fixed test

10 files changed, 168 insertions, 93 deletions

diff --git a/.github/how_to_use_github_to_contribute_to_gudhi.md b/.github/how_to_use_github_to_contribute_to_gudhi.md
index 6ab05e36..747ca39b 100644
--- a/.github/how_to_use_github_to_contribute_to_gudhi.md
+++ b/.github/how_to_use_github_to_contribute_to_gudhi.md
@@ -25,10 +25,10 @@ This creates a directory gudhi-devel, which you are free to move around or renam
 cd gudhi-devel
 ```
 
-Everytime you clone the repository, you will have to download the *submodules*.
+When you clone the repository, you also need to download the *submodules*.
 
 ## Submodules
-An interface to Hera for Wasserstein distance is available on an external git repository. To download it:
+Hera, used for Wasserstein distance, is available on an external git repository. To download it:
 ```bash
 git submodule update --init
 ```
@@ -60,8 +60,9 @@ This is a command you can run quite regularly.
 It tells git to check all that happened on github.
 It is safe, it will not mess with your files.
 
-**Reminder:** Everytime you checkout master or merge from master, afterwards, if the version of one the submodule has changed, or if a submodule was added, you will have to:
+**Reminder:** If the version of a submodule has changed, or if a submodule was added, you may need to:
 ```bash
+git submodule sync
 git submodule update --init
 ```
 
diff --git a/.gitmodules b/.gitmodules
index 6e8b3ab1..f70c570d 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "ext/hera"]
 	path = ext/hera
-	url = https://bitbucket.org/grey_narn/hera.git
+	url = https://github.com/grey-narn/hera.git
diff --git a/ext/hera b/ext/hera
-Subproject 9a89971855acefe39dce0e2adadf53b88ca8f68
+Subproject cb1838e682ec07f80720241cf9098400caeb83c
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 76608008..7b39a500 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1317,6 +1317,8 @@ class Simplex_tree {
    * \post Some simplex tree functions require the filtration to be valid. `make_filtration_non_decreasing()`
    * function is not launching `initialize_filtration()` but returns the filtration modification information. If the
    * complex has changed , please call `initialize_filtration()` to recompute it.
+   * 
+   * If a simplex has a `NaN` filtration value, it is considered lower than any other defined filtration value.
    */
   bool make_filtration_non_decreasing() {
     bool modified = false;
@@ -1347,7 +1349,9 @@ class Simplex_tree {
                                                               });
 
       Filtration_value max_filt_border_value = filtration(*max_border);
-      if (simplex.second.filtration() < max_filt_border_value) {
+      // Replacing if(f<max) with if(!(f>=max)) would mean that if f is NaN, we replace it with the max of the children.
+      // That seems more useful than keeping NaN.
+      if (!(simplex.second.filtration() >= max_filt_border_value)) {
         // Store the filtration modification information
         modified = true;
         simplex.second.assign_filtration(max_filt_border_value);
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index 8b9163f5..cf2b0153 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -28,3 +28,9 @@ if (TBB_FOUND)
   target_link_libraries(Simplex_tree_ctor_and_move_test_unit ${TBB_LIBRARIES})
 endif()
 gudhi_add_boost_test(Simplex_tree_ctor_and_move_test_unit)
+
+add_executable ( Simplex_tree_make_filtration_non_decreasing_test_unit simplex_tree_make_filtration_non_decreasing_unit_test.cpp )
+if (TBB_FOUND)
+  target_link_libraries(Simplex_tree_make_filtration_non_decreasing_test_unit ${TBB_LIBRARIES})
+endif()
+gudhi_add_boost_test(Simplex_tree_make_filtration_non_decreasing_test_unit)
diff --git a/src/Simplex_tree/test/simplex_tree_make_filtration_non_decreasing_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_make_filtration_non_decreasing_unit_test.cpp
new file mode 100644
index 00000000..4697ec05
--- /dev/null
+++ b/src/Simplex_tree/test/simplex_tree_make_filtration_non_decreasing_unit_test.cpp
@@ -0,0 +1,148 @@
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2020 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#include <iostream>
+#include <limits>  // for NaN
+#include <cmath>  // for isNaN
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "simplex_tree_make_filtration_non_decreasing"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
+
+//  ^
+// /!\ Nothing else from Simplex_tree shall be included to test includes are well defined.
