Use read_persistence_diagram_from_file in this example

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2440 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: cb5cbba3f968c6cd16025250076bbe1df4f2e11a
---
 .../example/bottleneck_read_file_example.cpp       | 31 +++-------------------
 1 file changed, 4 insertions(+), 27 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index bde05825..e50a243d 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -21,8 +21,10 @@
  */
 
 #define CGAL_HAS_THREADS
+#define DEBUG_TRACES
 
 #include <gudhi/Bottleneck.h>
+#include <gudhi/reader_utils.h>
 #include <iostream>
 #include <vector>
 #include <utility>  // for pair
@@ -30,39 +32,14 @@
 #include <sstream>
 #include <string>
 
-std::vector< std::pair<double, double> > read_diagram_from_file(const char* filename) {
-  std::ifstream in;
-  in.open(filename);
-  std::vector< std::pair<double, double> > result;
-  if (!in.is_open()) {
-    std::cerr << "File : " << filename << " do not exist. The program will now terminate \n";
-    throw "File do not exist \n";
-  }
-
-  std::string line;
-  while (!in.eof()) {
-    getline(in, line);
-    if (line.length() != 0) {
-      std::stringstream lineSS;
-      lineSS << line;
-      double beginn, endd;
-      lineSS >> beginn;
-      lineSS >> endd;
-      result.push_back(std::make_pair(beginn, endd));
-    }
-  }
-  in.close();
-  return result;
-}  // read_diagram_from_file
-
 int main(int argc, char** argv) {
   if (argc < 3) {
     std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
         "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
         " distance (set by default to zero). The program will now terminate \n";
   }
-  std::vector< std::pair< double, double > > diag1 = read_diagram_from_file(argv[1]);
-  std::vector< std::pair< double, double > > diag2 = read_diagram_from_file(argv[2]);
+  std::vector< std::pair< double, double > > diag1 = read_persistence_diagram_from_file(argv[1]);
+  std::vector< std::pair< double, double > > diag2 = read_persistence_diagram_from_file(argv[2]);
   double tolerance = 0.;
   if (argc == 4) {
     tolerance = atof(argv[3]);
-- 
cgit v1.2.3


From f8992aa852dc1a5ef1392837581f55650cccaebf Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 19 May 2017 08:52:58 +0000
Subject: Remove DEBUG_TRACES

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2446 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2290435a73db6bea9297fa79e10f7e36be10a43e
---
 src/Bottleneck_distance/example/bottleneck_read_file_example.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index e50a243d..67bd27db 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -21,7 +21,6 @@
  */
 
 #define CGAL_HAS_THREADS
-#define DEBUG_TRACES
 
 #include <gudhi/Bottleneck.h>
 #include <gudhi/reader_utils.h>
-- 
cgit v1.2.3


From 269fa842c2eaeb7ddf8040abfd6c18d23ac767e9 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 23 May 2017 09:10:41 +0000
Subject: read_persistence_diagram_from_file now uses an output iterator

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2455 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 3969666dcde3581a75789c5a4b62817dea553f9f
---
 .../example/bottleneck_read_file_example.cpp            | 15 +++++++++++++--
 src/common/include/gudhi/reader_utils.h                 | 17 ++++++++---------
 2 files changed, 21 insertions(+), 11 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 67bd27db..74c8d1ab 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -31,14 +31,25 @@
 #include <sstream>
 #include <string>
 
+struct Persistence_interval
+  : std::pair<double, double>
+{
+  Persistence_interval(std::tuple<int, double, double> data)
+    : std::pair<double, double>(std::make_pair(std::get<1>(data), std::get<2>(data)))
+  {}
+};
+
 int main(int argc, char** argv) {
   if (argc < 3) {
     std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
         "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
         " distance (set by default to zero). The program will now terminate \n";
   }
-  std::vector< std::pair< double, double > > diag1 = read_persistence_diagram_from_file(argv[1]);
-  std::vector< std::pair< double, double > > diag2 = read_persistence_diagram_from_file(argv[2]);
+  std::vector<Persistence_interval> diag1;
+  std::vector<Persistence_interval> diag2;
+  read_persistence_diagram_from_file(argv[1], std::back_inserter(diag1));
+  read_persistence_diagram_from_file(argv[2], std::back_inserter(diag2));
+
   double tolerance = 0.;
   if (argc == 4) {
     tolerance = atof(argv[3]);
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index ceee8daf..019a3db2 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -298,11 +298,11 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
 /**
 Reads a file containing persistance intervals.
 Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth, death);`
+where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
-
-std::vector< std::pair<double, double> > read_persistence_diagram_from_file(std::string const& filename) {
-
-  std::vector< std::pair<double, double> > result;
+template <typename OutputIterator>
+void read_persistence_diagram_from_file(std::string const& filename, OutputIterator out) {
 
   std::ifstream in;
   in.open(filename);
@@ -310,7 +310,6 @@ std::vector< std::pair<double, double> > read_persistence_diagram_from_file(std:
 #ifdef DEBUG_TRACES
     std::cerr << "File \"" << filename << "\" does not exist.\n";
 #endif  // DEBUG_TRACES
-    return result;
   }
 
   std::string line;
@@ -319,7 +318,9 @@ std::vector< std::pair<double, double> > read_persistence_diagram_from_file(std:
     if (line.length() != 0 && line[0] != '#') {
       double numbers[4];
       int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
-      result.push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
+      //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1);
+      int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+      *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
 #ifdef DEBUG_TRACES
       std::cerr << numbers[n - 2] << " - " << numbers[n - 1] << "\n";
 #endif  // DEBUG_TRACES
@@ -327,8 +328,6 @@ std::vector< std::pair<double, double> > read_persistence_diagram_from_file(std:
   }
 
   in.close();
-  return result;
-}  // read_diagram_from_file
-
+} // read_persistence_diagram_from_file
 
 #endif  // READER_UTILS_H_
-- 
cgit v1.2.3


From 71527e6ff81a7ac657f8a797a050bbcf7a131cb9 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 29 May 2017 16:22:49 +0000
Subject: Add 2 new variants of read_persistence_diagram_from_file

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2463 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: bd0dd2c981856c8e1a51b2b97ac10d9edd59f694
---
 .../example/bottleneck_read_file_example.cpp       |  6 +-
 src/common/include/gudhi/reader_utils.h            | 85 ++++++++++++++++++++--
 2 files changed, 82 insertions(+), 9 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 74c8d1ab..e26edd26 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -45,10 +45,8 @@ int main(int argc, char** argv) {
         "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
         " distance (set by default to zero). The program will now terminate \n";
   }
-  std::vector<Persistence_interval> diag1;
-  std::vector<Persistence_interval> diag2;
-  read_persistence_diagram_from_file(argv[1], std::back_inserter(diag1));
-  read_persistence_diagram_from_file(argv[2], std::back_inserter(diag2));
+  std::vector<std::pair<double, double>> diag1 = read_persistence_diagram_from_file(argv[1], -1);
+  std::vector<std::pair<double, double>> diag2 = read_persistence_diagram_from_file(argv[2], -1);
 
   double tolerance = 0.;
   if (argc == 4) {
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 019a3db2..7b371afc 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -310,24 +310,99 @@ void read_persistence_diagram_from_file(std::string const& filename, OutputItera
 #ifdef DEBUG_TRACES
     std::cerr << "File \"" << filename << "\" does not exist.\n";
 #endif  // DEBUG_TRACES
+    return;
   }
 
-  std::string line;
   while (!in.eof()) {
+    std::string line;
     getline(in, line);
     if (line.length() != 0 && line[0] != '#') {
       double numbers[4];
       int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
-      //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1);
-      int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
-      *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
+      if (n >= 2) {
+        //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1);
+        int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+        *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
+      }
+    }
+  }
+
+  in.close();
+} // read_persistence_diagram_from_file
+
+/**
+Reads a file containing persistance intervals.
+Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+The return value is an `std::map[dim, std::vector[std::pair[birth, death]]]`
+where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+**/
+std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_from_file(std::string const& filename) {
+
+  std::map<int, std::vector<std::pair<double, double>>> ret;
+
+  std::ifstream in;
+  in.open(filename);
+  if (!in.is_open()) {
 #ifdef DEBUG_TRACES
-      std::cerr << numbers[n - 2] << " - " << numbers[n - 1] << "\n";
+    std::cerr << "File \"" << filename << "\" does not exist.\n";
 #endif  // DEBUG_TRACES
+    return ret;
+  }
+
+  while (!in.eof()) {
+    std::string line;
+    getline(in, line);
+    if (line.length() != 0 && line[0] != '#') {
+      double numbers[4];
+      int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
+      if (n >= 2) {
+        int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+        ret[dim].push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
+      }
+    }
+  }
+
+  in.close();
+  return ret;
+} // read_persistence_diagram_from_file
+
+
+/**
+Reads a file containing persistance intervals.
+Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+If `only_this_dim` = -1, dimension is ignored and all lines are returned.
+If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` 
+(or where dimension is not specified) are returned.
+The return value is an `std::vector[std::pair[birth, death]]`
+where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+**/
+std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::string const& filename, int only_this_dim) {
+
+  std::vector<std::pair<double, double>> ret;
+
+  std::ifstream in;
+  in.open(filename);
+  if (!in.is_open()) {
+#ifdef DEBUG_TRACES
+    std::cerr << "File \"" << filename << "\" does not exist.\n";
+#endif  // DEBUG_TRACES
+    return ret;
+  }
+
+  while (!in.eof()) {
+    std::string line;
+    getline(in, line);
+    if (line.length() != 0 && line[0] != '#') {
+      double numbers[4];
+      int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
+      int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+      if (n >= 2 && (only_this_dim == -1 || dim == only_this_dim))
+        ret.push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
     }
   }
 
   in.close();
+  return ret;
 } // read_persistence_diagram_from_file
 
 #endif  // READER_UTILS_H_
-- 
cgit v1.2.3


From 006516d2df5eaa6e38765158f72fa29fea8fb610 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 30 May 2017 12:50:12 +0000
Subject: Remove debug code

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2473 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 458dcfcf18b36f8dd0023dfe5af0d6083d1c7684
---
 src/Bottleneck_distance/example/bottleneck_read_file_example.cpp | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index e26edd26..f6fd6501 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -20,8 +20,6 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#define CGAL_HAS_THREADS
-
 #include <gudhi/Bottleneck.h>
 #include <gudhi/reader_utils.h>
 #include <iostream>
-- 
cgit v1.2.3


From 6d4b5ec65b863abb5b183635a0e64341c19e7b4b Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 30 May 2017 13:00:15 +0000
Subject: Clean-up

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2474 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9586b4987dad745fa60bca1a433349a2f78fa9bd
---
 src/Bottleneck_distance/example/bottleneck_read_file_example.cpp | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index f6fd6501..de8c7f9d 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -29,14 +29,6 @@
 #include <sstream>
 #include <string>
 
-struct Persistence_interval
-  : std::pair<double, double>
-{
-  Persistence_interval(std::tuple<int, double, double> data)
-    : std::pair<double, double>(std::make_pair(std::get<1>(data), std::get<2>(data)))
-  {}
-};
-
 int main(int argc, char** argv) {
   if (argc < 3) {
     std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
-- 
cgit v1.2.3

-- 
cgit v1.2.3


From 53abf1ac75eefcecc1391d140183a49588f0d2d2 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 31 May 2017 11:30:58 +0000
Subject: Fix doc and shorten code

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2485 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 97dcd51c0dc9cef00a655e5e0ad078de752eabe8
---
 src/common/include/gudhi/reader_utils.h | 19 ++++++-------------
 1 file changed, 6 insertions(+), 13 deletions(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 7b371afc..df10d5a5 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -297,15 +297,14 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
 
 /**
 Reads a file containing persistance intervals.
-Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth, death);`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
 template <typename OutputIterator>
 void read_persistence_diagram_from_file(std::string const& filename, OutputIterator out) {
 
-  std::ifstream in;
-  in.open(filename);
+  std::ifstream in(filename);
   if (!in.is_open()) {
 #ifdef DEBUG_TRACES
     std::cerr << "File \"" << filename << "\" does not exist.\n";
@@ -326,13 +325,11 @@ void read_persistence_diagram_from_file(std::string const& filename, OutputItera
       }
     }
   }
-
-  in.close();
 } // read_persistence_diagram_from_file
 
 /**
 Reads a file containing persistance intervals.
-Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The return value is an `std::map[dim, std::vector[std::pair[birth, death]]]`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
@@ -340,8 +337,7 @@ std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_f
 
   std::map<int, std::vector<std::pair<double, double>>> ret;
 
-  std::ifstream in;
-  in.open(filename);
+  std::ifstream in(filename);
   if (!in.is_open()) {
 #ifdef DEBUG_TRACES
     std::cerr << "File \"" << filename << "\" does not exist.\n";
@@ -362,14 +358,13 @@ std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_f
     }
   }
 
-  in.close();
   return ret;
 } // read_persistence_diagram_from_file
 
 
 /**
 Reads a file containing persistance intervals.
-Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 If `only_this_dim` = -1, dimension is ignored and all lines are returned.
 If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` 
 (or where dimension is not specified) are returned.
@@ -380,8 +375,7 @@ std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::s
 
   std::vector<std::pair<double, double>> ret;
 
-  std::ifstream in;
-  in.open(filename);
+  std::ifstream in(filename);
   if (!in.is_open()) {
 #ifdef DEBUG_TRACES
     std::cerr << "File \"" << filename << "\" does not exist.\n";
@@ -401,7 +395,6 @@ std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::s
     }
   }
 
-  in.close();
   return ret;
 } // read_persistence_diagram_from_file
 
-- 
cgit v1.2.3


From 8457da40a4af813d6368cd85d1f60d2b2de52191 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 31 May 2017 11:36:20 +0000
Subject: Typo

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2486 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: dcc6134d95dea816a3c54a2a796535f384ccfc54
---
 src/common/include/gudhi/reader_utils.h | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index df10d5a5..55a1e875 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -296,7 +296,7 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
 }  // read_lower_triangular_matrix_from_csv_file
 
 /**
-Reads a file containing persistance intervals.
+Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth, death);`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
@@ -328,7 +328,7 @@ void read_persistence_diagram_from_file(std::string const& filename, OutputItera
 } // read_persistence_diagram_from_file
 
 /**
-Reads a file containing persistance intervals.
+Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The return value is an `std::map[dim, std::vector[std::pair[birth, death]]]`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
@@ -363,7 +363,7 @@ std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_f
 
 
 /**
-Reads a file containing persistance intervals.
+Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 If `only_this_dim` = -1, dimension is ignored and all lines are returned.
 If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` 
-- 
cgit v1.2.3


From cbcf098dbc2af8f385216d74d6ffbbe08deaff66 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 31 May 2017 11:44:16 +0000
Subject: Fix doc

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2487 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7be9a5da2a64835ff7558373e7a754647bc5b663
---
 src/common/include/gudhi/reader_utils.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 55a1e875..bb744b1c 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -330,7 +330,7 @@ void read_persistence_diagram_from_file(std::string const& filename, OutputItera
 /**
 Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
-The return value is an `std::map[dim, std::vector[std::pair[birth, death]]]`
+The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
 std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_from_file(std::string const& filename) {
@@ -368,7 +368,7 @@ Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 If `only_this_dim` = -1, dimension is ignored and all lines are returned.
 If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` 
 (or where dimension is not specified) are returned.
-The return value is an `std::vector[std::pair[birth, death]]`
+The return value is an `std::vector<std::pair<birth, death>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
 std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::string const& filename, int only_this_dim) {
-- 
cgit v1.2.3


From 66873d7ee6dd369dd3d8c1909d6376ed2bce4cc7 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 31 May 2017 11:54:55 +0000
Subject: Check if birth <= death

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2488 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: fc7aeca7ca7cd1ec2e9a9263849ec34d4dfa8414
---
 src/common/include/gudhi/reader_utils.h | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index bb744b1c..6a89ce90 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -24,6 +24,7 @@
 #define READER_UTILS_H_
 
 #include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Debug_utils.h>
 
 #include <boost/graph/adjacency_list.hpp>
 
@@ -321,6 +322,7 @@ void read_persistence_diagram_from_file(std::string const& filename, OutputItera
       if (n >= 2) {
         //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1);
         int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+        GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death.");
         *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
       }
     }
@@ -353,6 +355,7 @@ std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_f
       int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
       if (n >= 2) {
         int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+        GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death.");
         ret[dim].push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
       }
     }
@@ -391,7 +394,10 @@ std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::s
       int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
       int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
       if (n >= 2 && (only_this_dim == -1 || dim == only_this_dim))
+      {
+        GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death.");
         ret.push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
+      }
     }
   }
 
-- 
cgit v1.2.3


From df15aa4e16c00a7dc3bca01e01db8608b50dd4b9 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 31 May 2017 11:58:05 +0000
Subject: Add persistence diagram samples

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2489 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: bcad955589cbfccdb5f887e409df17a07288c9e4
---
 data/persistence_diagram/first.pers  | 5 +++++
 data/persistence_diagram/second.pers | 3 +++
 2 files changed, 8 insertions(+)
 create mode 100644 data/persistence_diagram/first.pers
 create mode 100644 data/persistence_diagram/second.pers

diff --git a/data/persistence_diagram/first.pers b/data/persistence_diagram/first.pers
new file mode 100644
index 00000000..193c60ba
--- /dev/null
+++ b/data/persistence_diagram/first.pers
@@ -0,0 +1,5 @@
+# Simple persistence diagram
+2.7 3.7
+9.6 14.
+34.2 34.974
+3. inf
\ No newline at end of file
diff --git a/data/persistence_diagram/second.pers b/data/persistence_diagram/second.pers
new file mode 100644
index 00000000..6292fde6
--- /dev/null
+++ b/data/persistence_diagram/second.pers
@@ -0,0 +1,3 @@
+2.8 4.45
+9.5 14.1
+3.2 inf
\ No newline at end of file
-- 
cgit v1.2.3


From 267f55ba68cd3c7beee9cd8c7bd9e13d90217848 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 31 May 2017 12:03:13 +0000
Subject: Test bottleneck_read_file_example

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2490 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: dbbce2ac4862dfdd3c01a619bf68120112ab44d5
---
 src/Bottleneck_distance/example/CMakeLists.txt | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index 0534a2c4..508e57bf 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -19,6 +19,10 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
       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")
 
+  add_test(NAME Bottleneck_read_file_example
+      COMMAND $<TARGET_FILE:bottleneck_read_file_example>
+      "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers")
+
   install(TARGETS bottleneck_read_file_example DESTINATION bin)
   install(TARGETS bottleneck_basic_example DESTINATION bin)
   install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
-- 
cgit v1.2.3


From 8493f7a38001930329ec6204e6b3e8dff1c67df1 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 1 Jun 2017 10:26:05 +0000
Subject: Use make_function_output_iterator to avoid code duplication

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2498 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7d9a9d3f72ef4af17f4a9b8263526df69498090c
---
 src/common/include/gudhi/reader_utils.h | 54 +++++----------------------------
 1 file changed, 7 insertions(+), 47 deletions(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 6a89ce90..f0903acc 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -25,6 +25,7 @@
 
 #include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/Debug_utils.h>
+#include <boost/function_output_iterator.hpp>
 
 #include <boost/graph/adjacency_list.hpp>
 
@@ -338,29 +339,9 @@ where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_from_file(std::string const& filename) {
 
   std::map<int, std::vector<std::pair<double, double>>> ret;
-
-  std::ifstream in(filename);
-  if (!in.is_open()) {
-#ifdef DEBUG_TRACES
-    std::cerr << "File \"" << filename << "\" does not exist.\n";
-#endif  // DEBUG_TRACES
-    return ret;
-  }
-
-  while (!in.eof()) {
-    std::string line;
-    getline(in, line);
-    if (line.length() != 0 && line[0] != '#') {
-      double numbers[4];
-      int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
-      if (n >= 2) {
-        int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
-        GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death.");
-        ret[dim].push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
-      }
-    }
-  }
-
+  read_persistence_diagram_from_file(
+    filename,
+    boost::make_function_output_iterator([&ret](auto t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); }));
   return ret;
 } // read_persistence_diagram_from_file
 
@@ -377,30 +358,9 @@ where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::string const& filename, int only_this_dim) {
 
   std::vector<std::pair<double, double>> ret;
-
-  std::ifstream in(filename);
-  if (!in.is_open()) {
-#ifdef DEBUG_TRACES
-    std::cerr << "File \"" << filename << "\" does not exist.\n";
-#endif  // DEBUG_TRACES
-    return ret;
-  }
-
-  while (!in.eof()) {
-    std::string line;
-    getline(in, line);
-    if (line.length() != 0 && line[0] != '#') {
-      double numbers[4];
-      int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
-      int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
-      if (n >= 2 && (only_this_dim == -1 || dim == only_this_dim))
-      {
-        GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death.");
-        ret.push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
-      }
-    }
-  }
-
+  read_persistence_diagram_from_file(
+    filename, 
+    boost::make_function_output_iterator([&ret](auto t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
   return ret;
 } // read_persistence_diagram_from_file
 
-- 
cgit v1.2.3


From 03f7d661f8b5d34320a075a826c0bfeafa16633f Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 1 Jun 2017 14:55:10 +0000
Subject: Doc for "pers" file format

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2500 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2da948fefffcb1961961e3111c89f400f23b65d3
---
 src/common/doc/main_page.h | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index bd4615f5..fba0a858 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -152,6 +152,27 @@
 </table>
  
  \section Toolbox Toolbox
+ \subsection FileFormats File Formats
+ \subsubsection FileFormatsPers Persistence Diagram
+
+ Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
+ Lines starting with `#` are ignored (comments).<br>
+ Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):
+ \code{.unparsed}
+   [[field] dimension] birth death
+ \endcode
+
+ Here is a simple sample file:
+ \code{.unparsed}
+   # Beautiful persistence diagram
+   2 2.7 3.7
+   2 9.6 14.
+   3 34.2 34.974
+   4 3. inf
+ \endcode
+
+ Other sample files can be found in the `data/persistence_diagram`.
+
  \subsection BottleneckDistanceToolbox Bottleneck distance
  \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge"
 <table border="0">
-- 
cgit v1.2.3


From c09268a046c43b4311f0f29ac4bfb14dcb2da30d Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 2 Jun 2017 14:10:20 +0000
Subject: Try to remove boost system

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2504 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: fd12c45af5ebeb72c4b49142abab91b46ce1a9da
---
 src/Alpha_complex/example/CMakeLists.txt            |  4 ++--
 src/Rips_complex/example/CMakeLists.txt             |  8 ++++----
 src/cmake/modules/GUDHI_third_party_libraries.cmake |  2 ++
 src/cython/CMakeLists.txt                           | 10 +---------
 4 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index 4badcb91..5bf553e9 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -5,9 +5,9 @@ project(Alpha_complex_examples)
 # cmake -DCGAL_DIR=~/workspace/CGAL-4.7 ..
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
   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})
+  target_link_libraries(Alpha_complex_example_from_points  ${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})
+  target_link_libraries(Alpha_complex_example_from_off ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Alpha_complex_example_from_points ${TBB_LIBRARIES})
     target_link_libraries(Alpha_complex_example_from_off ${TBB_LIBRARIES})
diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt
index 712db16e..d2d3e052 100644
--- a/src/Rips_complex/example/CMakeLists.txt
+++ b/src/Rips_complex/example/CMakeLists.txt
@@ -3,17 +3,17 @@ project(Rips_complex_examples)
 
 # Point cloud
 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})
+#target_link_libraries(Rips_complex_example_from_off  ${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})
+#target_link_libraries(Rips_complex_example_one_skeleton_from_points  ${Boost_SYSTEM_LIBRARY})
 
 # Distance matrix
 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})
+#target_link_libraries(Rips_complex_example_one_skeleton_from_distance_matrix  ${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})
+#target_link_libraries(Rips_complex_example_from_csv_distance_matrix  ${Boost_SYSTEM_LIBRARY})
 
 if (TBB_FOUND)
   target_link_libraries(Rips_complex_example_from_off ${TBB_LIBRARIES})
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 8cb01d3c..7b0cda3b 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -99,6 +99,8 @@ add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
 add_definitions(-DBOOST_ALL_NO_LIB)
 # problem with Visual Studio link on Boost program_options
 add_definitions( -DBOOST_ALL_DYN_LINK )
+# problem on Mac with boost_system and boost_thread
+#add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED )
 
 INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
 LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index d9f356f9..4b56122d 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -6,15 +6,7 @@ if(CYTHON_FOUND)
 
   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', ")
-  set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
-  if(WIN32)
-    set( returnValue "" )
-    find_the_lib (${returnValue} ${Boost_SYSTEM_LIBRARY})
-    set(BOOST_SYSTEM_LIB_NAME ${returnValue})
-  else()
-      set(BOOST_SYSTEM_LIB_NAME "boost_system")
-      endif()
-  set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${BOOST_SYSTEM_LIB_NAME}', ")
+  set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
 
   # Gudhi and CGAL compilation option
   if(MSVC)
-- 
cgit v1.2.3


From 7cd2fc5259aaa1b362652a026de1c2006ab3a78c Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 2 Jun 2017 16:55:18 +0000
Subject: Get rid of Boost_system library link

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2509 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 52deba0f2212767b99b801810d356e55417225db
---
 src/Alpha_complex/test/CMakeLists.txt              |  2 +-
 src/Bitmap_cubical_complex/example/CMakeLists.txt  |  3 ---
 src/Bitmap_cubical_complex/test/CMakeLists.txt     |  2 +-
 src/Bottleneck_distance/example/CMakeLists.txt     |  2 +-
 src/Bottleneck_distance/test/CMakeLists.txt        |  2 +-
 src/Contraction/example/CMakeLists.txt             |  4 ++--
 src/Persistent_cohomology/benchmark/CMakeLists.txt |  2 +-
 src/Persistent_cohomology/example/CMakeLists.txt   | 26 ++++++++++------------
 src/Persistent_cohomology/test/CMakeLists.txt      |  7 +++---
 src/Rips_complex/example/CMakeLists.txt            |  4 ----
 src/Rips_complex/test/CMakeLists.txt               |  2 +-
 src/Simplex_tree/example/CMakeLists.txt            |  2 +-
 src/Simplex_tree/test/CMakeLists.txt               |  2 +-
 src/Skeleton_blocker/example/CMakeLists.txt        |  2 +-
 src/Skeleton_blocker/test/CMakeLists.txt           |  6 ++---
 src/Spatial_searching/test/CMakeLists.txt          |  2 +-
 src/Tangential_complex/benchmark/CMakeLists.txt    |  2 +-
 src/Tangential_complex/test/CMakeLists.txt         |  2 +-
 src/Witness_complex/example/CMakeLists.txt         |  8 ++-----
 src/Witness_complex/test/CMakeLists.txt            |  4 ++--
 src/common/example/CMakeLists.txt                  |  6 ++---
 src/common/test/CMakeLists.txt                     |  4 ++--
 src/common/utilities/CMakeLists.txt                |  1 -
 23 files changed, 42 insertions(+), 55 deletions(-)

diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index d7f49b53..9e0b3b3c 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -5,7 +5,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
   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})
+  target_link_libraries(Alpha_complex_test_unit ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Alpha_complex_test_unit ${TBB_LIBRARIES})
   endif()
diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt
index 47f5e0c6..a0401619 100644
--- a/src/Bitmap_cubical_complex/example/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt
@@ -2,7 +2,6 @@ cmake_minimum_required(VERSION 2.6)
 project(Bitmap_cubical_complex_examples)
 
 add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp )
-target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
 if (TBB_FOUND)
   target_link_libraries(Bitmap_cubical_complex ${TBB_LIBRARIES})
 endif()
@@ -14,7 +13,6 @@ add_test(NAME Bitmap_cubical_complex_example_persistence_two_sphere COMMAND $<TA
     "${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()
@@ -22,7 +20,6 @@ add_test(NAME Bitmap_cubical_complex_example_random COMMAND $<TARGET_FILE:Random
     "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()
diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt
index b2895f85..02b026f2 100644
--- a/src/Bitmap_cubical_complex/test/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt
@@ -4,7 +4,7 @@ project(Bitmap_cubical_complex_tests)
 include(GUDHI_test_coverage)
 
 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})
+target_link_libraries(Bitmap_cubical_complex_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
   target_link_libraries(Bitmap_cubical_complex_test_unit ${TBB_LIBRARIES})
 endif()
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index 0534a2c4..9a37f02e 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -6,7 +6,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
 
   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})
+  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES})
     target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES})
diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt
index e1bbbbec..a165d472 100644
--- a/src/Bottleneck_distance/test/CMakeLists.txt
+++ b/src/Bottleneck_distance/test/CMakeLists.txt
@@ -5,7 +5,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   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})
+  target_link_libraries(Bottleneck_distance_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Bottleneck_distance_test_unit ${TBB_LIBRARIES})
   endif(TBB_FOUND)
diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt
index b2b38dea..6443323d 100644
--- a/src/Contraction/example/CMakeLists.txt
+++ b/src/Contraction/example/CMakeLists.txt
@@ -5,8 +5,8 @@ project(Contraction_examples)
 add_executable(RipsContraction Rips_contraction.cpp)
 add_executable(GarlandHeckbert Garland_heckbert.cpp)
 
-target_link_libraries(RipsContraction ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY})	
-target_link_libraries(GarlandHeckbert ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY})	
+target_link_libraries(RipsContraction ${Boost_TIMER_LIBRARY})
+target_link_libraries(GarlandHeckbert ${Boost_TIMER_LIBRARY})
 
 
 add_test(NAME Contraction_example_tore3D_0.2 COMMAND $<TARGET_FILE:RipsContraction>
diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt
index ea792c89..8b135ba1 100644
--- a/src/Persistent_cohomology/benchmark/CMakeLists.txt
+++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt
@@ -5,7 +5,7 @@ project(Persistent_cohomology_benchmark)
 if(GMP_FOUND)
    if(GMPXX_FOUND)
       add_executable ( performance_rips_persistence EXCLUDE_FROM_ALL performance_rips_persistence.cpp )
-      target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+      target_link_libraries(performance_rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
       if (TBB_FOUND)
         target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES})
       endif(TBB_FOUND)
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index a9884c49..f47de4c3 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -2,25 +2,23 @@ cmake_minimum_required(VERSION 2.6)
 project(Persistent_cohomology_examples)
 
 add_executable(plain_homology plain_homology.cpp)
-target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
 
 add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
-target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY})
 
 add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp)
-target_link_libraries(rips_distance_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
 add_executable(rips_persistence rips_persistence.cpp)
-target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
 add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp)
-target_link_libraries(rips_persistence_step_by_step ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_persistence_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
 add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp)
-target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
 add_executable(persistence_from_file persistence_from_file.cpp)
-target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(persistence_from_file ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
 if (TBB_FOUND)
   target_link_libraries(plain_homology ${TBB_LIBRARIES})
@@ -60,7 +58,7 @@ if(GMP_FOUND)
    if(GMPXX_FOUND)
       add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
       target_link_libraries(rips_multifield_persistence
-          ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+          ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
       if (TBB_FOUND)
         target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
       endif(TBB_FOUND)
@@ -72,11 +70,11 @@ endif(GMP_FOUND)
 
 if(CGAL_FOUND)
   add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
-  target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+  target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY})
   add_executable(exact_alpha_complex_3d_persistence exact_alpha_complex_3d_persistence.cpp)
-  target_link_libraries(exact_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+  target_link_libraries(exact_alpha_complex_3d_persistence ${CGAL_LIBRARY})
   add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp)
-  target_link_libraries(weighted_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+  target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY})
 
   if (TBB_FOUND)
     target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
@@ -97,13 +95,13 @@ if(CGAL_FOUND)
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
     target_link_libraries(alpha_complex_persistence
-        ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+        ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
     add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp)
-    target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+    target_link_libraries(periodic_alpha_complex_3d_persistence ${CGAL_LIBRARY})
 
     add_executable(custom_persistence_sort custom_persistence_sort.cpp)
-    target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+    target_link_libraries(custom_persistence_sort ${CGAL_LIBRARY})
 
     if (TBB_FOUND)
       target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt
index 11e9a951..45f53eb9 100644
--- a/src/Persistent_cohomology/test/CMakeLists.txt
+++ b/src/Persistent_cohomology/test/CMakeLists.txt
@@ -4,9 +4,9 @@ project(Persistent_cohomology_tests)
 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})
+target_link_libraries(Persistent_cohomology_test_unit ${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})
+target_link_libraries(Persistent_cohomology_test_betti_numbers ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
   target_link_libraries(Persistent_cohomology_test_unit ${TBB_LIBRARIES})
   target_link_libraries(Persistent_cohomology_test_betti_numbers ${TBB_LIBRARIES})
@@ -22,7 +22,8 @@ gudhi_add_coverage_test(Persistent_cohomology_test_betti_numbers)
 
 if(GMPXX_FOUND AND GMP_FOUND)
   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})
+  target_link_libraries(Persistent_cohomology_test_unit_multi_field
+      ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
   if (TBB_FOUND)
     target_link_libraries(Persistent_cohomology_test_unit_multi_field ${TBB_LIBRARIES})
   endif(TBB_FOUND)
diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt
index d2d3e052..2940f164 100644
--- a/src/Rips_complex/example/CMakeLists.txt
+++ b/src/Rips_complex/example/CMakeLists.txt
@@ -3,17 +3,13 @@ project(Rips_complex_examples)
 
 # Point cloud
 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 ( 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 ( 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 ( 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(Rips_complex_example_from_off ${TBB_LIBRARIES})
diff --git a/src/Rips_complex/test/CMakeLists.txt b/src/Rips_complex/test/CMakeLists.txt
index 57f780f1..3da9c90d 100644
--- a/src/Rips_complex/test/CMakeLists.txt
+++ b/src/Rips_complex/test/CMakeLists.txt
@@ -4,7 +4,7 @@ project(Rips_complex_tests)
 include(GUDHI_test_coverage)
 
 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})
+target_link_libraries(Rips_complex_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
   target_link_libraries(Rips_complex_test_unit ${TBB_LIBRARIES})
 endif()
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index d05bb187..e22cc92c 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -26,7 +26,7 @@ install(TARGETS Simplex_tree_example_mini_simplex_tree DESTINATION bin)
 # An example with Simplex-tree using CGAL alpha_shapes_3
 if(GMP_FOUND AND CGAL_FOUND)
   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})
+  target_link_libraries(Simplex_tree_example_alpha_shapes_3_from_off ${GMP_LIBRARIES} ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Simplex_tree_example_alpha_shapes_3_from_off ${TBB_LIBRARIES})
   endif()
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index 17b0f2c2..81999de6 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -4,7 +4,7 @@ project(Simplex_tree_tests)
 include(GUDHI_test_coverage)
 
 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})
+target_link_libraries(Simplex_tree_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
   target_link_libraries(Simplex_tree_test_unit ${TBB_LIBRARIES})
 endif()
diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt
index ce51ac39..6d685717 100644
--- a/src/Skeleton_blocker/example/CMakeLists.txt
+++ b/src/Skeleton_blocker/example/CMakeLists.txt
@@ -5,7 +5,7 @@ add_executable(Skeleton_blocker_example_from_simplices Skeleton_blocker_from_sim
 add_executable(Skeleton_blocker_example_iteration Skeleton_blocker_iteration.cpp)
 add_executable(Skeleton_blocker_example_link Skeleton_blocker_link.cpp)
 
-target_link_libraries(Skeleton_blocker_example_iteration ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY})
+target_link_libraries(Skeleton_blocker_example_iteration ${Boost_TIMER_LIBRARY})
 
 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>)
diff --git a/src/Skeleton_blocker/test/CMakeLists.txt b/src/Skeleton_blocker/test/CMakeLists.txt
index 0887fcff..4a363294 100644
--- a/src/Skeleton_blocker/test/CMakeLists.txt
+++ b/src/Skeleton_blocker/test/CMakeLists.txt
@@ -4,11 +4,11 @@ project(Skeleton_blocker_tests)
 include(GUDHI_test_coverage)
 
