Merge pull request #71 from MathieuCarriere/sklearn_tda

sklearn-tda

1 files changed, 44 insertions, 29 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index dbef7183..9af85eac 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -50,6 +50,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'euclidean_witness_complex', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'euclidean_strong_witness_complex', ")
     # Modules that should not be auto-imported in __init__.py
+    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'representations', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'wasserstein', ")
 
     add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
@@ -66,6 +67,9 @@ if(PYTHONINTERP_FOUND)
     if(SCIPY_FOUND)
       add_gudhi_debug_info("Scipy version ${SCIPY_VERSION}")
     endif()
+    if(SKLEARN_FOUND)
+      add_gudhi_debug_info("Scikit-learn version ${SKLEARN_VERSION}")
+    endif()
     if(OT_FOUND)
       add_gudhi_debug_info("POT version ${OT_VERSION}")
     endif()
@@ -204,6 +208,7 @@ if(PYTHONINTERP_FOUND)
 
     # Other .py files
     file(COPY "gudhi/persistence_graphical_tools.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
+    file(COPY "gudhi/representations" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/")
     file(COPY "gudhi/wasserstein.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
 
     add_custom_command(
@@ -382,42 +387,52 @@ if(PYTHONINTERP_FOUND)
       add_gudhi_py_test(test_wasserstein_distance)
     endif(OT_FOUND)
 
+    # Representations
+    if(SKLEARN_FOUND AND MATPLOTLIB_FOUND)
+      add_gudhi_py_test(test_representations)
+    endif()
+
     # Documentation generation is available through sphinx - requires all modules
     if(SPHINX_PATH)
       if(MATPLOTLIB_FOUND)
         if(NUMPY_FOUND)
           if(SCIPY_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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${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(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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${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)
-            else(OT_FOUND)
-              message("++ Python documentation module will not be compiled because POT 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(OT_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")