+#include "gudhi/Simplex_tree.h"
+
+using namespace Gudhi;
+
+typedef boost::mpl::list<Simplex_tree<>, Simplex_tree<Simplex_tree_options_fast_persistence>> list_of_tested_variants;
+
+BOOST_AUTO_TEST_CASE_TEMPLATE(make_filtration_non_decreasing, typeST, list_of_tested_variants) {
+  typeST st;
+
+  st.insert_simplex_and_subfaces({2, 1, 0}, 2.0);
+  st.insert_simplex_and_subfaces({3, 0}, 2.0);
+  st.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
+  
+  /* Inserted simplex:     */
+  /*    1                  */
+  /*    o                  */
+  /*   /X\                 */
+  /*  o---o---o---o        */
+  /*  2   0   3\X/4        */
+  /*            o          */
+  /*            5          */
+
+  std::cout << "Check default insertion ensures the filtration values are non decreasing" << std::endl;
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+
+  // Because of non decreasing property of simplex tree, { 0 } , { 1 } and { 0, 1 } are going to be set from value 2.0
+  // to 1.0
+  st.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
+  
+  // Inserted simplex:
+  //    1   6
+  //    o---o
+  //   /X\7/
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+  
+  std::cout << "Check default second insertion ensures the filtration values are non decreasing" << std::endl;
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+  
+  // Copy original simplex tree
+  typeST st_copy = st;
+
+  // Modify specific values for st to become like st_copy thanks to make_filtration_non_decreasing
+  st.assign_filtration(st.find({0,1,6,7}), 0.8);
+  st.assign_filtration(st.find({0,1,6}), 0.9);
+  st.assign_filtration(st.find({0,6}), 0.6);
+  st.assign_filtration(st.find({3,4,5}), 1.2);
+  st.assign_filtration(st.find({3,4}), 1.1);
+  st.assign_filtration(st.find({4,5}), 1.99);
+  
+  std::cout << "Check the simplex_tree is rolled back in case of decreasing filtration values" << std::endl;
+  BOOST_CHECK(st.make_filtration_non_decreasing());
+  BOOST_CHECK(st == st_copy);
+
+  // Other simplex tree
+  typeST st_other;
+  st_other.insert_simplex_and_subfaces({2, 1, 0}, 3.0);  // This one is different from st
+  st_other.insert_simplex_and_subfaces({3, 0}, 2.0);
+  st_other.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
+  st_other.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
+
+  // Modify specific values for st to become like st_other thanks to make_filtration_non_decreasing
+  st.assign_filtration(st.find({2}), 3.0);
+  // By modifying just the simplex {2}
+  // {0,1,2}, {1,2} and {0,2} will be modified
+  
+  std::cout << "Check the simplex_tree is repaired in case of decreasing filtration values" << std::endl;
+  BOOST_CHECK(st.make_filtration_non_decreasing());
+  BOOST_CHECK(st == st_other);
+
+  // Modify specific values for st still to be non-decreasing
+  st.assign_filtration(st.find({0,1,2}), 10.0);
+  st.assign_filtration(st.find({0,2}), 9.0);
+  st.assign_filtration(st.find({0,1,6,7}), 50.0);
+  st.assign_filtration(st.find({0,1,6}), 49.0);
+  st.assign_filtration(st.find({0,1,7}), 48.0);
+  // Other copy simplex tree
+  typeST st_other_copy = st;
+  
+  std::cout << "Check the simplex_tree is not modified in case of non-decreasing filtration values" << std::endl;
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+  BOOST_CHECK(st == st_other_copy);
+  
+}
+
+BOOST_AUTO_TEST_CASE_TEMPLATE(make_filtration_non_decreasing_on_nan_values, typeST, list_of_tested_variants) {
+  typeST st;
+
+  st.insert_simplex_and_subfaces({2, 1, 0}, std::numeric_limits<double>::quiet_NaN());
+  st.insert_simplex_and_subfaces({3, 0},    std::numeric_limits<double>::quiet_NaN());