 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})
+target_link_libraries(Skeleton_blocker_test_unit ${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})
+target_link_libraries(Skeleton_blocker_test_geometric_complex ${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})
+target_link_libraries(Skeleton_blocker_test_simplifiable ${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}/)
diff --git a/src/Spatial_searching/test/CMakeLists.txt b/src/Spatial_searching/test/CMakeLists.txt
index 2502ea5e..b9da7b4e 100644
--- a/src/Spatial_searching/test/CMakeLists.txt
+++ b/src/Spatial_searching/test/CMakeLists.txt
@@ -6,7 +6,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 
   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})
+    ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
   gudhi_add_coverage_test(Spatial_searching_test_Kd_tree_search)
 endif ()
diff --git a/src/Tangential_complex/benchmark/CMakeLists.txt b/src/Tangential_complex/benchmark/CMakeLists.txt
index ef772be8..8cb16e8c 100644
--- a/src/Tangential_complex/benchmark/CMakeLists.txt
+++ b/src/Tangential_complex/benchmark/CMakeLists.txt
@@ -4,7 +4,7 @@ project(Tangential_complex_benchmark)
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   add_executable(Tangential_complex_benchmark benchmark_tc.cpp)
   target_link_libraries(Tangential_complex_benchmark
-    ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+    ${Boost_DATE_TIME_LIBRARY} ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Tangential_complex_benchmark ${TBB_LIBRARIES})
   endif(TBB_FOUND)
diff --git a/src/Tangential_complex/test/CMakeLists.txt b/src/Tangential_complex/test/CMakeLists.txt
index fc710676..1948c8f6 100644
--- a/src/Tangential_complex/test/CMakeLists.txt
+++ b/src/Tangential_complex/test/CMakeLists.txt
@@ -5,7 +5,7 @@ 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})
+  target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Tangential_complex_test_TC ${TBB_LIBRARIES})
   endif()
diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index 1e18d024..cbc53902 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -2,7 +2,6 @@ cmake_minimum_required(VERSION 2.6)
 project(Witness_complex_examples)
 
 add_executable ( Witness_complex_example_nearest_landmark_table example_nearest_landmark_table.cpp )
-target_link_libraries(Witness_complex_example_nearest_landmark_table ${Boost_SYSTEM_LIBRARY})
 if (TBB_FOUND)
   target_link_libraries(Witness_complex_example_nearest_landmark_table ${TBB_LIBRARIES})
 endif()
@@ -14,17 +13,14 @@ install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin)
 # CGAL and Eigen3 are required for Euclidean version of Witness
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
   add_executable( Witness_complex_example_off example_witness_complex_off.cpp )
-  target_link_libraries(Witness_complex_example_off ${Boost_SYSTEM_LIBRARY})
   add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
-  target_link_libraries(Witness_complex_example_strong_off ${Boost_SYSTEM_LIBRARY})
   add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp )
-  target_link_libraries(Witness_complex_example_sphere ${Boost_SYSTEM_LIBRARY})
 
   add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp )
-  target_link_libraries(Witness_complex_example_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(Witness_complex_example_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
   add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp )
-  target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
   if (TBB_FOUND)
     target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES})
diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt
index 152e2f2c..0b523eaf 100644
--- a/src/Witness_complex/test/CMakeLists.txt
+++ b/src/Witness_complex/test/CMakeLists.txt
@@ -4,7 +4,7 @@ project(Witness_complex_tests)
 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})
+target_link_libraries(Witness_complex_test_simple_witness_complex ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
   target_link_libraries(Witness_complex_test_simple_witness_complex ${TBB_LIBRARIES})
 endif(TBB_FOUND)
@@ -14,7 +14,7 @@ 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)
   add_executable ( Witness_complex_test_euclidean_simple_witness_complex test_euclidean_simple_witness_complex.cpp )
-  target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${TBB_LIBRARIES})
   endif(TBB_FOUND)
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
index af3c2c9d..d0a3aa80 100644
--- a/src/common/example/CMakeLists.txt
+++ b/src/common/example/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 2.6)
 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})
+target_link_libraries(vector_double_off_reader ${CGAL_LIBRARY})
 add_test(NAME Common_example_vector_double_off_reader COMMAND $<TARGET_FILE:vector_double_off_reader>
     "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off")
 
@@ -10,14 +10,14 @@ install(TARGETS vector_double_off_reader DESTINATION bin)
 
 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})
+  target_link_libraries(cgal_3D_off_reader ${CGAL_LIBRARY})
   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})
+    target_link_libraries(cgal_off_reader ${CGAL_LIBRARY})
     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)
diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt
index c695fbf4..5aa426d7 100644
--- a/src/common/test/CMakeLists.txt
+++ b/src/common/test/CMakeLists.txt
@@ -4,10 +4,10 @@ project(Common_tests)
 include(GUDHI_test_coverage)
 
 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})
+target_link_libraries(Common_test_points_off_reader ${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})
+target_link_libraries(Common_test_distance_matrix_reader ${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}/)
diff --git a/src/common/utilities/CMakeLists.txt b/src/common/utilities/CMakeLists.txt
index c2e07e7e..b3e4b436 100644
--- a/src/common/utilities/CMakeLists.txt
+++ b/src/common/utilities/CMakeLists.txt
@@ -3,7 +3,6 @@ project(off_file_from_shape_generator)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
   add_executable ( off_file_from_shape_generator off_file_from_shape_generator.cpp )
-  target_link_libraries(off_file_from_shape_generator ${Boost_SYSTEM_LIBRARY})
   add_test(NAME off_file_from_shape_generator_on_sphere_1000_3_15.2 COMMAND $<TARGET_FILE:off_file_from_shape_generator>
       "on" "sphere" "onSphere.off" "1000" "3" "15.2")
   add_test(NAME off_file_from_shape_generator_in_sphere_100_2 COMMAND $<TARGET_FILE:off_file_from_shape_generator>
-- 
cgit v1.2.3


From 65bd15c84df2bf660918fcbf35a87b22510640cb Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 2 Jun 2017 16:59:15 +0000
Subject: Fix install issue

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2510 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c081183c9876761dace595a09ec04fe220846ed6
---
 src/common/example/CMakeLists.txt | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
index d0a3aa80..afe865d4 100644
--- a/src/common/example/CMakeLists.txt
+++ b/src/common/example/CMakeLists.txt
@@ -14,14 +14,15 @@ if(CGAL_FOUND)
   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
+  install(TARGETS cgal_3D_off_reader DESTINATION bin)
+
+  # need CGAL 4.7 and 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 ${CGAL_LIBRARY})
     add_test(NAME Common_example_vector_cgal_off_reader COMMAND $<TARGET_FILE:cgal_off_reader>
         "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off")
+    install(TARGETS cgal_off_reader DESTINATION bin)
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 
-  install(TARGETS cgal_3D_off_reader DESTINATION bin)
-  install(TARGETS cgal_off_reader DESTINATION bin)
 endif()
-- 
cgit v1.2.3


From f5d28342ee398c739c7345d8db4fbd653e9a0413 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 8 Jun 2017 07:17:36 +0000
Subject: Add modules as CMake options in order to be able to
 activate/desactivate compilation

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cmake_modules_for_gudhi@2515 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 53d5e669ad310c9d8d17c7f95f1e07c3bf658d77
---
 CMakeLists.txt                                    | 18 ++++--------------
 src/CMakeLists.txt                                |  8 ++++----
 src/cmake/modules/GUDHI_modules.cmake             | 23 +++++++++++++++++++----
 src/cmake/modules/GUDHI_user_version_target.cmake |  4 ++--
 4 files changed, 29 insertions(+), 24 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c9ceb92b..fbb359e1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -3,10 +3,7 @@ project(GUDHIdev)
 
 include(CMakeGUDHIVersion.txt)
 
-set(CMAKE_PREFIX_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
-set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
-message("CMAKE_PREFIX_PATH = ${CMAKE_PREFIX_PATH}")
-message("CMAKE_MODULE_PATH = ${CMAKE_MODULE_PATH}")
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
 
 enable_testing()
 
@@ -34,10 +31,8 @@ if (DEBUG_TRACES)
   add_definitions(-DDEBUG_TRACES)
 endif()
 
-# Modules list can be found in CMAKE_MODULE_PATH/GUDHI_modules.cmake
-include(GUDHI_modules)
-
 # Add your new module in the list, order is not important
+include(GUDHI_modules)
 
 add_gudhi_module(common)
 add_gudhi_module(Alpha_complex)
@@ -54,12 +49,7 @@ add_gudhi_module(Subsampling)
 add_gudhi_module(Tangential_complex)
 add_gudhi_module(Witness_complex)
 
-# Include module headers
-foreach(GUDHI_MODULE ${GUDHI_MODULES})
-  if(IS_DIRECTORY ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/include/)
-    include_directories(src/${GUDHI_MODULE}/include/)
-  endif()
-endforeach()
+message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
 
 # Include module CMake subdirectories
 # GUDHI_SUB_DIRECTORIES is managed in CMAKE_MODULE_PATH/GUDHI_modules.cmake
@@ -73,7 +63,7 @@ endforeach()
 
 add_subdirectory(src/GudhUI)
 
-if (NOT WITHOUT_GUDHI_PYTHON)
+if (WITH_GUDHI_PYTHON)
   # specific for cython module
   add_subdirectory(${GUDHI_CYTHON_PATH})
 endif()
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 8abfcf44..795005b1 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -7,10 +7,8 @@ enable_testing()
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
 
-# To be done first - Modules list can be found in CMAKE_MODULE_PATH/GUDHI_modules.cmake
-include(GUDHI_modules)
-
 # Add your new module in the list, order is not important
+include(GUDHI_modules)
 
 add_gudhi_module(common)
 add_gudhi_module(Alpha_complex)
@@ -27,6 +25,8 @@ add_gudhi_module(Subsampling)
 add_gudhi_module(Tangential_complex)
 add_gudhi_module(Witness_complex)
 
+message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
+
 # For "make doxygen" - Requires GUDHI_USER_VERSION_DIR to be set
 set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
 include(GUDHI_doxygen_target)
@@ -71,7 +71,7 @@ endforeach()
 
 add_subdirectory(GudhUI)
 
-if (NOT WITHOUT_GUDHI_PYTHON)
+if (WITH_GUDHI_PYTHON)
   # specific for cython module
   add_subdirectory(${GUDHI_CYTHON_PATH})
 endif()
diff --git a/src/cmake/modules/GUDHI_modules.cmake b/src/cmake/modules/GUDHI_modules.cmake
index 20fc8d17..f95d0c34 100644
--- a/src/cmake/modules/GUDHI_modules.cmake
+++ b/src/cmake/modules/GUDHI_modules.cmake
@@ -1,11 +1,26 @@
 # A function to add a new module in GUDHI
 
 set(GUDHI_MODULES "")
+set(GUDHI_MODULES_FULL_LIST "")
 function(add_gudhi_module file_path)
+  option("WITH_MODULE_GUDHI_${file_path}" "Activate/desactivate ${file_path} compilation and installation" ON)
+  if (WITH_MODULE_GUDHI_${file_path})
     set(GUDHI_MODULES ${GUDHI_MODULES} ${file_path} PARENT_SCOPE)
+  endif()
+  # Required by user_version
+  set(GUDHI_MODULES_FULL_LIST ${GUDHI_MODULES_FULL_LIST} ${file_path} PARENT_SCOPE)
+  # Include module headers is independant - You may ask for no Alpha complex module but Python interface i.e.
+  if(IS_DIRECTORY ${CMAKE_SOURCE_DIR}/src/${file_path}/include/)
+    include_directories(src/${file_path}/include/)
+  endif()
+
 endfunction(add_gudhi_module)
 
-# message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
+option(WITH_GUDHI_BENCHMARK "Activate/desactivate benchmark compilation" OFF)
+option(WITH_GUDHI_EXAMPLE "Activate/desactivate examples compilation and installation" OFF)
+option(WITH_GUDHI_PYTHON "Activate/desactivate python module compilation and installation" ON)
+option(WITH_GUDHI_TEST "Activate/desactivate examples compilation and installation" ON)
+option(WITH_GUDHI_UTILITIES "Activate/desactivate utilities compilation and installation" ON)
 
 if (WITH_GUDHI_BENCHMARK)
   set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};benchmark")
@@ -13,10 +28,10 @@ endif()
 if (WITH_GUDHI_EXAMPLE)
   set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};example")
 endif()
-if (NOT WITHOUT_GUDHI_TEST)
-    set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};test")
+if (WITH_GUDHI_TEST)
+  set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};test")
 endif()
-if (NOT WITHOUT_GUDHI_UTILITIES)
+if (WITH_GUDHI_UTILITIES)
   set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};utilities")
 endif()
 
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 8642d3bf..cff64ad2 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -50,7 +50,7 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
   set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
   set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches")
 
-  foreach(GUDHI_MODULE ${GUDHI_MODULES})
+  foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
     foreach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES})
       # Find files
       file(GLOB GUDHI_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_DIRECTORY}/*)
@@ -85,6 +85,6 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
       endforeach()
     endforeach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
 
-  endforeach(GUDHI_MODULE ${GUDHI_MODULES})
+  endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
 
 endif()
-- 
cgit v1.2.3


From 41991433af57269f1328c7c67e26eb111b060fa2 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 06:19:25 +0000
Subject: Add BOOST_SYSTEM_NO_DEPRECATED definition

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2524 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4718264666a9289a46f282cfcf3200481966c0db
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 7b0cda3b..5bee774a 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -100,7 +100,7 @@ add_definitions(-DBOOST_ALL_NO_LIB)
 # problem with Visual Studio link on Boost program_options
 add_definitions( -DBOOST_ALL_DYN_LINK )
 # problem on Mac with boost_system and boost_thread
-#add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED )
+add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED )
 
 INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
 LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
-- 
cgit v1.2.3


From 25b640d65879b719094e8d0e923812c2658c85c3 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 07:01:18 +0000
Subject: Tangential complex test must link with boost date time library

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2525 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2f62d58f2915eead697ba5fbb02e69719f6e471a
---
 src/Tangential_complex/test/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Tangential_complex/test/CMakeLists.txt b/src/Tangential_complex/test/CMakeLists.txt
index 1948c8f6..63e51c3e 100644
--- a/src/Tangential_complex/test/CMakeLists.txt
+++ b/src/Tangential_complex/test/CMakeLists.txt
@@ -5,7 +5,7 @@ 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_UNIT_TEST_FRAMEWORK_LIBRARY})
+  target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}  ${Boost_DATE_TIME_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Tangential_complex_test_TC ${TBB_LIBRARIES})
   endif()
-- 
cgit v1.2.3


From 4adbd857ff2ac187b5dfcfa25c37f32b887ae69b Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 07:48:54 +0000
Subject: No more need of find_the_lib cmake macro to find Windows boost lib
 name Fix cmake warning on if with quotes

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2527 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a352820ab0a596961b9851d4a30c40196a70ff98
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 13 -------------
 src/cython/CMakeLists.txt                           |  4 ++--
 2 files changed, 2 insertions(+), 15 deletions(-)

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 5bee774a..b4f3eb52 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -108,19 +108,6 @@ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
 message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
 message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
 
-macro( find_the_lib placeholder THE_LIBS )
-  set (THE_LIB_WE_FOUND "NO")
-  foreach(THE_LIB ${THE_LIBS})
-    if(EXISTS ${THE_LIB})
-      get_filename_component(THE_LIB_WE ${THE_LIB} NAME_WE)
-      if (NOT THE_LIB_WE_FOUND)
-        set (THE_LIB_WE_FOUND "YES")
-        set(returnValue "${THE_LIB_WE}")
-      endif(NOT THE_LIB_WE_FOUND)
-    endif(EXISTS ${THE_LIB})
-  endforeach(THE_LIB ${THE_LIBS})
-endmacro( find_the_lib )
-
 # Find the correct Python interpreter.
 # Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
 find_package(Cython)
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 4b56122d..adcc64e4 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -17,9 +17,9 @@ if(CYTHON_FOUND)
   if(CMAKE_COMPILER_IS_GNUCXX)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
   endif(CMAKE_COMPILER_IS_GNUCXX)
-  if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+  if (CMAKE_CXX_COMPILER_ID MATCHES Intel)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
-  endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+  endif(CMAKE_CXX_COMPILER_ID MATCHES Intel)
   if (DEBUG_TRACES)
     # For programs to be more verbose
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
-- 
cgit v1.2.3


From 26ccabbd6892ddc5313a7f75c98a92c268f15747 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 08:39:16 +0000
Subject: Remove boost timer and chrono dependencies

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2528 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5bfb8bd5a6e49dbea9fbfbdc1d748423fc930913
---
 src/Contraction/example/CMakeLists.txt                      | 4 ----
 src/Contraction/example/Garland_heckbert.cpp                | 3 ---
 src/Contraction/example/Rips_contraction.cpp                | 6 ------
 src/Skeleton_blocker/example/CMakeLists.txt                 | 2 --
 src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp | 4 ----
 src/cmake/modules/GUDHI_third_party_libraries.cmake         | 2 +-
 6 files changed, 1 insertion(+), 20 deletions(-)

diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt
index 6443323d..83594c0e 100644
--- a/src/Contraction/example/CMakeLists.txt
+++ b/src/Contraction/example/CMakeLists.txt
@@ -5,10 +5,6 @@ project(Contraction_examples)
 add_executable(RipsContraction Rips_contraction.cpp)
 add_executable(GarlandHeckbert Garland_heckbert.cpp)
 
-target_link_libraries(RipsContraction ${Boost_TIMER_LIBRARY})
-target_link_libraries(GarlandHeckbert ${Boost_TIMER_LIBRARY})
-
-
 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
diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp
index 8b5a6a6c..2b0dc973 100644
--- a/src/Contraction/example/Garland_heckbert.cpp
+++ b/src/Contraction/example/Garland_heckbert.cpp
@@ -30,7 +30,6 @@
 #include <gudhi/Skeleton_blocker.h>
 #include <gudhi/Off_reader.h>
 
-#include <boost/timer/timer.hpp>
 #include <iostream>
 
 #include "Garland_heckbert/Error_quadric.h"
@@ -165,8 +164,6 @@ int main(int argc, char *argv[]) {
 
   int num_contractions = atoi(argv[3]);
 
-  boost::timer::auto_cpu_timer t;
-
   // constructs the contractor object with Garland Heckbert policies.
   Complex_contractor contractor(complex,
                                 new GH_cost(complex),
diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp
index 8289b1d3..1b97f877 100644
--- a/src/Contraction/example/Rips_contraction.cpp
+++ b/src/Contraction/example/Rips_contraction.cpp
@@ -24,7 +24,6 @@
 #include <gudhi/Off_reader.h>
 #include <gudhi/Point.h>
 
-#include <boost/timer/timer.hpp>
 #include <iostream>
 
 struct Geometry_trait {
@@ -68,8 +67,6 @@ int main(int argc, char *argv[]) {
 
   build_rips(complex, atof(argv[2]));
 
-  boost::timer::auto_cpu_timer t;
-
   std::cout << "Initial complex has " <<
       complex.num_vertices() << " vertices and " <<
       complex.num_edges() << " edges" << std::endl;
@@ -90,9 +87,6 @@ int main(int argc, char *argv[]) {
       complex.num_blockers() << " blockers and " <<
       num_simplices << " simplices" << std::endl;
 
-
-  std::cout << "Time to simplify and enumerate simplices:\n";
-
   return EXIT_SUCCESS;
 }
 
diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt
index 6d685717..de70f089 100644
--- a/src/Skeleton_blocker/example/CMakeLists.txt
+++ b/src/Skeleton_blocker/example/CMakeLists.txt
@@ -5,8 +5,6 @@ add_executable(Skeleton_blocker_example_from_simplices Skeleton_blocker_from_sim
 add_executable(Skeleton_blocker_example_iteration Skeleton_blocker_iteration.cpp)
 add_executable(Skeleton_blocker_example_link Skeleton_blocker_link.cpp)
 
-target_link_libraries(Skeleton_blocker_example_iteration ${Boost_TIMER_LIBRARY})
-
 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/example/Skeleton_blocker_iteration.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
index 6a1bc480..4a0044e1 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
@@ -22,8 +22,6 @@
 
 #include <gudhi/Skeleton_blocker.h>
 
-#include <boost/timer/timer.hpp>
-
 #include <stdio.h>
 #include <stdlib.h>
 #include <string>
@@ -47,8 +45,6 @@ Complex build_complete_complex(int n) {
 }
 
 int main(int argc, char *argv[]) {
-  boost::timer::auto_cpu_timer t;
-
   const int n = 15;
 
   // build a full complex with n vertices and 2^n-1 simplices
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index b4f3eb52..2be79ee4 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -1,6 +1,6 @@
 # This files manage third party libraries required by GUDHI
 
-find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer date_time program_options thread)
+find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework date_time program_options thread)
 
 if(NOT Boost_FOUND)
   message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
-- 
cgit v1.2.3


From 05de4e9f4ed8f74e53a11455bc50470beba908eb Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 09:40:52 +0000
Subject: Remove boost date_time dependencies

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2529 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: daa13fc0046ffdd72577bb1b399fcbdc8ef5033c
---
 src/Tangential_complex/benchmark/CMakeLists.txt     |  3 +--
 src/Tangential_complex/example/CMakeLists.txt       |  4 ++--
 src/Tangential_complex/test/CMakeLists.txt          |  2 +-
 src/cmake/modules/GUDHI_third_party_libraries.cmake |  2 +-
 src/common/include/gudhi/Clock.h                    | 18 +++++++++---------
 5 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/src/Tangential_complex/benchmark/CMakeLists.txt b/src/Tangential_complex/benchmark/CMakeLists.txt
index 8cb16e8c..8729e394 100644
--- a/src/Tangential_complex/benchmark/CMakeLists.txt
+++ b/src/Tangential_complex/benchmark/CMakeLists.txt
@@ -3,8 +3,7 @@ project(Tangential_complex_benchmark)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   add_executable(Tangential_complex_benchmark benchmark_tc.cpp)
-  target_link_libraries(Tangential_complex_benchmark
-    ${Boost_DATE_TIME_LIBRARY} ${CGAL_LIBRARY})
+  target_link_libraries(Tangential_complex_benchmark ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Tangential_complex_benchmark ${TBB_LIBRARIES})
   endif(TBB_FOUND)
diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt
index 45c7642b..16d1339d 100644
--- a/src/Tangential_complex/example/CMakeLists.txt
+++ b/src/Tangential_complex/example/CMakeLists.txt
@@ -3,9 +3,9 @@ project(Tangential_complex_examples)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   add_executable( Tangential_complex_example_basic example_basic.cpp )
-  target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY})
+  target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY})
   add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp )
-  target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY})
+  target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES})
     target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES})
diff --git a/src/Tangential_complex/test/CMakeLists.txt b/src/Tangential_complex/test/CMakeLists.txt
index 63e51c3e..1948c8f6 100644
--- a/src/Tangential_complex/test/CMakeLists.txt
+++ b/src/Tangential_complex/test/CMakeLists.txt
@@ -5,7 +5,7 @@ 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_UNIT_TEST_FRAMEWORK_LIBRARY}  ${Boost_DATE_TIME_LIBRARY})
+  target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Tangential_complex_test_TC ${TBB_LIBRARIES})
   endif()
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 2be79ee4..8f486118 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -1,6 +1,6 @@
 # This files manage third party libraries required by GUDHI
 
-find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework date_time program_options thread)
+find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework program_options thread)
 
 if(NOT Boost_FOUND)
   message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
diff --git a/src/common/include/gudhi/Clock.h b/src/common/include/gudhi/Clock.h
index 77f196ca..eff48e41 100644
--- a/src/common/include/gudhi/Clock.h
+++ b/src/common/include/gudhi/Clock.h
@@ -23,9 +23,9 @@
 #ifndef CLOCK_H_
 #define CLOCK_H_
 
-#include <boost/date_time/posix_time/posix_time.hpp>
-
+#include <iostream>
 #include <string>
+#include <chrono>
 
 namespace Gudhi {
 
@@ -33,20 +33,20 @@ class Clock {
  public:
   // Construct and start the timer
   Clock(const std::string& msg_ = std::string())
-      : startTime(boost::posix_time::microsec_clock::local_time()),
+      : startTime(std::chrono::system_clock::now()),
       end_called(false),
       msg(msg_) { }
 
   // Restart the timer
   void begin() const {
     end_called = false;
-    startTime = boost::posix_time::microsec_clock::local_time();
+    startTime = std::chrono::system_clock::now();
   }
 
   // Stop the timer
   void end() const {
     end_called = true;
-    endTime = boost::posix_time::microsec_clock::local_time();
+    endTime = std::chrono::system_clock::now();
   }
 
   std::string message() const {
@@ -71,15 +71,15 @@ class Clock {
   // - or now otherwise. In this case, the timer is not stopped.
   double num_seconds() const {
     if (!end_called) {
-      auto end = boost::posix_time::microsec_clock::local_time();
-      return (end - startTime).total_milliseconds() / 1000.;
+      auto end = std::chrono::system_clock::now();
+      return std::chrono::duration_cast<std::chrono::milliseconds>(end-startTime).count() / 1000.;
     } else {
-      return (endTime - startTime).total_milliseconds() / 1000.;
+      return std::chrono::duration_cast<std::chrono::milliseconds>(endTime-startTime).count() / 1000.;
     }
   }
 
  private:
-  mutable boost::posix_time::ptime startTime, endTime;
+  mutable std::chrono::time_point<std::chrono::system_clock> startTime, endTime;
   mutable bool end_called;
   std::string msg;
 };
-- 
cgit v1.2.3


From 8a0f3bf13633cc0608e19a724873dc57e833837b Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 09:45:41 +0000
Subject: Homogenize DEFINE profiling name for subsampling

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2530 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 99176a6381a5c81298d94a781b996904ff2e1acc
---
 src/Subsampling/include/gudhi/pick_n_random_points.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Subsampling/include/gudhi/pick_n_random_points.h b/src/Subsampling/include/gudhi/pick_n_random_points.h
index f0e3f1f1..8c90b6bf 100644
--- a/src/Subsampling/include/gudhi/pick_n_random_points.h
+++ b/src/Subsampling/include/gudhi/pick_n_random_points.h
@@ -52,7 +52,7 @@ typename OutputIterator>
 void pick_n_random_points(Point_container const &points,
                           std::size_t final_size,
                           OutputIterator output_it) {
-#ifdef GUDHI_SUBS_PROFILING
+#ifdef GUDHI_SUBSAMPLING_PROFILING
   Gudhi::Clock t;
 #endif
 
@@ -72,7 +72,7 @@ void pick_n_random_points(Point_container const &points,
   for (int l : landmarks)
     *output_it++ = points[l];
 
-#ifdef GUDHI_SUBS_PROFILING
+#ifdef GUDHI_SUBSAMPLING_PROFILING
   t.end();
   std::cerr << "Random landmark choice took " << t.num_seconds()
       << " seconds." << std::endl;
-- 
cgit v1.2.3


From 3a7ffc0bfec712cb586d5c7ea154a4fd20be1a39 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 10:32:48 +0000
Subject: Change names and adapt example

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2531 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 833a51dd03ddccca38c6011834bb58667d63ccbf
---
 .../example/bottleneck_read_file_example.cpp                   |  4 ++--
 src/common/include/gudhi/reader_utils.h                        | 10 +++++-----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index de8c7f9d..94d9a148 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -35,8 +35,8 @@ int main(int argc, char** argv) {
         "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
         " distance (set by default to zero). The program will now terminate \n";
   }
-  std::vector<std::pair<double, double>> diag1 = read_persistence_diagram_from_file(argv[1], -1);
-  std::vector<std::pair<double, double>> diag2 = read_persistence_diagram_from_file(argv[2], -1);
+  std::vector<std::pair<double, double>> diag1 = read_persistence_intervals_in_dimension(argv[1]);
+  std::vector<std::pair<double, double>> diag2 = read_persistence_intervals_in_dimension(argv[2]);
 
   double tolerance = 0.;
   if (argc == 4) {
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index f0903acc..62b479ac 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -304,7 +304,7 @@ The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
 template <typename OutputIterator>
-void read_persistence_diagram_from_file(std::string const& filename, OutputIterator out) {
+void read_persistence_intervals_and_dimension(std::string const& filename, OutputIterator out) {
 
   std::ifstream in(filename);
   if (!in.is_open()) {
@@ -336,10 +336,10 @@ Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
-std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_from_file(std::string const& filename) {
+std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) {
 
   std::map<int, std::vector<std::pair<double, double>>> ret;
-  read_persistence_diagram_from_file(
+  read_persistence_intervals_and_dimension(
     filename,
     boost::make_function_output_iterator([&ret](auto t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); }));
   return ret;
@@ -355,10 +355,10 @@ If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim`
 The return value is an `std::vector<std::pair<birth, death>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
-std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::string const& filename, int only_this_dim) {
+std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
 
   std::vector<std::pair<double, double>> ret;
-  read_persistence_diagram_from_file(
+  read_persistence_intervals_and_dimension(
     filename, 
     boost::make_function_output_iterator([&ret](auto t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
   return ret;
-- 
cgit v1.2.3


From 2ceede5cd9f226e66bb1ecbe1798330c349c2aa0 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 10:39:31 +0000
Subject: Missing "return"

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2532 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 8905e0d3406cbe26615b83ab7056e7fd5bd8ed0e
---
 src/Bottleneck_distance/example/bottleneck_read_file_example.cpp | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 94d9a148..6cfbeafa 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -34,6 +34,7 @@ int main(int argc, char** argv) {
     std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
         "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
         " distance (set by default to zero). The program will now terminate \n";
+    //return -1;
   }
   std::vector<std::pair<double, double>> diag1 = read_persistence_intervals_in_dimension(argv[1]);
   std::vector<std::pair<double, double>> diag2 = read_persistence_intervals_in_dimension(argv[2]);
@@ -44,4 +45,6 @@ int main(int argc, char** argv) {
   }
   double b = Gudhi::persistence_diagram::bottleneck_distance(diag1, diag2, tolerance);
   std::cout << "The distance between the diagrams is : " << b << ". The tolerance is : " << tolerance << std::endl;
+
+  return 0;
 }
-- 
cgit v1.2.3


From 4918b9c752a2d269678791dc4772ae9276539051 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 10:42:12 +0000
Subject: Throw exceptions if file not found

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2533 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b412f432aeac6aef07ac2d9d65d50dc8f508c2e6
---
 src/common/include/gudhi/reader_utils.h | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 62b479ac..35af09bd 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -94,7 +94,10 @@ template< typename Graph_t, typename Filtration_value, typename Vertex_handle >
 Graph_t read_graph(std::string file_name) {
   std::ifstream in_(file_name.c_str(), std::ios::in);
   if (!in_.is_open()) {
-    std::cerr << "Unable to open file " << file_name << std::endl;
+    std::string error_str("read_graph - Unable to open file ");
+    error_str.append(file_name);
+    std::cerr << error_str << std::endl;
+    throw std::invalid_argument(error_str);
   }
 
   typedef std::pair< Vertex_handle, Vertex_handle > Edge_t;
@@ -308,10 +311,10 @@ void read_persistence_intervals_and_dimension(std::string const& filename, Outpu
 
   std::ifstream in(filename);
   if (!in.is_open()) {
-#ifdef DEBUG_TRACES
-    std::cerr << "File \"" << filename << "\" does not exist.\n";
-#endif  // DEBUG_TRACES
-    return;
+    std::string error_str("read_persistence_intervals_and_dimension - Unable to open file ");
+    error_str.append(filename);
+    std::cerr << error_str << std::endl;
+    throw std::invalid_argument(error_str);
   }
 
   while (!in.eof()) {
-- 
cgit v1.2.3


From 93c97a9a93b930a2f3c1c119d9e4d2567c54dacc Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 11:20:13 +0000
Subject: Create a new page for file formats

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2534 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: dc0d836b9df68a3f339dcbc6b8ff51577faf3d7b
---
 src/common/doc/file_formats.h | 25 +++++++++++++++++++++++++
 src/common/doc/main_page.h    | 23 ++---------------------
 2 files changed, 27 insertions(+), 21 deletions(-)
 create mode 100644 src/common/doc/file_formats.h

diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
new file mode 100644
index 00000000..1f7ba201
--- /dev/null
+++ b/src/common/doc/file_formats.h
@@ -0,0 +1,25 @@
+/*! \page fileformats File formats
+ 
+ \tableofcontents
+
+ \section FileFormatsPers Persistence Diagram
+
+ Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
+ Lines starting with `#` are ignored (comments).<br>
+ Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):
+ \code{.unparsed}
+   [[field] dimension] birth death
+ \endcode
+
+ Here is a simple sample file:
+ \code{.unparsed}
+   # Beautiful persistence diagram
+   2 2.7 3.7
+   2 9.6 14.
+   3 34.2 34.974
+   4 3. inf
+ \endcode
+
+ Other sample files can be found in the `data/persistence_diagram` folder.
+ 
+*/
\ No newline at end of file
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index fba0a858..b7f93ed2 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -152,27 +152,7 @@
 </table>
  
  \section Toolbox Toolbox
- \subsection FileFormats File Formats
- \subsubsection FileFormatsPers Persistence Diagram
-
- Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
- Lines starting with `#` are ignored (comments).<br>
- Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):
- \code{.unparsed}
-   [[field] dimension] birth death
- \endcode
-
- Here is a simple sample file:
- \code{.unparsed}
-   # Beautiful persistence diagram
-   2 2.7 3.7
-   2 9.6 14.
-   3 34.2 34.974
-   4 3. inf
- \endcode
-
- Other sample files can be found in the `data/persistence_diagram`.
-
+ 
  \subsection BottleneckDistanceToolbox Bottleneck distance
  \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge"
 <table border="0">
@@ -489,3 +469,4 @@ make doxygen
  * @example Witness_complex/example_witness_complex_sphere.cpp
  */
 
+#include "file_formats.h"
\ No newline at end of file
-- 
cgit v1.2.3


From 7260c86a2158b0df3f33b49f314201dd51044563 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 12:20:12 +0000
Subject: Rewrite Contraction and Skeleton blocker time display using
 Gudhi::Clock

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2535 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e2b5c1e152fd7bdca9d07db0390944409942ba53
---
 src/Contraction/example/Garland_heckbert.cpp                | 5 +++++
 src/Contraction/example/Rips_contraction.cpp                | 5 +++++
 src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp | 3 +++
 src/common/include/gudhi/Clock.h                            | 2 +-
 4 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp
index 2b0dc973..f0cde95e 100644
--- a/src/Contraction/example/Garland_heckbert.cpp
+++ b/src/Contraction/example/Garland_heckbert.cpp
@@ -29,6 +29,7 @@
 #include <gudhi/Edge_contraction.h>
 #include <gudhi/Skeleton_blocker.h>
 #include <gudhi/Off_reader.h>
+#include <gudhi/Clock.h>
 
 #include <iostream>
 
@@ -164,6 +165,8 @@ int main(int argc, char *argv[]) {
 
   int num_contractions = atoi(argv[3]);
 
+  Gudhi::Clock contraction_chrono("Time to simplify and enumerate simplices");
+
   // constructs the contractor object with Garland Heckbert policies.
   Complex_contractor contractor(complex,
                                 new GH_cost(complex),
@@ -179,6 +182,8 @@ int main(int argc, char *argv[]) {
       complex.num_edges() << " edges and " <<
       complex.num_triangles() << " triangles." << std::endl;
 
+  std::cout << contraction_chrono;
+
   // write simplified complex
   Gudhi::skeleton_blocker::Skeleton_blocker_off_writer<Complex> off_writer(argv[2], complex);
 
diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp
index 1b97f877..501b0e87 100644
--- a/src/Contraction/example/Rips_contraction.cpp
+++ b/src/Contraction/example/Rips_contraction.cpp
@@ -23,6 +23,7 @@
 #include <gudhi/Skeleton_blocker.h>
 #include <gudhi/Off_reader.h>
 #include <gudhi/Point.h>
+#include <gudhi/Clock.h>
 
 #include <iostream>
 
@@ -67,6 +68,8 @@ int main(int argc, char *argv[]) {
 
   build_rips(complex, atof(argv[2]));
 
+  Gudhi::Clock contraction_chrono("Time to simplify and enumerate simplices");
+
   std::cout << "Initial complex has " <<
       complex.num_vertices() << " vertices and " <<
       complex.num_edges() << " edges" << std::endl;
@@ -87,6 +90,8 @@ int main(int argc, char *argv[]) {
       complex.num_blockers() << " blockers and " <<
       num_simplices << " simplices" << std::endl;
 
+  std::cout << contraction_chrono;
+
   return EXIT_SUCCESS;
 }
 
diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
index 4a0044e1..08ff0264 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
@@ -21,6 +21,7 @@
  */
 
 #include <gudhi/Skeleton_blocker.h>
+#include <gudhi/Clock.h>
 
 #include <stdio.h>
 #include <stdlib.h>
@@ -45,6 +46,7 @@ Complex build_complete_complex(int n) {
 }
 
 int main(int argc, char *argv[]) {
+  Gudhi::Clock skbl_chrono("Time to build the complete complex, enumerate simplices and Euler Characteristic");
   const int n = 15;
 
   // build a full complex with n vertices and 2^n-1 simplices
@@ -78,5 +80,6 @@ int main(int argc, char *argv[]) {
   std::cout << "Saw " << num_vertices << " vertices, " << num_edges << " edges and " << num_simplices << " simplices"
       << std::endl;
   std::cout << "The Euler Characteristic is " << euler << std::endl;
+  std::cout << skbl_chrono;
   return EXIT_SUCCESS;
 }
diff --git a/src/common/include/gudhi/Clock.h b/src/common/include/gudhi/Clock.h
index eff48e41..b83de2f5 100644
--- a/src/common/include/gudhi/Clock.h
+++ b/src/common/include/gudhi/Clock.h
@@ -62,7 +62,7 @@ class Clock {
     if (!clock.msg.empty())
       stream << clock.msg << ": ";
 
-    stream << clock.num_seconds() << "s";
+    stream << clock.num_seconds() << "s\n";
     return stream;
   }
 
-- 
cgit v1.2.3


From 8b8689e9dc0c9970eee7c75cb8ea08433ce28196 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 13 Jun 2017 13:37:48 +0000
Subject: Add header and namespace + remove unnecessary include

