Fix python linkage (#1808)

* apply (manually) #1807 from @bp-kelley to modern_cxx branch and fix (hopefully) a windows problem

* another windows problem

* another windows problem

* windows now builds locally

* update link targets

CMakeLists.txt

@@ -169,11 +169,7 @@ if(RDK_BUILD_PYTHON_WRAPPERS)
     set(Python_ADDITIONAL_VERSIONS "${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}")
   endif (PYTHONINTERP_FOUND AND NOT Python_ADDITIONAL_VERSIONS)
   find_package(PythonLibs)
-  if(CMAKE_MAJOR_VERSION EQUAL 2 AND CMAKE_MINOR_VERSION EQUAL 6)
-    target_include_directories(rdkit_base INTERFACE ${PYTHON_INCLUDE_PATH})
-  else(CMAKE_MAJOR_VERSION EQUAL 2 AND CMAKE_MINOR_VERSION EQUAL 6)
-    target_include_directories(rdkit_base INTERFACE ${PYTHON_INCLUDE_DIR})
-  endif(CMAKE_MAJOR_VERSION EQUAL 2 AND CMAKE_MINOR_VERSION EQUAL 6)
+  target_include_directories(rdkit_base INTERFACE ${PYTHON_INCLUDE_DIR})
   find_package(NumPy REQUIRED)
   target_include_directories(rdkit_base INTERFACE ${PYTHON_NUMPY_INCLUDE_PATH})
 
@@ -235,6 +231,28 @@ if(RDK_BUILD_PYTHON_WRAPPERS)
 
   endif(RDK_INSTALL_INTREE)
 
+  # determine linkage of python
+  execute_process(
+      COMMAND
+      ${PYTHON_EXECUTABLE} -c "from distutils import sysconfig; print(sysconfig.get_config_var('Py_ENABLE_SHARED'))"
+      OUTPUT_VARIABLE Py_ENABLE_SHARED
+      OUTPUT_STRIP_TRAILING_WHITESPACE
+  )
+  if(NOT WIN32)
+    # See https://bugs.python.org/msg277944
+    # The "command to create shared modules". Used as variable in the "Makefile (and similar) templates to build python modules"
+    # for both in-python and third party modules. Initialized to hold the value which works for third party modules to link
+    # against the _installed_ python.
+    # We strip off the first word though (which will be the compiler name).
+    execute_process(
+        COMMAND
+        ${PYTHON_EXECUTABLE} -c "from distutils import sysconfig; print(sysconfig.get_config_var('LDSHARED').split(' ', 1)[1])"
+        OUTPUT_VARIABLE PYTHON_LDSHARED
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+     )
+     message("PYTHON Py_ENABLE_SHARED: ${Py_ENABLE_SHARED}")
+     message("PYTHON USING LINK LINE: ${PYTHON_LDSHARED}")
+  endif()
 else(RDK_BUILD_PYTHON_WRAPPERS)
   find_package(Boost 1.56.0 REQUIRED)
 endif(RDK_BUILD_PYTHON_WRAPPERS)

Code/RDBoost/CMakeLists.txt

@@ -1,5 +1,16 @@
-rdkit_library(RDBoost Wrap.cpp
-              LINK_LIBRARIES RDGeneral ${PYTHON_LIBRARIES} ${Boost_IMPORTED_LIBRARIES})
+if(WIN32 OR "${Py_ENABLE_SHARED}" STREQUAL "1")
+  rdkit_library(RDBoost Wrap.cpp
+                LINK_LIBRARIES RDGeneral ${PYTHON_LIBRARIES} ${Boost_IMPORTED_LIBRARIES})
+else()
+    rdkit_library(RDBoost Wrap.cpp
+                LINK_LIBRARIES RDGeneral ${Boost_IMPORTED_LIBRARIES})
+    if("${PYTHON_LDSHARED}" STREQUAL "")
+    else()
+       # fixes an apple issue
+       STRING(REGEX REPLACE "-bundle" "" LDSHARED ${PYTHON_LDSHARED})
+       set_target_properties(RDBoost PROPERTIES LINK_FLAGS ${LDSHARED})
+    endif()
+endif()
 
 rdkit_headers(Wrap.h PySequenceHolder.h
               list_indexing_suite.hpp
@@ -13,7 +24,7 @@ add_subdirectory(Wrap)
 if(RDK_BUILD_PYTHON_WRAPPERS)
   # this is a particularly nasty little bit of hackery.
   # cmake (as of 2.8) ignores the ADDITIONAL_MAKE_CLEAN_FILES argument
-  # unless it's in a directory that actualy has a target. So in order to 
+  # unless it's in a directory that actualy has a target. So in order to
   # cleanup files created by the python tests we have to put something
   # here with the ugly relative path
   IF(COMMAND cmake_policy)

Code/cmake/Modules/RDKitUtils.cmake

@@ -115,17 +115,29 @@ macro(rdkit_python_extension)
   if(RDK_BUILD_PYTHON_WRAPPERS)
     PYTHON_ADD_MODULE(${RDKPY_NAME} ${RDKPY_SOURCES})
     set_target_properties(${RDKPY_NAME} PROPERTIES PREFIX "")
-if(WIN32)
-    set_target_properties(${RDKPY_NAME} PROPERTIES SUFFIX ".pyd"
-                          LIBRARY_OUTPUT_DIRECTORY
-                          ${RDK_PYTHON_OUTPUT_DIRECTORY}/${RDKPY_DEST})
-else(WIN32)
-    set_target_properties(${RDKPY_NAME} PROPERTIES
-                          LIBRARY_OUTPUT_DIRECTORY
-                          ${RDK_PYTHON_OUTPUT_DIRECTORY}/${RDKPY_DEST})
-endif(WIN32)
-    target_link_libraries(${RDKPY_NAME} ${RDKPY_LINK_LIBRARIES}
-                          ${PYTHON_LIBRARIES} ${Boost_IMPORTED_LIBRARIES} )
+
+    if(WIN32)
+      set_target_properties(${RDKPY_NAME} PROPERTIES SUFFIX ".pyd"
+                           LIBRARY_OUTPUT_DIRECTORY
+                           ${RDK_PYTHON_OUTPUT_DIRECTORY}/${RDKPY_DEST})
+    else(WIN32)
+        set_target_properties(${RDKPY_NAME} PROPERTIES
+                              LIBRARY_OUTPUT_DIRECTORY
+                              ${RDK_PYTHON_OUTPUT_DIRECTORY}/${RDKPY_DEST})
+    endif(WIN32)
+
+    if(WIN32 OR "${Py_ENABLE_SHARED}" STREQUAL "1")
+      target_link_libraries(${RDKPY_NAME} ${RDKPY_LINK_LIBRARIES}
+                            ${PYTHON_LIBRARIES} ${Boost_IMPORTED_LIBRARIES} )
+    else()
+      target_link_libraries(${RDKPY_NAME} ${RDKPY_LINK_LIBRARIES}
+                            ${Boost_IMPORTED_LIBRARIES} )
+      if("${PYTHON_LDSHARED}" STREQUAL "")
+      else()
+        message("set_target_properties ${RDKPY_NAME} PROPERTIES LINK_FLAGS ${PYTHON_LDSHARED}")
+        set_target_properties(${RDKPY_NAME} PROPERTIES LINK_FLAGS ${PYTHON_LDSHARED})
+      endif()
+    endif()
 
     INSTALL(TARGETS ${RDKPY_NAME}
             LIBRARY DESTINATION ${RDKit_PythonDir}/${RDKPY_DEST} COMPONENT python)