+  st.insert_simplex_and_subfaces({3, 4, 5}, std::numeric_limits<double>::quiet_NaN());
+  
+  /* Inserted simplex:     */
+  /*    1                  */
+  /*    o                  */
+  /*   /X\                 */
+  /*  o---o---o---o        */
+  /*  2   0   3\X/4        */
+  /*            o          */
+  /*            5          */
+
+  std::cout << "SPECIFIC CASE:" << std::endl;
+  std::cout << "Insertion with NaN values does not ensure the filtration values are non decreasing" << std::endl;
+  st.make_filtration_non_decreasing();
+
+  std::cout << "Check all filtration values are NaN" << std::endl;
+  for (auto f_simplex : st.complex_simplex_range()) {
+    BOOST_CHECK(std::isnan(st.filtration(f_simplex)));
+  }
+
+  st.assign_filtration(st.find({0}), 0.);
+  st.assign_filtration(st.find({1}), 0.);
+  st.assign_filtration(st.find({2}), 0.);
+  st.assign_filtration(st.find({3}), 0.);
+  st.assign_filtration(st.find({4}), 0.);
+  st.assign_filtration(st.find({5}), 0.);
+
+  std::cout << "Check make_filtration_non_decreasing is modifying the simplicial complex" << std::endl;
+  BOOST_CHECK(st.make_filtration_non_decreasing());
+  
+  std::cout << "Check all filtration values are now defined" << std::endl;
+  for (auto f_simplex : st.complex_simplex_range()) {
+    BOOST_CHECK(!std::isnan(st.filtration(f_simplex)));
+  }
+}
\ No newline at end of file
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index 58bfa8db..e739ad0a 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -791,90 +791,6 @@ BOOST_AUTO_TEST_CASE(non_contiguous) {
   BOOST_CHECK(++i == std::end(b));
 }
 
-BOOST_AUTO_TEST_CASE(make_filtration_non_decreasing) {
-  std::cout << "********************************************************************" << std::endl;
-  std::cout << "MAKE FILTRATION NON DECREASING" << std::endl;
-  typedef Simplex_tree<> typeST;
-  typeST st;
-
-  st.insert_simplex_and_subfaces({2, 1, 0}, 2.0);
-  st.insert_simplex_and_subfaces({3, 0}, 2.0);
-  st.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
-  
-  /* Inserted simplex:     */
-  /*    1                  */
-  /*    o                  */
-  /*   /X\                 */
-  /*  o---o---o---o        */
-  /*  2   0   3\X/4        */
-  /*            o          */
-  /*            5          */
-
-  std::cout << "Check default insertion ensures the filtration values are non decreasing" << std::endl;
-  BOOST_CHECK(!st.make_filtration_non_decreasing());
-
-  // Because of non decreasing property of simplex tree, { 0 } , { 1 } and { 0, 1 } are going to be set from value 2.0
-  // to 1.0
-  st.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
-  
-  // Inserted simplex:
-  //    1   6
-  //    o---o
-  //   /X\7/
-  //  o---o---o---o
-  //  2   0   3\X/4
-  //            o
-  //            5
-  
-  std::cout << "Check default second insertion ensures the filtration values are non decreasing" << std::endl;
-  BOOST_CHECK(!st.make_filtration_non_decreasing());
-  
-  // Copy original simplex tree
-  typeST st_copy = st;
-
-  // Modify specific values for st to become like st_copy thanks to make_filtration_non_decreasing
-  st.assign_filtration(st.find({0,1,6,7}), 0.8);
-  st.assign_filtration(st.find({0,1,6}), 0.9);
-  st.assign_filtration(st.find({0,6}), 0.6);
-  st.assign_filtration(st.find({3,4,5}), 1.2);
-  st.assign_filtration(st.find({3,4}), 1.1);
-  st.assign_filtration(st.find({4,5}), 1.99);
-  
-  std::cout << "Check the simplex_tree is rolled back in case of decreasing filtration values" << std::endl;
-  BOOST_CHECK(st.make_filtration_non_decreasing());