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2537 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: fc2da43c18649c606ac4760a923684f9eef0c95e
---
 src/common/doc/file_formats.h | 33 +++++++++++++++++++++++++++++++--
 src/common/doc/main_page.h    |  3 +--
 2 files changed, 32 insertions(+), 4 deletions(-)

diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index 1f7ba201..c145b271 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -1,3 +1,30 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+*    (Geometric Understanding in Higher Dimensions) is a generic C++
+*    library for computational topology.
+*
+*    Author(s):       Clément Jamin
+*
+*    Copyright (C) 2017  INRIA
+*
+*    This program is free software: you can redistribute it and/or modify
+*    it under the terms of the GNU General Public License as published by
+*    the Free Software Foundation, either version 3 of the License, or
+*    (at your option) any later version.
+*
+*    This program is distributed in the hope that it will be useful,
+*    but WITHOUT ANY WARRANTY; without even the implied warranty of
+*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+*    GNU General Public License for more details.
+*
+*    You should have received a copy of the GNU General Public License
+*    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef DOC_COMMON_FILE_FORMAT_H_
+#define DOC_COMMON_FILE_FORMAT_H_
+
+namespace Gudhi {
+
 /*! \page fileformats File formats
  
  \tableofcontents
@@ -21,5 +48,7 @@
  \endcode
 
  Other sample files can be found in the `data/persistence_diagram` folder.
- 
-*/
\ No newline at end of file
+*/
+}  // namespace Gudhi
+
+#endif  // DOC_COMMON_FILE_FORMAT_H_
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index b7f93ed2..12012ecb 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -468,5 +468,4 @@ make doxygen
  * @example Witness_complex/example_witness_complex_persistence.cpp
  * @example Witness_complex/example_witness_complex_sphere.cpp
  */
-
-#include "file_formats.h"
\ No newline at end of file
+ 
\ No newline at end of file
-- 
cgit v1.2.3


From e6b1730fd0832fad2a9103863428465155f70986 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 13 Jun 2017 15:29:35 +0000
Subject: This should never have been commented out

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2540 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5e5fc971986908e5b9383130704536686e1b66ea
---
 src/Bottleneck_distance/example/bottleneck_read_file_example.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 6cfbeafa..238d99ad 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -34,7 +34,7 @@ int main(int argc, char** argv) {
     std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
         "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
         " distance (set by default to zero). The program will now terminate \n";
-    //return -1;
+    return -1;
   }
   std::vector<std::pair<double, double>> diag1 = read_persistence_intervals_in_dimension(argv[1]);
   std::vector<std::pair<double, double>> diag2 = read_persistence_intervals_in_dimension(argv[2]);
-- 
cgit v1.2.3


From 547a7c9cb50d1818c9412d10cca9655503db625c Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 13 Jun 2017 20:42:51 +0000
Subject: Try to fix Windows compilation for Conda

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2541 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: afa1b10e300aafbc92a85b3519f4b39add2ae6e4
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 4 ++++
 src/cython/CMakeLists.txt                           | 3 +++
 2 files changed, 7 insertions(+)

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 8f486118..7cd57b25 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -10,6 +10,10 @@ find_package(GMP)
 if(GMP_FOUND)
   message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
   INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
+  get_filename_component(lib_we ${GMP_LIBRARIES} NAME_WE)
+
+  message("++ lib_we = ${lib_we}")
+
   find_package(GMPXX)
   if(GMPXX_FOUND)
     message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index adcc64e4..2a0a3844 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -8,6 +8,9 @@ if(CYTHON_FOUND)
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
 
+  if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+    set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'boost_thread', ")
+  endif()
   # Gudhi and CGAL compilation option
   if(MSVC)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ")
-- 
cgit v1.2.3


From f6d8aaaacf4a2802d3aaad6d326f9510fdb2ddf7 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 14 Jun 2017 05:24:01 +0000
Subject: Add traces for debug

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2542 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a9e8098443114a4fe6e9c19e6410169580c134c6
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake |  4 ----
 src/cython/CMakeLists.txt                           | 10 ++++++++--
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 7cd57b25..8f486118 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -10,10 +10,6 @@ find_package(GMP)
 if(GMP_FOUND)
   message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
   INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
-  get_filename_component(lib_we ${GMP_LIBRARIES} NAME_WE)
-
-  message("++ lib_we = ${lib_we}")
-
   find_package(GMPXX)
   if(GMPXX_FOUND)
     message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 2a0a3844..eff36f93 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -8,6 +8,7 @@ if(CYTHON_FOUND)
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
 
+  message("++ Boost_THREAD_LIBRARY=${Boost_THREAD_LIBRARY} - Boost_thread_LIBRARY=${Boost_thread_LIBRARY} - ")
   if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'boost_thread', ")
   endif()
@@ -106,6 +107,7 @@ if(CYTHON_FOUND)
 
   if(CGAL_FOUND)
     # Add CGAL compilation args
+    message("++ CGAL_LIBRARIES = ${CGAL_LIBRARIES}")
     if(CGAL_HEADER_ONLY)
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
     else(CGAL_HEADER_ONLY)
@@ -119,10 +121,14 @@ if(CYTHON_FOUND)
     # GMP and GMPXX are not required, but if present, CGAL will link with them.
     if(GMP_FOUND)
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
+      get_filename_component(GMP_LIBRARY_FILE_NAME ${GMP_LIBRARIES} NAME_WE)
+      message("++ GMP_LIBRARY_FILE_NAME = ${GMP_LIBRARY_FILE_NAME}")
       if(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'libgmp-10', ")
+        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${GMP_LIBRARY_FILE_NAME}', ")
       else(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ")
+        STRING(REGEX REPLACE "lib" "" UNIX_GMP_LIBRARY_FILE_NAME ${GMP_LIBRARY_FILE_NAME})
+        message("++ UNIX_GMP_LIBRARY_FILE_NAME = ${UNIX_GMP_LIBRARY_FILE_NAME}")
+        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${UNIX_GMP_LIBRARY_FILE_NAME}', ")
       endif(WIN32)
         set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
       if(GMPXX_FOUND)
-- 
cgit v1.2.3


From e8c3b007c141551b68859ea178e79ddf618c6dca Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 14 Jun 2017 06:38:20 +0000
Subject: Fix try

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2543 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: da6eb0ef7b79c0d21d8e98d17d78459d1768a5db
---
 src/cython/CMakeLists.txt        | 42 +++++++++++++++++++++-------------------
 src/cython/cythonize_gudhi.py.in |  2 +-
 2 files changed, 23 insertions(+), 21 deletions(-)

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index eff36f93..739e1a89 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -1,6 +1,20 @@
 cmake_minimum_required(VERSION 2.8)
 project(Cython)
 
+function( add_gudhi_cython_lib THE_LIB )
+  if(EXISTS ${THE_LIB})
+    get_filename_component(THE_LIB_FILE_NAME ${THE_LIB} NAME_WE)
+    if(WIN32)
+      message("++ ${THE_LIB} => THE_LIB_FILE_NAME = ${THE_LIB_FILE_NAME}")
+      set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${THE_LIB_FILE_NAME}', " PARENT_SCOPE)
+    else(WIN32)
+      STRING(REGEX REPLACE "lib" "" UNIX_LIB_FILE_NAME ${THE_LIB_FILE_NAME})
+      message("++ ${THE_LIB} => UNIX_LIB_FILE_NAME = ${UNIX_LIB_FILE_NAME}")
+      set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${UNIX_LIB_FILE_NAME}', " PARENT_SCOPE)
+    endif(WIN32)
+  endif(EXISTS ${THE_LIB})
+endfunction( add_gudhi_cython_lib )
+
 if(CYTHON_FOUND)
   message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}")
 
@@ -8,9 +22,9 @@ if(CYTHON_FOUND)
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
 
-  message("++ Boost_THREAD_LIBRARY=${Boost_THREAD_LIBRARY} - Boost_thread_LIBRARY=${Boost_thread_LIBRARY} - ")
   if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
-    set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'boost_thread', ")
+    add_gudhi_cython_lib(${Boost_THREAD_LIBRARY})
+    set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
   endif()
   # Gudhi and CGAL compilation option
   if(MSVC)
@@ -107,33 +121,20 @@ if(CYTHON_FOUND)
 
   if(CGAL_FOUND)
     # Add CGAL compilation args
-    message("++ CGAL_LIBRARIES = ${CGAL_LIBRARIES}")
     if(CGAL_HEADER_ONLY)
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
     else(CGAL_HEADER_ONLY)
-      if(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL-vc140-mt-4.7', ")
-      else(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ")
-      endif(WIN32)
+      add_gudhi_cython_lib(${CGAL_LIBRARIES})
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
     endif(CGAL_HEADER_ONLY)
     # GMP and GMPXX are not required, but if present, CGAL will link with them.
     if(GMP_FOUND)
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
-      get_filename_component(GMP_LIBRARY_FILE_NAME ${GMP_LIBRARIES} NAME_WE)
-      message("++ GMP_LIBRARY_FILE_NAME = ${GMP_LIBRARY_FILE_NAME}")
-      if(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${GMP_LIBRARY_FILE_NAME}', ")
-      else(WIN32)
-        STRING(REGEX REPLACE "lib" "" UNIX_GMP_LIBRARY_FILE_NAME ${GMP_LIBRARY_FILE_NAME})
-        message("++ UNIX_GMP_LIBRARY_FILE_NAME = ${UNIX_GMP_LIBRARY_FILE_NAME}")
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${UNIX_GMP_LIBRARY_FILE_NAME}', ")
-      endif(WIN32)
-        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
+      add_gudhi_cython_lib(${GMP_LIBRARIES})
+      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
       if(GMPXX_FOUND)
         set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmpxx', ")
+        add_gudhi_cython_lib(${GMPXX_LIBRARIES})
         set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
       endif(GMPXX_FOUND)
     endif(GMP_FOUND)
@@ -154,7 +155,8 @@ if(CYTHON_FOUND)
 
   if (TBB_FOUND)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
-    set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'tbb', 'tbbmalloc', ")
+    add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY})
+    add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY})
     set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ")
     set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ")
   endif()
diff --git a/src/cython/cythonize_gudhi.py.in b/src/cython/cythonize_gudhi.py.in
index 5a97e9f3..cae4641b 100644
--- a/src/cython/cythonize_gudhi.py.in
+++ b/src/cython/cythonize_gudhi.py.in
@@ -42,7 +42,7 @@ setup(
     name = 'gudhi',
     author='Vincent Rouvreau',
     author_email='gudhi-contact@lists.gforge.inria.fr',
-    version='0.1.0',
+    version='@GUDHI_VERSION@',
     url='http://gudhi.gforge.inria.fr/',
     ext_modules = cythonize(gudhi),
 )
-- 
cgit v1.2.3


From a6b6f91bfd5a86ee88297b27f18c2bc7d38f6db4 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 14 Jun 2017 07:45:09 +0000
Subject: Remove birth<=death check (should be done by the caller if necessary)

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2544 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ce50159f4bf779a2a42d357cf1c2aa290feaf9b9
---
 src/common/include/gudhi/reader_utils.h | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 35af09bd..8df20dcc 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -305,6 +305,7 @@ Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth, death);`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+Note: the function does not check that birth <= death.
 **/
 template <typename OutputIterator>
 void read_persistence_intervals_and_dimension(std::string const& filename, OutputIterator out) {
@@ -326,7 +327,6 @@ void read_persistence_intervals_and_dimension(std::string const& filename, Outpu
       if (n >= 2) {
         //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1);
         int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
-        GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death.");
         *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
       }
     }
@@ -338,6 +338,7 @@ Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+Note: the function does not check that birth <= death.
 **/
 std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) {
 
@@ -357,6 +358,7 @@ If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim`
 (or where dimension is not specified) are returned.
 The return value is an `std::vector<std::pair<birth, death>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+Note: the function does not check that birth <= death.
 **/
 std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
 
-- 
cgit v1.2.3


From 30d31a1aabc2035e23eca7bcf3867a30536f11b7 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 16 Jun 2017 07:06:49 +0000
Subject: Fix Python module version numer Fix link with external libraries

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2547 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e2f47e860ea4608a4d298fa4772d750ac540be5a
---
 CMakeGUDHIVersion.txt            | 2 +-
 src/cython/cythonize_gudhi.py.in | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index bd0c57ac..3d9add66 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 2)
 set (GUDHI_MINOR_VERSION 0)
-set (GUDHI_PATCH_VERSION 0)
+set (GUDHI_PATCH_VERSION 1.beta)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/cython/cythonize_gudhi.py.in b/src/cython/cythonize_gudhi.py.in
index cae4641b..68a95916 100644
--- a/src/cython/cythonize_gudhi.py.in
+++ b/src/cython/cythonize_gudhi.py.in
@@ -35,6 +35,7 @@ gudhi = Extension(
     extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@],
     libraries=[@GUDHI_CYTHON_LIBRARIES@],
     library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@],
+    runtime_library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@],
     include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@],
 )
 
-- 
cgit v1.2.3


From 30b44fa282606a6a6b585e0e83b98dae4f2e6b2e Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 16 Jun 2017 08:12:26 +0000
Subject: Add warning about boost_thread link for the Mac GUDHI python module

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2548 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4a9f6c43f4868bd4f303579c22fdc7a54728e68c
---
 src/cython/CMakeLists.txt | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 739e1a89..84441591 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -22,6 +22,15 @@ if(CYTHON_FOUND)
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
 
+  # TODO: Something more clever could be done.
+  # This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h
+  # CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac).
+  # The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h
+  #   #if __has_feature(cxx_thread_local) || \
+  #       ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \
+  #       ( _MSC_VER >= 1900 )
+  #   #define CGAL_CAN_USE_CXX11_THREAD_LOCAL
+  #   #endif
   if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     add_gudhi_cython_lib(${Boost_THREAD_LIBRARY})
     set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
-- 
cgit v1.2.3


From 06f595c9bbe1f7fbc1d4e9dae7f5a0a384fe62c2 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 16 Jun 2017 09:27:12 +0000
Subject: Fix CUSTOMBUILD : error : don't know how to set runtime library
 search path for MSVC

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2549 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 94c7625b3bc8e943e3856e0e65dc65bb5d8cd0f7
---
 src/cython/CMakeLists.txt        | 8 ++++----
 src/cython/cythonize_gudhi.py.in | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 84441591..7586188c 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -170,6 +170,10 @@ if(CYTHON_FOUND)
     set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ")
   endif()
 
+  if(UNIX)
+    set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}")
+  endif(UNIX)
+
   # set sphinx-build in make files
   configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY)
   configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY)
@@ -187,10 +191,6 @@ if(CYTHON_FOUND)
   add_custom_target(cython ALL DEPENDS gudhi.so
                     COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
 
-  if(UNIX)
-    set( ENV{PYTHONPATH} $ENV{PYTHONPATH}:${CMAKE_CURRENT_BINARY_DIR}/ )
-  endif(UNIX)
-
   # For installation purpose
   # TODO(VR) : files matching pattern mechanism is copying all cython directory
   install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING
diff --git a/src/cython/cythonize_gudhi.py.in b/src/cython/cythonize_gudhi.py.in
index 68a95916..c1a1717a 100644
--- a/src/cython/cythonize_gudhi.py.in
+++ b/src/cython/cythonize_gudhi.py.in
@@ -35,8 +35,8 @@ gudhi = Extension(
     extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@],
     libraries=[@GUDHI_CYTHON_LIBRARIES@],
     library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@],
-    runtime_library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@],
     include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@],
+    runtime_library_dirs=[@GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS@],
 )
 
 setup(
-- 
cgit v1.2.3


From cdb39c39a60fe06009168c1ecb1d4ce5de0bed8c Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 16 Jun 2017 09:31:43 +0000
Subject: Fix auto lambda (requires C++14) compilation issue

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2550 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: df64cfdde77500b06f00432a1d1532518cd4dd37
---
 src/common/include/gudhi/reader_utils.h | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 8df20dcc..f1684d78 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -25,8 +25,8 @@
 
 #include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/Debug_utils.h>
-#include <boost/function_output_iterator.hpp>
 
+#include <boost/function_output_iterator.hpp>
 #include <boost/graph/adjacency_list.hpp>
 
 #include <iostream>
@@ -340,12 +340,12 @@ The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 Note: the function does not check that birth <= death.
 **/
-std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) {
+inline std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) {
 
   std::map<int, std::vector<std::pair<double, double>>> ret;
   read_persistence_intervals_and_dimension(
     filename,
-    boost::make_function_output_iterator([&ret](auto t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); }));
+    boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); }));
   return ret;
 } // read_persistence_diagram_from_file
 
@@ -360,12 +360,12 @@ The return value is an `std::vector<std::pair<birth, death>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 Note: the function does not check that birth <= death.
 **/
-std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
+inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
 
   std::vector<std::pair<double, double>> ret;
   read_persistence_intervals_and_dimension(
     filename, 
-    boost::make_function_output_iterator([&ret](auto t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
+    boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
   return ret;
 } // read_persistence_diagram_from_file
 
-- 
cgit v1.2.3


From 9d0b415512c166cda2985d1709fcf99fd770b799 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 20 Jun 2017 14:04:09 +0000
Subject: Missing typedef

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Spatial_searching-Add_radius_search@2556 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 3354bb63d0839ae8377e9c11ef2a1168cce7dd20
---
 src/Spatial_searching/include/gudhi/Kd_tree_search.h | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/Spatial_searching/include/gudhi/Kd_tree_search.h b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
index c4a15876..f13a98f7 100644
--- a/src/Spatial_searching/include/gudhi/Kd_tree_search.h
+++ b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
@@ -88,6 +88,10 @@ class Kd_tree_search {
     std::ptrdiff_t,
     Point_property_map,
     Traits_base>                                            STraits;
+  typedef CGAL::Distance_adapter<
+    std::ptrdiff_t,
+    Point_property_map,
+    CGAL::Euclidean_distance<Traits_base> >                 Orthogonal_distance;
 
   typedef CGAL::Orthogonal_k_neighbor_search<STraits>       K_neighbor_search;
   typedef typename K_neighbor_search::Tree                  Tree;
-- 
cgit v1.2.3


From 34487e33517c36ad65407743c46fd4c1df963628 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 28 Jun 2017 10:53:42 +0000
Subject: Add a comment

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2566 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 64cd59ca30ff82a1c116df20c4cee38a795dc518
---
 src/cython/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 5c98b09a..d801fb0b 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -151,6 +151,7 @@ if(CYTHON_FOUND)
     else(CGAL_HEADER_ONLY)
       add_gudhi_cython_lib(${CGAL_LIBRARIES})
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
+      # If CGAL is not header only, CGAL library may link with boost system,
       add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY})
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
     endif(CGAL_HEADER_ONLY)
-- 
cgit v1.2.3


From 2e7447cf1deb3a1ac08f2fe90cd780901da65016 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 3 Jul 2017 13:16:54 +0000
Subject: Rename cythonize_gudhi.py in setup.py to be conform with Python
 convention (for easy_install and pip)

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2578 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c514a7c5096293380254339e7e60782194040823
---
 src/cython/CMakeLists.txt        |  6 ++---
 src/cython/cythonize_gudhi.py.in | 49 ----------------------------------------
 src/cython/setup.py.in           | 49 ++++++++++++++++++++++++++++++++++++++++
 3 files changed, 52 insertions(+), 52 deletions(-)
 delete mode 100644 src/cython/cythonize_gudhi.py.in
 create mode 100644 src/cython/setup.py.in

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index d801fb0b..99badffb 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -197,15 +197,15 @@ if(CYTHON_FOUND)
   configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY)
   configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY)
 
-  # Generate cythonize_gudhi.py file to cythonize Gudhi
-  configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY)
+  # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
+  configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY)
   # Generate gudhi.pyx - Gudhi cython file
   configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
 
   add_custom_command(
       OUTPUT gudhi.so
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace")
+      COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
 
   add_custom_target(cython ALL DEPENDS gudhi.so
                     COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
diff --git a/src/cython/cythonize_gudhi.py.in b/src/cython/cythonize_gudhi.py.in
deleted file mode 100644
index c1a1717a..00000000
--- a/src/cython/cythonize_gudhi.py.in
+++ /dev/null
@@ -1,49 +0,0 @@
-from distutils.core import setup, Extension
-from Cython.Build import cythonize
-
-"""This file is part of the Gudhi Library. The Gudhi library
-   (Geometric Understanding in Higher Dimensions) is a generic C++
-   library for computational topology.
-
-   Author(s):       Vincent Rouvreau
-
-   Copyright (C) 2016  INRIA
-
-   This program is free software: you can redistribute it and/or modify
-   it under the terms of the GNU General Public License as published by
-   the Free Software Foundation, either version 3 of the License, or
-   (at your option) any later version.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License
-   along with this program.  If not, see <http://www.gnu.org/licenses/>.
-"""
-
-__author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016  INRIA"
-__license__ = "GPL v3"
-
-gudhi = Extension(
-    "gudhi",
-    sources = ['gudhi.pyx',],
-    language = 'c++',
-    extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@],
-    extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@],
-    libraries=[@GUDHI_CYTHON_LIBRARIES@],
-    library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@],
-    include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@],
-    runtime_library_dirs=[@GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS@],
-)
-
-setup(
-    name = 'gudhi',
-    author='Vincent Rouvreau',
-    author_email='gudhi-contact@lists.gforge.inria.fr',
-    version='@GUDHI_VERSION@',
-    url='http://gudhi.gforge.inria.fr/',
-    ext_modules = cythonize(gudhi),
-)
diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in
new file mode 100644
index 00000000..c1a1717a
--- /dev/null
+++ b/src/cython/setup.py.in
@@ -0,0 +1,49 @@
+from distutils.core import setup, Extension
+from Cython.Build import cythonize
+
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  INRIA
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA"
+__license__ = "GPL v3"
+
+gudhi = Extension(
+    "gudhi",
+    sources = ['gudhi.pyx',],
+    language = 'c++',
+    extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@],
+    extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@],
+    libraries=[@GUDHI_CYTHON_LIBRARIES@],
+    library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@],
+    include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@],
+    runtime_library_dirs=[@GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS@],
+)
+
+setup(
+    name = 'gudhi',
+    author='Vincent Rouvreau',
+    author_email='gudhi-contact@lists.gforge.inria.fr',
+    version='@GUDHI_VERSION@',
+    url='http://gudhi.gforge.inria.fr/',
+    ext_modules = cythonize(gudhi),
+)
-- 
cgit v1.2.3

-- 
cgit v1.2.3


From a4b7d528893f992115711225c7d4396de55c6c58 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 4 Jul 2017 13:37:29 +0000
Subject: Add Gudhi namespace for reader_utils Add confidence band in
 persistence_graphical_tools.py Persistence_diagram returns a plot that is no
 more showed.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2582 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4125f4f525057e89c8b0d5d164ea0b9d1df1bd72
---
 .../example/bottleneck_read_file_example.cpp       |  4 ++--
 .../example/rips_distance_matrix_persistence.cpp   |  2 +-
 ..._rips_complex_from_csv_distance_matrix_file.cpp |  2 +-
 src/Rips_complex/test/test_rips_complex.cpp        |  2 +-
 src/common/include/gudhi/reader_utils.h            | 10 +++++++---
 src/common/test/test_distance_matrix_reader.cpp    |  4 ++--
 src/cython/cython/persistence_graphical_tools.py   | 23 +++++++++++++++-------
 .../doc/persistence_graphical_tools_user.rst       | 10 ++++++----
 ...ex_diagram_persistence_from_off_file_example.py |  4 +++-
 9 files changed, 39 insertions(+), 22 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 238d99ad..1408681a 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -36,8 +36,8 @@ int main(int argc, char** argv) {
         " distance (set by default to zero). The program will now terminate \n";
     return -1;
   }
-  std::vector<std::pair<double, double>> diag1 = read_persistence_intervals_in_dimension(argv[1]);
-  std::vector<std::pair<double, double>> diag2 = read_persistence_intervals_in_dimension(argv[2]);
+  std::vector<std::pair<double, double>> diag1 = Gudhi::read_persistence_intervals_in_dimension(argv[1]);
+  std::vector<std::pair<double, double>> diag2 = Gudhi::read_persistence_intervals_in_dimension(argv[2]);
 
   double tolerance = 0.;
   if (argc == 4) {
diff --git a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
index 8517e7f6..d38808c7 100644
--- a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
@@ -57,7 +57,7 @@ int main(int argc, char * argv[]) {
 
   program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence);
 
-  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
+  Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
   Rips_complex rips_complex_from_file(distances, threshold);
 
   // Construct the Rips complex in a Simplex Tree
diff --git a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
index 7ae8126f..9e182f1e 100644
--- a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
+++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
@@ -32,7 +32,7 @@ int main(int argc, char **argv) {
   // Init of a Rips complex from a distance matrix in a csv file
   // Default separator is ';'
   // ----------------------------------------------------------------------------
-  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
+  Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
   Rips_complex rips_complex_from_file(distances, threshold);
 
   std::streambuf* streambufffer;
diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp
index fc2179f2..fc83f5f7 100644
--- a/src/Rips_complex/test/test_rips_complex.cpp
+++ b/src/Rips_complex/test/test_rips_complex.cpp
@@ -244,7 +244,7 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) {
   std::cout << "========== CSV FILE NAME = " << csv_file_name << " - Rips threshold=" <<
       rips_threshold << "==========" << std::endl;
 
-  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
+  Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
   Rips_complex rips_complex_from_file(distances, rips_threshold);
 
   const int DIMENSION_1 = 1;
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index f1684d78..8e99acfc 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -37,6 +37,8 @@
 #include <vector>
 #include <utility>  // for pair
 
+namespace Gudhi {
+
 // Keep this file tag for Doxygen to parse the code, otherwise, functions are not documented.
 // It is required for global functions and variables.
 
@@ -331,7 +333,7 @@ void read_persistence_intervals_and_dimension(std::string const& filename, Outpu
       }
     }
   }
-} // read_persistence_diagram_from_file
+}  // read_persistence_diagram_from_file
 
 /**
 Reads a file containing persistence intervals.
@@ -347,7 +349,7 @@ inline std::map<int, std::vector<std::pair<double, double>>> read_persistence_in
     filename,
     boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); }));
   return ret;
-} // read_persistence_diagram_from_file
+}  // read_persistence_diagram_from_file
 
 
 /**
@@ -367,6 +369,8 @@ inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dime
     filename, 
     boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
   return ret;
-} // read_persistence_diagram_from_file
+}  // read_persistence_diagram_from_file
+
+}  // namespace Gudhi
 
 #endif  // READER_UTILS_H_
diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp
index 95a73bd9..656e6f2e 100644
--- a/src/common/test/test_distance_matrix_reader.cpp
+++ b/src/common/test/test_distance_matrix_reader.cpp
@@ -36,7 +36,7 @@ BOOST_AUTO_TEST_CASE( lower_triangular_distance_matrix )
 {
   Distance_matrix from_lower_triangular;
   // Read lower_triangular_distance_matrix.csv file where the separator is a ','
-  from_lower_triangular = read_lower_triangular_matrix_from_csv_file<double>("lower_triangular_distance_matrix.csv",
+  from_lower_triangular = Gudhi::read_lower_triangular_matrix_from_csv_file<double>("lower_triangular_distance_matrix.csv",
                                                                              ',');
   for (auto& i : from_lower_triangular) {
     for (auto j : i) {
@@ -69,7 +69,7 @@ BOOST_AUTO_TEST_CASE( full_square_distance_matrix )
 {
   Distance_matrix from_full_square;
   // Read full_square_distance_matrix.csv file where the separator is the default one ';'
-  from_full_square = read_lower_triangular_matrix_from_csv_file<double>("full_square_distance_matrix.csv");
+  from_full_square = Gudhi::read_lower_triangular_matrix_from_csv_file<double>("full_square_distance_matrix.csv");
   for (auto& i : from_full_square) {
     for (auto j : i) {
       std::cout << j << " ";
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index a984633e..70ff6001 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -5,7 +5,7 @@ import numpy as np
    (Geometric Understanding in Higher Dimensions) is a generic C++
    library for computational topology.
 
-   Author(s):       Vincent Rouvreau
+   Author(s):       Vincent Rouvreau, Bertrand Michel
 
    Copyright (C) 2016 INRIA
 
@@ -27,11 +27,13 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
-def __min_birth_max_death(persistence):
+def __min_birth_max_death(persistence, band_boot=0.):
     """This function returns (min_birth, max_death) from the persistence.
 
     :param persistence: The persistence to plot.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param band_boot: bootstrap band
+    :type band_boot: float.
     :returns: (float, float) -- (min_birth, max_death).
     """
     # Look for minimum birth date and maximum death date for plot optimisation
@@ -45,6 +47,8 @@ def __min_birth_max_death(persistence):
             max_death = float(interval[1][0])
         if float(interval[1][0]) < min_birth:
             min_birth = float(interval[1][0])
+    if band_boot > 0.:
+        max_death += band_boot
     return (min_birth, max_death)
 
 """
@@ -108,16 +112,18 @@ def plot_persistence_barcode(persistence, alpha=0.6):
     plt.axis([axis_start, infinity, 0, ind])
     plt.show()
 
-def plot_persistence_diagram(persistence, alpha=0.6):
-    """This function plots the persistence diagram.
+def plot_persistence_diagram(persistence, alpha=0.6, band_boot=0.):
+    """This function plots the persistence diagram with confidence band.
 
     :param persistence: The persistence to plot.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
     :param alpha: alpha value in [0.0, 1.0] for points and horizontal infinity line (default is 0.6).
     :type alpha: float.
-    :returns: plot -- An diagram plot of persistence.
+    :param band_boot: bootstrap band
+    :type band_boot: float.
+    :returns: plot -- A diagram plot of persistence.
     """
-    (min_birth, max_death) = __min_birth_max_death(persistence)
+    (min_birth, max_death) = __min_birth_max_death(persistence, band_boot)
     ind = 0
     delta = ((max_death - min_birth) / 10.0)
     # Replace infinity values with max_death + delta for diagram to be more
@@ -131,6 +137,9 @@ def plot_persistence_diagram(persistence, alpha=0.6):
     plt.plot(x, x, color='k', linewidth=1.0)
     plt.plot(x, [infinity] * len(x), linewidth=1.0, color='k', alpha=alpha)
     plt.text(axis_start, infinity, r'$\infty$', color='k', alpha=alpha)
+    # bootstrap band
+    if band_boot > 0.:
+        plt.fill_between(x, x, x+band_boot, alpha=alpha, facecolor='red')
 
     # Draw points in loop
     for interval in reversed(persistence):
@@ -149,4 +158,4 @@ def plot_persistence_diagram(persistence, alpha=0.6):
     plt.ylabel('Death')
     # Ends plot on infinity value and starts a little bit before min_birth
     plt.axis([axis_start, infinity, axis_start, infinity + delta])
-    plt.show()
+    return plt
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index cae18323..bc731f12 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -51,16 +51,18 @@ This function can display the persistence result as a diagram:
 
     import gudhi
     
-    rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0)
+    rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
-    gudhi.plot_persistence_diagram(diag)
+    pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+    pplot.show()
 
 .. plot::
 
     import gudhi
 
-    rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0)
+    rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
-    gudhi.plot_persistence_diagram(diag)
+    pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+    pplot.show()
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
index 4c21b98e..5951eedf 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -39,6 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from '
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -64,7 +65,8 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
 
-- 
cgit v1.2.3


From 4832d865981bb74c8afc7240e953adc8f54c52b0 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 6 Jul 2017 15:38:44 +0000
Subject: Plot functions now returns a plot that can be modified before to be
 shown Add confidence band in plot_persistence_diagram Cythonization of
 read_lower_triangular_matrix_from_csv_file and read_persistence_intervals
 functions Add Python tests of read functions

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2590 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 522ec31e9ad3a9a688875612d246114704b8c74e
---
 src/common/include/gudhi/reader_utils.h            |  2 +-
 src/cython/CMakeLists.txt                          |  2 +-
 src/cython/cython/persistence_graphical_tools.py   |  4 +-
 src/cython/cython/reader_utils.pyx                 | 95 ++++++++++++++++++++++
 src/cython/doc/pyplots/barcode_persistence.py      |  2 +-
 src/cython/doc/pyplots/diagram_persistence.py      |  8 +-
 ...ex_diagram_persistence_from_off_file_example.py |  4 +-
 ...ex_diagram_persistence_from_off_file_example.py |  5 +-
 ...ex_diagram_persistence_from_off_file_example.py |  5 +-
 .../example/gudhi_graphical_tools_example.py       |  9 +-
 ...ersistence_from_distance_matrix_file_example.py |  4 +-
 src/cython/example/rips_persistence_diagram.py     |  3 +-
 ...complex_plain_homology_from_off_file_example.py |  4 +-
 src/cython/gudhi.pyx.in                            |  1 +
 src/cython/include/Reader_utils_interface.h        | 54 ++++++++++++
 src/cython/include/Rips_complex_interface.h        |  2 +-
 src/cython/test/test_reader_utils.py               | 81 ++++++++++++++++++
 17 files changed, 267 insertions(+), 18 deletions(-)
 create mode 100644 src/cython/cython/reader_utils.pyx
 create mode 100644 src/cython/include/Reader_utils_interface.h
 create mode 100755 src/cython/test/test_reader_utils.py

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 8e99acfc..f16ae61d 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -359,7 +359,7 @@ If `only_this_dim` = -1, dimension is ignored and all lines are returned.
 If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` 
 (or where dimension is not specified) are returned.
 The return value is an `std::vector<std::pair<birth, death>>`
-where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+where `birth` a `double`, and `death` a `double`.
 Note: the function does not check that birth <= death.
 **/
 inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 99badffb..f427b3c5 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -100,7 +100,7 @@ if(CYTHON_FOUND)
   file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
   # Persistence graphical tools examples
   file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+  file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
 
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     # If CGAL_VERSION >= 4.8.1, include subsampling
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 70ff6001..da709b8a 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -113,13 +113,13 @@ def plot_persistence_barcode(persistence, alpha=0.6):
     plt.show()
 
 def plot_persistence_diagram(persistence, alpha=0.6, band_boot=0.):
-    """This function plots the persistence diagram with confidence band.
+    """This function plots the persistence diagram with an optional confidence band.
 
