Merge branch 'master' of https://github.com/GUDHI/gudhi-devel into extended_persistence

28 files changed, 247 insertions, 90 deletions

diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index b0337934..2eecd50c 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -32,14 +32,18 @@ if (DIFF_PATH)
 
     add_test(Alpha_complex_example_from_off_60_diff_files ${DIFF_PATH}
         ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
+    set_tests_properties(Alpha_complex_example_from_off_60_diff_files PROPERTIES DEPENDS Alpha_complex_example_from_off_60) 
     add_test(Alpha_complex_example_from_off_32_diff_files ${DIFF_PATH}
         ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
+    set_tests_properties(Alpha_complex_example_from_off_32_diff_files PROPERTIES DEPENDS Alpha_complex_example_from_off_32) 
 
     add_test(Alpha_complex_example_fast_from_off_60_diff_files ${DIFF_PATH}
         ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
+    set_tests_properties(Alpha_complex_example_fast_from_off_60_diff_files PROPERTIES DEPENDS Alpha_complex_example_fast_from_off_60) 
     add_test(Alpha_complex_example_fast_from_off_32_diff_files ${DIFF_PATH}
         ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
-  endif()
+    set_tests_properties(Alpha_complex_example_fast_from_off_32_diff_files PROPERTIES DEPENDS Alpha_complex_example_fast_from_off_32) 
+endif()
 
   add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp )
   target_link_libraries(Alpha_complex_example_weighted_3d_from_points  ${CGAL_LIBRARY})
diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt
index 57b92942..2ffbdde0 100644
--- a/src/Alpha_complex/utilities/CMakeLists.txt
+++ b/src/Alpha_complex/utilities/CMakeLists.txt
@@ -2,7 +2,7 @@ project(Alpha_complex_utilities)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
-  target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} Boost::program_options)
 
   if (TBB_FOUND)
     target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
@@ -16,14 +16,20 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   if (DIFF_PATH)
     add_test(Alpha_complex_utilities_diff_exact_alpha_complex ${DIFF_PATH}
              "exact.pers" "safe.pers")
+    set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex PROPERTIES DEPENDS
+             "Alpha_complex_utilities_exact_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence")
+             
     add_test(Alpha_complex_utilities_diff_fast_alpha_complex ${DIFF_PATH}
              "fast.pers" "safe.pers")
+    set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex PROPERTIES DEPENDS
+             "Alpha_complex_utilities_fast_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence")
+
   endif()
   
   install(TARGETS alpha_complex_persistence DESTINATION bin)
 
   add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
-  target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} Boost::program_options)
   if (TBB_FOUND)
     target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
   endif(TBB_FOUND)
@@ -36,15 +42,19 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
           "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off"
           "-p" "2" "-m" "0.45" "-o" "exact_3d.pers" "-e")
 
-  add_test(NAME Alpha_complex_utilities_safe_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
+  add_test(NAME Alpha_complex_utilities_fast_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
           "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off"
           "-p" "2" "-m" "0.45" "-o" "fast_3d.pers" "-f")
 
   if (DIFF_PATH)
     add_test(Alpha_complex_utilities_diff_exact_alpha_complex_3d ${DIFF_PATH}
             "exact_3d.pers" "safe_3d.pers")
+    set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex_3d PROPERTIES DEPENDS
+            "Alpha_complex_utilities_exact_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d")
     add_test(Alpha_complex_utilities_diff_fast_alpha_complex_3d ${DIFF_PATH}
             "fast_3d.pers" "safe_3d.pers")
+    set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex_3d PROPERTIES DEPENDS
+            "Alpha_complex_utilities_fast_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d")
   endif()
 
   add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index 3d65963a..9839c59d 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -13,7 +13,7 @@ endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   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})
+  target_link_libraries(alpha_rips_persistence_bottleneck_distance Boost::program_options)
 
   if (TBB_FOUND)
     target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
diff --git a/src/Cech_complex/benchmark/CMakeLists.txt b/src/Cech_complex/benchmark/CMakeLists.txt
index b7697764..c04bca53 100644
--- a/src/Cech_complex/benchmark/CMakeLists.txt
+++ b/src/Cech_complex/benchmark/CMakeLists.txt
@@ -5,7 +5,7 @@ project(Cech_complex_benchmark)
 file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
 add_executable(cech_complex_benchmark cech_complex_benchmark.cpp)
-target_link_libraries(cech_complex_benchmark ${Boost_SYSTEM_LIBRARY} ${Boost_FILESYSTEM_LIBRARY})
+target_link_libraries(cech_complex_benchmark Boost::filesystem)
 
 if (TBB_FOUND)
   target_link_libraries(cech_complex_benchmark ${TBB_LIBRARIES})
diff --git a/src/Cech_complex/example/CMakeLists.txt b/src/Cech_complex/example/CMakeLists.txt
index ab391215..98757988 100644
--- a/src/Cech_complex/example/CMakeLists.txt
+++ b/src/Cech_complex/example/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 2.6)
 project(Cech_complex_examples)
 
