Merge remote-tracking branch 'upstream/master' into gspr/exact-betti-curve

1 files changed, 107 insertions, 84 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index e0e88880..26b8b7d6 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -41,13 +41,15 @@ function( add_gudhi_debug_info DEBUG_INFO )
 endfunction( add_gudhi_debug_info )
 
 if(PYTHONINTERP_FOUND)
-  if(PYBIND11_FOUND)
+  if(PYBIND11_FOUND AND CYTHON_FOUND)
     add_gudhi_debug_info("Pybind11 version ${PYBIND11_VERSION}")
+    # PyBind11 modules
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'bottleneck', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'hera', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'clustering', ")
-  endif()
-  if(CYTHON_FOUND)
+    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'datasets', ")
+
+    # Cython modules
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_reader', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'simplex_tree', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'rips_complex', ")
@@ -106,6 +108,16 @@ if(PYTHONINTERP_FOUND)
     if(TENSORFLOW_FOUND)
       add_gudhi_debug_info("TensorFlow version ${TENSORFLOW_VERSION}")
     endif()
+    if(SPHINX_FOUND)
+      add_gudhi_debug_info("Sphinx version ${SPHINX_VERSION}")
+    endif()
+    if(SPHINX_PARAMLINKS_FOUND)
+      add_gudhi_debug_info("Sphinx-paramlinks version ${SPHINX_PARAMLINKS_VERSION}")
+    endif()
+    if(PYTHON_DOCS_THEME_FOUND)
+      # Does not have a version number...
+      add_gudhi_debug_info("python_docs_theme found")
+    endif()
 
     set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
     set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
@@ -151,6 +163,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/wasserstein', ")
     set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/bottleneck', ")
     if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
+      set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'datasets/generators/_points', ")
       set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'bottleneck', ")
       set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ")
     endif ()
@@ -262,9 +275,12 @@ if(PYTHONINTERP_FOUND)
     file(COPY "gudhi/weighted_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/dtm_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/hera/__init__.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/hera")
+    file(COPY "gudhi/datasets" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi" FILES_MATCHING PATTERN "*.py")
+
 
     # Some files for pip package
     file(COPY "introduction.rst" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
+    file(COPY "pyproject.toml" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
 
     add_custom_command(
         OUTPUT gudhi.so
@@ -274,67 +290,69 @@ if(PYTHONINTERP_FOUND)
     add_custom_target(python ALL DEPENDS gudhi.so
                       COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
 