     :param persistence: The persistence to plot.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
     :param alpha: alpha value in [0.0, 1.0] for points and horizontal infinity line (default is 0.6).
     :type alpha: float.
-    :param band_boot: bootstrap band
+    :param band_boot: bootstrap band (not displayed if :math:`\leq` 0.)
     :type band_boot: float.
     :returns: plot -- A diagram plot of persistence.
     """
diff --git a/src/cython/cython/reader_utils.pyx b/src/cython/cython/reader_utils.pyx
new file mode 100644
index 00000000..14976167
--- /dev/null
+++ b/src/cython/cython/reader_utils.pyx
@@ -0,0 +1,95 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.string cimport string
+from libcpp.map cimport map
+from libcpp.pair cimport pair
+import os
+
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2017 INRIA
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2017 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Reader_utils_interface.h" namespace "Gudhi":
+    vector[vector[double]] read_matrix_from_csv_file(string off_file, char separator)
+    map[int, vector[pair[double, double]]] read_pers_intervals_grouped_by_dimension(string filename)
+    vector[pair[double, double]] read_pers_intervals_in_dimension(string filename, int only_this_dim)
+
+def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'):
+    """Read lower triangular matrix from a CSV style file.
+
+    :param csv_file: A CSV file style name.
+    :type csv_file: string
+    :param separator: The value separator in the CSV file. Default value is ';'
+    :type separator: char
+
+    :returns:  The lower triangular matrix.
+    :rtype: vector[vector[double]]
+    """
+    if csv_file is not '':
+        if os.path.isfile(csv_file):
+            return read_matrix_from_csv_file(str.encode(csv_file), str.encode(separator)[0])
+    print("file " + csv_file + " not set or not found.")
+    return []
+
+def read_persistence_intervals_grouped_by_dimension(persistence_file=''):
+    """Reads a file containing persistence intervals.
+    Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
+    The return value is an `map[dim, vector[pair[birth, death]]]`
+    where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+    Note: the function does not check that birth <= death.
+
+    :param persistence_file: A persistence file style name.
+    :type persistence_file: string
+
+    :returns:  The persistence pairs grouped by dimension.
+    :rtype: map[int, vector[pair[double, double]]]
+    """
+    if persistence_file is not '':
+        if os.path.isfile(persistence_file):
+            return read_pers_intervals_grouped_by_dimension(str.encode(persistence_file))
+    print("file " + persistence_file + " not set or not found.")
+    return []
+
+def read_persistence_intervals_in_dimension(persistence_file='', only_this_dim=-1):
+    """Reads a file containing persistence intervals.
+    Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
+    If `only_this_dim` = -1, dimension is ignored and all lines are returned.
+    If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim`
+    (or where dimension is not specified) are returned.
+    The return value is an `vector[pair[birth, death]]`
+    where `birth` a `double`, and `death` a `double`.
+    Note: the function does not check that birth <= death.
+
+    :param persistence_file: A persistence file style name.
+    :type persistence_file: string
+
+    :returns:  The persistence pairs grouped by dimension.
+    :rtype: map[int, vector[pair[double, double]]]
+    """
+    if persistence_file is not '':
+        if os.path.isfile(persistence_file):
+            return read_pers_intervals_in_dimension(str.encode(persistence_file), only_this_dim)
+    print("file " + persistence_file + " not set or not found.")
+    return []
diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py
index c06ac5a7..b021049f 100755
--- a/src/cython/doc/pyplots/barcode_persistence.py
+++ b/src/cython/doc/pyplots/barcode_persistence.py
@@ -1,5 +1,5 @@
 import gudhi
 
-periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='../3d_torus.txt')
+periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
 diag = periodic_cc.persistence()
 gudhi.plot_persistence_barcode(diag)
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
index b4714fe3..56d6c50f 100755
--- a/src/cython/doc/pyplots/diagram_persistence.py
+++ b/src/cython/doc/pyplots/diagram_persistence.py
@@ -1,5 +1,7 @@
 import gudhi
 
-alpha_complex = gudhi.AlphaComplex(off_file='../tore3D_300.off')
-diag = alpha_complex.persistence()
-gudhi.plot_persistence_diagram(diag)
+rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2)
+simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
+diag = simplex_tree.persistence()
+pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+pplot.show()
diff --git a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
index adedc7d2..b4487be4 100755
--- a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -38,6 +38,7 @@ parser = argparse.ArgumentParser(description='AlphaComplex creation from '
                                  'points from the given OFF file.')
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, default=0.5)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -63,7 +64,8 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
 
diff --git a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
index 2371c36c..e3f362dc 100755
--- a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -40,6 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
 parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
 parser.add_argument("-d", "--limit_dimension", type=int, required=True)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -70,8 +71,8 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
-
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
 
diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
index 5748aa8a..c236d992 100755
--- a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -40,6 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
 parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
 parser.add_argument("-d", "--limit_dimension", type=int, required=True)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -70,8 +71,8 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
-
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
 
diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py
index bc3b16ec..ed87806b 100755
--- a/src/cython/example/gudhi_graphical_tools_example.py
+++ b/src/cython/example/gudhi_graphical_tools_example.py
@@ -44,4 +44,11 @@ gudhi.plot_persistence_barcode(persistence)
 print("#####################################################################")
 print("Show diagram persistence example")
 
-gudhi.plot_persistence_diagram(persistence)
+pplot = gudhi.plot_persistence_diagram(persistence)
+pplot.show()
+
+print("#####################################################################")
+print("Show diagram persistence example with a confidence band")
+
+pplot = gudhi.plot_persistence_diagram(persistence, band_boot=0.2)
+pplot.show()
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 984dbf1b..3baebd17 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
@@ -39,6 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from '
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -61,4 +62,5 @@ print("betti_numbers()=")
 print(simplex_tree.betti_numbers())
 
 if args.no_diagram == False:
-    gudhi.plot_persistence_diagram(diag)
+    pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+    pplot.show()
diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py
index 4e5cd2c8..9bfea41c 100755
--- a/src/cython/example/rips_persistence_diagram.py
+++ b/src/cython/example/rips_persistence_diagram.py
@@ -39,4 +39,5 @@ simplex_tree = rips.create_simplex_tree(max_dimension=1)
 diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0)
 print("diag=", diag)
 
-gudhi.plot_persistence_diagram(diag)
+pplot = gudhi.plot_persistence_diagram(diag)
+pplot.show()
diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
index 4845eb47..6145e7f2 100755
--- a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
+++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
@@ -37,6 +37,7 @@ parser = argparse.ArgumentParser(description='TangentialComplex creation from '
                                  '- Constructs a tangential complex with the '
                                  'points from the given OFF file')
 parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -59,7 +60,8 @@ with open(args.file, 'r') as f:
         print(st.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
 
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index 34d7c3b5..ed2d28cc 100644
--- a/src/cython/gudhi.pyx.in
+++ b/src/cython/gudhi.pyx.in
@@ -30,6 +30,7 @@ include "cython/rips_complex.pyx"
 include "cython/cubical_complex.pyx"
 include "cython/periodic_cubical_complex.pyx"
 include "cython/persistence_graphical_tools.py"
+include "cython/reader_utils.pyx"
 include "cython/witness_complex.pyx"
 include "cython/strong_witness_complex.pyx"
 @GUDHI_CYTHON_ALPHA_COMPLEX@
diff --git a/src/cython/include/Reader_utils_interface.h b/src/cython/include/Reader_utils_interface.h
new file mode 100644
index 00000000..b87b6cca
--- /dev/null
+++ b/src/cython/include/Reader_utils_interface.h
@@ -0,0 +1,54 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2017 INRIA
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef INCLUDE_READER_UTILS_INTERFACE_H_
+#define INCLUDE_READER_UTILS_INTERFACE_H_
+
+#include <gudhi/reader_utils.h>
+
+#include <iostream>
+#include <vector>
+#include <string>
+
+namespace Gudhi {
+
+// Redefine functions with a different name in order the original name can be used in the Python version.
+std::vector<std::vector<double>> read_matrix_from_csv_file(const std::string& filename,
+                                                                const char separator = ';') {
+  return read_lower_triangular_matrix_from_csv_file<double>(filename, separator);
+}
+
+inline std::map<int, std::vector<std::pair<double, double>>>
+    read_pers_intervals_grouped_by_dimension(std::string const& filename) {
+  return read_persistence_intervals_grouped_by_dimension(filename);
+}
+
+inline std::vector<std::pair<double, double>>
+    read_pers_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
+  return read_persistence_intervals_in_dimension(filename, only_this_dim);
+}
+
+
+}  // namespace Gudhi
+
+
+#endif  // INCLUDE_READER_UTILS_INTERFACE_H_
diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
index 6d813f4a..d06ee4bd 100644
--- a/src/cython/include/Rips_complex_interface.h
+++ b/src/cython/include/Rips_complex_interface.h
@@ -66,7 +66,7 @@ class Rips_complex_interface {
     } else {
       // Rips construction where values is a distance matrix
       Distance_matrix distances =
-          read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
+          Gudhi::read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
       rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(distances, threshold);
     }
   }
diff --git a/src/cython/test/test_reader_utils.py b/src/cython/test/test_reader_utils.py
new file mode 100755
index 00000000..517bf109
--- /dev/null
+++ b/src/cython/test/test_reader_utils.py
@@ -0,0 +1,81 @@
+import gudhi
+
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2017 INRIA
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2017 INRIA"
+__license__ = "GPL v3"
+
+
+def test_non_existing_csv_file():
+    # Try to open a non existing file
+    matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file='pouetpouettralala.toubiloubabdou')
+    assert matrix == []
+
+def test_full_square_distance_matrix_csv_file():
+    # Create test file
+    test_file = open('full_square_distance_matrix.csv', 'w')
+    test_file.write('0;1;2;3;\n1;0;4;5;\n2;4;0;6;\n3;5;6;0;')
+    test_file.close()
+    matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file="full_square_distance_matrix.csv")
+    assert matrix == [[], [1.0], [2.0, 4.0], [3.0, 5.0, 6.0]]
+
+def test_lower_triangular_distance_matrix_csv_file():
+    # Create test file
+    test_file = open('lower_triangular_distance_matrix.csv', 'w')
+    test_file.write('\n1,\n2,3,\n4,5,6,\n7,8,9,10,')
+    test_file.close()
+    matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file="lower_triangular_distance_matrix.csv", separator=",")
+    assert matrix == [[], [1.0], [2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0, 10.0]]
+
+def test_non_existing_persistence_file():
+    # Try to open a non existing file
+    persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='pouetpouettralala.toubiloubabdou')
+    assert persistence == []
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='pouetpouettralala.toubiloubabdou', only_this_dim=1)
+    assert persistence == []
+
+def test_read_persistence_intervals_without_dimension():
+    # Create test file
+    test_file = open('persistence_intervals_without_dimension.pers', 'w')
+    test_file.write('# Simple persistence diagram without dimension\n2.7 3.7\n9.6 14.\n34.2 34.974\n3. inf')
+    test_file.close()
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers')
+    assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]]
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=15)
+    assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]]
+    persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_without_dimension.pers')
+    assert persistence == {-1: [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float('Inf'))]}
+
+def test_read_persistence_intervals_with_dimension():
+    # Create test file
+    test_file = open('persistence_intervals_with_dimension.pers', 'w')
+    test_file.write('# Simple persistence diagram with dimension\n0 2.7 3.7\n1 9.6 14.\n3 34.2 34.974\n1 3. inf')
+    test_file.close()
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers')
+    assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]]
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=1)
+    # BUG !!!
+    assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]]
+    persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_with_dimension.pers')
+    assert persistence == {0: [(2.7, 3.7)], 1: [(9.6, 14.0), (3.0, float('Inf'))], 3: [(34.2, 34.974)]}
-- 
cgit v1.2.3


From 2c353d0c3db1c5c8fc11cb28ea65c90c559766a1 Mon Sep 17 00:00:00 2001
From: glisse <glisse@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 10 Jul 2017 15:05:46 +0000
Subject: Cubical: use +inf instead of UINT_MAX as filtration value for
 non-simplices.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2595 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c578be16d9559b6d271cdb63be3a58a015735ab7
---
 .../include/gudhi/Bitmap_cubical_complex.h         | 27 +++++++++++-----------
 src/cython/test/test_cubical_complex.py            |  4 ++--
 2 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
index 5a87b9b8..f395de65 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
@@ -97,7 +97,7 @@ class Bitmap_cubical_complex : public T {
    * with filtration on top dimensional cells.
    **/
   Bitmap_cubical_complex(const std::vector<unsigned>& dimensions,
-                         const std::vector<typename T::filtration_type>& top_dimensional_cells) :
+                         const std::vector<Filtration_value>& top_dimensional_cells) :
       T(dimensions, top_dimensional_cells),
       key_associated_to_simplex(this->total_number_of_cells + 1) {
     for (size_t i = 0; i != this->total_number_of_cells; ++i) {
@@ -111,13 +111,13 @@ class Bitmap_cubical_complex : public T {
 
   /**
    * Constructor that requires vector of elements of type unsigned, which gives number of top dimensional cells
-   * in the following directions and vector of element of a type T::filtration_type
+   * in the following directions and vector of element of a type Filtration_value
    * with filtration on top dimensional cells. The last parameter of the constructor is a vector of boolean of a length
    * equal to the dimension of cubical complex.
    * If the position i on this vector is true, then we impose periodic boundary conditions in this direction.
    **/
   Bitmap_cubical_complex(const std::vector<unsigned>& dimensions,
-                         const std::vector<typename T::filtration_type>& top_dimensional_cells,
+                         const std::vector<Filtration_value>& top_dimensional_cells,
                          std::vector< bool > directions_in_which_periodic_b_cond_are_to_be_imposed) :
       T(dimensions, top_dimensional_cells, directions_in_which_periodic_b_cond_are_to_be_imposed),
       key_associated_to_simplex(this->total_number_of_cells + 1) {
@@ -170,20 +170,20 @@ class Bitmap_cubical_complex : public T {
     if (globalDbg) {
       std::cerr << "unsigned dimension(const Simplex_handle& sh)\n";
     }
-    if (sh != std::numeric_limits<Simplex_handle>::max()) return this->get_dimension_of_a_cell(sh);
+    if (sh != null_simplex()) return this->get_dimension_of_a_cell(sh);
     return -1;
   }
 
   /**
    * Return the filtration of a cell pointed by the Simplex_handle.
    **/
-  typename T::filtration_type filtration(Simplex_handle sh) {
+  Filtration_value filtration(Simplex_handle sh) {
     if (globalDbg) {
-      std::cerr << "T::filtration_type filtration(const Simplex_handle& sh)\n";
+      std::cerr << "Filtration_value filtration(const Simplex_handle& sh)\n";
     }
     // Returns the filtration value of a simplex.
-    if (sh != std::numeric_limits<Simplex_handle>::max()) return this->data[sh];
-    return std::numeric_limits<Simplex_handle>::max();
+    if (sh != null_simplex()) return this->data[sh];
+    return std::numeric_limits<Filtration_value>::infinity();
   }
 
   /**
@@ -203,7 +203,7 @@ class Bitmap_cubical_complex : public T {
     if (globalDbg) {
       std::cerr << "Simplex_key key(const Simplex_handle& sh)\n";
     }
-    if (sh != std::numeric_limits<Simplex_handle>::max()) {
+    if (sh != null_simplex()) {
       return this->key_associated_to_simplex[sh];
     }
     return this->null_key();
@@ -216,7 +216,7 @@ class Bitmap_cubical_complex : public T {
     if (globalDbg) {
       std::cerr << "Simplex_handle simplex(Simplex_key key)\n";
     }
-    if (key != std::numeric_limits<Simplex_handle>::max()) {
+    if (key != null_key()) {
       return this->simplex_associated_to_key[ key ];
     }
     return null_simplex();
@@ -229,7 +229,7 @@ class Bitmap_cubical_complex : public T {
     if (globalDbg) {
       std::cerr << "void assign_key(Simplex_handle& sh, Simplex_key key)\n";
     }
-    if (key == std::numeric_limits<Simplex_handle>::max()) return;
+    if (key == null_key()) return;
     this->key_associated_to_simplex[sh] = key;
     this->simplex_associated_to_key[key] = sh;
   }
@@ -566,8 +566,9 @@ class is_before_in_filtration {
   bool operator()(const typename Bitmap_cubical_complex<T>::Simplex_handle& sh1,
                   const typename Bitmap_cubical_complex<T>::Simplex_handle& sh2) const {
     // Not using st_->filtration(sh1) because it uselessly tests for null_simplex.
-    typename T::filtration_type fil1 = CC_->data[sh1];
-    typename T::filtration_type fil2 = CC_->data[sh2];
+    typedef typename T::filtration_type Filtration_value;
+    Filtration_value fil1 = CC_->data[sh1];
+    Filtration_value fil2 = CC_->data[sh2];
     if (fil1 != fil2) {
       return fil1 < fil2;
     }
diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py
index 2e281ee4..9a365823 100755
--- a/src/cython/test/test_cubical_complex.py
+++ b/src/cython/test/test_cubical_complex.py
@@ -67,7 +67,7 @@ def test_dimension_constructor():
                          top_dimensional_cells = [1,2,3,4,5,6,7,8,9])
     assert cub.__is_defined() == True
     assert cub.__is_persistence_defined() == False
-    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, 1.8446744073709552e+19))]
+    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, float('inf')))]
     assert cub.__is_persistence_defined() == True
     assert cub.betti_numbers() == [1, 0]
     assert cub.persistent_betti_numbers(0, 1000) == [0, 0]
@@ -80,7 +80,7 @@ def test_dimension_constructor():
     cub = CubicalComplex(perseus_file='CubicalOneSphere.txt')
     assert cub.__is_defined() == True
     assert cub.__is_persistence_defined() == False
-    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, 1.8446744073709552e+19))]
+    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, float('inf')))]
     assert cub.__is_persistence_defined() == True
     assert cub.betti_numbers() == [1, 0, 0]
     assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0]
-- 
cgit v1.2.3


From b8fdc4c7f6c30df5e7a28a0a23e697640f9d67cc Mon Sep 17 00:00:00 2001
From: glisse <glisse@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 10 Jul 2017 18:58:12 +0000
Subject: simplex / complex confusion

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2596 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 77c093029d3e2518260ce59705110df3fbfe11e3
---
 src/cython/cython/simplex_tree.pyx          | 48 ++++++++++++++---------------
 src/cython/include/Simplex_tree_interface.h |  8 ++---
 2 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 9d40a8b5..2acdac3c 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -183,10 +183,10 @@ cdef class SimplexTree:
         :returns:  true if the simplex was found, false otherwise.
         :rtype:  bool
         """
-        cdef vector[int] complex
+        cdef vector[int] csimplex
         for i in simplex:
-            complex.push_back(i)
-        return self.thisptr.find_simplex(complex)
+            csimplex.push_back(i)
+        return self.thisptr.find_simplex(csimplex)
 
     def insert(self, simplex, filtration=0.0):
         """This function inserts the given N-simplex and its subfaces with the
@@ -200,10 +200,10 @@ cdef class SimplexTree:
         :returns:  true if the simplex was found, false otherwise.
         :rtype:  bool
         """
-        cdef vector[int] complex
+        cdef vector[int] csimplex
         for i in simplex:
-            complex.push_back(i)
-        return self.thisptr.insert_simplex_and_subfaces(complex,
+            csimplex.push_back(i)
+        return self.thisptr.insert_simplex_and_subfaces(csimplex,
                                                         <double>filtration)
 
     def get_filtration(self):
@@ -232,35 +232,35 @@ cdef class SimplexTree:
         :returns:  The (simplices of the) skeleton of a maximum dimension.
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[pair[vector[int], double]] skeletons \
+        cdef vector[pair[vector[int], double]] skeleton \
             = self.thisptr.get_skeleton(<int>dimension)
         ct = []
-        for filtered_complex in skeletons:
+        for filtered_simplex in skeleton:
             v = []
-            for vertex in filtered_complex.first:
+            for vertex in filtered_simplex.first:
                 v.append(vertex)
-            ct.append((v, filtered_complex.second))
+            ct.append((v, filtered_simplex.second))
         return ct
 
     def get_star(self, simplex):
-        """This function returns the stars of a given N-simplex.
+        """This function returns the star of a given N-simplex.
 
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :returns:  The (simplices of the) star of a simplex.
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[int] complex
+        cdef vector[int] csimplex
         for i in simplex:
-            complex.push_back(i)
-        cdef vector[pair[vector[int], double]] stars \
-            = self.thisptr.get_star(complex)
+            csimplex.push_back(i)
+        cdef vector[pair[vector[int], double]] star \
+            = self.thisptr.get_star(csimplex)
         ct = []
-        for filtered_complex in stars:
+        for filtered_simplex in star:
             v = []
-            for vertex in filtered_complex.first:
+            for vertex in filtered_simplex.first:
                 v.append(vertex)
-            ct.append((v, filtered_complex.second))
+            ct.append((v, filtered_simplex.second))
         return ct
 
     def get_cofaces(self, simplex, codimension):
@@ -275,17 +275,17 @@ cdef class SimplexTree:
         :returns:  The (simplices of the) cofaces of a simplex
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[int] complex
+        cdef vector[int] csimplex
         for i in simplex:
-            complex.push_back(i)
+            csimplex.push_back(i)
         cdef vector[pair[vector[int], double]] cofaces \
-            = self.thisptr.get_cofaces(complex, <int>codimension)
+            = self.thisptr.get_cofaces(csimplex, <int>codimension)
         ct = []
-        for filtered_complex in cofaces:
+        for filtered_simplex in cofaces:
             v = []
-            for vertex in filtered_complex.first:
+            for vertex in filtered_simplex.first:
                 v.append(vertex)
-            ct.append((v, filtered_complex.second))
+            ct.append((v, filtered_simplex.second))
         return ct
 
     def remove_maximal_simplex(self, simplex):
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
index 45ce1916..09e7e992 100644
--- a/src/cython/include/Simplex_tree_interface.h
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -70,14 +70,14 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   }
 
   // Do not interface this function, only used in strong witness interface for complex creation
-  bool insert_simplex(const std::vector<std::size_t>& complex, Filtration_value filtration = 0) {
-    Insertion_result result = Base::insert_simplex(complex, filtration);
+  bool insert_simplex(const std::vector<std::size_t>& simplex, Filtration_value filtration = 0) {
+    Insertion_result result = Base::insert_simplex(simplex, filtration);
     return (result.second);
   }
 
   // Do not interface this function, only used in strong witness interface for complex creation
-  bool insert_simplex_and_subfaces(const std::vector<std::size_t>& complex, Filtration_value filtration = 0) {
-    Insertion_result result = Base::insert_simplex_and_subfaces(complex, filtration);
+  bool insert_simplex_and_subfaces(const std::vector<std::size_t>& simplex, Filtration_value filtration = 0) {
+    Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration);
     return (result.second);
   }
 
-- 
cgit v1.2.3


From 0f8c2b9623fcfd8b346944b637681144b4c58318 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 7 Aug 2017 13:27:32 +0000
Subject: Fix test reader utils

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2600 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 24bcf652d5374d158c6b4e90dd2233af7e153c49
---
 src/cython/test/test_reader_utils.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/cython/test/test_reader_utils.py b/src/cython/test/test_reader_utils.py
index 517bf109..79dc9064 100755
--- a/src/cython/test/test_reader_utils.py
+++ b/src/cython/test/test_reader_utils.py
@@ -61,9 +61,9 @@ def test_read_persistence_intervals_without_dimension():
     test_file.write('# Simple persistence diagram without dimension\n2.7 3.7\n9.6 14.\n34.2 34.974\n3. inf')
     test_file.close()
     persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers')
-    assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]]
+    assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))]
     persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=15)
-    assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]]
+    assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))]
     persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_without_dimension.pers')
     assert persistence == {-1: [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float('Inf'))]}
 
@@ -73,9 +73,9 @@ def test_read_persistence_intervals_with_dimension():
     test_file.write('# Simple persistence diagram with dimension\n0 2.7 3.7\n1 9.6 14.\n3 34.2 34.974\n1 3. inf')
     test_file.close()
     persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers')
-    assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]]
+    assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))]
     persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=1)
     # BUG !!!
-    assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]]
+    assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))]
     persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_with_dimension.pers')
     assert persistence == {0: [(2.7, 3.7)], 1: [(9.6, 14.0), (3.0, float('Inf'))], 3: [(34.2, 34.974)]}
-- 
cgit v1.2.3


From 1129608c2add6f15538b3e281d75119f0e1bc8b0 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 8 Aug 2017 12:48:40 +0000
Subject: Fix bug in read_persistence_intervals_in_dimension for only_this_dim
 Add unitary tests for read_persistence Add .clang-format to clang format new
 files

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2601 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 28e870973f9ebd686d503246202fa6d6a549e9e3
---
 src/.clang-format                                  |  90 ++++++
 src/common/include/gudhi/reader_utils.h            |  93 +++---
 src/common/test/CMakeLists.txt                     |   7 +
 src/common/test/README                             |   2 +-
 .../test/persistence_intervals_with_dimension.pers |   5 +
 .../test/persistence_intervals_with_field.pers     |   4 +
 .../persistence_intervals_without_dimension.pers   |   7 +
 .../test/test_persistence_intervals_reader.cpp     | 321 +++++++++++++++++++++
 8 files changed, 478 insertions(+), 51 deletions(-)
 create mode 100644 src/.clang-format
 create mode 100644 src/common/test/persistence_intervals_with_dimension.pers
 create mode 100644 src/common/test/persistence_intervals_with_field.pers
 create mode 100644 src/common/test/persistence_intervals_without_dimension.pers
 create mode 100644 src/common/test/test_persistence_intervals_reader.cpp

diff --git a/src/.clang-format b/src/.clang-format
new file mode 100644
index 00000000..dd4590c8
--- /dev/null
+++ b/src/.clang-format
@@ -0,0 +1,90 @@
+---
+Language:        Cpp
+# BasedOnStyle:  Google
+AccessModifierOffset: -1
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: true
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:   
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Attach
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+ColumnLimit:     120
+CommentPragmas:  '^ IWYU pragma:'
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: true
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+IncludeCategories: 
+  - Regex:           '^<.*\.h>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IndentCaseLabels: true
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    false
+SpaceAfterCStyleCast: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Auto
+TabWidth:        8
+UseTab:          Never
+...
+
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index f1684d78..bda93f4f 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -1,5 +1,5 @@
-/*    This file is part of the Gudhi Library. The Gudhi library 
- *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
  *    Author(s):       Clement Maria, Pawel Dlotko, Clement Jamin
@@ -36,6 +36,7 @@
 #include <string>
 #include <vector>
 #include <utility>  // for pair
+#include <tuple>  // for std::make_tuple
 
 // Keep this file tag for Doxygen to parse the code, otherwise, functions are not documented.
 // It is required for global functions and variables.
@@ -52,7 +53,7 @@
  * X21 X22 ... X2d<br>
  * etc<br>
  */
-inline void read_points(std::string file_name, std::vector< std::vector< double > > & points) {
+inline void read_points(std::string file_name, std::vector<std::vector<double>>& points) {
   std::ifstream in_file(file_name.c_str(), std::ios::in);
   if (!in_file.is_open()) {
     std::cerr << "Unable to open file " << file_name << std::endl;
@@ -62,14 +63,13 @@ inline void read_points(std::string file_name, std::vector< std::vector< double
   std::string line;
   double x;
   while (getline(in_file, line)) {
-    std::vector< double > point;
+    std::vector<double> point;
     std::istringstream iss(line);
     while (iss >> x) {
       point.push_back(x);
     }
     // Check for empty lines
-    if (!point.empty())
-      points.push_back(point);
+    if (!point.empty()) points.push_back(point);
   }
   in_file.close();
 }
@@ -90,7 +90,7 @@ inline void read_points(std::string file_name, std::vector< std::vector< double
  * Every simplex must appear exactly once.
  * Simplices of dimension more than 1 are ignored.
  */
-template< typename Graph_t, typename Filtration_value, typename Vertex_handle >
+template <typename Graph_t, typename Filtration_value, typename Vertex_handle>
 Graph_t read_graph(std::string file_name) {
   std::ifstream in_(file_name.c_str(), std::ios::in);
   if (!in_.is_open()) {
@@ -100,10 +100,10 @@ Graph_t read_graph(std::string file_name) {
     throw std::invalid_argument(error_str);
   }
 
-  typedef std::pair< Vertex_handle, Vertex_handle > Edge_t;
-  std::vector< Edge_t > edges;
-  std::vector< Filtration_value > edges_fil;
-  std::map< Vertex_handle, Filtration_value > vertices;
+  typedef std::pair<Vertex_handle, Vertex_handle> Edge_t;
+  std::vector<Edge_t> edges;
+  std::vector<Filtration_value> edges_fil;
+  std::map<Vertex_handle, Filtration_value> vertices;
 
   std::string line;
   int dim;
@@ -113,8 +113,7 @@ Graph_t read_graph(std::string file_name) {
     std::istringstream iss(line);
     while (iss >> dim) {
       switch (dim) {
-        case 0:
-        {
+        case 0: {
           iss >> u;
           iss >> fil;
           vertices[u] = fil;
@@ -123,8 +122,7 @@ Graph_t read_graph(std::string file_name) {
           }
           break;
         }
-        case 1:
-        {
+        case 1: {
           iss >> u;
           iss >> v;
           iss >> fil;
@@ -132,16 +130,13 @@ Graph_t read_graph(std::string file_name) {
           edges_fil.push_back(fil);
           break;
         }
-        default:
-        {
-          break;
-        }
+        default: { break; }
       }
     }
   }
   in_.close();
 
-  if ((size_t) (max_h + 1) != vertices.size()) {
+  if ((size_t)(max_h + 1) != vertices.size()) {
     std::cerr << "Error: vertices must be labeled from 0 to n-1 \n";
   }
 
@@ -169,8 +164,8 @@ Graph_t read_graph(std::string file_name) {
  * Every simplex must appear exactly once.
  * Simplices of dimension more than 1 are ignored.
  */
-template< typename Vertex_handle, typename Filtration_value >
-bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Filtration_value & fil) {
+template <typename Vertex_handle, typename Filtration_value>
+bool read_simplex(std::istream& in_, std::vector<Vertex_handle>& simplex, Filtration_value& fil) {
   int dim = 0;
   if (!(in_ >> dim)) return false;
   Vertex_handle v;
@@ -194,8 +189,8 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi
  * The key of a simplex is its position in the filtration order and also the number of its row in the file.
  * Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the filtration has dimension Dimi, filtration value
  * fil1 and simplices with key ki1 ... kiDimi in its boundary.*/
-template< typename Simplex_key, typename Filtration_value >
-bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundary, Filtration_value & fil) {
+template <typename Simplex_key, typename Filtration_value>
+bool read_hasse_simplex(std::istream& in_, std::vector<Simplex_key>& boundary, Filtration_value& fil) {
   int dim;
   if (!(in_ >> dim)) return false;
   if (dim == 0) {
@@ -214,7 +209,7 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar
 /**
  * @brief Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole
  * (square) matrix.
- * 
+ *
  * @author Pawel Dlotko
  *
  * Square matrix file format:<br>
@@ -231,13 +226,13 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar
  * Dj1;Dj2;...;Dj(j-1);<br>
  *
  **/
-template< typename Filtration_value >
-std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(const std::string& filename,
-                                                                                          const char separator = ';') {
+template <typename Filtration_value>
+std::vector<std::vector<Filtration_value>> read_lower_triangular_matrix_from_csv_file(const std::string& filename,
+                                                                                      const char separator = ';') {
 #ifdef DEBUG_TRACES
   std::cout << "Using procedure read_lower_triangular_matrix_from_csv_file \n";
 #endif  // DEBUG_TRACES
-  std::vector< std::vector< Filtration_value > > result;
+  std::vector<std::vector<Filtration_value>> result;
   std::ifstream in;
   in.open(filename.c_str());
   if (!in.is_open()) {
@@ -248,7 +243,7 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
 
   // the first line is emtpy, so we ignore it:
   std::getline(in, line);
-  std::vector< Filtration_value > values_in_this_line;
+  std::vector<Filtration_value> values_in_this_line;
   result.push_back(values_in_this_line);
 
   int number_of_line = 0;
@@ -256,11 +251,10 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
   // first, read the file line by line to a string:
   while (std::getline(in, line)) {
     // if line is empty, break
-    if (line.size() == 0)
-      break;
+    if (line.size() == 0) break;
 
     // if the last element of a string is comma:
-    if (line[ line.size() - 1 ] == separator) {
+    if (line[line.size() - 1] == separator) {
       // then shrink the string by one
       line.pop_back();
     }
@@ -273,7 +267,7 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
     // and now read the doubles.
 
     int number_of_entry = 0;
-    std::vector< Filtration_value > values_in_this_line;
+    std::vector<Filtration_value> values_in_this_line;
     while (iss.good()) {
       double entry;
       iss >> entry;
@@ -282,7 +276,7 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
       }
       ++number_of_entry;
     }
-    if (!values_in_this_line.empty())result.push_back(values_in_this_line);
+    if (!values_in_this_line.empty()) result.push_back(values_in_this_line);
     ++number_of_line;
   }
   in.close();
@@ -309,7 +303,6 @@ Note: the function does not check that birth <= death.
 **/
 template <typename OutputIterator>
 void read_persistence_intervals_and_dimension(std::string const& filename, OutputIterator out) {
-
   std::ifstream in(filename);
   if (!in.is_open()) {
     std::string error_str("read_persistence_intervals_and_dimension - Unable to open file ");
@@ -325,13 +318,12 @@ void read_persistence_intervals_and_dimension(std::string const& filename, Outpu
       double numbers[4];
       int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
       if (n >= 2) {
-        //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1);
         int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
         *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
       }
     }
   }
-} // read_persistence_diagram_from_file
+}
 
 /**
 Reads a file containing persistence intervals.
@@ -340,33 +332,34 @@ The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 Note: the function does not check that birth <= death.
 **/
-inline std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) {
-
+inline std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(
+    std::string const& filename) {
   std::map<int, std::vector<std::pair<double, double>>> ret;
   read_persistence_intervals_and_dimension(
-    filename,
-    boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); }));
+      filename, boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) {
+        ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t)));
+      }));
   return ret;
-} // read_persistence_diagram_from_file
-
+}
 
 /**
 Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 If `only_this_dim` = -1, dimension is ignored and all lines are returned.
-If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` 
+If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim`
 (or where dimension is not specified) are returned.
 The return value is an `std::vector<std::pair<birth, death>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 Note: the function does not check that birth <= death.
 **/
-inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
-
+inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename,
+                                                                                      int only_this_dim = -1) {
   std::vector<std::pair<double, double>> ret;
   read_persistence_intervals_and_dimension(
-    filename, 
-    boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
+      filename, boost::make_function_output_iterator([only_this_dim, &ret](std::tuple<int, double, double> t) {
+        if (only_this_dim == get<0>(t) || only_this_dim == -1) ret.emplace_back(get<1>(t), get<2>(t));
+      }));
   return ret;
-} // read_persistence_diagram_from_file
+}
 
 #endif  // READER_UTILS_H_
diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt
index 5aa426d7..de3e765a 100644
--- a/src/common/test/CMakeLists.txt
+++ b/src/common/test/CMakeLists.txt
@@ -9,10 +9,17 @@ target_link_libraries(Common_test_points_off_reader ${Boost_UNIT_TEST_FRAMEWORK_
 add_executable ( Common_test_distance_matrix_reader test_distance_matrix_reader.cpp )
 target_link_libraries(Common_test_distance_matrix_reader ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
+add_executable ( Common_test_persistence_intervals_reader test_persistence_intervals_reader.cpp )
+target_link_libraries(Common_test_persistence_intervals_reader ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+
 # Do not forget to copy test files in current binary dir
 file(COPY "${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 ${CMAKE_CURRENT_BINARY_DIR}/)
+file(COPY "${CMAKE_SOURCE_DIR}/src/common/test/persistence_intervals_with_dimension.pers" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+file(COPY "${CMAKE_SOURCE_DIR}/src/common/test/persistence_intervals_with_field.pers" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+file(COPY "${CMAKE_SOURCE_DIR}/src/common/test/persistence_intervals_without_dimension.pers" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
 gudhi_add_coverage_test(Common_test_points_off_reader)
 gudhi_add_coverage_test(Common_test_distance_matrix_reader)
+gudhi_add_coverage_test(Common_test_persistence_intervals_reader)
diff --git a/src/common/test/README b/src/common/test/README
index f2a7eb5a..a8e6efe9 100644
--- a/src/common/test/README
+++ b/src/common/test/README
@@ -7,7 +7,7 @@ make
 To launch with details:
 ***********************
 
-./dtoffrw_UT --report_level=detailed --log_level=all 
+./Common_test_points_off_reader --report_level=detailed --log_level=all
 