 add_executable ( Cech_complex_example_step_by_step cech_complex_step_by_step.cpp )
-target_link_libraries(Cech_complex_example_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(Cech_complex_example_step_by_step Boost::program_options)
 if (TBB_FOUND)
   target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES})
 endif()
diff --git a/src/Cech_complex/utilities/CMakeLists.txt b/src/Cech_complex/utilities/CMakeLists.txt
index 30b99729..253d7304 100644
--- a/src/Cech_complex/utilities/CMakeLists.txt
+++ b/src/Cech_complex/utilities/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 2.6)
 project(Cech_complex_utilities)
 
 add_executable(cech_persistence cech_persistence.cpp)
-target_link_libraries(cech_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(cech_persistence Boost::program_options)
 
 if (TBB_FOUND)
   target_link_libraries(cech_persistence ${TBB_LIBRARIES})
diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt
index f0dc885d..c5d31aca 100644
--- a/src/Contraction/example/CMakeLists.txt
+++ b/src/Contraction/example/CMakeLists.txt
@@ -4,7 +4,6 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
   add_executable(RipsContraction Rips_contraction.cpp)
 
   add_executable(GarlandHeckbert Garland_heckbert.cpp)
-  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")
diff --git a/src/Doxyfile.in b/src/Doxyfile.in
index ec551882..49e781bd 100644
--- a/src/Doxyfile.in
+++ b/src/Doxyfile.in
@@ -785,6 +785,7 @@ EXCLUDE                = data/                   \
 	                     GudhUI/                 \
                          cmake/                  \
                          python/                 \
+                         ext/                    \
                          README.md
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
diff --git a/src/Persistence_representations/utilities/CMakeLists.txt b/src/Persistence_representations/utilities/CMakeLists.txt
index fc51b1d6..85633b7b 100644
--- a/src/Persistence_representations/utilities/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/CMakeLists.txt
@@ -14,7 +14,7 @@ function(add_persistence_representation_creation_utility creation_utility)
     install(TARGETS ${creation_utility} DESTINATION bin)
 endfunction(add_persistence_representation_creation_utility)
 
-function(add_persistence_representation_plot_utility plot_utility tool_extension)
+function(add_persistence_representation_plot_utility creation_utility plot_utility tool_extension)
     add_executable ( ${plot_utility} ${plot_utility}.cpp )
 
     # as the function is called in a subdirectory level, need to '../' to find persistence heat maps files
@@ -22,17 +22,21 @@ function(add_persistence_representation_plot_utility plot_utility tool_extension
         "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}")
     #add_test(NAME Persistence_representation_utilities_${plot_utility}_second COMMAND $<TARGET_FILE:${plot_utility}>
     #    "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}")
+    set_tests_properties(Persistence_representation_utilities_${plot_utility}_first PROPERTIES DEPENDS
+                         Persistence_representation_utilities_${creation_utility})
     if(GNUPLOT_PATH)
         add_test(NAME Persistence_representation_utilities_${plot_utility}_first_gnuplot COMMAND ${GNUPLOT_PATH}
             "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}_GnuplotScript'")
         #add_test(NAME Persistence_representation_utilities_${plot_utility}_second_gnuplot COMMAND ${GNUPLOT_PATH}
         #    "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}_GnuplotScript'")
+        set_tests_properties(Persistence_representation_utilities_${plot_utility}_first_gnuplot PROPERTIES DEPENDS
+                             Persistence_representation_utilities_${plot_utility}_first)
     endif()
 
     install(TARGETS ${plot_utility} DESTINATION bin)
 endfunction(add_persistence_representation_plot_utility)
 
-function(add_persistence_representation_function_utility function_utility tool_extension)
+function(add_persistence_representation_function_utility creation_utility function_utility tool_extension)
     add_executable ( ${function_utility} ${function_utility}.cpp )
 
     # ARGV2 is an optional argument
@@ -48,6 +52,8 @@ function(add_persistence_representation_function_utility function_utility tool_e
             "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}"
             "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}")
     endif()
+    set_tests_properties(Persistence_representation_utilities_${function_utility} PROPERTIES DEPENDS
+                         Persistence_representation_utilities_${creation_utility})
 
     install(TARGETS ${function_utility} DESTINATION bin)
 endfunction(add_persistence_representation_function_utility)
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt
index 89ef232f..e4c471c2 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt
@@ -2,13 +2,24 @@ project(Persistence_representations_heat_maps_utilities)
 
 add_persistence_representation_creation_utility(create_pssk  "10" "-1" "-1" "4" "-1")
 add_persistence_representation_creation_utility(create_p_h_m_weighted_by_arctan_of_their_persistence "10" "-1" "-1" "4" "-1")
+
 add_persistence_representation_creation_utility(create_p_h_m_weighted_by_distance_from_diagonal "10" "-1" "-1" "4" "-1")
+# Tests output the same file
+set_tests_properties(Persistence_representation_utilities_create_p_h_m_weighted_by_distance_from_diagonal PROPERTIES DEPENDS
+                     Persistence_representation_utilities_create_p_h_m_weighted_by_arctan_of_their_persistence)
+
 add_persistence_representation_creation_utility(create_p_h_m_weighted_by_squared_diag_distance "10" "-1" "-1" "4" "-1")
+# Tests output the same file
+set_tests_properties(Persistence_representation_utilities_create_p_h_m_weighted_by_squared_diag_distance PROPERTIES DEPENDS
+                     Persistence_representation_utilities_create_p_h_m_weighted_by_distance_from_diagonal)
+
 # Need to set grid min and max for further average, distance and scalar_product
 add_persistence_representation_creation_utility(create_persistence_heat_maps "10" "0" "35" "10" "-1")
+set_tests_properties(Persistence_representation_utilities_create_persistence_heat_maps PROPERTIES DEPENDS
+                     Persistence_representation_utilities_create_p_h_m_weighted_by_squared_diag_distance)
 
