Code review: rename cython as python (make target and directory

.appveyor.yml

@@ -54,8 +54,8 @@ build_script:
   - cd build
   - cmake -G "Visual Studio 15 2017 Win64" %CMAKE_FLAGS% -DCMAKE_TOOLCHAIN_FILE=c:/Tools/vcpkg/scripts/buildsystems/vcpkg.cmake ..
   - if [%target%]==[Python] (
-      cd src/cython &
-      MSBuild Cython.sln /m /p:Configuration=Release /p:Platform=x64 &
+      cd src/python &
+      MSBuild Python.sln /m /p:Configuration=Release /p:Platform=x64 &
       ctest -j 1 -C Release
     ) else (
       MSBuild GUDHIdev.sln /m /p:Configuration=Release /p:Platform=x64 &

.circleci/config.yml

@@ -56,7 +56,7 @@ jobs:
             cd build;            
             cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..;
             make all test sphinx;
-            cp -R cython/sphinx /tmp/sphinx;
+            cp -R python/sphinx /tmp/sphinx;
 
       - store_artifacts:
           path: /tmp/sphinx

.gitignore

@@ -2,21 +2,7 @@
 build/
 
 # Generated by Cython
-src/cython/gudhi/simplex_tree.cpp
-src/cython/gudhi/alpha_complex.cpp
-src/cython/gudhi/bottleneck.cpp
-src/cython/gudhi/cubical_complex.cpp
-src/cython/gudhi/euclidean_strong_witness_complex.cpp
-src/cython/gudhi/off_reader.cpp
-src/cython/gudhi/periodic_cubical_complex.cpp
-src/cython/gudhi/reader_utils.cpp
-src/cython/gudhi/rips_complex.cpp
-src/cython/gudhi/subsampling.cpp
-src/cython/gudhi/euclidean_witness_complex.cpp
-src/cython/gudhi/nerve_gic.cpp
-src/cython/gudhi/strong_witness_complex.cpp
-src/cython/gudhi/tangential_complex.cpp
-src/cython/gudhi/witness_complex.cpp
+src/python/gudhi/*.cpp
 
 # Generated by tests
 data/points/COIL_database/lucky_cat.off_dist

CMakeLists.txt

@@ -11,7 +11,7 @@ set(GUDHI_MODULES "" CACHE INTERNAL "GUDHI_MODULES")
 set(GUDHI_MISSING_MODULES "" CACHE INTERNAL "GUDHI_MISSING_MODULES")
 
 # This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path
-set(GUDHI_CYTHON_PATH "src/cython")
+set(GUDHI_PYTHON_PATH "src/python")
 
 # For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
 include(GUDHI_third_party_libraries NO_POLICY_SCOPE)
@@ -54,7 +54,7 @@ add_subdirectory(src/GudhUI)
 
 if (WITH_GUDHI_PYTHON)
   # specific for cython module
-  add_subdirectory(${GUDHI_CYTHON_PATH})
+  add_subdirectory(${GUDHI_PYTHON_PATH})
 else()
   message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF")
   set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python")

src/CMakeLists.txt

@@ -10,7 +10,7 @@ set(GUDHI_MODULES "" CACHE INTERNAL "GUDHI_MODULES")
 set(GUDHI_MISSING_MODULES "" CACHE INTERNAL "GUDHI_MISSING_MODULES")
 
 # This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path
-set(GUDHI_CYTHON_PATH "cython")
+set(GUDHI_PYTHON_PATH "python")
 