    ==> echo $? returns 0 in case of success (non-zero otherwise)
 
diff --git a/src/common/test/persistence_intervals_with_dimension.pers b/src/common/test/persistence_intervals_with_dimension.pers
new file mode 100644
index 00000000..406748c8
--- /dev/null
+++ b/src/common/test/persistence_intervals_with_dimension.pers
@@ -0,0 +1,5 @@
+# Simple persistence diagram with dimension
+0 2.7 3.7
+1 9.6 14.
+3 34.2 34.974
+1 3. inf
diff --git a/src/common/test/persistence_intervals_with_field.pers b/src/common/test/persistence_intervals_with_field.pers
new file mode 100644
index 00000000..41dd9f1e
--- /dev/null
+++ b/src/common/test/persistence_intervals_with_field.pers
@@ -0,0 +1,4 @@
+3 0 2.7 3.7
+3 1 9.6 14.
+3 3 34.2 34.974
+3 1 3. inf
diff --git a/src/common/test/persistence_intervals_without_dimension.pers b/src/common/test/persistence_intervals_without_dimension.pers
new file mode 100644
index 00000000..76fa27f3
--- /dev/null
+++ b/src/common/test/persistence_intervals_without_dimension.pers
@@ -0,0 +1,7 @@
+# Simple persistence diagram without dimension
+2.7 3.7
+9.6 14.
+# Another comment
+34.2 34.974
+3. inf
+# End of file
diff --git a/src/common/test/test_persistence_intervals_reader.cpp b/src/common/test/test_persistence_intervals_reader.cpp
new file mode 100644
index 00000000..a06fff1e
--- /dev/null
+++ b/src/common/test/test_persistence_intervals_reader.cpp
@@ -0,0 +1,321 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2017  INRIA
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/reader_utils.h>
+
+#include <iostream>
+#include <vector>
+#include <utility>  // for pair
+#include <tuple>
+#include <limits>  // for inf
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "persistence_intervals_reader"
+#include <boost/test/unit_test.hpp>
+
+using Persistence_intervals_by_dimension = std::map<int, std::vector<std::pair<double, double>>>;
+using Persistence_intervals = std::vector<std::pair<double, double>>;
+// Test files with only 2 parameters (persistence birth and death) per line in file
+BOOST_AUTO_TEST_CASE( persistence_intervals_without_dimension )
+{
+  Persistence_intervals_by_dimension expected_intervals_by_dimension;
+  expected_intervals_by_dimension[-1].push_back(std::make_pair(2.7, 3.7));
+  expected_intervals_by_dimension[-1].push_back(std::make_pair(9.6, 14.));
+  expected_intervals_by_dimension[-1].push_back(std::make_pair(34.2, 34.974));
+  expected_intervals_by_dimension[-1].push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
+
+  Persistence_intervals_by_dimension persistence_intervals_by_dimension =
+      read_persistence_intervals_grouped_by_dimension("persistence_intervals_without_dimension.pers");
+
+  std::cout << "\nread_persistence_intervals_grouped_by_dimension - expected\n";
+  for (auto map_iter : expected_intervals_by_dimension) {
+    std::cout << "key=" << map_iter.first;
+    for (auto vec_iter : map_iter.second)
+      std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+  }
+
+  std::cout << "\nread_persistence_intervals_grouped_by_dimension - read\n";
+  for (auto map_iter : persistence_intervals_by_dimension) {
+    std::cout << "key=" << map_iter.first;
+    for (auto vec_iter : map_iter.second)
+      std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+  }
+
+  BOOST_CHECK(persistence_intervals_by_dimension == expected_intervals_by_dimension);
+
+  Persistence_intervals expected_intervals_in_dimension;
+  expected_intervals_in_dimension.push_back(std::make_pair(2.7, 3.7));
+  expected_intervals_in_dimension.push_back(std::make_pair(9.6, 14.));
+  expected_intervals_in_dimension.push_back(std::make_pair(34.2, 34.974));
+  expected_intervals_in_dimension.push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
+
+  Persistence_intervals persistence_intervals_in_dimension =
+      read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers");
+
+  std::cout << "\nread_persistence_intervals_in_dimension - expected\n";
+  for (auto vec_iter : expected_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  std::cout << "\nread_persistence_intervals_in_dimension - read\n";
+  for (auto vec_iter : expected_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+  expected_intervals_in_dimension.clear();
+  persistence_intervals_in_dimension =
+        read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers", 0);
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+  expected_intervals_in_dimension.clear();
+  persistence_intervals_in_dimension =
+        read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers", 1);
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+  expected_intervals_in_dimension.clear();
+  persistence_intervals_in_dimension =
+        read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers", 2);
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+  expected_intervals_in_dimension.clear();
+  persistence_intervals_in_dimension =
+        read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers", 3);
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+}
+// Test files with 3 parameters (dimension birth death) per line in file
+BOOST_AUTO_TEST_CASE( persistence_intervals_with_dimension )
+{
+  Persistence_intervals_by_dimension expected_intervals_by_dimension;
+  expected_intervals_by_dimension[0].push_back(std::make_pair(2.7, 3.7));
+  expected_intervals_by_dimension[1].push_back(std::make_pair(9.6, 14.));
+  expected_intervals_by_dimension[3].push_back(std::make_pair(34.2, 34.974));
+  expected_intervals_by_dimension[1].push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
+
+  Persistence_intervals_by_dimension persistence_intervals_by_dimension =
+      read_persistence_intervals_grouped_by_dimension("persistence_intervals_with_dimension.pers");
+
+  std::cout << "\nread_persistence_intervals_grouped_by_dimension - expected\n";
+  for (auto map_iter : expected_intervals_by_dimension) {
+    std::cout << "key=" << map_iter.first;
+    for (auto vec_iter : map_iter.second)
+      std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+  }
+
+  std::cout << "\nread_persistence_intervals_grouped_by_dimension - read\n";
+  for (auto map_iter : persistence_intervals_by_dimension) {
+    std::cout << "key=" << map_iter.first;
+    for (auto vec_iter : map_iter.second)
+      std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+  }
+
+  BOOST_CHECK(persistence_intervals_by_dimension == expected_intervals_by_dimension);
+
+  Persistence_intervals expected_intervals_in_dimension;
+  expected_intervals_in_dimension.push_back(std::make_pair(2.7, 3.7));
+  expected_intervals_in_dimension.push_back(std::make_pair(9.6, 14.));
+  expected_intervals_in_dimension.push_back(std::make_pair(34.2, 34.974));
+  expected_intervals_in_dimension.push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
+
+  Persistence_intervals persistence_intervals_in_dimension =
+      read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers");
+
+  std::cout << "\nread_persistence_intervals_in_dimension - expected\n";
+  for (auto vec_iter : expected_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  std::cout << "\nread_persistence_intervals_in_dimension - read\n";
+  for (auto vec_iter : persistence_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+  expected_intervals_in_dimension.clear();
+  expected_intervals_in_dimension.push_back(std::make_pair(2.7, 3.7));
+  persistence_intervals_in_dimension =
+        read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers", 0);
+
+  std::cout << "\nread_persistence_intervals_in_dimension 0 - expected\n";
+  for (auto vec_iter : expected_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  std::cout << "\nread_persistence_intervals_in_dimension 0 - read\n";
+  for (auto vec_iter : persistence_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+  expected_intervals_in_dimension.clear();
+  expected_intervals_in_dimension.push_back(std::make_pair(9.6, 14.));
+  expected_intervals_in_dimension.push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
+  persistence_intervals_in_dimension =
+        read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers", 1);
+
+  std::cout << "\nread_persistence_intervals_in_dimension 1 - expected\n";
+  for (auto vec_iter : expected_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  std::cout << "\nread_persistence_intervals_in_dimension 1 - read\n";
+  for (auto vec_iter : persistence_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+  expected_intervals_in_dimension.clear();
+  persistence_intervals_in_dimension =
+        read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers", 2);
+
+  std::cout << "\nread_persistence_intervals_in_dimension 2 - expected\n";
+  for (auto vec_iter : expected_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  std::cout << "\nread_persistence_intervals_in_dimension 2 - read\n";
+  for (auto vec_iter : persistence_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+  expected_intervals_in_dimension.clear();
+  expected_intervals_in_dimension.push_back(std::make_pair(34.2, 34.974));
+  persistence_intervals_in_dimension =
+        read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers", 3);
+
+  std::cout << "\nread_persistence_intervals_in_dimension 3 - expected\n";
+  for (auto vec_iter : expected_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  std::cout << "\nread_persistence_intervals_in_dimension 3 - read\n";
+  for (auto vec_iter : persistence_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+}
+
+// Test files with 4 parameters (field dimension birth death) per line in file
+BOOST_AUTO_TEST_CASE( persistence_intervals_with_field )
+{
+  Persistence_intervals_by_dimension expected_intervals_by_dimension;
+  expected_intervals_by_dimension[0].push_back(std::make_pair(2.7, 3.7));
+  expected_intervals_by_dimension[1].push_back(std::make_pair(9.6, 14.));
+  expected_intervals_by_dimension[3].push_back(std::make_pair(34.2, 34.974));
+  expected_intervals_by_dimension[1].push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
+
+  Persistence_intervals_by_dimension persistence_intervals_by_dimension =
+      read_persistence_intervals_grouped_by_dimension("persistence_intervals_with_field.pers");
+
+  std::cout << "\nread_persistence_intervals_grouped_by_dimension - expected\n";
+  for (auto map_iter : expected_intervals_by_dimension) {
+    std::cout << "key=" << map_iter.first;
+    for (auto vec_iter : map_iter.second)
+      std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+  }
+
+  std::cout << "\nread_persistence_intervals_grouped_by_dimension - read\n";
+  for (auto map_iter : persistence_intervals_by_dimension) {
+    std::cout << "key=" << map_iter.first;
+    for (auto vec_iter : map_iter.second)
+      std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+  }
+
+  BOOST_CHECK(persistence_intervals_by_dimension == expected_intervals_by_dimension);
+
+  Persistence_intervals expected_intervals_in_dimension;
+  expected_intervals_in_dimension.push_back(std::make_pair(2.7, 3.7));
+  expected_intervals_in_dimension.push_back(std::make_pair(9.6, 14.));
+  expected_intervals_in_dimension.push_back(std::make_pair(34.2, 34.974));
+  expected_intervals_in_dimension.push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
+
+  Persistence_intervals persistence_intervals_in_dimension =
+      read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers");
+
+  std::cout << "\nread_persistence_intervals_in_dimension - expected\n";
+  for (auto vec_iter : expected_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  std::cout << "\nread_persistence_intervals_in_dimension - read\n";
+  for (auto vec_iter : persistence_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+  expected_intervals_in_dimension.clear();
+  expected_intervals_in_dimension.push_back(std::make_pair(2.7, 3.7));
+  persistence_intervals_in_dimension =
+        read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers", 0);
+
+  std::cout << "\nread_persistence_intervals_in_dimension 0 - expected\n";
+  for (auto vec_iter : expected_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  std::cout << "\nread_persistence_intervals_in_dimension 0 - read\n";
+  for (auto vec_iter : persistence_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+  expected_intervals_in_dimension.clear();
+  expected_intervals_in_dimension.push_back(std::make_pair(9.6, 14.));
+  expected_intervals_in_dimension.push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
+  persistence_intervals_in_dimension =
+        read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers", 1);
+
+  std::cout << "\nread_persistence_intervals_in_dimension 1 - expected\n";
+  for (auto vec_iter : expected_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  std::cout << "\nread_persistence_intervals_in_dimension 1 - read\n";
+  for (auto vec_iter : persistence_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+  expected_intervals_in_dimension.clear();
+  persistence_intervals_in_dimension =
+        read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers", 2);
+
+  std::cout << "\nread_persistence_intervals_in_dimension 2 - expected\n";
+  for (auto vec_iter : expected_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  std::cout << "\nread_persistence_intervals_in_dimension 2 - read\n";
+  for (auto vec_iter : persistence_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+  expected_intervals_in_dimension.clear();
+  expected_intervals_in_dimension.push_back(std::make_pair(34.2, 34.974));
+  persistence_intervals_in_dimension =
+        read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers", 3);
+
+  std::cout << "\nread_persistence_intervals_in_dimension 3 - expected\n";
+  for (auto vec_iter : expected_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  std::cout << "\nread_persistence_intervals_in_dimension 3 - read\n";
+  for (auto vec_iter : persistence_intervals_in_dimension)
+    std::cout << " [" << vec_iter.first << " ," << vec_iter.second << "] ";
+
+  BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
+
+}
-- 
cgit v1.2.3


From 295d60787357806ae9aac1bfab98f3fefcd759a0 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 8 Aug 2017 13:15:33 +0000
Subject: Fix persistence files reader unitary tests

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2603 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1b3ab678420a63b6607d15f350697eccc42b56f7
---
 src/cython/test/test_reader_utils.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/cython/test/test_reader_utils.py b/src/cython/test/test_reader_utils.py
index 79dc9064..25591fb3 100755
--- a/src/cython/test/test_reader_utils.py
+++ b/src/cython/test/test_reader_utils.py
@@ -62,8 +62,10 @@ def test_read_persistence_intervals_without_dimension():
     test_file.close()
     persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers')
     assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))]
-    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=15)
-    assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))]
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=0)
+    assert persistence == []
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=1)
+    assert persistence == []
     persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_without_dimension.pers')
     assert persistence == {-1: [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float('Inf'))]}
 
@@ -74,8 +76,13 @@ def test_read_persistence_intervals_with_dimension():
     test_file.close()
     persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers')
     assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))]
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=0)
+    assert persistence == [(2.7, 3.7)]
     persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=1)
-    # BUG !!!
-    assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))]
+    assert persistence == [(9.6, 14.), (3., float('Inf'))]
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=2)
+    assert persistence == []
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=3)
+    assert persistence == [(34.2, 34.974)]
     persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_with_dimension.pers')
     assert persistence == {0: [(2.7, 3.7)], 1: [(9.6, 14.0), (3.0, float('Inf'))], 3: [(34.2, 34.974)]}
-- 
cgit v1.2.3


From fb19e46931baeb83f7547ea0cf734593e2a949a1 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 10 Aug 2017 07:12:08 +0000
Subject: Add Gudhi namespace

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2605 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 6f004d1f7f8a741081181c1ead026fb952a21e6c
---
 .../test/test_persistence_intervals_reader.cpp     | 37 +++++++++++-----------
 1 file changed, 19 insertions(+), 18 deletions(-)

diff --git a/src/common/test/test_persistence_intervals_reader.cpp b/src/common/test/test_persistence_intervals_reader.cpp
index a06fff1e..be299376 100644
--- a/src/common/test/test_persistence_intervals_reader.cpp
+++ b/src/common/test/test_persistence_intervals_reader.cpp
@@ -27,6 +27,7 @@
 #include <utility>  // for pair
 #include <tuple>
 #include <limits>  // for inf
+#include <map>
 
 #define BOOST_TEST_DYN_LINK
 #define BOOST_TEST_MODULE "persistence_intervals_reader"
@@ -44,7 +45,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_without_dimension )
   expected_intervals_by_dimension[-1].push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
 
   Persistence_intervals_by_dimension persistence_intervals_by_dimension =
-      read_persistence_intervals_grouped_by_dimension("persistence_intervals_without_dimension.pers");
+      Gudhi::read_persistence_intervals_grouped_by_dimension("persistence_intervals_without_dimension.pers");
 
   std::cout << "\nread_persistence_intervals_grouped_by_dimension - expected\n";
   for (auto map_iter : expected_intervals_by_dimension) {
@@ -69,7 +70,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_without_dimension )
   expected_intervals_in_dimension.push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
 
   Persistence_intervals persistence_intervals_in_dimension =
-      read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers");
+      Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers");
 
   std::cout << "\nread_persistence_intervals_in_dimension - expected\n";
   for (auto vec_iter : expected_intervals_in_dimension)
@@ -83,22 +84,22 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_without_dimension )
 
   expected_intervals_in_dimension.clear();
   persistence_intervals_in_dimension =
-        read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers", 0);
+        Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers", 0);
   BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
 
   expected_intervals_in_dimension.clear();
   persistence_intervals_in_dimension =
-        read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers", 1);
+        Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers", 1);
   BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
 
   expected_intervals_in_dimension.clear();
   persistence_intervals_in_dimension =
-        read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers", 2);
+        Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers", 2);
   BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
 
   expected_intervals_in_dimension.clear();
   persistence_intervals_in_dimension =
-        read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers", 3);
+        Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_without_dimension.pers", 3);
   BOOST_CHECK(persistence_intervals_in_dimension == expected_intervals_in_dimension);
 
 }
@@ -112,7 +113,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_with_dimension )
   expected_intervals_by_dimension[1].push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
 
   Persistence_intervals_by_dimension persistence_intervals_by_dimension =
-      read_persistence_intervals_grouped_by_dimension("persistence_intervals_with_dimension.pers");
+      Gudhi::read_persistence_intervals_grouped_by_dimension("persistence_intervals_with_dimension.pers");
 
   std::cout << "\nread_persistence_intervals_grouped_by_dimension - expected\n";
   for (auto map_iter : expected_intervals_by_dimension) {
@@ -137,7 +138,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_with_dimension )
   expected_intervals_in_dimension.push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
 
   Persistence_intervals persistence_intervals_in_dimension =
-      read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers");
+      Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers");
 
   std::cout << "\nread_persistence_intervals_in_dimension - expected\n";
   for (auto vec_iter : expected_intervals_in_dimension)
@@ -152,7 +153,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_with_dimension )
   expected_intervals_in_dimension.clear();
   expected_intervals_in_dimension.push_back(std::make_pair(2.7, 3.7));
   persistence_intervals_in_dimension =
-        read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers", 0);
+        Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers", 0);
 
   std::cout << "\nread_persistence_intervals_in_dimension 0 - expected\n";
   for (auto vec_iter : expected_intervals_in_dimension)
@@ -168,7 +169,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_with_dimension )
   expected_intervals_in_dimension.push_back(std::make_pair(9.6, 14.));
   expected_intervals_in_dimension.push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
   persistence_intervals_in_dimension =
-        read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers", 1);
+        Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers", 1);
 
   std::cout << "\nread_persistence_intervals_in_dimension 1 - expected\n";
   for (auto vec_iter : expected_intervals_in_dimension)
@@ -182,7 +183,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_with_dimension )
 
   expected_intervals_in_dimension.clear();
   persistence_intervals_in_dimension =
-        read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers", 2);
+        Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers", 2);
 
   std::cout << "\nread_persistence_intervals_in_dimension 2 - expected\n";
   for (auto vec_iter : expected_intervals_in_dimension)
@@ -197,7 +198,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_with_dimension )
   expected_intervals_in_dimension.clear();
   expected_intervals_in_dimension.push_back(std::make_pair(34.2, 34.974));
   persistence_intervals_in_dimension =
-        read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers", 3);
+        Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_with_dimension.pers", 3);
 
   std::cout << "\nread_persistence_intervals_in_dimension 3 - expected\n";
   for (auto vec_iter : expected_intervals_in_dimension)
@@ -221,7 +222,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_with_field )
   expected_intervals_by_dimension[1].push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
 
   Persistence_intervals_by_dimension persistence_intervals_by_dimension =
-      read_persistence_intervals_grouped_by_dimension("persistence_intervals_with_field.pers");
+      Gudhi::read_persistence_intervals_grouped_by_dimension("persistence_intervals_with_field.pers");
 
   std::cout << "\nread_persistence_intervals_grouped_by_dimension - expected\n";
   for (auto map_iter : expected_intervals_by_dimension) {
@@ -246,7 +247,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_with_field )
   expected_intervals_in_dimension.push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
 
   Persistence_intervals persistence_intervals_in_dimension =
-      read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers");
+      Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers");
 
   std::cout << "\nread_persistence_intervals_in_dimension - expected\n";
   for (auto vec_iter : expected_intervals_in_dimension)
@@ -261,7 +262,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_with_field )
   expected_intervals_in_dimension.clear();
   expected_intervals_in_dimension.push_back(std::make_pair(2.7, 3.7));
   persistence_intervals_in_dimension =
-        read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers", 0);
+        Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers", 0);
 
   std::cout << "\nread_persistence_intervals_in_dimension 0 - expected\n";
   for (auto vec_iter : expected_intervals_in_dimension)
@@ -277,7 +278,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_with_field )
   expected_intervals_in_dimension.push_back(std::make_pair(9.6, 14.));
   expected_intervals_in_dimension.push_back(std::make_pair(3., std::numeric_limits<double>::infinity()));
   persistence_intervals_in_dimension =
-        read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers", 1);
+        Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers", 1);
 
   std::cout << "\nread_persistence_intervals_in_dimension 1 - expected\n";
   for (auto vec_iter : expected_intervals_in_dimension)
@@ -291,7 +292,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_with_field )
 
   expected_intervals_in_dimension.clear();
   persistence_intervals_in_dimension =
-        read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers", 2);
+        Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers", 2);
 
   std::cout << "\nread_persistence_intervals_in_dimension 2 - expected\n";
   for (auto vec_iter : expected_intervals_in_dimension)
@@ -306,7 +307,7 @@ BOOST_AUTO_TEST_CASE( persistence_intervals_with_field )
   expected_intervals_in_dimension.clear();
   expected_intervals_in_dimension.push_back(std::make_pair(34.2, 34.974));
   persistence_intervals_in_dimension =
-        read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers", 3);
+        Gudhi::read_persistence_intervals_in_dimension("persistence_intervals_with_field.pers", 3);
 
   std::cout << "\nread_persistence_intervals_in_dimension 3 - expected\n";
   for (auto vec_iter : expected_intervals_in_dimension)
-- 
cgit v1.2.3


From b633404a13fe7acd2f0518b88219212f93758a49 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 10 Aug 2017 08:41:44 +0000
Subject: utf8 file format

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2606 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0541d16e8818dfc9cd6ecd7960c0ec5638cd8277
---
 src/common/doc/file_formats.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index c145b271..e1d1426e 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -2,7 +2,7 @@
 *    (Geometric Understanding in Higher Dimensions) is a generic C++
 *    library for computational topology.
 *
-*    Author(s):       Clément Jamin
+*    Author(s):       Clément Jamin
 *
 *    Copyright (C) 2017  INRIA
 *
-- 
cgit v1.2.3


From c7da4a2e7f8cb26c63ebc5c226c0cfefb5290755 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 10 Aug 2017 08:50:04 +0000
Subject: Fix Python2 compatibility

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2607 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b8744511b527f7117d3432c559dcb68b59253e53
---
 src/cython/cython/reader_utils.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cython/cython/reader_utils.pyx b/src/cython/cython/reader_utils.pyx
index 14976167..3a17c5a0 100644
--- a/src/cython/cython/reader_utils.pyx
+++ b/src/cython/cython/reader_utils.pyx
@@ -49,7 +49,7 @@ def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'):
     """
     if csv_file is not '':
         if os.path.isfile(csv_file):
-            return read_matrix_from_csv_file(str.encode(csv_file), str.encode(separator)[0])
+            return read_matrix_from_csv_file(str.encode(csv_file), ord(separator[0]))
     print("file " + csv_file + " not set or not found.")
     return []
 
-- 
cgit v1.2.3


From 6166aad3e082119ead02413659cfb6ea2e661ef7 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 10 Aug 2017 09:22:04 +0000
Subject: Some modifications to file format documentation (utf8 test)

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2608 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2590184676603521a3ab175834670bb47a80c93b
---
 src/common/doc/file_formats.h | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index e1d1426e..9d0415b1 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -34,18 +34,19 @@ namespace Gudhi {
  Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
  Lines starting with `#` are ignored (comments).<br>
  Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):
- \code{.unparsed}
+ \verbatim
    [[field] dimension] birth death
- \endcode
+ \endverbatim
 
  Here is a simple sample file:
- \code{.unparsed}
-   # Beautiful persistence diagram
+ \verbatim
+   # Persistence diagram example
    2 2.7 3.7
    2 9.6 14.
+   # Some comments
    3 34.2 34.974
    4 3. inf
- \endcode
+ \endverbatim
 
  Other sample files can be found in the `data/persistence_diagram` folder.
 */
-- 
cgit v1.2.3


From 2fc118133e76f05fc55d86cf32883223191fe473 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 17 Aug 2017 16:10:46 +0000
Subject: Add file formats for Python. Binding for persistence write files
 Launch py.test with the command "python -m pytest" (shall work everywhere)

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2611 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9443a7eb5b580ece7708ff57949ad08339c1c5c3
---
 .../include/gudhi/Persistent_cohomology.h          | 13 +++++++---
 .../modules/GUDHI_third_party_libraries.cmake      |  2 --
 src/common/doc/file_formats.h                      |  6 ++++-
 src/cython/CMakeLists.txt                          | 14 +++++-----
 src/cython/cython/simplex_tree.pyx                 | 22 +++++++++++++++-
 src/cython/doc/_templates/layout.html              |  1 +
 src/cython/doc/fileformats.rst                     | 30 ++++++++++++++++++++++
 src/cython/doc/reader_utils_ref.rst                | 11 ++++++++
 8 files changed, 84 insertions(+), 15 deletions(-)
 create mode 100644 src/cython/doc/fileformats.rst
 create mode 100644 src/cython/doc/reader_utils_ref.rst

diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index 672fda48..e0a147b3 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -591,10 +591,17 @@ class Persistent_cohomology {
     std::ofstream diagram_out(diagram_name.c_str());
     cmp_intervals_by_length cmp(cpx_);
     std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp);
+    bool has_infinity = std::numeric_limits<Filtration_value>::has_infinity;
     for (auto pair : persistent_pairs_) {
-    diagram_out << cpx_->dimension(get<0>(pair)) << " "
-          << cpx_->filtration(get<0>(pair)) << " "
-          << cpx_->filtration(get<1>(pair)) << std::endl;
+      // Special case on windows, inf is "1.#INF"
+      if (has_infinity && cpx_->filtration(get<1>(pair)) == std::numeric_limits<Filtration_value>::infinity()) {
+        diagram_out << cpx_->dimension(get<0>(pair)) << " "
+              << cpx_->filtration(get<0>(pair)) << " inf" << std::endl;
+      } else {
+        diagram_out << cpx_->dimension(get<0>(pair)) << " "
+              << cpx_->filtration(get<0>(pair)) << " "
+              << cpx_->filtration(get<1>(pair)) << std::endl;
+      }
     }
   }
 
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 8f486118..e29ba40c 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -117,8 +117,6 @@ if(NOT GUDHI_CYTHON_PATH)
 endif(NOT GUDHI_CYTHON_PATH)
 
 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)
     # Documentation generation is available through sphinx
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index 9d0415b1..d715aa4d 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -26,7 +26,7 @@
 namespace Gudhi {
 
 /*! \page fileformats File formats
- 
+
  \tableofcontents
 
  \section FileFormatsPers Persistence Diagram
@@ -49,6 +49,10 @@ namespace Gudhi {
  \endverbatim
 
  Other sample files can be found in the `data/persistence_diagram` folder.
+
+ Such files can be generated with `Gudhi::persistent_cohomology::Persistent_cohomology::output_diagram()` and read with
+ `Gudhi::read_persistence_intervals_and_dimension()`, `Gudhi::read_persistence_intervals_grouped_by_dimension()` or
+ `Gudhi::read_persistence_intervals_in_dimension()`.
 */
 }  // namespace Gudhi
 
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index f427b3c5..a06be008 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -16,7 +16,7 @@ function( add_gudhi_cython_lib THE_LIB )
 endfunction( add_gudhi_cython_lib )
 
 if(CYTHON_FOUND)
-  message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}")
+  message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - 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', ")
@@ -305,13 +305,11 @@ if(CYTHON_FOUND)
   set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   # Unitary tests are available through py.test
-  if(PYTEST_PATH)
-    add_test(
-        NAME gudhi_cython_py_test
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTHON_EXECUTABLE} "${PYTEST_PATH}")
-    set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-  endif(PYTEST_PATH)
+  add_test(
+      NAME gudhi_cython_py_test
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest)
+  set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   # Documentation generation is available through sphinx
   if(SPHINX_PATH)
diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 2acdac3c..9e3b2345 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -61,6 +61,7 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
         vector[int] betti_numbers()
         vector[int] persistent_betti_numbers(double from_value, double to_value)
         vector[pair[double,double]] intervals_in_dimension(int dimension)
+        void write_output_diagram(string diagram_file_name)
 
 # SimplexTree python interface
 cdef class SimplexTree:
@@ -385,7 +386,7 @@ cdef class SimplexTree:
         complex in a specific dimension.
 
         :param dimension: The specific dimension.
-        :type from_value: int.
+        :type dimension: int.
         :returns: The persistence intervals.
         :rtype:  list of pair of float
 
@@ -399,3 +400,22 @@ cdef class SimplexTree:
             print("intervals_in_dim function requires persistence function"
                   " to be launched first.")
         return intervals_result
+
+    def write_persistence_diagram(self, persistence_file=''):
+        """This function writes the persistence intervals of the simplicial
+        complex in a user given file name.
+
+        :param persistence_file: The specific dimension.
+        :type persistence_file: string.
+
+        :note: intervals_in_dim function requires persistence function to be
+            launched first.
+        """
+        if self.pcohptr != NULL:
+            if persistence_file != '':
+                self.pcohptr.write_output_diagram(str.encode(persistence_file))
+            else:
+                print("persistence_file must be specified")
+        else:
+            print("intervals_in_dim function requires persistence function"
+                  " to be launched first.")
diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html
index b11c1236..243f33c6 100644
--- a/src/cython/doc/_templates/layout.html
+++ b/src/cython/doc/_templates/layout.html
@@ -65,6 +65,7 @@
             {#- old style sidebars: using blocks -- should be deprecated #}
             {%- block sidebartoc %}
 <h2><a href="index.html">GUDHI</a></h2>
+<h2><a href="fileformats.html">File formats</a></h2>
 <h2><a href="installation.html">GUDHI installation</a></h2>
 <h2><a href="citation.html">Acknowledging the GUDHI library</a></h2>
 <h2><a href="genindex.html">Index</a></h2>
diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst
new file mode 100644
index 00000000..36225b6d
--- /dev/null
+++ b/src/cython/doc/fileformats.rst
@@ -0,0 +1,30 @@
+File formats
+############
+
+To find the correct function to read the files, please refer to :doc:`reader_utils_ref`
+
+Persistence Diagram
+*******************
+
+Such a file, whose extension is usually ``.pers``, contains a list of persistence intervals.
+
+Lines starting with ``#`` are ignored (comments).
+
+Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines)::
+
+    [[field] dimension] birth death
+
+Here is a simple sample file::
+
+    # Persistence diagram example
+    2 2.7 3.7
+    2 9.6 14.
+    # Some comments
+    3 34.2 34.974
+    4 3. inf
+
+Other sample files can be found in the data/persistence_diagram folder.
+
+Such files can be generated with :meth:`gudhi.SimplexTree.write_persistence_diagram` and read with
+:meth:`gudhi.read_persistence_intervals_grouped_by_dimension`, or
+:meth:`gudhi.read_persistence_intervals_in_dimension`.
diff --git a/src/cython/doc/reader_utils_ref.rst b/src/cython/doc/reader_utils_ref.rst
new file mode 100644
index 00000000..9c1ea6fc
--- /dev/null
+++ b/src/cython/doc/reader_utils_ref.rst
@@ -0,0 +1,11 @@
+=============================
+Reader utils reference manual
+=============================
+
+.. autofunction:: gudhi.read_off
+
+.. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file
+
+.. autofunction:: gudhi.read_persistence_intervals_grouped_by_dimension
+
+.. autofunction:: gudhi.read_persistence_intervals_in_dimension
-- 
cgit v1.2.3


From 5b92662a7ed71546efb4a3697bc0b3e2b315fefc Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 18 Aug 2017 06:19:31 +0000
Subject: Add display function in file format doc

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2612 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b51ffdf8f7be07c6745ca2b6501c51a350deffd2
---
 src/cython/doc/fileformats.rst | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst
index 36225b6d..156ef4e4 100644
--- a/src/cython/doc/fileformats.rst
+++ b/src/cython/doc/fileformats.rst
@@ -1,16 +1,16 @@
 File formats
 ############
 
-To find the correct function to read the files, please refer to :doc:`reader_utils_ref`
-
 Persistence Diagram
 *******************
 
-Such a file, whose extension is usually ``.pers``, contains a list of persistence intervals.
+Such a file, whose extension is usually ``.pers``, contains a list of
+persistence intervals.
 
 Lines starting with ``#`` are ignored (comments).
 
-Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines)::
+Other lines might contain 2, 3 or 4 values (the number of values on each line
+must be the same for all lines)::
 
     [[field] dimension] birth death
 
@@ -25,6 +25,9 @@ Here is a simple sample file::
 
 Other sample files can be found in the data/persistence_diagram folder.
 
-Such files can be generated with :meth:`gudhi.SimplexTree.write_persistence_diagram` and read with
+Such files can be generated with
+:meth:`gudhi.SimplexTree.write_persistence_diagram`, read with
 :meth:`gudhi.read_persistence_intervals_grouped_by_dimension`, or
-:meth:`gudhi.read_persistence_intervals_in_dimension`.
+:meth:`gudhi.read_persistence_intervals_in_dimension` and displayed with
+:meth:`gudhi.plot_persistence_barcode` or
+:meth:`gudhi.plot_persistence_diagram`.
-- 
cgit v1.2.3


From ef36c8b63bc353ac9d4e6982b9bba6797d546e51 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 18 Aug 2017 09:40:19 +0000
Subject: Fix sphinx bug when python3 is not in /usr/bin

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2613 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 07f67d4cc1f3b558b191115e0979ce3ce0580206
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake |  2 +-
 src/cython/CMakeLists.txt                           |  1 +
 src/cython/doc/python3-sphinx-build                 | 11 -----------
 src/cython/doc/python3-sphinx-build.in              | 11 +++++++++++
 4 files changed, 13 insertions(+), 12 deletions(-)
 delete mode 100755 src/cython/doc/python3-sphinx-build
 create mode 100755 src/cython/doc/python3-sphinx-build.in

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index e29ba40c..dbf2106a 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -123,7 +123,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
     # No sphinx-build in Pyton3, just hack it
-    set(SPHINX_PATH "${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${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)
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index a06be008..ab5ea9ef 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -194,6 +194,7 @@ if(CYTHON_FOUND)
   endif(UNIX)
 
   # set sphinx-build in make files
+  configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
   configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY)
   configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY)
 
diff --git a/src/cython/doc/python3-sphinx-build b/src/cython/doc/python3-sphinx-build
deleted file mode 100755
index 44b94169..00000000
--- a/src/cython/doc/python3-sphinx-build
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/python3
-
-"""
-Emulate sphinx-build for python3
-"""
-
-from sys import exit, argv
-from sphinx import main
-
-if __name__ == '__main__':
-    exit(main(argv))
diff --git a/src/cython/doc/python3-sphinx-build.in b/src/cython/doc/python3-sphinx-build.in
new file mode 100755
index 00000000..c97965f5
--- /dev/null
+++ b/src/cython/doc/python3-sphinx-build.in
@@ -0,0 +1,11 @@
+#!@PYTHON_EXECUTABLE@
+
+"""
+Emulate sphinx-build for python3
+"""
+
+from sys import exit, argv
+from sphinx import main
+
+if __name__ == '__main__':
+    exit(main(argv))
-- 
cgit v1.2.3


From 962ed22cc9f8a3de681e8543f3558b37525a5681 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 22 Aug 2017 13:19:58 +0000
Subject: Version files modification for new release

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2616 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 8296050aef9e6658cd98080075f4047487e21b68
---
 CMakeGUDHIVersion.txt  | 2 +-
 src/Doxyfile           | 2 +-
 src/cython/doc/conf.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index 3d9add66..d5620218 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 2)
 set (GUDHI_MINOR_VERSION 0)
-set (GUDHI_PATCH_VERSION 1.beta)
+set (GUDHI_PATCH_VERSION 1-rc1)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/Doxyfile b/src/Doxyfile
index 2fecf5fb..6c01aefc 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME           = "GUDHI"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "2.0.0"
+PROJECT_NUMBER         = "2.0.1-rc1"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py
index 42bfd59c..072f7a94 100755
--- a/src/cython/doc/conf.py
+++ b/src/cython/doc/conf.py
@@ -69,7 +69,7 @@ copyright = u'2016, GUDHI Editorial Board'
 # The short X.Y version.
 version = '2.0'
 # The full version, including alpha/beta/rc tags.
-release = '2.0.0'
+release = '2.0.1-rc1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-- 
cgit v1.2.3

-- 
cgit v1.2.3


From ff75dab4aa40bcea9400f861bbdf1bd133f892d1 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 25 Aug 2017 06:31:41 +0000
Subject: bug in Python SimplexTree (needs string) Doc issue in alpha_complex
 user doc

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2629 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ab35f6f64af33414002d6899275170f781e9cfa8
---
 src/cython/cython/simplex_tree.pyx    | 1 +
 src/cython/doc/alpha_complex_user.rst | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 9e3b2345..47aa5311 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -2,6 +2,7 @@ from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 from libcpp cimport bool
+from libcpp.string cimport string
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst
index e8268ef1..ff62390b 100644
--- a/src/cython/doc/alpha_complex_user.rst
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -142,7 +142,7 @@ Prune above given filtration value
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The simplex tree is pruned from the given maximum alpha squared value (cf. `Simplex_tree::prune_above_filtration()`
-int he `C++ version <http://gudhi.gforge.inria.fr/doc/latest/index.html>`_).
+in the `C++ version <http://gudhi.gforge.inria.fr/doc/latest/index.html>`_).
 In the following example, the value is given by the user as argument of the program.
 