-add_persistence_representation_plot_utility(plot_persistence_heat_map ".mps")
+add_persistence_representation_plot_utility(create_persistence_heat_maps plot_persistence_heat_map ".mps")
 
-add_persistence_representation_function_utility(average_persistence_heat_maps ".mps")
-add_persistence_representation_function_utility(compute_distance_of_persistence_heat_maps ".mps" "1")
-add_persistence_representation_function_utility(compute_scalar_product_of_persistence_heat_maps ".mps")
+add_persistence_representation_function_utility(create_persistence_heat_maps average_persistence_heat_maps ".mps")
+add_persistence_representation_function_utility(create_persistence_heat_maps compute_distance_of_persistence_heat_maps ".mps" "1")
+add_persistence_representation_function_utility(create_persistence_heat_maps compute_scalar_product_of_persistence_heat_maps ".mps")
diff --git a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt
index a025183e..118c1e9b 100644
--- a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt
@@ -3,17 +3,16 @@ project(Persistence_representations_intervals_utilities)
 
 add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp )
 
-add_test(NAME plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths>
+add_test(NAME Persistence_representation_utilities_plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths>
     "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1")
 
 install(TARGETS plot_histogram_of_intervals_lengths DESTINATION bin)
 
-add_persistence_representation_plot_utility(plot_persistence_intervals "")
-add_persistence_representation_plot_utility(plot_persistence_Betti_numbers "")
+add_persistence_representation_plot_utility(plot_histogram_of_intervals_lengths plot_persistence_intervals "")
+add_persistence_representation_plot_utility(plot_histogram_of_intervals_lengths plot_persistence_Betti_numbers "")
 
 add_persistence_representation_creation_utility(compute_birth_death_range_in_persistence_diagram "-1")
 
-
 add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp )
 add_test(NAME Persistence_representation_utilities_compute_number_of_dominant_intervals
     COMMAND $<TARGET_FILE:compute_number_of_dominant_intervals>
diff --git a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt
index 6b24d032..4df84d36 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt
@@ -2,8 +2,8 @@ project(Persistence_representations_landscapes_utilities)
 
 add_persistence_representation_creation_utility(create_landscapes "-1")
 
-add_persistence_representation_plot_utility(plot_landscapes ".land")
+add_persistence_representation_plot_utility(create_landscapes plot_landscapes ".land")
 
-add_persistence_representation_function_utility(average_landscapes ".land")
-add_persistence_representation_function_utility(compute_distance_of_landscapes ".land" "1")
-add_persistence_representation_function_utility(compute_scalar_product_of_landscapes ".land")
+add_persistence_representation_function_utility(create_landscapes average_landscapes ".land")
+add_persistence_representation_function_utility(create_landscapes compute_distance_of_landscapes ".land" "1")
+add_persistence_representation_function_utility(create_landscapes compute_scalar_product_of_landscapes ".land")
diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt
index 36f3196b..8cd965f1 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt
@@ -3,8 +3,8 @@ project(Persistence_representations_lanscapes_on_grid_utilities)
 # Need to set grid min and max for further average, distance and scalar_product
 add_persistence_representation_creation_utility(create_landscapes_on_grid "100" "0" "35" "-1")
 
-add_persistence_representation_plot_utility(plot_landscapes_on_grid ".g_land")
+add_persistence_representation_plot_utility(create_landscapes_on_grid plot_landscapes_on_grid ".g_land")
 
-add_persistence_representation_function_utility(average_landscapes_on_grid ".g_land")
-add_persistence_representation_function_utility(compute_distance_of_landscapes_on_grid ".g_land" "1")
-add_persistence_representation_function_utility(compute_scalar_product_of_landscapes_on_grid ".g_land")
+add_persistence_representation_function_utility(create_landscapes_on_grid average_landscapes_on_grid ".g_land")
+add_persistence_representation_function_utility(create_landscapes_on_grid compute_distance_of_landscapes_on_grid ".g_land" "1")
+add_persistence_representation_function_utility(create_landscapes_on_grid compute_scalar_product_of_landscapes_on_grid ".g_land")
diff --git a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt
index bc982094..5b22ca84 100644
--- a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt
@@ -2,8 +2,8 @@ project(Persistence_vectors_utilities)
 
 add_persistence_representation_creation_utility(create_persistence_vectors "-1")
 
-add_persistence_representation_plot_utility(plot_persistence_vectors ".vect")
+add_persistence_representation_plot_utility(create_persistence_vectors plot_persistence_vectors ".vect")
 