-  BOOST_CHECK(st == st_copy);
-
-  // Other simplex tree
-  typeST st_other;
-  st_other.insert_simplex_and_subfaces({2, 1, 0}, 3.0);  // This one is different from st
-  st_other.insert_simplex_and_subfaces({3, 0}, 2.0);
-  st_other.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
-  st_other.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
-
-  // Modify specific values for st to become like st_other thanks to make_filtration_non_decreasing
-  st.assign_filtration(st.find({2}), 3.0);
-  // By modifying just the simplex {2}
-  // {0,1,2}, {1,2} and {0,2} will be modified
-  
-  std::cout << "Check the simplex_tree is repaired in case of decreasing filtration values" << std::endl;
-  BOOST_CHECK(st.make_filtration_non_decreasing());
-  BOOST_CHECK(st == st_other);
-
-  // Modify specific values for st still to be non-decreasing
-  st.assign_filtration(st.find({0,1,2}), 10.0);
-  st.assign_filtration(st.find({0,2}), 9.0);
-  st.assign_filtration(st.find({0,1,6,7}), 50.0);
-  st.assign_filtration(st.find({0,1,6}), 49.0);
-  st.assign_filtration(st.find({0,1,7}), 48.0);
-  // Other copy simplex tree
-  typeST st_other_copy = st;
-  
-  std::cout << "Check the simplex_tree is not modified in case of non-decreasing filtration values" << std::endl;
-  BOOST_CHECK(!st.make_filtration_non_decreasing());
-  BOOST_CHECK(st == st_other_copy);
-  
-}
-
 
 typedef boost::mpl::list<boost::adjacency_list<boost::setS, boost::vecS, boost::directedS,
                                                boost::property<vertex_filtration_t, double>,
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 6db2c76b..2d010483 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -68,7 +68,7 @@ if(CGAL_FOUND)
 endif()
 
 # For those who dislike bundled dependencies, this indicates where to find a preinstalled Hera.
-set(HERA_WASSERSTEIN_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/geom_matching/wasserstein/include CACHE PATH "Directory where one can find Hera's wasserstein.h")
+set(HERA_WASSERSTEIN_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include CACHE PATH "Directory where one can find Hera's wasserstein.h")
 
 option(WITH_GUDHI_USE_TBB "Build with Intel TBB parallelization" ON)
 
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 5047252f..257d1939 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -55,7 +55,7 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
 
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                   copy_directory ${CMAKE_SOURCE_DIR}/ext/hera/geom_matching/wasserstein/include ${GUDHI_USER_VERSION_DIR}/ext/hera/geom_matching/wasserstein/include)
+                   copy_directory ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include ${GUDHI_USER_VERSION_DIR}/ext/hera/wasserstein/include)
 
 set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
 
diff --git a/src/python/test/test_cubical_complex.py b/src/python/test/test_cubical_complex.py
index 8af63355..b20f77c1 100755
--- a/src/python/test/test_cubical_complex.py
+++ b/src/python/test/test_cubical_complex.py
@@ -148,7 +148,7 @@ def test_connected_sublevel_sets():
     assert cub.persistence() == [(0, (2.0, float("inf")))]
     assert cub.betti_numbers() == [1, 0, 0]
 
-def test_connected_sublevel_sets():
+def test_cubical_generators():
     cub = CubicalComplex(top_dimensional_cells = [[0, 0, 0], [0, 1, 0], [0, 0, 0]])
     cub.persistence()
-    assert cub.cofaces_of_persistence_pairs() == np.array([[1, 7, 4], [0, 8, -1]])
+    assert np.array_equal(cub.cofaces_of_persistence_pairs(), np.array([[1, 7, 4], [0, 8, -1]]))