 
-- 
cgit v1.2.3


From 94bf43f9d92f546837f5120379ffdc08bf274302 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 5 Sep 2017 15:47:24 +0000
Subject: Tests and compilation are now from sources (even if doc and examples
 are copied) This modification does not fix it for the doc

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2645 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0fa4850747d3f18cd54e0622ef1831d5d5c5a0df
---
 src/cython/CMakeLists.txt | 123 ++++++++++++++++++++++++++++++++++------------
 src/cython/gudhi.pyx.in   |  18 +++----
 src/cython/setup.py.in    |   2 +-
 3 files changed, 102 insertions(+), 41 deletions(-)

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index ab5ea9ef..a12b6029 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -73,13 +73,11 @@ if(CYTHON_FOUND)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
   endif (EIGEN3_FOUND)
 
-  # Copy recursively include, cython, example, doc and test repositories before packages finding
+  # Copy recursively example and doc repositories before packages finding
   # Some tests and doc files are removed in case some packages are not found
-  file(COPY include DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY cython DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
   file(COPY example DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
   file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
   # Developper version for doc images
   file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png")
   file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
@@ -104,9 +102,9 @@ if(CYTHON_FOUND)
 
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     # If CGAL_VERSION >= 4.8.1, include subsampling
-    set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'")
-    set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'")
-    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'")
+    set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
+    set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
+    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
   else (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     # Remove subsampling unitary tests
     file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py)
@@ -125,7 +123,7 @@ if(CYTHON_FOUND)
   endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
     # If CGAL_VERSION >= 4.7.0, include alpha
-    set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'")
+    set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
   else (NOT CGAL_VERSION VERSION_LESS 4.7.0)
     # Remove alpha complex unitary tests
     file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py)
@@ -136,9 +134,9 @@ if(CYTHON_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
     # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex
     set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
-        "include 'cython/euclidean_witness_complex.pyx'\ninclude 'cython/euclidean_strong_witness_complex.pyx'\n")
+        "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
   else (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    # Remove alpha complex unitary tests
+    # Remove euclidean witness complex unitary tests
     file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py)
     file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst")
     file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst")
@@ -177,6 +175,7 @@ if(CYTHON_FOUND)
   # Loop on INCLUDE_DIRECTORIES PROPERTY
   get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
   foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
+    message("  ---  ${GUDHI_INCLUDE_DIRECTORY} ---")
     set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ")
   endforeach()
   set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ")
@@ -220,97 +219,159 @@ if(CYTHON_FOUND)
 
   # Test examples
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    # Bottleneck
     add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
              -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
     set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
     add_test(NAME bottleneck_basic_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/bottleneck_basic_example.py")
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
     set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
+    add_test(
+        NAME test_bottleneck_distance_py_test
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
+    set_tests_properties(test_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+    # Tangential
     add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
     set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
+    add_test(
+        NAME test_tangential_complex_py_test
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py)
+    set_tests_properties(test_tangential_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+    # Euclidean witness
     add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
     set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
     add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
     set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+    add_test(
+        NAME test_euclidean_witness_complex_py_test
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py)
+    set_tests_properties(test_euclidean_witness_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
   endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
 
   if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    # Alpha
     add_test(NAME alpha_complex_from_points_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_from_points_example.py")
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
     set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
     add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
     set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
 
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+    add_test(
+        NAME test_alpha_complex_py_test
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py)
+    set_tests_properties(test_alpha_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
 
+  # Cubical
   add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
            --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
   set_tests_properties(periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME random_cubical_complex_persistence_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/random_cubical_complex_persistence_example.py"
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
            10 10 10)
   set_tests_properties(random_cubical_complex_persistence_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
+  add_test(
+      NAME test_cubical_complex_py_test
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_cubical_complex.py)
+  set_tests_properties(test_cubical_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  # Rips
   add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
            --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
   set_tests_properties(rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
            --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
   set_tests_properties(rips_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME rips_complex_from_points_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_from_points_example.py)
+           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
   set_tests_properties(rips_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
+  add_test(
+      NAME test_rips_complex_py_test
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_rips_complex.py)
+  set_tests_properties(test_rips_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  # Simplex tree
   add_test(NAME simplex_tree_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/simplex_tree_example.py)
+           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
   set_tests_properties(simplex_tree_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
+  add_test(
+      NAME test_simplex_tree_py_test
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_simplex_tree.py)
+  set_tests_properties(test_simplex_tree_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  # Witness
   add_test(NAME witness_complex_from_nearest_landmark_table_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/witness_complex_from_nearest_landmark_table.py)
+           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
   set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
-  # Unitary tests are available through py.test
   add_test(
-      NAME gudhi_cython_py_test
+      NAME test_witness_complex_py_test
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_witness_complex.py)
+  set_tests_properties(test_witness_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  # Reader utils
+  add_test(
+      NAME test_reader_utils_py_test
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py)
+  set_tests_properties(test_reader_utils_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  # Subsampling
+  add_test(
+      NAME test_subsampling_py_test
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest)
-  set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
+  set_tests_properties(test_subsampling_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   # Documentation generation is available through sphinx
   if(SPHINX_PATH)
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index ed2d28cc..1141673a 100644
--- a/src/cython/gudhi.pyx.in
+++ b/src/cython/gudhi.pyx.in
@@ -24,15 +24,15 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016  INRIA"
 __license__ = "GPL v3"
 
-include "cython/off_reader.pyx"
-include "cython/simplex_tree.pyx"
-include "cython/rips_complex.pyx"
-include "cython/cubical_complex.pyx"
-include "cython/periodic_cubical_complex.pyx"
-include "cython/persistence_graphical_tools.py"
-include "cython/reader_utils.pyx"
-include "cython/witness_complex.pyx"
-include "cython/strong_witness_complex.pyx"
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/off_reader.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/simplex_tree.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/rips_complex.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/cubical_complex.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/periodic_cubical_complex.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/persistence_graphical_tools.py'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/reader_utils.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/witness_complex.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/strong_witness_complex.pyx'
 @GUDHI_CYTHON_ALPHA_COMPLEX@
 @GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX@
 @GUDHI_CYTHON_SUBSAMPLING@
diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in
index c1a1717a..fefa36bb 100644
--- a/src/cython/setup.py.in
+++ b/src/cython/setup.py.in
@@ -29,7 +29,7 @@ __license__ = "GPL v3"
 
 gudhi = Extension(
     "gudhi",
-    sources = ['gudhi.pyx',],
+    sources = ['@CMAKE_CURRENT_BINARY_DIR@/gudhi.pyx',],
     language = 'c++',
     extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@],
     extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@],
-- 
cgit v1.2.3


From c15a3570fa54e837c27f0e5b862e7bb5c16302d7 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 7 Sep 2017 13:17:19 +0000
Subject: Python documentation is now built from sources to the build
 directory. Missing bibtex and images to be "as before"

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2649 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0deda91875e34ce534c88a601cfb167d9c7dfa01
---
 src/cython/CMakeLists.txt                          | 200 ++++++++-------------
 src/cython/doc/Makefile.in                         |  44 -----
 src/cython/doc/alpha_complex_user.rst              |   3 +-
 src/cython/doc/conf.py                             |  90 +---------
 src/cython/doc/cubical_complex_user.rst            |  10 +-
 src/cython/doc/examples.rst                        |  19 +-
 src/cython/doc/generate_examples.py                |  43 -----
 src/cython/doc/make.bat.in                         |  67 -------
 .../doc/persistence_graphical_tools_user.rst       |  13 +-
 src/cython/doc/pyplots/barcode_persistence.py      |   3 +-
 src/cython/doc/pyplots/diagram_persistence.py      |   3 +-
 src/cython/doc/rips_complex_user.rst               |   6 +-
 src/cython/doc/tangential_complex_user.rst         |   3 +-
 src/cython/gudhi.pyx.in                            |   3 +
 14 files changed, 131 insertions(+), 376 deletions(-)
 delete mode 100644 src/cython/doc/Makefile.in
 delete mode 100755 src/cython/doc/generate_examples.py
 delete mode 100644 src/cython/doc/make.bat.in

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index a12b6029..6c8232ea 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -73,33 +73,6 @@ if(CYTHON_FOUND)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
   endif (EIGEN3_FOUND)
 
-  # Copy recursively example and doc repositories before packages finding
-  # Some tests and doc files are removed in case some packages are not found
-  file(COPY example DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-
-  # Developper version for doc images
-  file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png")
-  file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.svg")
-  file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  # User version for doc images
-  file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png")
-  file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.svg")
-  file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  # Biblio
-  file(GLOB GUDHI_BIB_FILES "${CMAKE_SOURCE_DIR}/biblio/*.bib")
-  file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  # Cubical complex perseus doc example
-  file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt")
-  file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  # Persistence graphical tools examples
-  file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     # If CGAL_VERSION >= 4.8.1, include subsampling
     set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
@@ -192,11 +165,6 @@ if(CYTHON_FOUND)
     set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}")
   endif(UNIX)
 
-  # set sphinx-build in make files
-  configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
-  configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY)
-  configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY)
-
   # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
   configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY)
   # Generate gudhi.pyx - Gudhi cython file
@@ -222,52 +190,46 @@ if(CYTHON_FOUND)
     # Bottleneck
     add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
              -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
-    set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
     add_test(NAME bottleneck_basic_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
-    set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
 
-    add_test(
-        NAME test_bottleneck_distance_py_test
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
-    set_tests_properties(test_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    add_test(NAME test_bottleneck_distance_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
 
     # Tangential
     add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
-    set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
-    add_test(
-        NAME test_tangential_complex_py_test
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py)
-    set_tests_properties(test_tangential_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    add_test(NAME test_tangential_complex_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py)
 
     # Euclidean witness
     add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-    set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
     add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-    set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
-    add_test(
-        NAME test_euclidean_witness_complex_py_test
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py)
-    set_tests_properties(test_euclidean_witness_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    add_test(NAME test_euclidean_witness_complex_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py)
 
   endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
 
@@ -275,115 +237,105 @@ if(CYTHON_FOUND)
     # Alpha
     add_test(NAME alpha_complex_from_points_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
-    set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
 
     add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
-    set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
-    add_test(
-        NAME test_alpha_complex_py_test
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py)
-    set_tests_properties(test_alpha_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    add_test(NAME test_alpha_complex_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py)
 
   endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
 
   # Cubical
   add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
            --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
-  set_tests_properties(periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME random_cubical_complex_persistence_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
            10 10 10)
-  set_tests_properties(random_cubical_complex_persistence_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
-  add_test(
-      NAME test_cubical_complex_py_test
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_cubical_complex.py)
-  set_tests_properties(test_cubical_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+  add_test(NAME test_cubical_complex_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_cubical_complex.py)
 
   # Rips
   add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
            --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
-  set_tests_properties(rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
            --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
-  set_tests_properties(rips_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME rips_complex_from_points_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
-  set_tests_properties(rips_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
 
-  add_test(
-      NAME test_rips_complex_py_test
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_rips_complex.py)
-  set_tests_properties(test_rips_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+  add_test(NAME test_rips_complex_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_rips_complex.py)
 
   # Simplex tree
   add_test(NAME simplex_tree_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
-  set_tests_properties(simplex_tree_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
 
-  add_test(
-      NAME test_simplex_tree_py_test
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_simplex_tree.py)
-  set_tests_properties(test_simplex_tree_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+  add_test(NAME test_simplex_tree_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_simplex_tree.py)
 
   # Witness
   add_test(NAME witness_complex_from_nearest_landmark_table_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
-  set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
 
-  add_test(
-      NAME test_witness_complex_py_test
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_witness_complex.py)
-  set_tests_properties(test_witness_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+  add_test(NAME test_witness_complex_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_witness_complex.py)
 
   # Reader utils
-  add_test(
-      NAME test_reader_utils_py_test
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py)
-  set_tests_properties(test_reader_utils_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+  add_test(NAME test_reader_utils_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py)
 
   # Subsampling
-  add_test(
-      NAME test_subsampling_py_test
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
-  set_tests_properties(test_subsampling_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-
-  # Documentation generation is available through sphinx
-  if(SPHINX_PATH)
-    if (UNIX)
-      add_custom_target(sphinx
-          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
-          DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
-          COMMAND make html doctest)
-    else (UNIX)
-      add_custom_target(sphinx
-          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
-          COMMAND make.bat html doctest)
-    endif (UNIX)
-  endif(SPHINX_PATH)
+  add_test(NAME test_subsampling_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
+
+  # Documentation generation is available through sphinx - requires all modules
+  if(SPHINX_PATH AND NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    # set sphinx-build in make files
+    configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
+
+    add_custom_target(sphinx
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
+        COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+        ${SPHINX_PATH} -b html . "${CMAKE_CURRENT_BINARY_DIR}/sphinx"
+        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so")
+
+    add_test(NAME sphinx_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc "${CMAKE_CURRENT_BINARY_DIR}/sphinx")
+
+  endif(SPHINX_PATH AND NOT CGAL_VERSION VERSION_LESS 4.8.1)
 endif(CYTHON_FOUND)
diff --git a/src/cython/doc/Makefile.in b/src/cython/doc/Makefile.in
deleted file mode 100644
index 526350b3..00000000
--- a/src/cython/doc/Makefile.in
+++ /dev/null
@@ -1,44 +0,0 @@
-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = @SPHINX_PATH@
-PAPER         =
-BUILDDIR      = _build
-
-# User-friendly check for sphinx-build
-ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
-endif
-
-# Internal variables.
-PAPEROPT_a4     = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
-
-help:
-	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       to make standalone HTML files"
-	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
-
-clean:
-	rm -f examples.inc
-	rm -rf $(BUILDDIR)/*
-
-# GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean)
-
-html:
-	./generate_examples.py
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-doctest:
-	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
-	@echo "Testing of doctests in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst
index e8268ef1..e541e6d3 100644
--- a/src/cython/doc/alpha_complex_user.rst
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -158,7 +158,8 @@ Then, it is asked to display information about the alpha complex:
 .. testcode::
 
     import gudhi
-    alpha_complex = gudhi.AlphaComplex(off_file='alphacomplexdoc.off')
+    alpha_complex = gudhi.AlphaComplex(off_file=gudhi.__root_source_dir__ + \
+        '/data/points/alphacomplexdoc.off')
     simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=59.0)
     result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py
index 072f7a94..19a880d4 100755
--- a/src/cython/doc/conf.py
+++ b/src/cython/doc/conf.py
@@ -21,7 +21,7 @@ import os
 #sys.path.insert(0, os.path.abspath('.'))
 
 # Path to Gudhi.so from source path
-sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath('.'))
 
 # -- General configuration ------------------------------------------------
 
@@ -58,18 +58,20 @@ source_suffix = '.rst'
 # The master toctree document.
 master_doc = 'index'
 
+import gudhi
+
 # General information about the project.
-project = u'GUDHI'
-copyright = u'2016, GUDHI Editorial Board'
+project = gudhi.__name__
+copyright = gudhi.__copyright__
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '2.0'
+version = gudhi.__version__
 # The full version, including alpha/beta/rc tags.
-release = '2.0.1-rc1'
+#release = '2.0.1-rc1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -198,81 +200,3 @@ html_static_path = ['_static']
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'GUDHIdoc'
 
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-  ('index', 'GUDHI.tex', u'GUDHI Documentation',
-   u'Vincent Rouvreau', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-#latex_logo = None
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# If true, show page references after internal links.
-#latex_show_pagerefs = False
-
-# If true, show URL addresses after external links.
-#latex_show_urls = False
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_domain_indices = True
-
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    ('index', 'gudhi', u'GUDHI Documentation',
-     [u'Vincent Rouvreau'], 1)
-]
-
-# If true, show URL addresses after external links.
-#man_show_urls = False
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-  ('index', 'GUDHI', u'GUDHI Documentation',
-   u'Vincent Rouvreau', 'GUDHI', 'One line description of project.',
-   'Miscellaneous'),
-]
-
-# Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
-
-# If false, no module index is generated.
-#texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
-
-# If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
index 344b9554..8c9a3ed6 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -97,12 +97,13 @@ The input file for the following complex is:
 
 .. literalinclude:: cubicalcomplexdoc.txt
 
-.. centered:: cubicalcomplexdoc.txt
+.. centered:: data/bitmap/cubicalcomplexdoc.txt
 
 .. testcode::
 
     import gudhi
-    cubical_complex = gudhi.CubicalComplex(perseus_file='cubicalcomplexdoc.txt')
+    cubical_complex = gudhi.CubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
+        '/data/bitmap/cubicalcomplexdoc.txt')
     result_str = 'Cubical complex is of dimension ' + repr(cubical_complex.dimension()) + ' - ' + \
         repr(cubical_complex.num_simplices()) + ' simplices.'
     print(result_str)
@@ -129,14 +130,15 @@ For instance:
 
 .. literalinclude:: periodiccubicalcomplexdoc.txt
 
-.. centered:: periodiccubicalcomplexdoc.txt
+.. centered:: data/bitmap/periodiccubicalcomplexdoc.txt
 
 Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
 
 .. testcode::
 
     import gudhi
-    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='periodiccubicalcomplexdoc.txt')
+    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
+        '/data/bitmap/periodiccubicalcomplexdoc.txt')
     result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \
         repr(periodic_cc.num_simplices()) + ' simplices.'
     print(result_str)
diff --git a/src/cython/doc/examples.rst b/src/cython/doc/examples.rst
index a89e0596..1e596e18 100644
--- a/src/cython/doc/examples.rst
+++ b/src/cython/doc/examples.rst
@@ -1,4 +1,21 @@
 Examples
 ########
 
-.. include:: examples.inc
+.. only:: builder_html
+
+    * :download:`rips_complex_from_points_example.py <../example/rips_complex_from_points_example.py>`
+    * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>`
+    * :download:`simplex_tree_example.py <../example/simplex_tree_example.py>`
+    * :download:`alpha_rips_persistence_bottleneck_distance.py <../example/alpha_rips_persistence_bottleneck_distance.py>`
+    * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
+    * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
+    * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>`
+    * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>`
+    * :download:`witness_complex_from_nearest_landmark_table.py <../example/witness_complex_from_nearest_landmark_table.py>`
+    * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>`
+    * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>`
+    * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>`
diff --git a/src/cython/doc/generate_examples.py b/src/cython/doc/generate_examples.py
deleted file mode 100755
index d64d506c..00000000
--- a/src/cython/doc/generate_examples.py
+++ /dev/null
@@ -1,43 +0,0 @@
-#!/usr/bin/env python
-
-from os import listdir
-
-"""This file is part of the Gudhi Library. The Gudhi library
-   (Geometric Understanding in Higher Dimensions) is a generic C++
-   library for computational topology.
-
-   Author(s):       Vincent Rouvreau
-
-   Copyright (C) 2017 INRIA
-
-   This program is free software: you can redistribute it and/or modify
-   it under the terms of the GNU General Public License as published by
-   the Free Software Foundation, either version 3 of the License, or
-   (at your option) any later version.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License
-   along with this program.  If not, see <http://www.gnu.org/licenses/>.
-"""
-
-__author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2017 INRIA"
-__license__ = "GPL v3"
-
-"""
-generate_examples.py generates examples.inc to be included in examples.rst.
-Refer to Makefile and make.bat to see if it is correctly launched.
-"""
-
-output_file = open('examples.inc','w')
-
-output_file.write('.. only:: builder_html\n\n')
-
-for file in listdir('../example/'):
-    output_file.write("    * :download:`" + file + " <../example/" + file + ">`\n")
-
-output_file.close()
diff --git a/src/cython/doc/make.bat.in b/src/cython/doc/make.bat.in
deleted file mode 100644
index ff1a6d56..00000000
--- a/src/cython/doc/make.bat.in
+++ /dev/null
@@ -1,67 +0,0 @@
-@ECHO OFF
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-        set SPHINXBUILD=@SPHINX_PATH@
-)
-set BUILDDIR=_build
-set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
-set I18NSPHINXOPTS=%SPHINXOPTS% .
-if NOT "%PAPER%" == "" (
-	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
-	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
-)
-
-if "%1" == "" goto help
-
-if "%1" == "help" (
-	:help
-	echo.Please use `make ^<target^>` where ^<target^> is one of
-	echo.  html       to make standalone HTML files
-	echo.  doctest    to run all doctests embedded in the documentation if enabled
-	goto end
-)
-
-if "%1" == "clean" (
-	del examples.inc
-	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
-	del /q /s %BUILDDIR%\*
-	goto end
-)
-
-
-%SPHINXBUILD% 2> nul
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-:: GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean)
-
-if "%1" == "html" (
-	generate_examples.py
-	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
-	goto end
-)
-
-if "%1" == "doctest" (
-	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Testing of doctests in the sources finished, look at the ^
-results in %BUILDDIR%/doctest/output.txt.
-	goto end
-)
-
-:end
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index 13198162..9033331f 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -32,7 +32,8 @@ This function can display the persistence result as a barcode:
 
     import gudhi
     
-    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
+    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
+        '/data/bitmap/3d_torus.txt')
     diag = periodic_cc.persistence()
     plt = gudhi.plot_persistence_barcode(diag)
     plt.show()
@@ -41,8 +42,10 @@ This function can display the persistence result as a barcode:
 
     import gudhi
 
-    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
+    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
+        '/data/bitmap/3d_torus.txt')
     diag = periodic_cc.persistence()
+    print("diag = ", diag)
     plt = gudhi.plot_persistence_barcode(diag)
     plt.show()
 
@@ -55,7 +58,8 @@ This function can display the persistence result as a diagram:
 
     import gudhi
     
-    rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2)
+    rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \
+        '/data/points/tore3D_1307.off', max_edge_length=0.2)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
     plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
@@ -65,7 +69,8 @@ This function can display the persistence result as a diagram:
 
     import gudhi
 
-    rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2)
+    rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \
+        '/data/points/tore3D_1307.off', max_edge_length=0.2)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
     plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py
index 9cd3149d..de33d506 100755
--- a/src/cython/doc/pyplots/barcode_persistence.py
+++ b/src/cython/doc/pyplots/barcode_persistence.py
@@ -1,6 +1,7 @@
 import gudhi
 
-periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
+periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
+    '/data/bitmap/3d_torus.txt')
 diag = periodic_cc.persistence()
 plt = gudhi.plot_persistence_barcode(diag)
 plt.show()
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
index 30661965..c2fbf801 100755
--- a/src/cython/doc/pyplots/diagram_persistence.py
+++ b/src/cython/doc/pyplots/diagram_persistence.py
@@ -1,6 +1,7 @@
 import gudhi
 
-rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2)
+rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \
+    '/data/points/tore3D_1307.off', max_edge_length=0.2)
 simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
 diag = simplex_tree.persistence()
 plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
index f9760976..6b48422b 100644
--- a/src/cython/doc/rips_complex_user.rst
+++ b/src/cython/doc/rips_complex_user.rst
@@ -101,7 +101,8 @@ Finally, it is asked to display information about the Rips complex.
 .. testcode::
 
     import gudhi
-    rips_complex = gudhi.RipsComplex(off_file='alphacomplexdoc.off', max_edge_length=12.0)
+    rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \
+        '/data/points/alphacomplexdoc.off', max_edge_length=12.0)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
     result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
@@ -205,7 +206,8 @@ Finally, it is asked to display information about the Rips complex.
 .. testcode::
 
     import gudhi
-    rips_complex = gudhi.RipsComplex(csv_file='full_square_distance_matrix.csv', max_edge_length=12.0)
+    rips_complex = gudhi.RipsComplex(csv_file=gudhi.__root_source_dir__ + \
+        '/data/distance_matrix/full_square_distance_matrix.csv', max_edge_length=12.0)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
     result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
index 03f9fea6..d670cfdb 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -122,7 +122,8 @@ This example builds the Tangential complex of point set read in an OFF file.
 .. testcode::
 
     import gudhi
-    tc = gudhi.TangentialComplex(off_file='alphacomplexdoc.off')
+    tc = gudhi.TangentialComplex(off_file=gudhi.__root_source_dir__ + \
+        '/data/points/alphacomplexdoc.off')
     result_str = 'Tangential contains ' + repr(tc.num_simplices()) + \
         ' simplices - ' + repr(tc.num_vertices()) + ' vertices.'
     print(result_str)
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index 1141673a..a8dd9f80 100644
--- a/src/cython/gudhi.pyx.in
+++ b/src/cython/gudhi.pyx.in
@@ -23,6 +23,9 @@
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016  INRIA"
 __license__ = "GPL v3"
+__version__ = "@GUDHI_VERSION@"
+# This variable is used by doctest to find files
+__root_source_dir__ = "@CMAKE_SOURCE_DIR@"
 
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/off_reader.pyx'
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/simplex_tree.pyx'
-- 
cgit v1.2.3


From ef8a5bca22be47df00f61d660e84948f1f45f9ba Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 7 Sep 2017 16:07:41 +0000
Subject: Fix doc for user_version

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2650 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 18aebd67968fd48ccfcfcfbff75c614496f4424e
---
 src/cython/doc/alpha_complex_sum.rst          |  2 +-
 src/cython/doc/alpha_complex_user.rst         |  6 +++---
 src/cython/doc/bottleneck_distance_sum.rst    |  2 +-
 src/cython/doc/cubical_complex_sum.rst        | 22 +++++++++++-----------
 src/cython/doc/cubical_complex_user.rst       |  2 +-
 src/cython/doc/index.rst                      |  8 +++++---
 src/cython/doc/persistent_cohomology_sum.rst  |  2 +-
 src/cython/doc/persistent_cohomology_user.rst |  2 +-
 src/cython/doc/rips_complex_sum.rst           |  2 +-
 src/cython/doc/rips_complex_user.rst          |  2 +-
 src/cython/doc/simplex_tree_sum.rst           |  2 +-
 src/cython/doc/tangential_complex_sum.rst     |  4 ++--
 src/cython/doc/tangential_complex_user.rst    | 14 +++++++-------
 src/cython/doc/witness_complex_sum.rst        | 26 ++++++++++++++------------
 src/cython/doc/witness_complex_user.rst       |  4 ++--
 15 files changed, 52 insertions(+), 48 deletions(-)

diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst
index a5f6420a..1680a712 100644
--- a/src/cython/doc/alpha_complex_sum.rst
+++ b/src/cython/doc/alpha_complex_sum.rst
@@ -5,7 +5,7 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | Alpha_complex is a simplicial complex constructed from the finite      |
-|      img/alpha_complex_representation.png                      | cells of a Delaunay Triangulation.                                     |
+|      ../../doc/Alpha_complex/alpha_complex_representation.png  | cells of a Delaunay Triangulation.                                     |
 |      :alt: Alpha complex representation                        |                                                                        |
 |      :figclass: align-center                                   | The filtration value of each simplex is computed as the square of the  |
 |                                                                | circumradius of the simplex if the circumsphere is empty (the simplex  |
diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst
index e541e6d3..c3a13bef 100644
--- a/src/cython/doc/alpha_complex_user.rst
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -75,7 +75,7 @@ In order to build the alpha complex, first, a Simplex tree is built from the cel
 (The filtration value is set to NaN, which stands for unknown value):
 
 .. figure::
-    img/alpha_complex_doc.png
+    ../../doc/Alpha_complex/alpha_complex_doc.png
     :figclass: align-center
     :alt: Simplex tree structure construction example
 
@@ -112,7 +112,7 @@ computes the filtration value of the triangle, and then propagates the filtratio
 here:
 
 .. figure::
-    img/alpha_complex_doc_420.png
+    ../../doc/Alpha_complex/alpha_complex_doc_420.png
     :figclass: align-center
     :alt: Filtration value propagation example
 
@@ -201,6 +201,6 @@ the program output is:
 CGAL citations
 ==============
 
-.. bibliography:: how_to_cite_cgal.bib
+.. bibliography:: ../../biblio/how_to_cite_cgal.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/bottleneck_distance_sum.rst b/src/cython/doc/bottleneck_distance_sum.rst
index 5c475d0d..030fad9e 100644
--- a/src/cython/doc/bottleneck_distance_sum.rst
+++ b/src/cython/doc/bottleneck_distance_sum.rst
@@ -5,7 +5,7 @@
 
 +-----------------------------------------------------------------+----------------------------------------------------------------------+
 | .. figure::                                                     | Bottleneck distance measures the similarity between two persistence  |
-|      img/perturb_pd.png                                         | diagrams. It's the shortest distance b for which there exists a      |
+|      ../../doc/Bottleneck_distance/perturb_pd.png               | diagrams. It's the shortest distance b for which there exists a      |
 |      :figclass: align-center                                    | perfect matching between the points of the two diagrams (+ all the   |
 |                                                                 | diagonal points) such that any couple of matched points are at       |
 |      Bottleneck distance is the length of                       | distance at most b.                                                  |
diff --git a/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.rst
index 3ddf6375..280ad0e0 100644
--- a/src/cython/doc/cubical_complex_sum.rst
+++ b/src/cython/doc/cubical_complex_sum.rst
@@ -2,14 +2,14 @@
 :Author: Pawel Dlotko                                              :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
 =================================================================  ===================================  ===================================
 
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| .. figure::                                                     | The cubical complex is an example of a structured complex useful in  |
-|      img/Cubical_complex_representation.png                     | computational mathematics (specially rigorous numerics) and image    |
-|      :alt: Cubical complex representation                       | analysis.                                                            |
-|      :figclass: align-center                                    |                                                                      |
-|                                                                 |                                                                      |
-|      Cubical complex representation                             |                                                                      |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| :doc:`cubical_complex_user`                                     | * :doc:`cubical_complex_ref`                                         |
-|                                                                 | * :doc:`periodic_cubical_complex_ref`                                |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
++--------------------------------------------------------------------------+----------------------------------------------------------------------+
+| .. figure::                                                              | The cubical complex is an example of a structured complex useful in  |
+|      ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image    |
+|      :alt: Cubical complex representation                                | analysis.                                                            |
+|      :figclass: align-center                                             |                                                                      |
+|                                                                          |                                                                      |
+|      Cubical complex representation                                      |                                                                      |
++--------------------------------------------------------------------------+----------------------------------------------------------------------+
+| :doc:`cubical_complex_user`                                              | * :doc:`cubical_complex_ref`                                         |
+|                                                                          | * :doc:`periodic_cubical_complex_ref`                                |
++--------------------------------------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
index 8c9a3ed6..36fa3ba9 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -157,6 +157,6 @@ End user programs are available in cython/example/ folder.
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst
index f6d10567..3945d72a 100644
--- a/src/cython/doc/index.rst
+++ b/src/cython/doc/index.rst
@@ -1,8 +1,10 @@
 GUDHI Python module documentation
 #################################
 
-.. image:: img/Gudhi_banner.png
-   :align: center
+.. figure::
+     ../../doc/common/Gudhi_banner.png
+     :alt: Gudhi banner
+     :figclass: align-center
 
 Introduction
 ************
@@ -81,6 +83,6 @@ Persistence graphical tools
 Bibliography
 ************
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst
index d1f79cb4..a26df1dc 100644
--- a/src/cython/doc/persistent_cohomology_sum.rst
+++ b/src/cython/doc/persistent_cohomology_sum.rst
@@ -4,7 +4,7 @@
 
 +-----------------------------------------------------------------+-----------------------------------------------------------------------+
 | .. figure::                                                     | The theory of homology consists in attaching to a topological space   |
-|      img/3DTorus_poch.png                                       | a sequence of (homology) groups, capturing global topological         |
+|      ../../doc/Persistent_cohomology/3DTorus_poch.png           | a sequence of (homology) groups, capturing global topological         |
 |      :figclass: align-center                                    | features like connected components, holes, cavities, etc. Persistent  |
 |                                                                 | homology studies the evolution -- birth, life and death -- of these   |
 |      Rips Persistent Cohomology on a 3D                         | features when the topological space is changing. Consequently, the    |
diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst
index 72f1a7f7..bf90c163 100644
--- a/src/cython/doc/persistent_cohomology_user.rst
+++ b/src/cython/doc/persistent_cohomology_user.rst
@@ -109,6 +109,6 @@ We provide several example files: run these examples with -h for details on thei
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/rips_complex_sum.rst b/src/cython/doc/rips_complex_sum.rst
index 2b65fc19..5616bfa9 100644
--- a/src/cython/doc/rips_complex_sum.rst
+++ b/src/cython/doc/rips_complex_sum.rst
@@ -4,7 +4,7 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | Rips complex is a simplicial complex constructed from a one skeleton   |
-|      img/rips_complex_representation.png                       | graph.                                                                 |
+|      ../../doc/Rips_complex/rips_complex_representation.png    | graph.                                                                 |
 |      :figclass: align-center                                   |                                                                        |
 |                                                                | The filtration value of each edge is computed from a user-given        |
 |      Rips complex representation                               | distance function and is inserted until a user-given threshold         |
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
index 6b48422b..96ba9944 100644
--- a/src/cython/doc/rips_complex_user.rst
+++ b/src/cython/doc/rips_complex_user.rst
@@ -26,7 +26,7 @@ structure, and then expands the simplicial complex when required.
 Vertex name correspond to the index of the point in the given range (aka. the point cloud).
 
 .. figure::
-    img/rips_complex_representation.png
+    ../../doc/Rips_complex/rips_complex_representation.png
     :align: center
 
     Rips-complex one skeleton graph representation
diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst
index 3174fb62..fb0e54c1 100644
--- a/src/cython/doc/simplex_tree_sum.rst
+++ b/src/cython/doc/simplex_tree_sum.rst
@@ -4,7 +4,7 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | The simplex tree is an efficient and flexible data structure for       |
-|      img/Simplex_tree_representation.png                       | representing general (filtered) simplicial complexes.                  |
+|      ../../doc/Simplex_tree/Simplex_tree_representation.png    | representing general (filtered) simplicial complexes.                  |
 |      :alt: Simplex tree representation                         |                                                                        |
 |      :figclass: align-center                                   | The data structure is described in                                     |
 |                                                                | :cite:`boissonnatmariasimplextreealgorithmica`                         |
diff --git a/src/cython/doc/tangential_complex_sum.rst b/src/cython/doc/tangential_complex_sum.rst
index 2b05bc10..72b4d7ba 100644
--- a/src/cython/doc/tangential_complex_sum.rst
+++ b/src/cython/doc/tangential_complex_sum.rst
@@ -5,10 +5,10 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | A Tangential Delaunay complex is a simplicial complex designed to      |
-|      img/tc_examples.png                                       | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`-    |
+|      ../../doc/Tangential_complex/tc_examples.png              | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`-    |
 |      :figclass: align-center                                   | dimensional Euclidean space. The input is a point sample coming from   |
 |                                                                | an unknown manifold. The running time depends only linearly on the     |
-|      **Tangential complex representation**                     | extrinsic dimension :math:`d` and exponentially on the intrinsic       |
+|      Tangential complex representation                         | extrinsic dimension :math:`d` and exponentially on the intrinsic       |
 |                                                                | dimension :math:`k`.                                                   |
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | :doc:`tangential_complex_user`                                 | :doc:`tangential_complex_ref`                                          |
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
index d670cfdb..efa6d7ce 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -22,7 +22,7 @@ Let us start with the description of the Tangential complex of a simple
 example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
 :math:`P` located on a curve embedded in 2D.
 
-.. figure:: img/tc_example_01.png
+.. figure:: ../../doc/Tangential_complex/tc_example_01.png
     :alt: The input
     :figclass: align-center
 
@@ -31,7 +31,7 @@ example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
 For each point :math:`p`, estimate its tangent subspace :math:`T_p` (e.g.
 using PCA). 
 
-.. figure:: img/tc_example_02.png
+.. figure:: ../../doc/Tangential_complex/tc_example_02.png
     :alt: The estimated normals
     :figclass: align-center
 
@@ -42,7 +42,7 @@ Let us add the Voronoi diagram of the points in orange. For each point
 :math:`p`, construct its star in the Delaunay triangulation of :math:`P`
 restricted to :math:`T_p`.
 
-.. figure:: img/tc_example_03.png
+.. figure:: ../../doc/Tangential_complex/tc_example_03.png
     :alt: The Voronoi diagram
     :figclass: align-center
 
@@ -62,7 +62,7 @@ simplex is not in the star of all its vertices.
 
 Let us take the same example.
 
-.. figure:: img/tc_example_07_before.png
+.. figure:: ../../doc/Tangential_complex/tc_example_07_before.png
     :alt: Before
     :figclass: align-center
 
@@ -70,7 +70,7 @@ Let us take the same example.
 
 Let us slightly move the tangent subspace :math:`T_q`
 
-.. figure:: img/tc_example_07_after.png
+.. figure:: ../../doc/Tangential_complex/tc_example_07_after.png
     :alt: After
     :figclass: align-center
 
@@ -79,7 +79,7 @@ Let us slightly move the tangent subspace :math:`T_q`
 Now, the star of :math:`Q` contains :math:`QP`, but the star of :math:`P` does
 not contain :math:`QP`. We have an inconsistency.
 
-.. figure:: img/tc_example_08.png
+.. figure:: ../../doc/Tangential_complex/tc_example_08.png
     :alt: After
     :figclass: align-center
 
@@ -191,6 +191,6 @@ The output is:
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.rst
index b65522ba..a8a126a0 100644
--- a/src/cython/doc/witness_complex_sum.rst
+++ b/src/cython/doc/witness_complex_sum.rst
@@ -3,15 +3,17 @@
 :Euclidean version requires: CGAL :math:`\geq` 4.6.0               Eigen3
 =================================================================  ===================================  ===================================
 
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| .. image::                                                      | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on  |
-|      img/Witness_complex_representation.png                     | two sets of points in :math:`\mathbb{R}^D`.                          |
-|                                                                 |                                                                      |
-|                                                                 | The data structure is described in                                   |
-|                                                                 | :cite:`boissonnatmariasimplextreealgorithmica`.                      |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| :doc:`witness_complex_user`                                     | * :doc:`witness_complex_ref`                                         |
-|                                                                 | * :doc:`strong_witness_complex_ref`                                  |
-|                                                                 | * :doc:`euclidean_witness_complex_ref`                               |
-|                                                                 | * :doc:`euclidean_strong_witness_complex_ref`                        |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
++-------------------------------------------------------------------+----------------------------------------------------------------------+
+| .. figure::                                                       | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on  |
+|      ../../doc/Witness_complex/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`.                          |
+|      :alt: Witness complex representation                         |                                                                      |
+|      :figclass: align-center                                      | The data structure is described in                                   |
+|                                                                   | :cite:`boissonnatmariasimplextreealgorithmica`.                      |
+|                                                                   |                                                                      |
+|      Witness complex representation                               |                                                                      |
++-------------------------------------------------------------------+----------------------------------------------------------------------+
+| :doc:`witness_complex_user`                                       | * :doc:`witness_complex_ref`                                         |
+|                                                                   | * :doc:`strong_witness_complex_ref`                                  |
+|                                                                   | * :doc:`euclidean_witness_complex_ref`                               |
+|                                                                   | * :doc:`euclidean_strong_witness_complex_ref`                        |
++-------------------------------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst
index aa9cbb2c..29413269 100644
--- a/src/cython/doc/witness_complex_user.rst
+++ b/src/cython/doc/witness_complex_user.rst
@@ -33,7 +33,7 @@ Both definitions can be relaxed by a real value :math:`\alpha`:
 which leads to definitions of **weak relaxed witness complex** (or just relaxed witness complex for short) and
 **strong relaxed witness complex** respectively.
 