-add_persistence_representation_function_utility(average_persistence_vectors ".vect")
-add_persistence_representation_function_utility(compute_distance_of_persistence_vectors ".vect" "1")
-add_persistence_representation_function_utility(compute_scalar_product_of_persistence_vectors ".vect")
+add_persistence_representation_function_utility(create_persistence_vectors average_persistence_vectors ".vect")
+add_persistence_representation_function_utility(create_persistence_vectors compute_distance_of_persistence_vectors ".vect" "1")
+add_persistence_representation_function_utility(create_persistence_vectors compute_scalar_product_of_persistence_vectors ".vect")
diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt
index 2bb3b0c7..f38cc543 100644
--- a/src/Persistent_cohomology/benchmark/CMakeLists.txt
+++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt
@@ -3,7 +3,7 @@ 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_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+      target_link_libraries(performance_rips_persistence Boost::program_options ${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 94ec13c5..4c08cd68 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -5,13 +5,13 @@ add_executable(plain_homology plain_homology.cpp)
 add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
 
 add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp)
-target_link_libraries(rips_persistence_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_persistence_step_by_step Boost::program_options)
 
 add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp)
-target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_persistence_via_boundary_matrix Boost::program_options)
 
 add_executable(persistence_from_file persistence_from_file.cpp)
-target_link_libraries(persistence_from_file ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(persistence_from_file Boost::program_options)
 
 if (TBB_FOUND)
   target_link_libraries(plain_homology ${TBB_LIBRARIES})
@@ -43,7 +43,7 @@ if(GMP_FOUND)
    if(GMPXX_FOUND)
       add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
       target_link_libraries(rips_multifield_persistence
-          ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+          Boost::program_options ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
       if (TBB_FOUND)
         target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
       endif(TBB_FOUND)
diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt
index e7772bdb..244a93ec 100644
--- a/src/Rips_complex/example/CMakeLists.txt
+++ b/src/Rips_complex/example/CMakeLists.txt
@@ -53,15 +53,23 @@ if (DIFF_PATH)
   add_test(Rips_complex_example_from_off_doc_12_1_diff_files ${DIFF_PATH}
       ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt
       ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt)
+  set_tests_properties(Rips_complex_example_from_off_doc_12_1_diff_files PROPERTIES DEPENDS Rips_complex_example_from_off_doc_12_1) 
+
   add_test(Rips_complex_example_from_off_doc_12_3_diff_files ${DIFF_PATH}
       ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt
       ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt)
+  set_tests_properties(Rips_complex_example_from_off_doc_12_3_diff_files PROPERTIES DEPENDS Rips_complex_example_from_off_doc_12_3) 
+
   add_test(Rips_complex_example_from_csv_distance_matrix_doc_12_1_diff_files ${DIFF_PATH}
       ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt
       ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt)
+  set_tests_properties(Rips_complex_example_from_csv_distance_matrix_doc_12_1_diff_files PROPERTIES DEPENDS Rips_complex_example_from_csv_distance_matrix_doc_12_1) 
+
   add_test(Rips_complex_example_from_csv_distance_matrix_doc_12_3_diff_files ${DIFF_PATH}
       ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt
       ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt)
+  set_tests_properties(Rips_complex_example_from_csv_distance_matrix_doc_12_3_diff_files PROPERTIES DEPENDS Rips_complex_example_from_csv_distance_matrix_doc_12_3) 
+
 endif()
 
 install(TARGETS Rips_complex_example_from_off DESTINATION bin)
diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt
index 4b565628..d2448d7b 100644
--- a/src/Rips_complex/utilities/CMakeLists.txt
+++ b/src/Rips_complex/utilities/CMakeLists.txt
@@ -1,16 +1,16 @@
 project(Rips_complex_utilities)
 
 add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp)
-target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_distance_matrix_persistence Boost::program_options)
 
 add_executable(rips_persistence rips_persistence.cpp)
-target_link_libraries(rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_persistence Boost::program_options)
 
 add_executable(rips_correlation_matrix_persistence rips_correlation_matrix_persistence.cpp)
-target_link_libraries(rips_correlation_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_correlation_matrix_persistence Boost::system Boost::program_options)
 
 add_executable(sparse_rips_persistence sparse_rips_persistence.cpp)
-target_link_libraries(sparse_rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(sparse_rips_persistence Boost::program_options)
 
 if (TBB_FOUND)
   target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES})
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index 8a8cac58..a0aabee2 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -35,7 +35,7 @@ endif()
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   add_executable ( Simplex_tree_example_cech_complex_cgal_mini_sphere_3d cech_complex_cgal_mini_sphere_3d.cpp )
-  target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${Boost_PROGRAM_OPTIONS_LIBRARY} ${CGAL_LIBRARY})
+  target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d Boost::program_options ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${TBB_LIBRARIES})
   endif()
diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt
index 3ee0c2f6..d986d2d1 100644
--- a/src/Witness_complex/utilities/CMakeLists.txt
+++ b/src/Witness_complex/utilities/CMakeLists.txt
@@ -4,10 +4,10 @@ project(Witness_complex_utilities)
 if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   
   add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp )
-  target_link_libraries(Witness_complex_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(Witness_complex_strong_witness_persistence Boost::program_options)
 
