Merge remote-tracking branch 'origin/master' into sklearn_tda

1 files changed, 41 insertions, 26 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 2756d547..2cc578a6 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -50,6 +50,8 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'euclidean_witness_complex', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'euclidean_strong_witness_complex', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'sktda', ")
+    # Modules that should not be auto-imported in __init__.py
+    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'wasserstein', ")
 
     add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
     add_gudhi_debug_info("Cython version ${CYTHON_VERSION}")
@@ -67,6 +69,8 @@ if(PYTHONINTERP_FOUND)
     endif()
     if(SKLEARN_FOUND)
       add_gudhi_debug_info("Scikit-learn version ${SKLEARN_VERSION}")
+    if(OT_FOUND)
+      add_gudhi_debug_info("POT version ${OT_VERSION}")
     endif()
 
     set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
@@ -77,7 +81,7 @@ if(PYTHONINTERP_FOUND)
     if(MSVC)
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ")
     else(MSVC)
-      set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ")
+      set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-std=c++14', ")
     endif(MSVC)
     if(CMAKE_COMPILER_IS_GNUCXX)
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
@@ -204,6 +208,7 @@ if(PYTHONINTERP_FOUND)
     # Other .py files
     file(COPY "gudhi/persistence_graphical_tools.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/sktda" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/")
+    file(COPY "gudhi/wasserstein.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
 
     add_custom_command(
         OUTPUT gudhi.so
@@ -376,37 +381,47 @@ if(PYTHONINTERP_FOUND)
     # Reader utils
     add_gudhi_py_test(test_reader_utils)
 
+    # Wasserstein
+    if(OT_FOUND)
+      add_gudhi_py_test(test_wasserstein_distance)
+    endif(OT_FOUND)
+
     # Documentation generation is available through sphinx - requires all modules
     if(SPHINX_PATH)
       if(MATPLOTLIB_FOUND)
         if(NUMPY_FOUND)
           if(SCIPY_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(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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${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")
+                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)
+            endif(OT_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")