backmerge of trunk

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@722 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 10b585b7050b993a1c2a4e7876ba9f6d85339ad9

8 files changed, 52 insertions, 67 deletions

diff --git a/src/Bottleneck/test/bottleneck_unit_test.cpp b/src/Bottleneck/test/bottleneck_unit_test.cpp
index 068b8690..c60f5d8a 100644
--- a/src/Bottleneck/test/bottleneck_unit_test.cpp
+++ b/src/Bottleneck/test/bottleneck_unit_test.cpp
@@ -1,6 +1,6 @@
-#define BOOST_TEST_MODULE bottleneck test
-
-#include <boost/test/included/unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "bottleneck"
+#include <boost/test/unit_test.hpp>
 
 #include "gudhi/Graph_matching.h"
 #include <iostream>
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index 8bd265d8..896a7a9f 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -336,18 +336,18 @@ class Persistent_cohomology {
 
       if (ds_parent_[key] == key  // root of its tree
       && zero_cocycles_.find(key) == zero_cocycles_.end()) {
-        persistent_pairs_.push_back(
-            Persistent_interval(cpx_->simplex(key), cpx_->null_simplex(), coeff_field_.characteristic()));
+        persistent_pairs_.emplace_back(
+            cpx_->simplex(key), cpx_->null_simplex(), coeff_field_.characteristic());
       }
     }
     for (auto zero_idx : zero_cocycles_) {
-      persistent_pairs_.push_back(
-          Persistent_interval(cpx_->simplex(zero_idx.second), cpx_->null_simplex(), coeff_field_.characteristic()));
+      persistent_pairs_.emplace_back(
+          cpx_->simplex(zero_idx.second), cpx_->null_simplex(), coeff_field_.characteristic());
     }
 // Compute infinite interval of dimension > 0
     for (auto cocycle : transverse_idx_) {
-      persistent_pairs_.push_back(
-          Persistent_interval(cpx_->simplex(cocycle.first), cpx_->null_simplex(), cocycle.second.characteristics_));
+      persistent_pairs_.emplace_back(
+          cpx_->simplex(cocycle.first), cpx_->null_simplex(), cocycle.second.characteristics_);
     }
   }
 
@@ -387,8 +387,8 @@ class Persistent_cohomology {
       if (cpx_->filtration(cpx_->simplex(idx_coc_u))
           < cpx_->filtration(cpx_->simplex(idx_coc_v))) {  // Kill cocycle [idx_coc_v], which is younger.
         if (interval_length_policy(cpx_->simplex(idx_coc_v), sigma)) {
-          persistent_pairs_.push_back(
-              Persistent_interval(cpx_->simplex(idx_coc_v), sigma, coeff_field_.characteristic()));
+          persistent_pairs_.emplace_back(
+              cpx_->simplex(idx_coc_v), sigma, coeff_field_.characteristic());
         }
         // Maintain the index of the 0-cocycle alive.
         if (kv != idx_coc_v) {
@@ -402,8 +402,8 @@ class Persistent_cohomology {
         }
       } else {  // Kill cocycle [idx_coc_u], which is younger.
         if (interval_length_policy(cpx_->simplex(idx_coc_u), sigma)) {
-          persistent_pairs_.push_back(
-              Persistent_interval(cpx_->simplex(idx_coc_u), sigma, coeff_field_.characteristic()));
+          persistent_pairs_.emplace_back(
+              cpx_->simplex(idx_coc_u), sigma, coeff_field_.characteristic());
         }
         // Maintain the index of the 0-cocycle alive.
         if (ku != idx_coc_u) {
@@ -553,9 +553,9 @@ class Persistent_cohomology {
                        Arith_element charac) {
     // Create a finite persistent interval for which the interval exists
     if (interval_length_policy(cpx_->simplex(death_key), sigma)) {
-      persistent_pairs_.push_back(Persistent_interval(cpx_->simplex(death_key)  // creator
-          , sigma                                                               // destructor
-          , charac));                                                           // fields
+      persistent_pairs_.emplace_back(cpx_->simplex(death_key)  // creator
+          , sigma                                              // destructor
+          , charac);                                           // fields
     }
 
     auto death_key_row = transverse_idx_.find(death_key);  // Find the beginning of the row.
@@ -695,7 +695,7 @@ class Persistent_cohomology {
   void output_diagram(std::ostream& ostream = std::cout) {
 