   add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp )
-  target_link_libraries(Witness_complex_weak_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(Witness_complex_weak_witness_persistence Boost::program_options)
 
   if (TBB_FOUND)
     target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES})
diff --git a/src/cmake/modules/GUDHI_boost_test.cmake b/src/cmake/modules/GUDHI_boost_test.cmake
index c3b29883..4a13404b 100644
--- a/src/cmake/modules/GUDHI_boost_test.cmake
+++ b/src/cmake/modules/GUDHI_boost_test.cmake
@@ -9,7 +9,6 @@ if (WITH_GUDHI_BOOST_TEST_COVERAGE)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
   endif()
   set(GUDHI_UT_LOG_FORMAT "--log_format=XML")
-  set(GUDHI_UT_LOG_SINK "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml")
   set(GUDHI_UT_LOG_LEVEL "--log_level=test_suite")
   set(GUDHI_UT_REPORT_LEVEL "--report_level=no")
 else (WITH_GUDHI_BOOST_TEST_COVERAGE)
@@ -19,7 +18,11 @@ else (WITH_GUDHI_BOOST_TEST_COVERAGE)
 endif(WITH_GUDHI_BOOST_TEST_COVERAGE)
 
 function(gudhi_add_boost_test unitary_test)
-  target_link_libraries(${unitary_test} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  if (WITH_GUDHI_BOOST_TEST_COVERAGE)
+    set(GUDHI_UT_LOG_SINK "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml")
+  endif(WITH_GUDHI_BOOST_TEST_COVERAGE)
+  
+  target_link_libraries(${unitary_test} Boost::unit_test_framework)
   add_test(NAME ${unitary_test} COMMAND $<TARGET_FILE:${unitary_test}>
       ${GUDHI_UT_LOG_FORMAT} ${GUDHI_UT_LOG_SINK}
       ${GUDHI_UT_LOG_LEVEL} ${GUDHI_UT_REPORT_LEVEL})
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 359d1c12..6db2c76b 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -6,6 +6,38 @@ if(NOT Boost_FOUND)
   message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
 endif(NOT Boost_FOUND)
 
+# cf. https://cliutils.gitlab.io/modern-cmake/chapters/packages/Boost.html
+# This is needed if your Boost version is newer than your CMake version
+# or if you have an old version of CMake (<3.5)
+if(NOT TARGET Boost::program_options)
+    add_library(Boost::program_options IMPORTED INTERFACE)
+    set_property(TARGET Boost::program_options PROPERTY
+        INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
+    set_property(TARGET Boost::program_options PROPERTY
+        INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES})
+endif()
+if(NOT TARGET Boost::filesystem)
+    add_library(Boost::filesystem IMPORTED INTERFACE)
+    set_property(TARGET Boost::filesystem PROPERTY
+        INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
+    set_property(TARGET Boost::filesystem PROPERTY
+        INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES})
+endif()
+if(NOT TARGET Boost::unit_test_framework)
+    add_library(Boost::unit_test_framework IMPORTED INTERFACE)
+    set_property(TARGET Boost::unit_test_framework PROPERTY
+        INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
+    set_property(TARGET Boost::unit_test_framework PROPERTY
+        INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES})
+endif()
+if(NOT TARGET Boost::system)
+    add_library(Boost::system IMPORTED INTERFACE)
+    set_property(TARGET Boost::system PROPERTY
+        INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
+    set_property(TARGET Boost::system PROPERTY
+        INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES})
+endif()
+
 find_package(GMP)
 if(GMP_FOUND)
   INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
@@ -85,9 +117,6 @@ 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})
-
 message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
 message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
 
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
index 583a0027..fa8eb98c 100644
--- a/src/common/example/CMakeLists.txt
+++ b/src/common/example/CMakeLists.txt
@@ -12,6 +12,7 @@ if (DIFF_PATH)
 
   add_test(Common_example_vector_double_off_reader_diff_files ${DIFF_PATH}
       ${CMAKE_CURRENT_BINARY_DIR}/vectordoubleoffreader_result.txt ${CMAKE_CURRENT_BINARY_DIR}/alphacomplexdoc.off.txt)
+  set_tests_properties(Common_example_vector_double_off_reader_diff_files PROPERTIES DEPENDS Common_example_vector_double_off_reader) 
 endif()
 
 if(NOT CGAL_VERSION VERSION_LESS 4.11.0)
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 090a7446..20e72a5f 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -181,7 +181,7 @@ if(PYTHONINTERP_FOUND)
         set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${MPFR_LIBRARIES_DIR}', ")
         message("** Add mpfr ${MPFR_LIBRARIES}")
       endif(MPFR_FOUND)
-endif(CGAL_FOUND)
+    endif(CGAL_FOUND)
 
     # Specific for Mac
     if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
diff --git a/src/python/doc/persistence_graphical_tools_sum.inc b/src/python/doc/persistence_graphical_tools_sum.inc
index 0cdf8072..ef376802 100644
--- a/src/python/doc/persistence_graphical_tools_sum.inc
+++ b/src/python/doc/persistence_graphical_tools_sum.inc
@@ -2,11 +2,11 @@
    :widths: 30 50 20
 