 # For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
 include(GUDHI_third_party_libraries NO_POLICY_SCOPE)
@@ -61,7 +61,7 @@ add_subdirectory(GudhUI)
 
 if (WITH_GUDHI_PYTHON)
   # specific for cython module
-  add_subdirectory(${GUDHI_CYTHON_PATH})
+  add_subdirectory(${GUDHI_PYTHON_PATH})
 else()
   message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF")
   set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python")

src/Doxyfile.in

@@ -784,7 +784,7 @@ EXCLUDE                = data/                   \
 	                     example/                \
 	                     GudhUI/                 \
                          cmake/                  \
-                         cython/                 \
+                         python/                 \
                          README.md
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or

src/cmake/modules/GUDHI_third_party_libraries.cmake

@@ -101,16 +101,18 @@ function( find_python_module PYTHON_MODULE_NAME )
           RESULT_VARIABLE PYTHON_MODULE_RESULT
           OUTPUT_VARIABLE PYTHON_MODULE_VERSION
           ERROR_VARIABLE PYTHON_MODULE_ERROR)
-  message ("PYTHON_MODULE_NAME = ${PYTHON_MODULE_NAME}
-   - PYTHON_MODULE_RESULT = ${PYTHON_MODULE_RESULT}
-   - PYTHON_MODULE_VERSION = ${PYTHON_MODULE_VERSION}
-   - PYTHON_MODULE_ERROR = ${PYTHON_MODULE_ERROR}")
   if(PYTHON_MODULE_RESULT EQUAL 0)
     # Remove carriage return
     string(STRIP ${PYTHON_MODULE_VERSION} PYTHON_MODULE_VERSION)
+    message ("++ Python module ${PYTHON_MODULE_NAME} - Version ${PYTHON_MODULE_VERSION} found")
+
     set(${PYTHON_MODULE_NAME_UP}_VERSION ${PYTHON_MODULE_VERSION} PARENT_SCOPE)
     set(${PYTHON_MODULE_NAME_UP}_FOUND TRUE PARENT_SCOPE)
   else()
+    message ("PYTHON_MODULE_NAME = ${PYTHON_MODULE_NAME}
+     - PYTHON_MODULE_RESULT = ${PYTHON_MODULE_RESULT}
+     - PYTHON_MODULE_VERSION = ${PYTHON_MODULE_VERSION}
+     - PYTHON_MODULE_ERROR = ${PYTHON_MODULE_ERROR}")
     unset(${PYTHON_MODULE_NAME_UP}_VERSION PARENT_SCOPE)
     set(${PYTHON_MODULE_NAME_UP}_FOUND FALSE PARENT_SCOPE)
   endif()
@@ -125,11 +127,11 @@ if( PYTHONINTERP_FOUND )
   find_python_module("sphinx")
 endif()
 
-if(NOT GUDHI_CYTHON_PATH)
-  message(FATAL_ERROR "ERROR: GUDHI_CYTHON_PATH is not valid.")
-endif(NOT GUDHI_CYTHON_PATH)
+if(NOT GUDHI_PYTHON_PATH)
+  message(FATAL_ERROR "ERROR: GUDHI_PYTHON_PATH is not valid.")
+endif(NOT GUDHI_PYTHON_PATH)
 
-option(WITH_GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "Build with setting runtime_library_dirs. Usefull when setting rpath is not allowed" ON)
+option(WITH_GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS "Build with setting runtime_library_dirs. Usefull when setting rpath is not allowed" ON)
 
 if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
   if(SPHINX_FOUND)
@@ -139,7 +141,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     if(NOT SPHINX_PATH)
       if(PYTHON_VERSION_MAJOR EQUAL 3)
         # In Python3, just hack sphinx-build if it does not exist
-        set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build.py")
+        set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_PYTHON_PATH}/doc/python3-sphinx-build.py")
       endif(PYTHON_VERSION_MAJOR EQUAL 3)
     endif(NOT SPHINX_PATH)
   endif(SPHINX_FOUND)

src/cmake/modules/GUDHI_user_version_target.cmake

@@ -42,7 +42,7 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy_directory ${CMAKE_SOURCE_DIR}/biblio ${GUDHI_USER_VERSION_DIR}/biblio)
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                   copy_directory ${CMAKE_SOURCE_DIR}/src/cython ${GUDHI_USER_VERSION_DIR}/cython)
+                   copy_directory ${CMAKE_SOURCE_DIR}/${GUDHI_PYTHON_PATH} ${GUDHI_USER_VERSION_DIR}/python)
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy_directory ${CMAKE_SOURCE_DIR}/data ${GUDHI_USER_VERSION_DIR}/data)
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E