-.. figure:: img/swit.svg
+.. figure:: ../../doc/Witness_complex/swit.svg
     :alt: Strongly witnessed simplex
     :figclass: align-center
 
@@ -126,6 +126,6 @@ Here is an example of constructing a strong witness complex filtration and compu
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
-- 
cgit v1.2.3


From df9030e6c1df5fb735914eadd44cf27b86fce239 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 11 Sep 2017 15:12:01 +0000
Subject: Add comment for the dependency

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2655 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ab03b16bc884fe3291e3308e4a975b7c6232a861
---
 src/cython/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 6c8232ea..ea6e840a 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -326,6 +326,7 @@ if(CYTHON_FOUND)
     # set sphinx-build in make files
     configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
 
+    # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
     add_custom_target(sphinx
         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
         COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-- 
cgit v1.2.3


From 03bb8ee15f7c8b71fd922a27ed02bca4c98825d9 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 11 Sep 2017 15:16:39 +0000
Subject: remove debug traces

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2656 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4ea039d0564268458ca64950113fbffdc86c10b3
---
 src/cython/CMakeLists.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index ea6e840a..7cf31a03 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -148,7 +148,6 @@ if(CYTHON_FOUND)
   # Loop on INCLUDE_DIRECTORIES PROPERTY
   get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
   foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
-    message("  ---  ${GUDHI_INCLUDE_DIRECTORY} ---")
     set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ")
   endforeach()
   set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ")
-- 
cgit v1.2.3


From 04fe614e8a859257b57aadfdb5aa14fc3d78babb Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 08:30:31 +0000
Subject: Euclidean witness requires CGAL 4.6.0 Subsampling requires CGAL 4.8.1
 All modules requiring CGAL requires also Eigen3

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2662 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: df4c03882b8c5eb91f12939b460b3c9b85cbb870
---
 src/cython/CMakeLists.txt | 96 +++++++++++++++++------------------------------
 1 file changed, 35 insertions(+), 61 deletions(-)

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 7cf31a03..db23d42b 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -73,47 +73,18 @@ if(CYTHON_FOUND)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
   endif (EIGEN3_FOUND)
 
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    # If CGAL_VERSION >= 4.8.1, include subsampling
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
     set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
     set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
-  else (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    # Remove subsampling unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_user.rst")
-    # Remove tangential complex and bottleneck unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py)
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_bottleneck_distance.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_user.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_user.rst")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    # If CGAL_VERSION >= 4.7.0, include alpha
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
-  else (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    # Remove alpha complex unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_user.rst")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
     set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
         "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
-  else (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    # Remove euclidean witness complex unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
 
   if(CGAL_FOUND)
     # Add CGAL compilation args
@@ -185,7 +156,7 @@ if(CYTHON_FOUND)
       PATTERN "*.pyd")
 
   # Test examples
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     # Bottleneck
     add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -213,26 +184,14 @@ if(CYTHON_FOUND)
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py)
 
-    # Euclidean witness
-    add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
-    add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
-    add_test(NAME test_euclidean_witness_complex_py_test
+    # Subsampling
+    add_test(NAME test_subsampling_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py)
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
 
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     # Alpha
     add_test(NAME alpha_complex_from_points_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -249,7 +208,27 @@ if(CYTHON_FOUND)
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py)
 
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+    # Euclidean witness
+    add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+    add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+    add_test(NAME test_euclidean_witness_complex_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py)
+
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
 
   # Cubical
   add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
@@ -315,13 +294,8 @@ if(CYTHON_FOUND)
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
            COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py)
 
-  # Subsampling
-  add_test(NAME test_subsampling_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
-
   # Documentation generation is available through sphinx - requires all modules
-  if(SPHINX_PATH AND NOT CGAL_VERSION VERSION_LESS 4.8.1)
+  if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     # set sphinx-build in make files
     configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
 
@@ -337,5 +311,5 @@ if(CYTHON_FOUND)
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
              ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc "${CMAKE_CURRENT_BINARY_DIR}/sphinx")
 
-  endif(SPHINX_PATH AND NOT CGAL_VERSION VERSION_LESS 4.8.1)
+  endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 endif(CYTHON_FOUND)
-- 
cgit v1.2.3


From 5470c3565cfb4b9e3827a42bfdc3fbec461638a5 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 10:05:46 +0000
Subject: Fix in Python3 if sphinx is not installed

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2663 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0005d7fe2e7e8513a276543295c02351456595cc
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index dbf2106a..4cf2f445 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -122,8 +122,12 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     # Documentation generation is available through sphinx
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
-    # No sphinx-build in Pyton3, just hack it
-    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+    execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from sphinx import main"
+                    RESULT_VARIABLE SPHINX_MODULE_IS_INSTALLED)
+    if(SPHINX_MODULE_IS_INSTALLED)
+      # No sphinx-build in Pyton3, just hack it
+      set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+    endif(SPHINX_MODULE_IS_INSTALLED)
   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)
-- 
cgit v1.2.3


From 3dd4db9ad872eecae58e6edf3c16915ca1ec7ccc Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 11:26:30 +0000
Subject: Add debug traces

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2664 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e4c572d98f4628e7f9b36fd9925ba7ce68e3cf81
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 4cf2f445..799d28b6 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -124,6 +124,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
     execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from sphinx import main"
                     RESULT_VARIABLE SPHINX_MODULE_IS_INSTALLED)
+    message("  --- SPHINX_MODULE_IS_INSTALLED --- ${SPHINX_MODULE_IS_INSTALLED}")
     if(SPHINX_MODULE_IS_INSTALLED)
       # No sphinx-build in Pyton3, just hack it
       set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
-- 
cgit v1.2.3


From 90f4783f287e266d3d8787d0d18b84d27f8b96b6 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 12:45:20 +0000
Subject: Modification rollback

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2665 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2f977f8b93c6104d2b7c8f16c13da974b36f1535
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 799d28b6..dbf2106a 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -122,13 +122,8 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     # Documentation generation is available through sphinx
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
-    execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from sphinx import main"
-                    RESULT_VARIABLE SPHINX_MODULE_IS_INSTALLED)
-    message("  --- SPHINX_MODULE_IS_INSTALLED --- ${SPHINX_MODULE_IS_INSTALLED}")
-    if(SPHINX_MODULE_IS_INSTALLED)
-      # No sphinx-build in Pyton3, just hack it
-      set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
-    endif(SPHINX_MODULE_IS_INSTALLED)
+    # No sphinx-build in Pyton3, just hack it
+    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_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)
-- 
cgit v1.2.3


From 9a3df180af4976242fb45d7dcd49c3632e65f04c Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 20:36:58 +0000
Subject: Bottleneck does not require Eigen3 (C++ and Python) Doc issue about
 examples requiring Eigen3

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2666 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5e127d4e8137a44ee3bd688c32653acfb4a55007
---
 src/Bottleneck_distance/benchmark/CMakeLists.txt |  4 ++--
 src/Bottleneck_distance/example/CMakeLists.txt   | 26 ++++++++++++++++--------
 src/Bottleneck_distance/test/CMakeLists.txt      |  4 ++--
 src/common/doc/main_page.h                       | 20 ++++++++++++++++--
 src/cython/CMakeLists.txt                        | 26 ++++++++++++++----------
 5 files changed, 54 insertions(+), 26 deletions(-)

diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt
index 170081ce..20a4e47b 100644
--- a/src/Bottleneck_distance/benchmark/CMakeLists.txt
+++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt
@@ -1,9 +1,9 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_benchmark)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   add_executable ( bottleneck_chrono bottleneck_chrono.cpp )
   if (TBB_FOUND)
     target_link_libraries(bottleneck_chrono ${TBB_LIBRARIES})
   endif(TBB_FOUND)
-endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+endif(NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index dc1da31c..eac617db 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -1,30 +1,38 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_examples)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_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_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
-  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES})
     target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES})
-    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
   endif(TBB_FOUND)
 
   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")
-
   add_test(NAME Bottleneck_read_file_example
       COMMAND $<TARGET_FILE:bottleneck_read_file_example>
       "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers")
 
   install(TARGETS bottleneck_read_file_example DESTINATION bin)
   install(TARGETS bottleneck_basic_example DESTINATION bin)
-  install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
 
+endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+
+# Eigen3 and CGAL > 4.7.0 is required for alpha complex
+# CGAL > 4.8.1 is required for bottleneck distance =>
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
+  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+  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")
+
+  install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
+  if (TBB_FOUND)
+    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt
index a165d472..2676b82c 100644
--- a/src/Bottleneck_distance/test/CMakeLists.txt
+++ b/src/Bottleneck_distance/test/CMakeLists.txt
@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_tests)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   include(GUDHI_test_coverage)
 
   add_executable ( Bottleneck_distance_test_unit bottleneck_unit_test.cpp )
@@ -12,4 +12,4 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 
   gudhi_add_coverage_test(Bottleneck_distance_test_unit)
 
-endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index bd4615f5..1a7994a5 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -160,7 +160,7 @@
       <b>Author:</b> Fran&ccedil;ois Godi<br>
       <b>Introduced in:</b> GUDHI 2.0.0<br>
       <b>Copyright:</b> GPL v3<br>
-      <b>Requires:</b> \ref cgal &ge; 4.8.1 and \ref eigen3
+      <b>Requires:</b> \ref cgal &ge; 4.8.1
     </td>
     <td width="75%">
     Bottleneck distance measures the similarity between two persistence diagrams. 
@@ -329,13 +329,29 @@ make doxygen
  * Alpha_complex/Alpha_complex_from_off.cpp</a>
  * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
+ * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
  * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
  * Persistent_cohomology/alpha_complex_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
  * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * 
+ * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
+ * Spatial_searching/example_spatial_searching.cpp</a>
+ * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
+ * Subsampling/example_choose_n_farthest_points.cpp</a>
+ * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html">
+ * Subsampling/example_custom_kernel.cpp</a>
+ * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
+ * Subsampling/example_pick_n_random_points.cpp</a>
+ * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
+ * Subsampling/example_sparsify_point_set.cpp</a>
+ * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
+ * Tangential_complex/example_basic.cpp</a>
+ * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
+ * Tangential_complex/example_with_perturb.cpp</a>
+ *
  * \subsection tbb Threading Building Blocks
  * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel&reg; TBB</a> lets you easily write parallel
  * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index db23d42b..baeeb203 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -73,10 +73,12 @@ if(CYTHON_FOUND)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
   endif (EIGEN3_FOUND)
 
+  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
     set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
-    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
@@ -157,22 +159,13 @@ if(CYTHON_FOUND)
 
   # Test examples
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-    # Bottleneck
+    # Bottleneck and Alpha
     add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
              -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
 
-    add_test(NAME bottleneck_basic_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
-
-    add_test(NAME test_bottleneck_distance_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
-
     # Tangential
     add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -190,6 +183,17 @@ if(CYTHON_FOUND)
              COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
 
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    # Bottleneck
+    add_test(NAME bottleneck_basic_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
+
+    add_test(NAME test_bottleneck_distance_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
+  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
 
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     # Alpha
-- 
cgit v1.2.3


From 8a22b7c6111b41e91766cdd53c0116b845e068b5 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 21:47:19 +0000
Subject: Fix sphinx build for python3 on Ubuntu

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2667 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c720b8be2919344e06f3d71cefdd7693439f63f0
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake |  2 +-
 src/cython/CMakeLists.txt                           |  9 +++------
 src/cython/doc/python3-sphinx-build.in              | 11 -----------
 src/cython/doc/python3-sphinx-build.py              | 11 +++++++++++
 4 files changed, 15 insertions(+), 18 deletions(-)
 delete mode 100755 src/cython/doc/python3-sphinx-build.in
 create mode 100755 src/cython/doc/python3-sphinx-build.py

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index dbf2106a..f2bbafdc 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -123,7 +123,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
     # No sphinx-build in Pyton3, just hack it
-    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+    set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build.py")
   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)
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index baeeb203..d1761f47 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -75,7 +75,7 @@ if(CYTHON_FOUND)
 
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
     set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
@@ -300,20 +300,17 @@ if(CYTHON_FOUND)
 
   # Documentation generation is available through sphinx - requires all modules
   if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-    # set sphinx-build in make files
-    configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
-
     # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
     add_custom_target(sphinx
         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
         COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-        ${SPHINX_PATH} -b html . "${CMAKE_CURRENT_BINARY_DIR}/sphinx"
+        ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc sphinx
         DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so")
 
     add_test(NAME sphinx_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc "${CMAKE_CURRENT_BINARY_DIR}/sphinx")
+             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc doctest)
 
   endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 endif(CYTHON_FOUND)
diff --git a/src/cython/doc/python3-sphinx-build.in b/src/cython/doc/python3-sphinx-build.in
deleted file mode 100755
index c97965f5..00000000
--- a/src/cython/doc/python3-sphinx-build.in
+++ /dev/null
@@ -1,11 +0,0 @@
-#!@PYTHON_EXECUTABLE@
-
-"""
-Emulate sphinx-build for python3
-"""
-
-from sys import exit, argv
-from sphinx import main
-
-if __name__ == '__main__':
-    exit(main(argv))
diff --git a/src/cython/doc/python3-sphinx-build.py b/src/cython/doc/python3-sphinx-build.py
new file mode 100755
index 00000000..44b94169
--- /dev/null
+++ b/src/cython/doc/python3-sphinx-build.py
@@ -0,0 +1,11 @@
+#!/usr/bin/python3
+
+"""
+Emulate sphinx-build for python3
+"""
+
+from sys import exit, argv
+from sphinx import main
+
+if __name__ == '__main__':
+    exit(main(argv))
-- 
cgit v1.2.3

-- 
cgit v1.2.3


From 624126c4af0a0b7d50a347968a24789ca69adbfe Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 13 Sep 2017 13:42:16 +0000
Subject: radius search => near search

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/call_it_near_search@2669 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e77c8b7de12df9cf5d0a6ef8d79e4b14a28237b3
---
 src/Spatial_searching/doc/Intro_spatial_searching.h         | 2 +-
 src/Spatial_searching/example/example_spatial_searching.cpp | 6 +++---
 src/Spatial_searching/include/gudhi/Kd_tree_search.h        | 2 +-
 src/Spatial_searching/test/test_Kd_tree_search.cpp          | 4 ++--
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/Spatial_searching/doc/Intro_spatial_searching.h b/src/Spatial_searching/doc/Intro_spatial_searching.h
index 9a3c1b65..22652ac4 100644
--- a/src/Spatial_searching/doc/Intro_spatial_searching.h
+++ b/src/Spatial_searching/doc/Intro_spatial_searching.h
@@ -46,7 +46,7 @@ namespace spatial_searching {
  * 
  * \section spatial_searching_examples Example
  * 
- * This example generates 500 random points, then performs radius search, and queries for nearest and farthest points using different methods.
+ * This example generates 500 random points, then performs near search, and queries for nearest and farthest points using different methods.
  * 
  * \include Spatial_searching/example_spatial_searching.cpp
  * 
diff --git a/src/Spatial_searching/example/example_spatial_searching.cpp b/src/Spatial_searching/example/example_spatial_searching.cpp
index 9e6a8f32..201b589e 100644
--- a/src/Spatial_searching/example/example_spatial_searching.cpp
+++ b/src/Spatial_searching/example/example_spatial_searching.cpp
@@ -48,10 +48,10 @@ int main(void) {
   for (auto ifs_iterator = ifn_range.begin(); ifs_iterator->first != 0; ++ifs_iterator)
     std::cout << ifs_iterator->first << " (sq. dist. = " << ifs_iterator->second << ")\n";
 
-  // Radius search
-  std::cout << "Radius search:\n";
+  // Near search
+  std::cout << "Near search:\n";
   std::vector<std::size_t> rs_result;
-  points_ds.radius_search(points[45], 0.5, std::back_inserter(rs_result));
+  points_ds.near_search(points[45], 0.5, std::back_inserter(rs_result));
   K k;
   for (auto const& p_idx : rs_result)
     std::cout << p_idx << " (sq. dist. = " << k.squared_distance_d_object()(points[p_idx], points[45]) << ")\n";
diff --git a/src/Spatial_searching/include/gudhi/Kd_tree_search.h b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
index f13a98f7..a4385c84 100644
--- a/src/Spatial_searching/include/gudhi/Kd_tree_search.h
+++ b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
@@ -264,7 +264,7 @@ class Kd_tree_search {
   ///                Note: `it` is used this way: `*it++ = each_point`.
   /// @param[in] eps Approximation factor.
   template <typename OutputIterator>
-  void radius_search(
+  void near_search(
     Point const& p,
     FT radius,
     OutputIterator it,
diff --git a/src/Spatial_searching/test/test_Kd_tree_search.cpp b/src/Spatial_searching/test/test_Kd_tree_search.cpp
index f79114bc..663a103a 100644
--- a/src/Spatial_searching/test/test_Kd_tree_search.cpp
+++ b/src/Spatial_searching/test/test_Kd_tree_search.cpp
@@ -110,10 +110,10 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) {
   // Same result for KFN and IFN?
   BOOST_CHECK(kfn_result == ifn_result);
 
-  // Test radius search
+  // Test near search
   Point rs_q(rd.get_double(-1., 1), rd.get_double(-1., 1), rd.get_double(-1., 1), rd.get_double(-1., 1));
   std::vector<std::size_t> rs_result;
-  points_ds.radius_search(rs_q, 0.5, std::back_inserter(rs_result));
+  points_ds.near_search(rs_q, 0.5, std::back_inserter(rs_result));
   K k;
   for (auto const& p_idx : rs_result)
     BOOST_CHECK(k.squared_distance_d_object()(points[p_idx], rs_q) <= 0.5);
-- 
cgit v1.2.3


From bc62d9afbb151279a9da1e082a53788d3fd0d242 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 18 Sep 2017 09:37:20 +0000
Subject: Add warning for developper version that sphinx is configured for user
 version Removes GudhUI ERROR mesages (just warnings

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2677 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0111272d9f6d6dc10e370360b2242eff4828611b
---
 src/GudhUI/CMakeLists.txt | 34 +++-------------------------------
 src/cython/CMakeLists.txt | 13 ++++++++++---
 2 files changed, 13 insertions(+), 34 deletions(-)

diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index 57861946..374195d0 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -5,28 +5,6 @@ find_package(Qt5 COMPONENTS Widgets Xml OpenGL)
 find_package(QGLViewer)
 find_package(OpenGL)
 
-if (CGAL_VERSION VERSION_EQUAL 4.8.0)
-  message(ERROR " GudhUI does not compile with CGAL 4.8.0. 4.8.1, 4.8.2 and 4.9 are OK.")
-endif()
-
-if (NOT CGAL_FOUND)
-  message(ERROR " GudhUI requires CGAL and will not be compiled.")
-endif()
-
-if (NOT Qt5_FOUND)
-  message(ERROR " GudhUI requires Qt5 and will not be compiled.")
-endif()
-
-if (NOT OPENGL_FOUND)
-  message(ERROR " GudhUI requires OpenGL and will not be compiled.")
-endif()
-
-if (NOT QGLVIEWER_FOUND)
-  message(ERROR " GudhUI requires QGLViewer and will not be compiled.")
-endif()
-
-
-
 if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_VERSION VERSION_EQUAL 4.8.0)
 
   set(CMAKE_AUTOMOC ON)
@@ -37,8 +15,6 @@ if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_
   SET(Boost_USE_MULTITHREAD OFF)
   include_directories (${QGLVIEWER_INCLUDE_DIR})
  
-  #####################################################################
-
   add_executable  ( GudhUI 
     gui/gudhui.cpp
     gui/MainWindow.cpp
@@ -52,14 +28,10 @@ if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_
   target_link_libraries( GudhUI Qt5::Widgets Qt5::Xml Qt5::OpenGL )
   target_link_libraries( GudhUI ${QGLVIEWER_LIBRARIES} )
   target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )	
-if (TBB_FOUND)
-  target_link_libraries( GudhUI ${TBB_LIBRARIES})
-endif()
+  if (TBB_FOUND)
+    target_link_libraries( GudhUI ${TBB_LIBRARIES})
+  endif()
 
   install(TARGETS GudhUI DESTINATION bin)
 
-###############################################################################
-
-else()
-  message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt5, and will not be compiled.")
 endif()
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index d1761f47..ed0aace1 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -300,17 +300,24 @@ if(CYTHON_FOUND)
 
   # Documentation generation is available through sphinx - requires all modules
   if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+    set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
+    # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
+    # Images and biblio warnings because not found on developper version
+    if (GUDHI_CYTHON_PATH STREQUAL "src/cython")
+      set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
+    endif()
     # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
     add_custom_target(sphinx
         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
         COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-        ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc sphinx
-        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so")
+        ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
+        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+        COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
 
     add_test(NAME sphinx_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc doctest)
+             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
 
   endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 endif(CYTHON_FOUND)
-- 
cgit v1.2.3


From 7f7aac2010f5cda05dfd1057827d8deaea186cf5 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 18 Sep 2017 12:58:10 +0000
Subject: Add a function to launch py.test as required for no cache files in
 sources

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2678 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 92ca1aabcbe276198fa29ea75f763fb0aa3c504f
---
 src/cython/CMakeLists.txt | 50 +++++++++++++++++++----------------------------
 1 file changed, 20 insertions(+), 30 deletions(-)

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index ed0aace1..ec8589f0 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -15,6 +15,16 @@ function( add_gudhi_cython_lib THE_LIB )
   endif(EXISTS ${THE_LIB})
 endfunction( add_gudhi_cython_lib )
 
+# THE_TEST is the python test file name (without .py extension) containing tests functions
+function( add_gudhi_py_test THE_TEST )
+  # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python
+  # use py.test no cache provider, otherwise a .cache file is created in sources by py.test
+  add_test(NAME ${THE_TEST}_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py)
+endfunction( add_gudhi_py_test )
+
+
 if(CYTHON_FOUND)
   message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - Sphinx is ${SPHINX_PATH}")
 
@@ -173,14 +183,10 @@ if(CYTHON_FOUND)
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
 
-    add_test(NAME test_tangential_complex_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py)
+    add_gudhi_py_test(test_tangential_complex)
 
     # Subsampling
-    add_test(NAME test_subsampling_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
+    add_gudhi_py_test(test_subsampling)
 
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
@@ -190,9 +196,7 @@ if(CYTHON_FOUND)
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
 
-    add_test(NAME test_bottleneck_distance_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
+    add_gudhi_py_test(test_bottleneck_distance)
   endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
 
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
@@ -208,9 +212,7 @@ if(CYTHON_FOUND)
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
 
-    add_test(NAME test_alpha_complex_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py)
+    add_gudhi_py_test(test_alpha_complex)
 
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 
@@ -228,9 +230,7 @@ if(CYTHON_FOUND)
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
 
-    add_test(NAME test_euclidean_witness_complex_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py)
+    add_gudhi_py_test(test_euclidean_witness_complex)
 
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
 
@@ -247,9 +247,7 @@ if(CYTHON_FOUND)
            ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
            10 10 10)
 
-  add_test(NAME test_cubical_complex_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_cubical_complex.py)
+  add_gudhi_py_test(test_cubical_complex)
 
   # Rips
   add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
@@ -269,9 +267,7 @@ if(CYTHON_FOUND)
            COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
            ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
 
-  add_test(NAME test_rips_complex_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_rips_complex.py)
+  add_gudhi_py_test(test_rips_complex)
 
   # Simplex tree
   add_test(NAME simplex_tree_example_py_test
@@ -279,9 +275,7 @@ if(CYTHON_FOUND)
            COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
            ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
 
-  add_test(NAME test_simplex_tree_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_simplex_tree.py)
+  add_gudhi_py_test(test_simplex_tree)
 
   # Witness
   add_test(NAME witness_complex_from_nearest_landmark_table_py_test
@@ -289,14 +283,10 @@ if(CYTHON_FOUND)
            COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
            ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
 
-  add_test(NAME test_witness_complex_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_witness_complex.py)
+  add_gudhi_py_test(test_witness_complex)
 
   # Reader utils
-  add_test(NAME test_reader_utils_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py)
+  add_gudhi_py_test(test_reader_utils)
 
   # Documentation generation is available through sphinx - requires all modules
   if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-- 
cgit v1.2.3

-- 
cgit v1.2.3


From 18c1daaba21430c54647f4823eec9c7ed52c2878 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 19 Sep 2017 12:09:27 +0000
Subject: Fix memory leak

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_memory_leak_fix@2686 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a8fd65accb5be293e9d3f5fe411225745cb76b0b
---
 src/cython/include/Rips_complex_interface.h | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
index d06ee4bd..02985727 100644
--- a/src/cython/include/Rips_complex_interface.h
+++ b/src/cython/include/Rips_complex_interface.h
@@ -71,6 +71,10 @@ class Rips_complex_interface {
     }
   }
 
+  ~Rips_complex_interface() {
+    delete rips_complex_;
+  }
+
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) {
     rips_complex_->create_complex(*simplex_tree, dim_max);
     simplex_tree->initialize_filtration();
-- 
cgit v1.2.3

-- 
cgit v1.2.3


From 3534c24fd805f8cf0ed8f1d5faea183513966b9f Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 22 Sep 2017 06:59:33 +0000
Subject: Remove global filtration attribute of te simplex tree (including
 getter and setter)

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2705 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a6c179ae47e61d1ca12d1f54c4ae1fc0e3c1fde2
---
 src/Hasse_complex/include/gudhi/Hasse_complex.h    | 10 +---------
 .../example/alpha_complex_3d_persistence.cpp       |  2 --
 .../example/exact_alpha_complex_3d_persistence.cpp |  2 --
 .../periodic_alpha_complex_3d_persistence.cpp      |  2 --
 .../example/persistence_from_file.cpp              |  3 +--
 .../persistence_from_simple_simplex_tree.cpp       |  3 +--
 .../weighted_alpha_complex_3d_persistence.cpp      |  2 --
 .../test/persistent_cohomology_unit_test.cpp       |  3 +--
 ...persistent_cohomology_unit_test_multi_field.cpp |  3 +--
 src/Simplex_tree/example/simple_simplex_tree.cpp   |  3 +--
 src/Simplex_tree/include/gudhi/Simplex_tree.h      | 22 ----------------------
 src/Simplex_tree/test/simplex_tree_unit_test.cpp   | 22 ++++------------------
 src/cython/cython/simplex_tree.pyx                 | 10 ----------
 src/cython/example/simplex_tree_example.py         |  1 -
 src/cython/test/test_simplex_tree.py               |  1 -
 15 files changed, 10 insertions(+), 79 deletions(-)

diff --git a/src/Hasse_complex/include/gudhi/Hasse_complex.h b/src/Hasse_complex/include/gudhi/Hasse_complex.h
index 8b06b771..834201a5 100644
--- a/src/Hasse_complex/include/gudhi/Hasse_complex.h
+++ b/src/Hasse_complex/include/gudhi/Hasse_complex.h
@@ -104,7 +104,6 @@ class Hasse_complex {
   Hasse_complex(Complex_ds & cpx)
       : complex_(cpx.num_simplices())
       , vertices_()
-      , threshold_(cpx.filtration())
       , num_vertices_()
       , dim_max_(cpx.dimension()) {
     int size = complex_.size();
@@ -125,7 +124,6 @@ class Hasse_complex {
   Hasse_complex()
       : complex_()
       , vertices_()
-      , threshold_(0)
       , num_vertices_(0)
       , dim_max_(-1) { }
 
@@ -157,15 +155,11 @@ class Hasse_complex {
 
   Filtration_value filtration(Simplex_handle sh) {
     if (sh == null_simplex()) {
-      return filtration();
+      return INFINITY;
     }
     return complex_[sh].filtration_;
   }
 
-  Filtration_value filtration() {
-    return threshold_;
-  }
-
   int dimension(Simplex_handle sh) {
     if (complex_[sh].boundary_.empty()) return 0;
     return complex_[sh].boundary_.size() - 1;
@@ -206,7 +200,6 @@ class Hasse_complex {
 
   std::vector< Hasse_simp, Gudhi::no_init_allocator<Hasse_simp> > complex_;
   std::vector<Simplex_handle> vertices_;
-  Filtration_value threshold_;
   size_t num_vertices_;
   int dim_max_;
 };
@@ -245,7 +238,6 @@ std::istream& operator>>(std::istream & is
   }
 
   hcpx.dim_max_ = max_dim;
-  hcpx.threshold_ = max_fil;
 
   return is;
 }
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index fd227b82..53e50a69 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -202,7 +202,6 @@ int main(int argc, char * const argv[]) {
     else
       std::cout << "This shall not happen" << std::endl;
   }
-  simplex_tree.set_filtration(filtration_max);
   simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
@@ -216,7 +215,6 @@ int main(int argc, char * const argv[]) {
   std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
   std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
   std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
-  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
 #endif  // DEBUG_TRACES
 
 #ifdef DEBUG_TRACES
diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
index 8a335075..acb34bcb 100644
--- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
@@ -204,7 +204,6 @@ int main(int argc, char * const argv[]) {
     else
       std::cout << "This shall not happen" << std::endl;
   }
-  simplex_tree.set_filtration(filtration_max);
   simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
@@ -218,7 +217,6 @@ int main(int argc, char * const argv[]) {
   std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
   std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
   std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
-  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
 #endif  // DEBUG_TRACES
 
 #ifdef DEBUG_TRACES
diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
index 8928cfc2..f731d349 100644
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -221,7 +221,6 @@ int main(int argc, char * const argv[]) {
     else
       std::cout << "This shall not happen" << std::endl;
   }
-  simplex_tree.set_filtration(filtration_max);
   simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
@@ -235,7 +234,6 @@ int main(int argc, char * const argv[]) {
   std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
   std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
   std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
-  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
 #endif  // DEBUG_TRACES
 
 #ifdef DEBUG_TRACES
diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp
index 67235467..eafa3fd5 100644
--- a/src/Persistent_cohomology/example/persistence_from_file.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_file.cpp
@@ -61,8 +61,7 @@ int main(int argc, char * argv[]) {
   simplex_tree_stream >> simplex_tree;
 
   std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl;
-  std::cout << "   - dimension " << simplex_tree.dimension() << "   - filtration " << simplex_tree.filtration()
-      << std::endl;
+  std::cout << "   - dimension " << simplex_tree.dimension() << std::endl;
 
   /*
   std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
index 7ca9410a..8214d66a 100644
--- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
@@ -143,11 +143,10 @@ int main(int argc, char * const argv[]) {
   /*   An edge [10,12,2]      */
 
   st.set_dimension(2);
-  st.set_filtration(0.4);
 
   std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices "
       << std::endl;
-  std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
+  std::cout << "   - dimension " << st.dimension() << std::endl;
   std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:"
       << std::endl;
   std::cout << "**************************************************************" << std::endl;
diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
index 34b90933..9728f22d 100644
--- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
@@ -222,7 +222,6 @@ int main(int argc, char * const argv[]) {
     else
       std::cout << "This shall not happen" << std::endl;
   }
-  simplex_tree.set_filtration(filtration_max);
   simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
@@ -236,7 +235,6 @@ int main(int argc, char * const argv[]) {
   std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
   std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
   std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
-  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
 #endif  // DEBUG_TRACES
 
 #ifdef DEBUG_TRACES
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
index f8174020..f53987b6 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
@@ -31,12 +31,11 @@ std::string test_rips_persistence(int coefficient, int min_persistence) {
 
   // Display the Simplex_tree
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension()
-      << " - filtration= " << st.filtration() << std::endl;
+      << std::endl;
 
   // Check
   BOOST_CHECK(st.num_simplices() == 98);
   BOOST_CHECK(st.dimension() == 3);
-  BOOST_CHECK(st.filtration() == 1.89);
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();
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 3537cfa4..9e767943 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
@@ -31,12 +31,11 @@ std::string test_rips_persistence(int min_coefficient, int max_coefficient, doub
 
   // Display the Simplex_tree
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension()
-      << " - filtration= " << st.filtration() << std::endl;
+      << std::endl;
 
   // Check
   BOOST_CHECK(st.num_simplices() == 58);
   BOOST_CHECK(st.dimension() == 3);
-  BOOST_CHECK(st.filtration() == 0.4);
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();
diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp
index 60f9a35e..d8318f03 100644
--- a/src/Simplex_tree/example/simple_simplex_tree.cpp
+++ b/src/Simplex_tree/example/simple_simplex_tree.cpp
@@ -185,13 +185,12 @@ int main(int argc, char * const argv[]) {
   }
 
   // ++ GENERAL VARIABLE SET
-  simplexTree.set_filtration(FOURTH_FILTRATION_VALUE);  // Max filtration value
   simplexTree.set_dimension(2);  // Max dimension = 2 -> (2,1,0)
 
   std::cout << "********************************************************************\n";
   // Display the Simplex_tree - Can not be done in the middle of 2 inserts
   std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices\n";
-  std::cout << "   - dimension " << simplexTree.dimension() << "   - filtration " << simplexTree.filtration() << "\n";
+  std::cout << "   - dimension " << simplexTree.dimension() << "\n";
   std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n";
   for (auto f_simplex : simplexTree.filtration_simplex_range()) {
     std::cout << "   " << "[" << simplexTree.filtration(f_simplex) << "] ";
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 317bce23..8c91cc67 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -289,7 +289,6 @@ class Simplex_tree {
   /** \brief Constructs an empty simplex tree. */
   Simplex_tree()
       : null_vertex_(-1),
-      threshold_(0),
       root_(nullptr, null_vertex_),
       filtration_vect_(),
       dimension_(-1) { }
@@ -297,7 +296,6 @@ class Simplex_tree {
   /** \brief User-defined copy constructor reproduces the whole tree structure. */
   Simplex_tree(const Simplex_tree& simplex_source)
       : null_vertex_(simplex_source.null_vertex_),
-      threshold_(simplex_source.threshold_),
       root_(nullptr, null_vertex_ , simplex_source.root_.members_),
       filtration_vect_(),
       dimension_(simplex_source.dimension_) {
@@ -323,12 +321,10 @@ class Simplex_tree {
   /** \brief User-defined move constructor moves the whole tree structure. */
   Simplex_tree(Simplex_tree && old)
       : null_vertex_(std::move(old.null_vertex_)),
-      threshold_(std::move(old.threshold_)),
       root_(std::move(old.root_)),
       filtration_vect_(std::move(old.filtration_vect_)),
       dimension_(std::move(old.dimension_)) {
     old.dimension_ = -1;
-    old.threshold_ = 0;
     old.root_ = Siblings(nullptr, null_vertex_);
   }
 
@@ -356,7 +352,6 @@ class Simplex_tree {
   /** \brief Checks if two simplex trees are equal. */
   bool operator==(Simplex_tree& st2) {
     if ((null_vertex_ != st2.null_vertex_) ||
-        (threshold_ != st2.threshold_) ||
         (dimension_ != st2.dimension_))
       return false;
     return rec_equal(&root_, &st2.root_);
@@ -427,11 +422,6 @@ class Simplex_tree {
     sh->second.assign_filtration(fv);
   }
 
-  /** \brief Returns an upper bound of the filtration values of the simplices. */
-  Filtration_value filtration() const {
-    return threshold_;
-  }
-
   /** \brief Returns a Simplex_handle different from all Simplex_handles
    * associated to the simplices in the simplicial complex.
    *
@@ -757,11 +747,6 @@ class Simplex_tree {
     return &root_;
   }
 
-  /** Set an upper bound for the filtration values. */
-  void set_filtration(Filtration_value fil) {
-    threshold_ = fil;
-  }
-
   /** Set a dimension for the simplicial complex. */
   void set_dimension(int dimension) {
     dimension_ = dimension;
@@ -1215,8 +1200,6 @@ class Simplex_tree {
 
  private:
   Vertex_handle null_vertex_;
-  /** \brief Upper bound on the filtration values of the simplices.*/
-  Filtration_value threshold_;
   /** \brief Total number of simplices in the complex, without the empty simplex.*/
   /** \brief Set of simplex tree Nodes representing the vertices.*/
   Siblings root_;
@@ -1244,7 +1227,6 @@ std::istream& operator>>(std::istream & is, Simplex_tree<T...> & st) {
   typedef Simplex_tree<T...> ST;
   std::vector<typename ST::Vertex_handle> simplex;
   typename ST::Filtration_value fil;
-  typename ST::Filtration_value max_fil = 0;
   int max_dim = -1;
   while (read_simplex(is, simplex, fil)) {
     // read all simplices in the file as a list of vertices
@@ -1253,15 +1235,11 @@ std::istream& operator>>(std::istream & is, Simplex_tree<T...> & st) {
     if (max_dim < dim) {
       max_dim = dim;
     }
-    if (max_fil < fil) {
-      max_fil = fil;
-    }
     // insert every simplex in the simplex tree
     st.insert_simplex(simplex, fil);
     simplex.clear();
   }
   st.set_dimension(max_dim);
-  st.set_filtration(max_fil);
 
   return is;
 }
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index b06d7ec9..17ddc605 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -26,7 +26,6 @@ void test_empty_simplex_tree(typeST& tst) {
   typedef typename typeST::Vertex_handle Vertex_handle;
   const Vertex_handle DEFAULT_VERTEX_VALUE = Vertex_handle(- 1);
   BOOST_CHECK(tst.null_vertex() == DEFAULT_VERTEX_VALUE);
-  BOOST_CHECK(tst.filtration() == 0.0);
   BOOST_CHECK(tst.num_vertices() == (size_t) 0);
   BOOST_CHECK(tst.num_simplices() == (size_t) 0);
   typename typeST::Siblings* STRoot = tst.root();
@@ -98,12 +97,11 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_from_file, typeST, list_of_tested_var
 
   // Display the Simplex_tree
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
-  std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
+  std::cout << "   - dimension " << st.dimension() << std::endl;
 
   // Check
   BOOST_CHECK(st.num_simplices() == 143353);
   BOOST_CHECK(st.dimension() == 3);
-  BOOST_CHECK(AreAlmostTheSame(st.filtration(), 0.4));
 
   int previous_size = 0;
   for (auto f_simplex : st.filtration_simplex_range()) {
@@ -147,7 +145,6 @@ void test_simplex_tree_insert_returns_true(const typePairSimplexBool& returnValu
 }
 
 // Global variables
-double max_fil = 0.0;
 int dim_max = -1;
 
 template<class typeST, class Filtration_value>
@@ -158,15 +155,8 @@ void set_and_test_simplex_tree_dim_fil(typeST& simplexTree, int vectorSize, cons
     std::cout << "   set_and_test_simplex_tree_dim_fil - dim_max=" << dim_max
         << std::endl;
   }
-  if (fil > max_fil) {
-    max_fil = fil;
-    simplexTree.set_filtration(max_fil);
-    std::cout << "   set_and_test_simplex_tree_dim_fil - max_fil=" << max_fil
-        << std::endl;
-  }
 
   BOOST_CHECK(simplexTree.dimension() == dim_max);
-  BOOST_CHECK(AreAlmostTheSame(simplexTree.filtration(), max_fil));
 
   // Another way to count simplices:
   size_t num_simp = 0;
@@ -190,7 +180,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var
   const Filtration_value FOURTH_FILTRATION_VALUE = 0.4;
   // reset since we run the test several times
   dim_max = -1;
-  max_fil = 0.0;
 
   // TEST OF INSERTION
   std::cout << "********************************************************************" << std::endl;
@@ -310,7 +299,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var
   BOOST_CHECK(shReturned == typename typeST::Simplex_handle(nullptr));
   BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !!
   BOOST_CHECK(st.dimension() == dim_max);
-  BOOST_CHECK(AreAlmostTheSame(st.filtration(), max_fil));
 
   // ++ ELEVENTH
   std::cout << "   - INSERT (2,1,0) (already inserted)" << std::endl;
@@ -325,7 +313,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var
   BOOST_CHECK(shReturned == typename typeST::Simplex_handle(nullptr));
   BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !!
   BOOST_CHECK(st.dimension() == dim_max);
-  BOOST_CHECK(AreAlmostTheSame(st.filtration(), max_fil));
 
   /* Inserted simplex:        */
   /*    1                     */
@@ -365,7 +352,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var
 
   // Display the Simplex_tree - Can not be done in the middle of 2 inserts
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
-  std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
+  std::cout << "   - dimension " << st.dimension() << std::endl;
   std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
   for (auto f_simplex : st.filtration_simplex_range()) {
     std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
@@ -575,7 +562,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(NSimplexAndSubfaces_tree_insertion, typeST, list_o
 
   // Display the Simplex_tree - Can not be done in the middle of 2 inserts
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
-  std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
+  std::cout << "   - dimension " << st.dimension() << std::endl;
   std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
   for (auto f_simplex : st.filtration_simplex_range()) {
     std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
@@ -756,7 +743,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(copy_move_on_simplex_tree, typeST, list_of_tested_
   typeST st_empty;
   // Check st has been emptied by the move
   BOOST_CHECK(st == st_empty);
-  BOOST_CHECK(st.filtration() == 0);
   BOOST_CHECK(st.dimension() == -1);
   BOOST_CHECK(st.num_simplices() == 0);
   BOOST_CHECK(st.num_vertices() == (size_t)0);
@@ -1149,4 +1135,4 @@ BOOST_AUTO_TEST_CASE(mini_prune_above_filtration) {
   // Display the Simplex_tree
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
 
-}
\ No newline at end of file
+}
diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 47aa5311..45487158 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -36,9 +36,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
 
     cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>":
         Simplex_tree()
-        double filtration()
         double simplex_filtration(vector[int] simplex)
-        void set_filtration(double filtration)
         void initialize_filtration()
         int num_vertices()
         int num_simplices()
@@ -115,14 +113,6 @@ cdef class SimplexTree:
         """
         return self.thisptr.simplex_filtration(simplex)
 
-    def set_filtration(self, filtration):
-        """This function sets the main simplicial complex filtration value.
-
-        :param filtration: The filtration value.
-        :type filtration: float.
-        """
-        self.thisptr.set_filtration(<double> filtration)
-
     def initialize_filtration(self):
         """This function initializes and sorts the simplicial complex
         filtration vector.
diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py
index 3af20fcf..831d9da8 100755
--- a/src/cython/example/simplex_tree_example.py
+++ b/src/cython/example/simplex_tree_example.py
@@ -52,7 +52,6 @@ else:
 st.set_dimension(3)
 print("dimension=", st.dimension())
 
-st.set_filtration(4.0)
 st.initialize_filtration()
 print("filtration=", st.get_filtration())
 print("filtration[1, 2]=", st.filtration([1, 2]))
diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py
index 3ae537e3..4d452d7d 100755
--- a/src/cython/test/test_simplex_tree.py
+++ b/src/cython/test/test_simplex_tree.py
@@ -53,7 +53,6 @@ def test_insertion():
     assert st.find([2, 3]) == False
 
     # filtration test
-    st.set_filtration(5.0)
     st.initialize_filtration()
     assert st.filtration([0, 1, 2]) == 4.0
     assert st.filtration([0, 2]) == 4.0
-- 
cgit v1.2.3

-- 
cgit v1.2.3


From d965a53c39266dd37cd9058837b80469347fc5d3 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 25 Sep 2017 08:47:06 +0000
Subject: Fix weighted alpha complex 3d

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/weighted_alpha_complex_fix@2709 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 3e7d1f73038d193b566e790a3095b6f802c48b48
---
 .../example/weighted_alpha_complex_3d_persistence.cpp                  | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
index 34b90933..ce45d16d 100644
--- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
@@ -115,6 +115,7 @@ int main(int argc, char * const argv[]) {
   if (weights_ifstr.good()) {
     double weight = 0.0;
     std::size_t index = 0;
+    wp.reserve(lp.size());
     // Attempt read the weight in a double format, return false if it fails
     while ((weights_ifstr >> weight) && (index < lp.size())) {
       wp.push_back(Weighted_point_3(lp[index], weight));
@@ -130,7 +131,7 @@ int main(int argc, char * const argv[]) {
   }
 
   // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
-  Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL);
+  Alpha_shape_3 as(wp.begin(), wp.end(), 0, Alpha_shape_3::GENERAL);
 #ifdef DEBUG_TRACES
   std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
 #endif  // DEBUG_TRACES
-- 
cgit v1.2.3


From 6965bcc31dfc44ba82524637b4184f8dfdd86e9c Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 25 Sep 2017 15:44:28 +0000
Subject: Do not advertise nor use the exact bottleneck distance version

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2711 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e441b042d15bfbe727789803ca17b17711a48d9c
---
 .../example/bottleneck_read_file_example.cpp                 | 12 ++++++------
 src/cython/doc/bottleneck_distance_user.rst                  |  4 ++--
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 1408681a..24d73c57 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -25,21 +25,21 @@
 #include <iostream>
 #include <vector>
 #include <utility>  // for pair
-#include <fstream>
-#include <sstream>
 #include <string>
+#include <limits>  // for numeric_limits
 
 int main(int argc, char** argv) {
   if (argc < 3) {
-    std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
-        "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
-        " distance (set by default to zero). The program will now terminate \n";
+    std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file" <<
+        " should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
+        " distance (set by default to the smallest positive double value). If you set the error bound to 0, be" <<
+        " aware this version is exact but expensive. The program will now terminate \n";
     return -1;
   }
   std::vector<std::pair<double, double>> diag1 = Gudhi::read_persistence_intervals_in_dimension(argv[1]);
   std::vector<std::pair<double, double>> diag2 = Gudhi::read_persistence_intervals_in_dimension(argv[2]);
 
-  double tolerance = 0.;
+  double tolerance = std::numeric_limits<double>::min();
   if (argc == 4) {
     tolerance = atof(argv[3]);
   }
diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst
index 0066992f..7692dce2 100644
--- a/src/cython/doc/bottleneck_distance_user.rst
+++ b/src/cython/doc/bottleneck_distance_user.rst
@@ -25,7 +25,7 @@ This example computes the bottleneck distance from 2 persistence diagrams:
     message = "Bottleneck distance approximation=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0.1)
     print(message)
 
-    message = "Bottleneck distance exact value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0)
+    message = "Bottleneck distance value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2)
     print(message)
 
 The output is:
@@ -33,4 +33,4 @@ The output is:
 .. testoutput::
 
     Bottleneck distance approximation=0.81
-    Bottleneck distance exact value=0.75
+    Bottleneck distance value=0.75
-- 
cgit v1.2.3


From 822765550b4f944bef11e6fe7de56fb72fb00640 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 26 Sep 2017 08:27:39 +0000
Subject: Gudhi 2.0.1-rc2 version

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2715 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 76499766ca670017df0c963c3b5a49c343eb1a47
---
 CMakeGUDHIVersion.txt | 2 +-
 src/Doxyfile          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index d5620218..87daf28e 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 2)
 set (GUDHI_MINOR_VERSION 0)
-set (GUDHI_PATCH_VERSION 1-rc1)
+set (GUDHI_PATCH_VERSION 1-rc2)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/Doxyfile b/src/Doxyfile
index 6c01aefc..7f5975eb 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME           = "GUDHI"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "2.0.1-rc1"
+PROJECT_NUMBER         = "2.0.1-rc2"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
-- 
cgit v1.2.3


From 914398be0187ab7d21ef1100533ed7a3c7983c76 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 27 Sep 2017 20:10:05 +0000
Subject: Replace INFINITY with
 std::numeric_limits<Filtration_value>::infinity()

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2719 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b24d3381da60cd634142e3024d5f5ed53294f8e8
---
 src/Hasse_complex/include/gudhi/Hasse_complex.h | 3 ++-
 src/Simplex_tree/include/gudhi/Simplex_tree.h   | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/Hasse_complex/include/gudhi/Hasse_complex.h b/src/Hasse_complex/include/gudhi/Hasse_complex.h
index 834201a5..e67f7609 100644
--- a/src/Hasse_complex/include/gudhi/Hasse_complex.h
+++ b/src/Hasse_complex/include/gudhi/Hasse_complex.h
@@ -30,6 +30,7 @@
 #include <algorithm>
 #include <utility>  // for pair
 #include <vector>
+#include <limits>  // for infinity value
 
 #ifdef GUDHI_USE_TBB
 #include <tbb/parallel_for.h>
@@ -155,7 +156,7 @@ class Hasse_complex {
 
   Filtration_value filtration(Simplex_handle sh) {
     if (sh == null_simplex()) {
-      return INFINITY;
+      return std::numeric_limits<Filtration_value>::infinity();
     }
     return complex_[sh].filtration_;
   }
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 8c91cc67..37b3ea97 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -402,14 +402,14 @@ class Simplex_tree {
 
   /** \brief Returns the filtration value of a simplex.
    *
-   * Called on the null_simplex, returns INFINITY.
+   * Called on the null_simplex, it returns infinity.
    * If SimplexTreeOptions::store_filtration is false, returns 0.
    */
   static Filtration_value filtration(Simplex_handle sh) {
     if (sh != null_simplex()) {
       return sh->second.filtration();
     } else {
-      return INFINITY;
+      return std::numeric_limits<Filtration_value>::infinity();
     }
   }
 
-- 
cgit v1.2.3


From 526625e6faa7b01430b481d5c21d7d7dfe16e290 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 27 Sep 2017 20:25:21 +0000
Subject: Fix some cpplints

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2721 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 76b127e54d9511b70294ab48336ca6dbd6fdb1d6
---
 ...Bitmap_cubical_complex_periodic_boundary_conditions.cpp |  1 +
 src/Bottleneck_distance/include/gudhi/Neighbors_finder.h   |  8 ++++----
 src/Spatial_searching/include/gudhi/Kd_tree_search.h       | 14 ++++++--------
 src/common/utilities/off_file_from_shape_generator.cpp     |  2 +-
 src/cython/include/Reader_utils_interface.h                |  2 ++
 5 files changed, 14 insertions(+), 13 deletions(-)

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 f8754345..122160a2 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
@@ -30,6 +30,7 @@
 #include <iostream>
 #include <sstream>
 #include <vector>
+#include <string>
 
 int main(int argc, char** argv) {
   std::cout << "This program computes persistent homology, by using " <<
diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
index bdc47578..a6b9b021 100644
--- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
+++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
@@ -44,16 +44,16 @@ struct Square_query {
   typedef Internal_point Point_d;
   typedef double FT;
   bool contains(Point_d p) const {
-    return std::abs(p.x()-c.x())<=size && std::abs(p.y()-c.y())<=size;
+    return std::abs(p.x()-c.x()) <= size && std::abs(p.y()-c.y()) <= size;
   }
-  bool inner_range_intersects(CGAL::Kd_tree_rectangle<FT,D> const&r) const {
+  bool inner_range_intersects(CGAL::Kd_tree_rectangle<FT, D> const&r) const {
     return
       r.max_coord(0) >= c.x() - size &&
       r.min_coord(0) <= c.x() + size &&
       r.max_coord(1) >= c.y() - size &&
       r.min_coord(1) <= c.y() + size;
   }
-  bool outer_range_contains(CGAL::Kd_tree_rectangle<FT,D> const&r) const {
+  bool outer_range_contains(CGAL::Kd_tree_rectangle<FT, D> const&r) const {
     return
       r.min_coord(0) >= c.x() - size &&
       r.max_coord(0) <= c.x() + size &&
@@ -146,7 +146,7 @@ inline int Neighbors_finder::pull_near(int u_point_index) {
     // Is the query point near to a V point in the plane ?
     Internal_point u_point = g.get_u_point(u_point_index);
     auto neighbor = kd_t.search_any_point(Square_query{u_point, r});
-    if(!neighbor)
+    if (!neighbor)
       return null_point_index();
     tmp = neighbor->point_index;
     auto point = g.get_v_point(tmp);
diff --git a/src/Spatial_searching/include/gudhi/Kd_tree_search.h b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
index a4385c84..af04736b 100644
--- a/src/Spatial_searching/include/gudhi/Kd_tree_search.h
+++ b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
@@ -193,7 +193,7 @@ class Kd_tree_search {
   /// \brief Search incrementally for the nearest neighbors from a query point.
   /// @param[in] p The query point.
   /// @param[in] eps Approximation factor.
-  /// @return A range (whose `value_type` is `std::size_t`) containing the 
+  /// @return A range (whose `value_type` is `std::size_t`) containing the
   /// neighbors sorted by their distance to p.
   /// All the neighbors are not computed by this function, but they will be
   /// computed incrementally when the iterator on the range is incremented.
@@ -239,7 +239,7 @@ class Kd_tree_search {
   /// \brief Search incrementally for the farthest neighbors from a query point.
   /// @param[in] p The query point.
   /// @param[in] eps Approximation factor.
-  /// @return A range (whose `value_type` is `std::size_t`) 
+  /// @return A range (whose `value_type` is `std::size_t`)
   /// containing the neighbors sorted by their distance to p.
   /// All the neighbors are not computed by this function, but they will be
   /// computed incrementally when the iterator on the range is incremented.
@@ -264,12 +264,10 @@ class Kd_tree_search {
   ///                Note: `it` is used this way: `*it++ = each_point`.
   /// @param[in] eps Approximation factor.
   template <typename OutputIterator>
-  void near_search(
-    Point const& p,
-    FT radius,
-    OutputIterator it,
-    FT eps = FT(0)) const {
-    
+  void near_search(Point const& p,
+                   FT radius,
+                   OutputIterator it,
+                   FT eps = FT(0)) const {
     m_tree.search(it, Fuzzy_sphere(p, radius, eps, m_tree.traits()));
   }
 
diff --git a/src/common/utilities/off_file_from_shape_generator.cpp b/src/common/utilities/off_file_from_shape_generator.cpp
index 0f310a13..afcd558c 100644
--- a/src/common/utilities/off_file_from_shape_generator.cpp
+++ b/src/common/utilities/off_file_from_shape_generator.cpp
@@ -77,7 +77,7 @@ int main(int argc, char **argv) {
       usage(argv[0]);
   }
 
-  enum class Data_shape { sphere, cube, curve, torus, klein, undefined } ;
+  enum class Data_shape { sphere, cube, curve, torus, klein, undefined};
 
   Data_shape shape = Data_shape::undefined;
   if (memcmp(argv[2], "sphere", sizeof("sphere")) == 0) {
diff --git a/src/cython/include/Reader_utils_interface.h b/src/cython/include/Reader_utils_interface.h
index b87b6cca..8ec34f61 100644
--- a/src/cython/include/Reader_utils_interface.h
+++ b/src/cython/include/Reader_utils_interface.h
@@ -28,6 +28,8 @@
 #include <iostream>
 #include <vector>
 #include <string>
+#include <map>
+#include <utility>  // for pair<>
 
 namespace Gudhi {
 
-- 
cgit v1.2.3


From 768c70aa382a7b0b561ea842720f5963a412b88e Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 29 Sep 2017 08:40:52 +0000
Subject: Rename a few functions in Kd_tree_search

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2730 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: f009977d25c76cc0f6116093a448fab258c8626b
---
 .../doc/Intro_spatial_searching.h                  |  2 +-
 .../example/example_spatial_searching.cpp          | 22 +++++++-------
 .../include/gudhi/Kd_tree_search.h                 | 34 +++++++++++-----------
 src/Spatial_searching/test/test_Kd_tree_search.cpp | 24 +++++++--------
 src/Subsampling/include/gudhi/sparsify_point_set.h |  2 +-
 .../include/gudhi/Tangential_complex.h             | 16 +++++-----
 .../gudhi/Euclidean_strong_witness_complex.h       |  2 +-
 .../include/gudhi/Euclidean_witness_complex.h      |  2 +-
 .../test/test_euclidean_simple_witness_complex.cpp |  2 +-
 9 files changed, 52 insertions(+), 54 deletions(-)

diff --git a/src/Spatial_searching/doc/Intro_spatial_searching.h b/src/Spatial_searching/doc/Intro_spatial_searching.h
index 22652ac4..1ee5e92e 100644
--- a/src/Spatial_searching/doc/Intro_spatial_searching.h
+++ b/src/Spatial_searching/doc/Intro_spatial_searching.h
@@ -46,7 +46,7 @@ namespace spatial_searching {
  * 
  * \section spatial_searching_examples Example
  * 
- * This example generates 500 random points, then performs near search, and queries for nearest and farthest points using different methods.
+ * This example generates 500 random points, then performs all-near-neighbors searches, and queries for nearest and furthest neighbors using different methods.
  * 
  * \include Spatial_searching/example_spatial_searching.cpp
  * 
diff --git a/src/Spatial_searching/example/example_spatial_searching.cpp b/src/Spatial_searching/example/example_spatial_searching.cpp
index 201b589e..034ad24a 100644
--- a/src/Spatial_searching/example/example_spatial_searching.cpp
+++ b/src/Spatial_searching/example/example_spatial_searching.cpp
@@ -24,34 +24,34 @@ int main(void) {
 
   // 10-nearest neighbor query
   std::cout << "10 nearest neighbors from points[20]:\n";
-  auto knn_range = points_ds.query_k_nearest_neighbors(points[20], 10, true);
+  auto knn_range = points_ds.k_nearest_neighbors(points[20], 10, true);
   for (auto const& nghb : knn_range)
     std::cout << nghb.first << " (sq. dist. = " << nghb.second << ")\n";
 
   // Incremental nearest neighbor query
   std::cout << "Incremental nearest neighbors:\n";
-  auto inn_range = points_ds.query_incremental_nearest_neighbors(points[45]);
+  auto inn_range = points_ds.incremental_nearest_neighbors(points[45]);
   // Get the neighbors in distance order until we hit the first point
   for (auto ins_iterator = inn_range.begin(); ins_iterator->first != 0; ++ins_iterator)
     std::cout << ins_iterator->first << " (sq. dist. = " << ins_iterator->second << ")\n";
 
-  // 10-farthest neighbor query
-  std::cout << "10 farthest neighbors from points[20]:\n";
-  auto kfn_range = points_ds.query_k_farthest_neighbors(points[20], 10, true);
+  // 10-furthest neighbor query
+  std::cout << "10 furthest neighbors from points[20]:\n";
+  auto kfn_range = points_ds.k_furthest_neighbors(points[20], 10, true);
   for (auto const& nghb : kfn_range)
     std::cout << nghb.first << " (sq. dist. = " << nghb.second << ")\n";
 
-  // Incremental farthest neighbor query
-  std::cout << "Incremental farthest neighbors:\n";
-  auto ifn_range = points_ds.query_incremental_farthest_neighbors(points[45]);
+  // Incremental furthest neighbor query
+  std::cout << "Incremental furthest neighbors:\n";
+  auto ifn_range = points_ds.incremental_furthest_neighbors(points[45]);
   // Get the neighbors in distance reverse order until we hit the first point
   for (auto ifs_iterator = ifn_range.begin(); ifs_iterator->first != 0; ++ifs_iterator)
     std::cout << ifs_iterator->first << " (sq. dist. = " << ifs_iterator->second << ")\n";
 
-  // Near search
-  std::cout << "Near search:\n";
+  // All-near-neighbors search
+  std::cout << "All-near-neighbors search:\n";
   std::vector<std::size_t> rs_result;
-  points_ds.near_search(points[45], 0.5, std::back_inserter(rs_result));
+  points_ds.all_near_neighbors(points[45], 0.5, std::back_inserter(rs_result));
   K k;
   for (auto const& p_idx : rs_result)
     std::cout << p_idx << " (sq. dist. = " << k.squared_distance_d_object()(points[p_idx], points[45]) << ")\n";
diff --git a/src/Spatial_searching/include/gudhi/Kd_tree_search.h b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
index af04736b..ef428002 100644
--- a/src/Spatial_searching/include/gudhi/Kd_tree_search.h
+++ b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
@@ -42,19 +42,19 @@ namespace spatial_searching {
 
   /**
   * \class Kd_tree_search Kd_tree_search.h gudhi/Kd_tree_search.h
-  * \brief Spatial tree data structure to perform (approximate) nearest and farthest neighbor search.
+  * \brief Spatial tree data structure to perform (approximate) nearest and furthest neighbor search.
   *
   * \ingroup spatial_searching
   *
   * \details
   * The class Kd_tree_search is a tree-based data structure, based on
   * <a target="_blank" href="http://doc.cgal.org/latest/Spatial_searching/index.html">CGAL dD spatial searching data structures</a>.
-  * It provides a simplified API to perform (approximate) nearest and farthest neighbor searches. Contrary to CGAL default behavior, the tree
+  * It provides a simplified API to perform (approximate) nearest and furthest neighbor searches. Contrary to CGAL default behavior, the tree
   * does not store the points themselves, but stores indices.
   *
-  * There are two types of queries: the <i>k-nearest or k-farthest neighbor query</i>, where <i>k</i> is fixed and the <i>k</i> nearest 
-  * or farthest points are computed right away,
-  * and the <i>incremental nearest or farthest neighbor query</i>, where no number of neighbors is provided during the call, as the
+  * There are two types of queries: the <i>k-nearest or k-furthest neighbor query</i>, where <i>k</i> is fixed and the <i>k</i> nearest 
+  * or furthest points are computed right away,
+  * and the <i>incremental nearest or furthest neighbor query</i>, where no number of neighbors is provided during the call, as the
   * neighbors will be computed incrementally when the iterator on the range is incremented.
   *
   * \tparam Search_traits must be a model of the <a target="_blank"
@@ -96,7 +96,7 @@ class Kd_tree_search {
   typedef CGAL::Orthogonal_k_neighbor_search<STraits>       K_neighbor_search;
   typedef typename K_neighbor_search::Tree                  Tree;
   typedef typename K_neighbor_search::Distance              Distance;
-  /// \brief The range returned by a k-nearest or k-farthest neighbor search.
+  /// \brief The range returned by a k-nearest or k-furthest neighbor search.
   /// Its value type is `std::pair<std::size_t, FT>` where `first` is the index
   /// of a point P and `second` is the squared distance between P and the query point.
   typedef K_neighbor_search                                 KNS_range;
@@ -104,7 +104,7 @@ class Kd_tree_search {
   typedef CGAL::Orthogonal_incremental_neighbor_search<
     STraits, Distance, CGAL::Sliding_midpoint<STraits>, Tree>
                                                    Incremental_neighbor_search;
-  /// \brief The range returned by an incremental nearest or farthest neighbor search.
+  /// \brief The range returned by an incremental nearest or furthest neighbor search.
   /// Its value type is `std::pair<std::size_t, FT>` where `first` is the index
   /// of a point P and `second` is the squared distance between P and the query point.
   typedef Incremental_neighbor_search                       INS_range;
@@ -171,7 +171,7 @@ class Kd_tree_search {
   /// @param[in] sorted Indicates if the computed sequence of k-nearest neighbors needs to be sorted.
   /// @param[in] eps Approximation factor.
   /// @return A range (whose `value_type` is `std::size_t`) containing the k-nearest neighbors.
-  KNS_range query_k_nearest_neighbors(
+  KNS_range k_nearest_neighbors(
     Point const& p,
     unsigned int k,
     bool sorted = true,
@@ -197,7 +197,7 @@ class Kd_tree_search {
   /// neighbors sorted by their distance to p.
   /// All the neighbors are not computed by this function, but they will be
   /// computed incrementally when the iterator on the range is incremented.
-  INS_range query_incremental_nearest_neighbors(Point const& p, FT eps = FT(0)) const {
+  INS_range incremental_nearest_neighbors(Point const& p, FT eps = FT(0)) const {
     // Initialize the search structure, and search all N points
     // Note that we need to pass the Distance explicitly since it needs to
     // know the property map
@@ -211,13 +211,13 @@ class Kd_tree_search {
     return search;
   }
 
-  /// \brief Search for the k-farthest points from a query point.
+  /// \brief Search for the k-furthest points from a query point.
   /// @param[in] p The query point.
-  /// @param[in] k Number of farthest points to search.
-  /// @param[in] sorted Indicates if the computed sequence of k-farthest neighbors needs to be sorted.
+  /// @param[in] k Number of furthest points to search.
+  /// @param[in] sorted Indicates if the computed sequence of k-furthest neighbors needs to be sorted.
   /// @param[in] eps Approximation factor.
-  /// @return A range (whose `value_type` is `std::size_t`) containing the k-farthest neighbors.
-  KNS_range query_k_farthest_neighbors(
+  /// @return A range (whose `value_type` is `std::size_t`) containing the k-furthest neighbors.
+  KNS_range k_furthest_neighbors(
     Point const& p,
     unsigned int k,
     bool sorted = true,
@@ -236,14 +236,14 @@ class Kd_tree_search {
     return search;
   }
 
-  /// \brief Search incrementally for the farthest neighbors from a query point.
+  /// \brief Search incrementally for the furthest neighbors from a query point.
   /// @param[in] p The query point.
   /// @param[in] eps Approximation factor.
   /// @return A range (whose `value_type` is `std::size_t`)
   /// containing the neighbors sorted by their distance to p.
   /// All the neighbors are not computed by this function, but they will be
   /// computed incrementally when the iterator on the range is incremented.
-  INS_range query_incremental_farthest_neighbors(Point const& p, FT eps = FT(0)) const {
+  INS_range incremental_furthest_neighbors(Point const& p, FT eps = FT(0)) const {
     // Initialize the search structure, and search all N points
     // Note that we need to pass the Distance explicitly since it needs to
     // know the property map
@@ -264,7 +264,7 @@ class Kd_tree_search {
   ///                Note: `it` is used this way: `*it++ = each_point`.
   /// @param[in] eps Approximation factor.
   template <typename OutputIterator>
-  void near_search(Point const& p,
+  void all_near_neighbors(Point const& p,
                    FT radius,
                    OutputIterator it,
                    FT eps = FT(0)) const {
diff --git a/src/Spatial_searching/test/test_Kd_tree_search.cpp b/src/Spatial_searching/test/test_Kd_tree_search.cpp
index 663a103a..8a8334c3 100644
--- a/src/Spatial_searching/test/test_Kd_tree_search.cpp
+++ b/src/Spatial_searching/test/test_Kd_tree_search.cpp
@@ -48,12 +48,12 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) {
 
   Points_ds points_ds(points);
 
-  // Test query_k_nearest_neighbors
+  // Test k_nearest_neighbors
   std::size_t closest_pt_index =
-      points_ds.query_k_nearest_neighbors(points[10], 1, false).begin()->first;
+      points_ds.k_nearest_neighbors(points[10], 1, false).begin()->first;
   BOOST_CHECK(closest_pt_index == 10);
 
-  auto kns_range = points_ds.query_k_nearest_neighbors(points[20], 10, true);
+  auto kns_range = points_ds.k_nearest_neighbors(points[20], 10, true);
 
   std::vector<std::size_t> knn_result;
   FT last_dist = -1.;
@@ -63,12 +63,12 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) {
     last_dist = nghb.second;
   }
 
-  // Test query_incremental_nearest_neighbors 
+  // Test incremental_nearest_neighbors 
   closest_pt_index =
-      points_ds.query_incremental_nearest_neighbors(points[10]).begin()->first;
+      points_ds.incremental_nearest_neighbors(points[10]).begin()->first;
   BOOST_CHECK(closest_pt_index == 10);
 
-  auto inn_range = points_ds.query_incremental_nearest_neighbors(points[20]);
+  auto inn_range = points_ds.incremental_nearest_neighbors(points[20]);
 
   std::vector<std::size_t> inn_result;
   last_dist = -1.;
@@ -83,8 +83,8 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) {
   // Same result for KNN and INN?
   BOOST_CHECK(knn_result == inn_result);
 
-  // Test query_k_farthest_neighbors
-  auto kfn_range = points_ds.query_k_farthest_neighbors(points[20], 10, true);
+  // Test k_furthest_neighbors
+  auto kfn_range = points_ds.k_furthest_neighbors(points[20], 10, true);
 
   std::vector<std::size_t> kfn_result;
   last_dist = kfn_range.begin()->second;
@@ -94,8 +94,8 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) {
     last_dist = nghb.second;
   }
 
-  // Test query_k_farthest_neighbors
-  auto ifn_range = points_ds.query_incremental_farthest_neighbors(points[20]);
+  // Test k_furthest_neighbors
+  auto ifn_range = points_ds.incremental_furthest_neighbors(points[20]);
 
   std::vector<std::size_t> ifn_result;
   last_dist = ifn_range.begin()->second;
@@ -110,10 +110,10 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) {
   // Same result for KFN and IFN?
   BOOST_CHECK(kfn_result == ifn_result);
 
-  // Test near search
+  // Test all_near_neighbors
   Point rs_q(rd.get_double(-1., 1), rd.get_double(-1., 1), rd.get_double(-1., 1), rd.get_double(-1., 1));
   std::vector<std::size_t> rs_result;
-  points_ds.near_search(rs_q, 0.5, std::back_inserter(rs_result));
+  points_ds.all_near_neighbors(rs_q, 0.5, std::back_inserter(rs_result));
   K k;
   for (auto const& p_idx : rs_result)
     BOOST_CHECK(k.squared_distance_d_object()(points[p_idx], rs_q) <= 0.5);
diff --git a/src/Subsampling/include/gudhi/sparsify_point_set.h b/src/Subsampling/include/gudhi/sparsify_point_set.h
index 507f8c79..7d3b97fb 100644
--- a/src/Subsampling/include/gudhi/sparsify_point_set.h
+++ b/src/Subsampling/include/gudhi/sparsify_point_set.h
@@ -83,7 +83,7 @@ sparsify_point_set(
 
     *output_it++ = *it_pt;
 
-    auto ins_range = points_ds.query_incremental_nearest_neighbors(*it_pt);
+    auto ins_range = points_ds.incremental_nearest_neighbors(*it_pt);
 
     // If another point Q is closer that min_squared_dist, mark Q to be dropped
     for (auto const& neighbor : ins_range) {
diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h
index 9fa7c825..a5cefd6a 100644
--- a/src/Tangential_complex/include/gudhi/Tangential_complex.h
+++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h
@@ -1093,8 +1093,8 @@ class Tangential_complex {
     std::size_t num_inserted_points = 1;
 #endif
     // const int NUM_NEIGHBORS = 150;
-    // KNS_range ins_range = m_points_ds.query_k_nearest_neighbors(center_pt, NUM_NEIGHBORS);
-    INS_range ins_range = m_points_ds.query_incremental_nearest_neighbors(center_pt);
+    // KNS_range ins_range = m_points_ds.k_nearest_neighbors(center_pt, NUM_NEIGHBORS);
+    INS_range ins_range = m_points_ds.incremental_nearest_neighbors(center_pt);
 
     // While building the local triangulation, we keep the radius
     // of the sphere "star sphere" centered at "center_vertex"
@@ -1203,7 +1203,7 @@ class Tangential_complex {
     Point center_point = compute_perturbed_point(i);
     // Among updated point, what is the closer from our center point?
     std::size_t closest_pt_index =
-        updated_pts_ds.query_k_nearest_neighbors(center_point, 1, false).begin()->first;
+        updated_pts_ds.k_nearest_neighbors(center_point, 1, false).begin()->first;
 
     typename K::Construct_weighted_point_d k_constr_wp =
         m_k.construct_weighted_point_d_object();
@@ -1315,11 +1315,10 @@ class Tangential_complex {
         m_k.compute_coordinate_d_object();
 
 #ifdef GUDHI_TC_USE_ANOTHER_POINT_SET_FOR_TANGENT_SPACE_ESTIM
-    KNS_range kns_range = m_points_ds_for_tse.query_k_nearest_neighbors(
-                                                                        p, num_pts_for_pca, false);
+    KNS_range kns_range = m_points_ds_for_tse.k_nearest_neighbors(p, num_pts_for_pca, false);
     const Points &points_for_pca = m_points_for_tse;
 #else
-    KNS_range kns_range = m_points_ds.query_k_nearest_neighbors(p, num_pts_for_pca, false);
+    KNS_range kns_range = m_points_ds.k_nearest_neighbors(p, num_pts_for_pca, false);
     const Points &points_for_pca = m_points;
 #endif
 
@@ -1413,11 +1412,10 @@ class Tangential_complex {
       const Point &p = m_points[*it_index];
 
 #ifdef GUDHI_TC_USE_ANOTHER_POINT_SET_FOR_TANGENT_SPACE_ESTIM
-      KNS_range kns_range = m_points_ds_for_tse.query_k_nearest_neighbors(
-                                                                          p, num_pts_for_pca, false);
+      KNS_range kns_range = m_points_ds_for_tse.k_nearest_neighbors(p, num_pts_for_pca, false);
       const Points &points_for_pca = m_points_for_tse;
 #else
-      KNS_range kns_range = m_points_ds.query_k_nearest_neighbors(p, num_pts_for_pca, false);
+      KNS_range kns_range = m_points_ds.k_nearest_neighbors(p, num_pts_for_pca, false);
       const Points &points_for_pca = m_points;
 #endif
 
diff --git a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h
index fb669ef8..4f3cef4f 100644
--- a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h
@@ -84,7 +84,7 @@ class Euclidean_strong_witness_complex
     : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks_) {
     nearest_landmark_table_.reserve(boost::size(witnesses));
     for (auto w : witnesses)
-      nearest_landmark_table_.push_back(landmark_tree_.query_incremental_nearest_neighbors(w));
+      nearest_landmark_table_.push_back(landmark_tree_.incremental_nearest_neighbors(w));
   }
 
   /** \brief Returns the point corresponding to the given vertex.
diff --git a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h
index 6afe9a5d..ff8bb139 100644
--- a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h
@@ -86,7 +86,7 @@ class Euclidean_witness_complex
     : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks) {
     nearest_landmark_table_.reserve(boost::size(witnesses));
     for (auto w : witnesses)
-      nearest_landmark_table_.push_back(landmark_tree_.query_incremental_nearest_neighbors(w));
+      nearest_landmark_table_.push_back(landmark_tree_.incremental_nearest_neighbors(w));
   }
 
   /** \brief Returns the point corresponding to the given vertex.
diff --git a/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp b/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp
index 62fd1157..4f718203 100644
--- a/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp
+++ b/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp
@@ -75,7 +75,7 @@ BOOST_AUTO_TEST_CASE(simple_witness_complex) {
   Kd_tree landmark_tree(landmarks);
   Nearest_landmark_table nearest_landmark_table;
   for (auto w: witnesses)
-    nearest_landmark_table.push_back(landmark_tree.query_incremental_nearest_neighbors(w));
+    nearest_landmark_table.push_back(landmark_tree.incremental_nearest_neighbors(w));
 
   // Weak witness complex: Euclidean version
   EuclideanWitnessComplex eucl_witness_complex(landmarks,
-- 
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