    +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+
-   | .. figure::                                                     | These graphical tools comes on top of persistence results and allows  | :Author: Vincent Rouvreau                     |
-   |      img/graphical_tools_representation.png                     | the user to build easily persistence barcode, diagram or density.     |                                               |
+   | .. figure::                                                     | These graphical tools comes on top of persistence results and allows  | :Author: Vincent Rouvreau, Theo Lacombe       |
+   |      img/graphical_tools_representation.png                     | the user to display easily persistence barcode, diagram or density.   |                                               |
    |                                                                 |                                                                       | :Introduced in: GUDHI 2.0.0                   |
-   |                                                                 |                                                                       |                                               |
-   |                                                                 |                                                                       | :Copyright: MIT                               |
+   |                                                                 | Note that these functions return the matplotlib axis, allowing        |                                               |
+   |                                                                 | for further modifications (title, aspect, etc.)                       | :Copyright: MIT                               |
    |                                                                 |                                                                       |                                               |
    |                                                                 |                                                                       | :Requires: matplotlib, numpy and scipy        |
    +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+
diff --git a/src/python/doc/persistence_graphical_tools_user.rst b/src/python/doc/persistence_graphical_tools_user.rst
index 80002db6..91e52703 100644
--- a/src/python/doc/persistence_graphical_tools_user.rst
+++ b/src/python/doc/persistence_graphical_tools_user.rst
@@ -20,7 +20,7 @@ This function can display the persistence result as a barcode:
 .. plot::
    :include-source:
 
-    import matplotlib.pyplot as plot
+    import matplotlib.pyplot as plt
     import gudhi
 
     off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off'
@@ -31,7 +31,7 @@ This function can display the persistence result as a barcode:
     diag = simplex_tree.persistence(min_persistence=0.4)
 
     gudhi.plot_persistence_barcode(diag)
-    plot.show()
+    plt.show()
 
 Show persistence as a diagram
 -----------------------------
@@ -44,15 +44,31 @@ This function can display the persistence result as a diagram:
 .. plot::
    :include-source:
 
-    import matplotlib.pyplot as plot
+    import matplotlib.pyplot as plt
     import gudhi
 
     # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method
     persistence_file=gudhi.__root_source_dir__ + \
         '/data/persistence_diagram/rips_on_tore3D_1307.pers'
-    gudhi.plot_persistence_diagram(persistence_file=persistence_file,
+    ax = gudhi.plot_persistence_diagram(persistence_file=persistence_file,
         legend=True)
-    plot.show()
+    # We can modify the title, aspect, etc.
+    ax.set_title("Persistence diagram of a torus")
+    ax.set_aspect("equal")  # forces to be square shaped
+    plt.show()
+
+Note that (as barcode and density) it can also take a simple `np.array` 
+of shape (N x 2) encoding a persistence diagram (in a given dimension).
+
+.. plot::
+    :include-source:
+    
+    import matplotlib.pyplot as plt
+    import gudhi
+    import numpy as np
+    d = np.array([[0, 1], [1, 2], [1, np.inf]])
+    gudhi.plot_persistence_diagram(d)
+    plt.show()
 
 Persistence density
 -------------------
@@ -65,7 +81,7 @@ If you want more information on a specific dimension, for instance:
 .. plot::
    :include-source:
 
-    import matplotlib.pyplot as plot
+    import matplotlib.pyplot as plt
     import gudhi
     # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method
     persistence_file=gudhi.__root_source_dir__ + \
@@ -75,9 +91,9 @@ If you want more information on a specific dimension, for instance:
         only_this_dim=1)
     pers_diag = [(1, elt) for elt in birth_death]
     # Use subplots to display diagram and density side by side
-    fig, axes = plot.subplots(nrows=1, ncols=2, figsize=(12, 5))
+    fig, axes = plt.subplots(nrows=1, ncols=2, figsize=(12, 5))
     gudhi.plot_persistence_diagram(persistence=pers_diag,
         axes=axes[0])
     gudhi.plot_persistence_density(persistence=pers_diag,
         dimension=1, legend=True, axes=axes[1])
-    plot.show()
+    plt.show()
diff --git a/src/python/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx
index 382e71c5..45cc8eba 100644
--- a/src/python/gudhi/nerve_gic.pyx
+++ b/src/python/gudhi/nerve_gic.pyx
@@ -187,7 +187,7 @@ cdef class CoverComplex:
 
     def set_automatic_resolution(self):
         """Computes the optimal length of intervals (i.e. the smallest interval
-        length avoiding discretization artifacts—see :cite:`Carriere17c`) for a
+        length avoiding discretization artifacts - see :cite:`Carriere17c`) for a
         functional cover.
 
         :rtype: double
@@ -288,7 +288,7 @@ cdef class CoverComplex:
 
     def set_graph_from_automatic_rips(self, N=100):
         """Creates a graph G from a Rips complex whose threshold value is
-        automatically tuned with subsampling—see.
+        automatically tuned with subsampling - see :cite:`Carriere17c`.
 