     cmp_intervals_by_length cmp(cpx_);
-    persistent_pairs_.sort(cmp);
+    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_) {
       // Special case on windows, inf is "1.#INF" (cf. unitary tests and R package TDA)
@@ -714,7 +714,7 @@ class Persistent_cohomology {
   {
     std::ofstream           diagram_out(diagram_name.c_str());
     cmp_intervals_by_length cmp( cpx_ );
-    persistent_pairs_.sort( cmp );
+    std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp);
     for(auto pair : persistent_pairs_)
     {
     diagram_out << cpx_->dimension(get<0>(pair)) << " "
@@ -761,7 +761,7 @@ class Persistent_cohomology {
   /*  Key -> row. */
   std::map<Simplex_key, cocycle> transverse_idx_;
   /* Persistent intervals. */
-  std::list<Persistent_interval> persistent_pairs_;
+  std::vector<Persistent_interval> persistent_pairs_;
   length_interval interval_length_policy;
 
   boost::object_pool<Column> column_pool_;
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
index 2a4c8692..a12019f8 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
@@ -41,9 +41,7 @@ class Field_Zp {
 
   Field_Zp()
       : Prime(0),
-        inverse_(),
-        mult_id_all(1),
-        add_id_all(0) {
+        inverse_() {
   }
 
   void init(int charac) {
@@ -81,14 +79,14 @@ class Field_Zp {
   }
 
   /** \brief Returns the additive idendity \f$0_{\Bbbk}\f$ of the field.*/
-  const Element& additive_identity() const {
-    return add_id_all;
+  Element additive_identity() const {
+    return 0;
   }
   /** \brief Returns the multiplicative identity \f$1_{\Bbbk}\f$ of the field.*/
-  const Element& multiplicative_identity(Element = 0) const {
-    return mult_id_all;
+  Element multiplicative_identity(Element = 0) const {
+    return 1;
   }
-  /** Returns the inverse in the field. Modifies P.*/
+  /** Returns the inverse in the field. Modifies P. ??? */
   std::pair<Element, Element> inverse(Element x, Element P) {
     return std::pair<Element, Element>(inverse_[x], P);
   }  // <------ return the product of field characteristic for which x is invertible
@@ -101,7 +99,7 @@ class Field_Zp {
   }
 
   /** \brief Returns the characteristic \f$p\f$ of the field.*/
-  const int& characteristic() const {
+  int characteristic() const {
     return Prime;
   }
 
@@ -109,8 +107,6 @@ class Field_Zp {
   int Prime;
   /** Property map Element -> Element, which associate to an element its inverse in the field.*/
   std::vector<Element> inverse_;
-  const Element mult_id_all;
-  const Element add_id_all;
 };
 
 }  // namespace persistent_cohomology
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
index c6fd5282..555d696f 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
@@ -142,7 +142,7 @@ class Multi_field {
     return prod_characteristics_;
   }
 
-  /** Returns the inverse in the field. Modifies P.*/
+  /** Returns the inverse in the field. Modifies P. ??? */
   std::pair<Element, Element> inverse(Element x, Element QS) {
     Element QR;
     mpz_gcd(QR.get_mpz_t(), x.get_mpz_t(), QS.get_mpz_t());  // QR <- gcd(x,QS)
@@ -153,12 +153,12 @@ class Multi_field {
     mpz_invert(inv_qt.get_mpz_t(), x.get_mpz_t(), QT.get_mpz_t());
 
     assert(prod_characteristics_ > 0);  // division by zero + non negative values
-    return std::pair<Element, Element>(
-        (inv_qt * multiplicative_identity(QT)) % prod_characteristics_, QT);
+    return { (inv_qt * multiplicative_identity(QT)) % prod_characteristics_, QT };
   }
   /** Returns -x * y.*/
   Element times_minus(const Element& x, const Element& y) {
     assert(prod_characteristics_ > 0);  // division by zero + non negative values
+    /* This assumes that (x*y)%pc cannot be zero, but Field_Zp has specific code for the 0 case ??? */
     return prod_characteristics_ - ((x * y) % prod_characteristics_);
   }
 
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
index 55bc7066..194b3e74 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
@@ -1,15 +1,14 @@
-#define BOOST_TEST_MODULE persistent_cohomology test
-#include <boost/test/included/unit_test.hpp>
-#include <boost/system/error_code.hpp>
-#include <boost/chrono/thread_clock.hpp>
 #include <iostream>
 #include <string>
-
+#include <algorithm>
 #include <utility> // std::pair, std::make_pair
-
 #include <cmath> // float comparison
 #include <limits>
 
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "persistent_cohomology"
+#include <boost/test/unit_test.hpp>
+
 #include "gudhi/graph_simplicial_complex.h"
 #include "gudhi/reader_utils.h"
 #include "gudhi/Simplex_tree.h"
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 18a4725e..703682e1 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
@@ -1,15 +1,14 @@
-#define BOOST_TEST_MODULE persistent_cohomology_multi_field test
-#include <boost/test/included/unit_test.hpp>
-#include <boost/system/error_code.hpp>
-#include <boost/chrono/thread_clock.hpp>
 #include <iostream>
 #include <string>
-
+#include <algorithm>
 #include <utility> // std::pair, std::make_pair
-
 #include <cmath> // float comparison
 #include <limits>
 
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "persistent_cohomology_multi_field"
+#include <boost/test/unit_test.hpp>
+
 #include "gudhi/graph_simplicial_complex.h"
 #include "gudhi/reader_utils.h"
 #include "gudhi/Simplex_tree.h"
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
index 977fafa1..de350f2d 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
@@ -77,8 +77,8 @@ class Simplex_tree_siblings {
         parent_(parent),
         members_(boost::container::ordered_unique_range, members.begin(),
                  members.end()) {
-    for (auto map_it = members_.begin(); map_it != members_.end(); map_it++) {
-      map_it->second.assign_children(this);
+    for (auto& map_el : members_) {
+      map_el.second.assign_children(this);
     }
   }
 
@@ -90,19 +90,12 @@ class Simplex_tree_siblings {
    * present in the node.
    */
   void insert(Vertex_handle v, Filtration_value filtration_value) {
-    typename Dictionary::iterator sh = members_.find(v);
-    if (sh != members_.end() && sh->second.filtration() > filtration_value) {
-      sh->second.assign_filtration(filtration_value);
-      return;
-    }
-    if (sh == members_.end()) {
-      members_.insert(
-          std::pair<Vertex_handle, Node>(v, Node(this, filtration_value)));
-      return;
-    }
+    auto ins = members_.emplace(v, Node(this, filtration_value));
+    if (!ins.second && filtration(ins.first) > filtration_value)
+      ins.first->second.assign_filtration(filtration_value);
   }
 
-  typename Dictionary::iterator find(Vertex_handle v) {
+  Dictionary_it find(Vertex_handle v) {
     return members_.find(v);
   }
 
@@ -110,7 +103,7 @@ class Simplex_tree_siblings {
     return oncles_;
   }
 
-  Vertex_handle parent() {
+  Vertex_handle parent() const {
     return parent_;
   }
 
@@ -118,7 +111,7 @@ class Simplex_tree_siblings {
     return members_;
   }
 
-  size_t size() {
+  size_t size() const {
     return members_.size();
   }
 
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index 7f2172a2..566d6d90 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -1,17 +1,14 @@
-#define BOOST_TEST_MODULE simplex_tree test
-#include <boost/test/included/unit_test.hpp>
-#include <boost/range/adaptor/reversed.hpp>
-#include <boost/system/error_code.hpp>
-#include <boost/chrono/thread_clock.hpp>
 #include <iostream>
 #include <string>
 #include <algorithm>
-
 #include <utility> // std::pair, std::make_pair
-
 #include <cmath> // float comparison
 #include <limits>
 
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "simplex_tree"
+#include <boost/test/unit_test.hpp>
+
 #include "gudhi/graph_simplicial_complex.h"
 #include "gudhi/reader_utils.h"
 #include "gudhi/Simplex_tree.h"
@@ -112,6 +109,7 @@ BOOST_AUTO_TEST_CASE(simplex_tree_from_file) {
     // Size of simplex
     int size = 0;
     for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      (void) vertex;
       size++;
     }
     BOOST_CHECK(AreAlmostTheSame(st.filtration(f_simplex), (0.1 * size))); // Specific test: filtration = 0.1 * simplex_size