-    install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)")
-
+  set(GUDHI_PYTHON_PATH_ENV "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PYTHONPATH}")
   # Documentation generation is available through sphinx - requires all modules
   # Make it first as sphinx test is by far the longest test which is nice when testing in parallel
   if(SPHINX_PATH)
-    if(MATPLOTLIB_FOUND)
-      if(NUMPY_FOUND)
-        if(SCIPY_FOUND)
-          if(SKLEARN_FOUND)
-            if(OT_FOUND)
-              if(PYBIND11_FOUND)
-                if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
-                  set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
-                  # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
-                  # Images and biblio warnings because not found on developper version
-                  if (GUDHI_PYTHON_PATH STREQUAL "src/python")
-                    set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
-                  endif()
-                  # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
-                  add_custom_target(sphinx
-                      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
-                      COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-                      ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
-                      DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
-                      COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
-
-                  add_test(NAME sphinx_py_test
-                           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-                           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-                           ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
-
-                  # Set missing or not modules
-                  set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES")
-                else(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
-                  message("++ Python documentation module will not be compiled because it requires a Eigen3 and CGAL version >= 4.11.0")
+    if(SPHINX_PARAMLINKS_FOUND)
+      if(PYTHON_DOCS_THEME_FOUND)
+        if(MATPLOTLIB_FOUND)
+          if(NUMPY_FOUND)
+            if(SCIPY_FOUND)
+              if(SKLEARN_FOUND)
+                if(OT_FOUND)
+                  if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+                    set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
+                    # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
+                    # Images and biblio warnings because not found on developper version
+                    if (GUDHI_PYTHON_PATH STREQUAL "src/python")
+                      set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
+                    endif()
+                    # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
+                    add_custom_target(sphinx
+                        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
+                        COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
+                        ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
+                        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+                        COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
+                    add_test(NAME sphinx_py_test
+                             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
+                             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
+                    # Set missing or not modules
+                    set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES")
+                  else(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+                    message("++ Python documentation module will not be compiled because it requires a Eigen3 and CGAL version >= 4.11.0")
+                    set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+                  endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+                else(OT_FOUND)
+                  message("++ Python documentation module will not be compiled because POT was not found")
                   set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
-                endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
-              else(PYBIND11_FOUND)
-                message("++ Python documentation module will not be compiled because pybind11 was not found")
+                endif(OT_FOUND)
+              else(SKLEARN_FOUND)
+                message("++ Python documentation module will not be compiled because scikit-learn was not found")
                 set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
-              endif(PYBIND11_FOUND)
-            else(OT_FOUND)
-              message("++ Python documentation module will not be compiled because POT was not found")
+              endif(SKLEARN_FOUND)
+            else(SCIPY_FOUND)
+              message("++ Python documentation module will not be compiled because scipy was not found")
               set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
-            endif(OT_FOUND)
-          else(SKLEARN_FOUND)
-            message("++ Python documentation module will not be compiled because scikit-learn was not found")
+            endif(SCIPY_FOUND)
+          else(NUMPY_FOUND)
+            message("++ Python documentation module will not be compiled because numpy was not found")
             set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
-          endif(SKLEARN_FOUND)
-        else(SCIPY_FOUND)
-          message("++ Python documentation module will not be compiled because scipy was not found")
+          endif(NUMPY_FOUND)
+        else(MATPLOTLIB_FOUND)
+          message("++ Python documentation module will not be compiled because matplotlib was not found")
           set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
-        endif(SCIPY_FOUND)
-      else(NUMPY_FOUND)
-        message("++ Python documentation module will not be compiled because numpy was not found")
+        endif(MATPLOTLIB_FOUND)
+      else(PYTHON_DOCS_THEME_FOUND)
+        message("++ Python documentation module will not be compiled because python-docs-theme was not found")
         set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
-      endif(NUMPY_FOUND)
-    else(MATPLOTLIB_FOUND)
-      message("++ Python documentation module will not be compiled because matplotlib was not found")
+      endif(PYTHON_DOCS_THEME_FOUND)
+    else(SPHINX_PARAMLINKS_FOUND)
+      message("++ Python documentation module will not be compiled because sphinxcontrib-paramlinks was not found")
       set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
-    endif(MATPLOTLIB_FOUND)
+    endif(SPHINX_PARAMLINKS_FOUND)
   else(SPHINX_PATH)
     message("++ Python documentation module will not be compiled because sphinx and sphinxcontrib-bibtex were not found")
     set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
@@ -346,13 +364,13 @@ if(PYTHONINTERP_FOUND)
       # Bottleneck and Alpha
       add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
                -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
       # Tangential
       add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
                --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
 
@@ -361,13 +379,13 @@ if(PYTHONINTERP_FOUND)
       # Witness complex
       add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
                --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
 
       add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
                --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
 
@@ -379,12 +397,10 @@ if(PYTHONINTERP_FOUND)
       # Bottleneck
       add_test(NAME bottleneck_basic_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
 
-      if (PYBIND11_FOUND)
-        add_gudhi_py_test(test_bottleneck_distance)
-      endif()
+      add_gudhi_py_test(test_bottleneck_distance)
 
       # Cover complex
       file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
@@ -392,26 +408,26 @@ if(PYTHONINTERP_FOUND)
       file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
       add_test(NAME cover_complex_nerve_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
                -f human.off -c 2 -r 10 -g 0.3)
 
       add_test(NAME cover_complex_coordinate_gic_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
                -f human.off -c 0 -v)
 
       add_test(NAME cover_complex_functional_gic_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
                -o lucky_cat.off
                -f lucky_cat_PCA1 -v)
 
       add_test(NAME cover_complex_voronoi_gic_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
                -f human.off -n 700 -v)
 
@@ -422,13 +438,17 @@ if(PYTHONINTERP_FOUND)
       # Alpha
       add_test(NAME alpha_complex_from_points_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
+      add_test(NAME alpha_complex_from_generated_points_on_sphere_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_generated_points_on_sphere_example.py")
       add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
       add_gudhi_py_test(test_alpha_complex)
     endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
 
@@ -436,18 +456,21 @@ if(PYTHONINTERP_FOUND)
       # Euclidean witness
       add_gudhi_py_test(test_euclidean_witness_complex)
 
+      # Datasets generators
+      add_gudhi_py_test(test_datasets_generators) # TODO separate full python datasets generators in another test file independant from CGAL ?
+
     endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
 
     # Cubical
     add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
              --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
 
     add_test(NAME random_cubical_complex_persistence_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
              10 10 10)
 
@@ -456,19 +479,19 @@ if(PYTHONINTERP_FOUND)
     # Rips
     add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -s , -e 12.0 -d 3)
 
     add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
 
     add_test(NAME rips_complex_from_points_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
 
     add_gudhi_py_test(test_rips_complex)
@@ -476,7 +499,7 @@ if(PYTHONINTERP_FOUND)
     # Simplex tree
     add_test(NAME simplex_tree_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
 
     add_gudhi_py_test(test_simplex_tree)
@@ -485,7 +508,7 @@ if(PYTHONINTERP_FOUND)
     # Witness
     add_test(NAME witness_complex_from_nearest_landmark_table_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
 
     add_gudhi_py_test(test_witness_complex)
@@ -494,14 +517,14 @@ if(PYTHONINTERP_FOUND)
     add_gudhi_py_test(test_reader_utils)
 
     # Wasserstein
-    if(OT_FOUND AND PYBIND11_FOUND)
+    if(OT_FOUND)
       # EagerPy dependency because of enable_autodiff=True
       if(EAGERPY_FOUND)
         add_gudhi_py_test(test_wasserstein_distance)
       endif()
+
       add_gudhi_py_test(test_wasserstein_barycenter)
-    endif()
-    if(OT_FOUND)
+
       if(TORCH_FOUND AND TENSORFLOW_FOUND AND EAGERPY_FOUND)
         add_gudhi_py_test(test_wasserstein_with_tensors)
       endif()
@@ -527,7 +550,7 @@ if(PYTHONINTERP_FOUND)
     endif()
 
     # Tomato
-    if(SCIPY_FOUND AND SKLEARN_FOUND AND PYBIND11_FOUND)
+    if(SCIPY_FOUND AND SKLEARN_FOUND)
       add_gudhi_py_test(test_tomato)
     endif()
 
@@ -544,10 +567,10 @@ if(PYTHONINTERP_FOUND)
 
     # Set missing or not modules
     set(GUDHI_MODULES ${GUDHI_MODULES} "python" CACHE INTERNAL "GUDHI_MODULES")
-  else(CYTHON_FOUND)
-    message("++ Python module will not be compiled because cython was not found")
+  else(PYBIND11_FOUND AND CYTHON_FOUND)
+    message("++ Python module will not be compiled because cython and/or pybind11 was/were not found")
     set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES")
-  endif(CYTHON_FOUND)
+  endif(PYBIND11_FOUND AND CYTHON_FOUND)
 else(PYTHONINTERP_FOUND)
   message("++ Python module will not be compiled because no Python interpreter was found")
   set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES")