Merge last master modification and fix merge conflict

6 files changed, 30 insertions, 20 deletions

diff --git a/Dockerfile_gudhi_installation b/Dockerfile_gudhi_installation
index 9fe20730..d5d86338 100644
--- a/Dockerfile_gudhi_installation
+++ b/Dockerfile_gudhi_installation
@@ -50,14 +50,16 @@ RUN pip3 install \
     numpy \
     matplotlib \
     scipy \
-    Cython
+    Cython \
+    POT \
+    scikit-learn
 
 # apt clean up
 RUN apt autoremove && rm -rf /var/lib/apt/lists/*
 
-RUN curl -LO "https://github.com/GUDHI/gudhi-devel/releases/download/tags%2Fgudhi-release-3.0.0/gudhi.3.0.0.tar.gz" \
-&& tar xf gudhi.3.0.0.tar.gz \
-&& cd gudhi.3.0.0 \
+RUN curl -LO "https://github.com/GUDHI/gudhi-devel/releases/download/tags%2Fgudhi-release-3.1.0/gudhi.3.1.0.tar.gz" \
+&& tar xf gudhi.3.1.0.tar.gz \
+&& cd gudhi.3.1.0 \
 && mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_PYTHON=OFF -DPython_ADDITIONAL_VERSIONS=3 ..  \
 && make all test install \
 && cmake -DWITH_GUDHI_PYTHON=ON . \
diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h
index ab099c04..61db6508 100644
--- a/src/Nerve_GIC/include/gudhi/GIC.h
+++ b/src/Nerve_GIC/include/gudhi/GIC.h
@@ -14,7 +14,7 @@
 
 #ifdef GUDHI_USE_TBB
 #include <tbb/parallel_for.h>
-#include <tbb/mutex.h>
+#include <mutex>
 #endif
 
 #include <gudhi/Debug_utils.h>
@@ -459,7 +459,7 @@ class Cover_complex {
     // This cannot be parallelized if thread_local is not defined
     // thread_local is not defined for XCode < v.8
     #if defined(GUDHI_USE_TBB) && defined(GUDHI_CAN_USE_CXX11_THREAD_LOCAL)
-    tbb::mutex deltamutex;
+    std::mutex deltamutex;
     tbb::parallel_for(0, N, [&](int i){
         std::vector<int> samples(m);
         SampleWithoutReplacement(n, m, samples);
@@ -765,7 +765,7 @@ class Cover_complex {
 
     #ifdef GUDHI_USE_TBB
       if (verbose) std::clog << "Computing connected components (parallelized)..." << std::endl;
-      tbb::mutex covermutex, idmutex;
+      std::mutex covermutex, idmutex;
       tbb::parallel_for(0, res, [&](int i){
         // Compute connected components
         Graph G = one_skeleton.create_subgraph();
@@ -895,7 +895,7 @@ class Cover_complex {
     // Compute the geodesic distances to subsamples with Dijkstra
     #ifdef GUDHI_USE_TBB
       if (verbose) std::clog << "Computing geodesic distances (parallelized)..." << std::endl;
-      tbb::mutex coverMutex; tbb::mutex mindistMutex;
+      std::mutex coverMutex; tbb::mutex mindistMutex;
       tbb::parallel_for(0, m, [&](int i){
         int seed = voronoi_subsamples[i];
         std::vector<double> dmap(n);
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index f99b164c..8a8cac58 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -16,6 +16,9 @@ endif()
 add_test(NAME Simplex_tree_example_simple_simplex_tree COMMAND $<TARGET_FILE:Simplex_tree_example_simple_simplex_tree>)
 
 add_executable ( Simplex_tree_example_mini_simplex_tree mini_simplex_tree.cpp )
+if (TBB_FOUND)
+  target_link_libraries(Simplex_tree_example_mini_simplex_tree ${TBB_LIBRARIES})
+endif()
 add_test(NAME Simplex_tree_example_mini_simplex_tree COMMAND $<TARGET_FILE:Simplex_tree_example_mini_simplex_tree>)
 
 # An example with Simplex-tree using CGAL alpha_shapes_3
diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h
index f058fa9f..f007bdd5 100644
--- a/src/Tangential_complex/include/gudhi/Tangential_complex.h
+++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h
@@ -60,7 +60,7 @@
 #ifdef GUDHI_USE_TBB
 #include <tbb/parallel_for.h>
 #include <tbb/combinable.h>
-#include <tbb/mutex.h>
+#include <mutex>
 #endif
 
 // #define GUDHI_TC_EXPORT_NORMALS // Only for 3D surfaces (k=2, d=3)
@@ -147,7 +147,7 @@ class Tangential_complex {
   typedef typename Tr_traits::Vector_d Tr_vector;
 
 #if defined(GUDHI_USE_TBB)
-  typedef tbb::mutex Mutex_for_perturb;
+  typedef std::mutex Mutex_for_perturb;
   typedef Vector Translation_for_perturb;
   typedef std::vector<Atomic_wrapper<FT> > Weights;
 #else
diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index 5860f3a3..2659798e 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -12,10 +12,18 @@ 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 4.11.0)
   add_executable( Witness_complex_example_off example_witness_complex_off.cpp )
+  if (TBB_FOUND)
+    target_link_libraries(Witness_complex_example_off ${TBB_LIBRARIES})
+  endif()
   add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp )
+  if (TBB_FOUND)
+    target_link_libraries(Witness_complex_example_sphere ${TBB_LIBRARIES})
+  endif()
   
   add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
-  target_link_libraries(Witness_complex_example_strong_off)
+  if (TBB_FOUND)
+    target_link_libraries(Witness_complex_example_strong_off ${TBB_LIBRARIES})
+  endif()
 
   add_test(NAME Witness_complex_example_off_test_torus
       COMMAND $<TARGET_FILE:Witness_complex_example_off>
diff --git a/src/python/doc/alpha_complex_sum.inc b/src/python/doc/alpha_complex_sum.inc
index a1184663..b5af0d27 100644
--- a/src/python/doc/alpha_complex_sum.inc
+++ b/src/python/doc/alpha_complex_sum.inc
@@ -5,16 +5,13 @@
    | .. figure::                                                    | Alpha complex is a simplicial complex constructed from the finite      | :Author: Vincent Rouvreau                                                                                                   |
    |      ../../doc/Alpha_complex/alpha_complex_representation.png  | cells of a Delaunay Triangulation.                                     |                                                                                                                             |
    |      :alt: Alpha complex representation                        |                                                                        | :Introduced in: GUDHI 2.0.0                                                                                                 |
-   |      :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  | :Copyright: MIT (`GPL v3 </licensing/>`_)                                                                                   |
-   |                                                                | is then said to be Gabriel), and as the minimum of the filtration      |                                                                                                                             |
-   |                                                                | values of the codimension 1 cofaces that make it not Gabriel           | :Requires: `Eigen <installation.html#eigen>`__ :math:`\geq` 3.1.0 and `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 |
-   |                                                                | otherwise. All simplices that have a filtration value                  |                                                                                                                             |
-   |                                                                | :math:`> \alpha^2` are removed from the Delaunay complex               |                                                                                                                             |
-   |                                                                | when creating the simplicial complex if it is specified.               |                                                                                                                             |
+   |      :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      | :Copyright: MIT (`GPL v3 </licensing/>`_)                                                                                   |
+   |                                                                | simplex is then said to be Gabriel), and as the minimum of the         |                                                                                                                             |
+   |                                                                | filtration values of the codimension 1 cofaces that make it not        | :Requires: `Eigen <installation.html#eigen>`__ :math:`\geq` 3.1.0 and `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 |
+   |                                                                | Gabriel otherwise.                                                     |                                                                                                                             |
    |                                                                |                                                                        |                                                                                                                             |
-   |                                                                | This package requires having CGAL version 4.7 or higher (4.8.1 is      |                                                                                                                             |
-   |                                                                | advised for better performance).                                       |                                                                                                                             |
+   |                                                                | For performances reasons, it is advised to use CGAL ≥ 5.0.0.           |                                                                                                                             |
    +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------+
    | * :doc:`alpha_complex_user`                                    | * :doc:`alpha_complex_ref`                                                                                                                                                                           |
    +----------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+