         :param N: Number of subsampling iteration (the default reasonable value
             is 100, but there is no guarantee on how to choose it).
diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py
index 246280de..cc3db467 100644
--- a/src/python/gudhi/persistence_graphical_tools.py
+++ b/src/python/gudhi/persistence_graphical_tools.py
@@ -5,6 +5,7 @@
 # Copyright (C) 2016 Inria
 #
 # Modification(s):
+#   - 2020/02 Theo Lacombe: Added more options for improved rendering and more flexibility.
 #   - YYYY/MM Author: Description of the modification
 
 from os import path
@@ -14,7 +15,7 @@ import numpy as np
 from gudhi.reader_utils import read_persistence_intervals_in_dimension
 from gudhi.reader_utils import read_persistence_intervals_grouped_by_dimension
 
-__author__ = "Vincent Rouvreau, Bertrand Michel"
+__author__ = "Vincent Rouvreau, Bertrand Michel, Theo Lacombe"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
 
@@ -43,6 +44,19 @@ def __min_birth_max_death(persistence, band=0.0):
         max_death += band
     return (min_birth, max_death)
 
+
+def _array_handler(a):
+    '''
+    :param a: if array, assumes it is a (n x 2) np.array and return a
+                persistence-compatible list (padding with 0), so that the
+                plot can be performed seamlessly.
+    '''
+    if isinstance(a[0][1], np.float64) or isinstance(a[0][1], float):
+        return [[0, x] for x in a]
+    else:
+        return a
+
+
 def plot_persistence_barcode(
     persistence=[],
     persistence_file="",
@@ -52,13 +66,16 @@ def plot_persistence_barcode(
     inf_delta=0.1,
     legend=False,
     colormap=None,
-    axes=None
+    axes=None,
+    fontsize=16,
 ):
     """This function plots the persistence bar code from persistence values list
+    , a np.array of shape (N x 2) (representing a diagram 
+    in a single homology dimension), 
     or from a :doc:`persistence file <fileformats>`.
 
-    :param persistence: Persistence intervals values list grouped by dimension.
-    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence: Persistence intervals values list. Can be grouped by dimension or not.
+    :type persistence: an array of (dimension, array of (birth, death)) or an array of (birth, death).
     :param persistence_file: A :doc:`persistence file <fileformats>` style name
         (reset persistence if both are set).
     :type persistence_file: string
@@ -81,11 +98,19 @@ def plot_persistence_barcode(
     :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on
         a new set of axes.
     :type axes: `matplotlib.axes.Axes`
+    :param fontsize: Fontsize to use in axis.
+    :type fontsize: int
     :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn.
     """
     try:
         import matplotlib.pyplot as plt
         import matplotlib.patches as mpatches
+        from matplotlib import rc
+        plt.rc('text', usetex=True)
+        plt.rc('font', family='serif')
+
+
+        persistence = _array_handler(persistence)
 
         if persistence_file != "":
             if path.isfile(persistence_file):
@@ -163,7 +188,7 @@ def plot_persistence_barcode(
                 loc="lower right",
             )
 
-        axes.set_title("Persistence barcode")
+        axes.set_title("Persistence barcode", fontsize=fontsize)
 
         # Ends plot on infinity value and starts a little bit before min_birth
         axes.axis([axis_start, infinity, 0, ind])
@@ -183,13 +208,16 @@ def plot_persistence_diagram(
     inf_delta=0.1,
     legend=False,
     colormap=None,
-    axes=None
+    axes=None,
+    fontsize=16,
+    greyblock=True
 ):
     """This function plots the persistence diagram from persistence values
-    list or from a :doc:`persistence file <fileformats>`.
+    list, a np.array of shape (N x 2) representing a diagram in a single
+    homology dimension, or from a :doc:`persistence file <fileformats>`.
 
-    :param persistence: Persistence intervals values list grouped by dimension.
-    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence: Persistence intervals values list. Can be grouped by dimension or not.
+    :type persistence: an array of (dimension, array of (birth, death)) or an array of (birth, death).
     :param persistence_file: A :doc:`persistence file <fileformats>` style name
         (reset persistence if both are set).
     :type persistence_file: string
@@ -214,11 +242,20 @@ def plot_persistence_diagram(
     :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on
         a new set of axes.
     :type axes: `matplotlib.axes.Axes`
+    :param fontsize: Fontsize to use in axis.
+    :type fontsize: int
+    :param greyblock: if we want to plot a grey patch on the lower half plane for nicer rendering. Default True.
+    :type greyblock: boolean
     :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn.
     """
     try:
         import matplotlib.pyplot as plt
         import matplotlib.patches as mpatches
+        from matplotlib import rc
+        plt.rc('text', usetex=True)
+        plt.rc('font', family='serif')
+
+        persistence = _array_handler(persistence)
 
         if persistence_file != "":
             if path.isfile(persistence_file):
@@ -256,19 +293,18 @@ def plot_persistence_diagram(
         # Replace infinity values with max_death + delta for diagram to be more
         # readable
         infinity = max_death + delta
+        axis_end = max_death + delta / 2
         axis_start = min_birth - delta
 
-        # line display of equation : birth = death
-        x = np.linspace(axis_start, infinity, 1000)
-        # infinity line and text
-        axes.plot(x, x, color="k", linewidth=1.0)
-        axes.plot(x, [infinity] * len(x), linewidth=1.0, color="k", alpha=alpha)
-        axes.text(axis_start, infinity, r"$\infty$", color="k", alpha=alpha)
         # bootstrap band
         if band > 0.0:
+            x = np.linspace(axis_start, infinity, 1000)
             axes.fill_between(x, x, x + band, alpha=alpha, facecolor="red")
-
+        # lower diag patch
+        if greyblock:
+            axes.add_patch(mpatches.Polygon([[axis_start, axis_start], [axis_end, axis_start], [axis_end, axis_end]], fill=True, color='lightgrey'))
         # Draw points in loop
+        pts_at_infty = False  # Records presence of pts at infty
         for interval in reversed(persistence):
             if float(interval[1][1]) != float("inf"):
                 # Finite death case
@@ -279,10 +315,23 @@ def plot_persistence_diagram(
                     color=colormap[interval[0]],
                 )
             else:
+                pts_at_infty = True
                 # Infinite death case for diagram to be nicer
                 axes.scatter(
                     interval[1][0], infinity, alpha=alpha, color=colormap[interval[0]]
                 )
+        if pts_at_infty:
+            # infinity line and text
+            axes.plot([axis_start, axis_end], [axis_start, axis_end], linewidth=1.0, color="k")
+            axes.plot([axis_start, axis_end], [infinity, infinity], linewidth=1.0, color="k", alpha=alpha)
+            # Infinity label
+            yt = axes.get_yticks()
+            yt = yt[np.where(yt < axis_end)] # to avoid ploting ticklabel higher than infinity
+            yt = np.append(yt, infinity)
+            ytl = ["%.3f" % e for e in yt]  # to avoid float precision error
+            ytl[-1] = r'$+\infty$'
+            axes.set_yticks(yt)
+            axes.set_yticklabels(ytl)
 
         if legend:
             dimensions = list(set(item[0] for item in persistence))
@@ -293,11 +342,11 @@ def plot_persistence_diagram(
                 ]
             )
 
-        axes.set_xlabel("Birth")
-        axes.set_ylabel("Death")
+        axes.set_xlabel("Birth", fontsize=fontsize)
+        axes.set_ylabel("Death", fontsize=fontsize)
+        axes.set_title("Persistence diagram", fontsize=fontsize)
         # Ends plot on infinity value and starts a little bit before min_birth
-        axes.axis([axis_start, infinity, axis_start, infinity + delta])
-        axes.set_title("Persistence diagram")
+        axes.axis([axis_start, axis_end, axis_start, infinity + delta/2])
         return axes
 
     except ImportError:
@@ -313,16 +362,22 @@ def plot_persistence_density(
     dimension=None,
     cmap=None,
     legend=False,
-    axes=None
+    axes=None,
+    fontsize=16,
+    greyblock=False
 ):
     """This function plots the persistence density from persistence
-    values list or from a :doc:`persistence file <fileformats>`. Be
+    values list, np.array of shape (N x 2) representing a diagram
+    in a single homology dimension,
+    or from a :doc:`persistence file <fileformats>`. Be
     aware that this function does not distinguish the dimension, it is
     up to you to select the required one. This function also does not handle
     degenerate data set (scipy correlation matrix inversion can fail).
 
-    :param persistence: Persistence intervals values list grouped by dimension.
-    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence: Persistence intervals values list. 
+                        Can be grouped by dimension or not.
+    :type persistence: an array of (dimension, array of (birth, death)) 
+                        or an array of (birth, death).
     :param persistence_file: A :doc:`persistence file <fileformats>`
         style name (reset persistence if both are set).
     :type persistence_file: string
@@ -355,11 +410,22 @@ def plot_persistence_density(
     :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on
         a new set of axes.
     :type axes: `matplotlib.axes.Axes`
+    :param fontsize: Fontsize to use in axis.
+    :type fontsize: int
+    :param greyblock: if we want to plot a grey patch on the lower half plane 
+                         for nicer rendering. Default False.
+    :type greyblock: boolean
     :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn.
     """
     try:
         import matplotlib.pyplot as plt
+        import matplotlib.patches as mpatches
         from scipy.stats import kde
+        from matplotlib import rc
+        plt.rc('text', usetex=True)
+        plt.rc('font', family='serif')
+
+        persistence = _array_handler(persistence)
 
         if persistence_file != "":
             if dimension is None:
@@ -418,12 +484,16 @@ def plot_persistence_density(
         # Make the plot
         img = axes.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
 
+        if greyblock:
+            axes.add_patch(mpatches.Polygon([[birth.min(), birth.min()], [death.max(), birth.min()], [death.max(), death.max()]], fill=True, color='lightgrey'))
+
         if legend:
             plt.colorbar(img, ax=axes)
 
-        axes.set_xlabel("Birth")
-        axes.set_ylabel("Death")
-        axes.set_title("Persistence density")
+        axes.set_xlabel("Birth", fontsize=fontsize)
+        axes.set_ylabel("Death", fontsize=fontsize)
+        axes.set_title("Persistence density", fontsize=fontsize)
+
         return axes
 
     except ImportError: