Some cmake cleanup work (rdkit#7720)

* cmake modernization

- get rid of some warnings
- switch to what I hope is the correct way of doing things
- bump min cmake version to 3.16
- bump min boost version to 1.70

This builds on linux

* remove some usages of PYTHON_EXECUTABLE

* remove old-school python usage from coverage tests

* remove unused CI file

* bump boost version for windows builds to 1.84

* still trying to get the ci builds working

* typo

* eventually the CI will work

* robustify some tests

.azure-pipelines/vs_build.yml

@@ -6,12 +6,14 @@ steps:
     conda info -a
     conda install -n base conda-libmamba-solver
     conda config --set solver libmamba
-    conda create --name rdkit_build ^
-        boost-cpp=$(boost_version) boost=$(boost_version) ^
-        py-boost=$(boost_version) libboost=$(boost_version) ^
-        numpy matplotlib=3.8 cairo pillow eigen pandas=2.1
+    conda create --name rdkit_build -c conda-forge $(python) ^
+        boost=$(boost_version) boost-cpp=$(boost_version) ^
+        libboost-python-devel=(boost_version) ^
+        libboost=$(boost_version) ^
+        libboost-devel=$(boost_version) ^
+        numpy matplotlib cairo pillow eigen pandas=2.1
     call activate rdkit_build
-    conda install -c conda-forge sphinx myst-parser ipython=8.20 jupyter pytest nbval
+    conda install -c conda-forge sphinx myst-parser ipython jupyter pytest nbval
     conda install -c conda-forge cmake
   displayName: Install dependencies
 - script: |
@@ -40,8 +42,6 @@ steps:
     -DRDK_BUILD_CFFI_LIB=ON ^
     -DRDK_SWIG_STATIC=OFF ^
     -DRDK_TEST_MULTITHREADED=ON ^
-    -DRDK_BOOST_PYTHON3_NAME=$(python_name) ^
-    -DBoost_NO_BOOST_CMAKE=TRUE ^
     -DCMAKE_INCLUDE_PATH=%CONDA_PREFIX%/Library/include ^
     -DCMAKE_LIBRARY_PATH="%CONDA_PREFIX%/Library/lib
   displayName: Configure build (Run CMake)

.azure-pipelines/vs_build_dll.yml

@@ -6,12 +6,14 @@ steps:
     conda info -a
     conda install -n base conda-libmamba-solver
     conda config --set solver libmamba
-    conda create --name rdkit_build ^
-        boost-cpp=$(boost_version) boost=$(boost_version) ^
+    conda create --name rdkit_build -c conda-forge $(python) ^
+        boost=$(boost_version) boost-cpp=$(boost_version) ^
+        libboost-python-devel=(boost_version) ^
         libboost=$(boost_version) ^
-        numpy matplotlib=3.8 cairo pillow eigen pandas=2.1
+        libboost-devel=$(boost_version) ^
+        numpy matplotlib cairo pillow eigen pandas=2.1
     call activate rdkit_build
-    conda install -c conda-forge cmake ipython=8.20 pytest nbval
+    conda install -c conda-forge cmake ipython pytest nbval
   displayName: Install dependencies
 - script: |
     set Boost_ROOT=
@@ -39,7 +41,6 @@ steps:
     -DRDK_BUILD_SWIG_WRAPPERS=OFF ^
     -DRDK_SWIG_STATIC=OFF ^
     -DRDK_TEST_MULTITHREADED=ON ^
-    -DBoost_NO_BOOST_CMAKE=TRUE ^
     -DCMAKE_INCLUDE_PATH=%CONDA_PREFIX%/Library/include ^
     -DCMAKE_LIBRARY_PATH="%CONDA_PREFIX%/Library/lib
   displayName: Configure build (Run CMake)

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.14)
+cmake_minimum_required(VERSION 3.16)
 
 project (RDKit)
 
@@ -71,7 +71,7 @@ option(RDK_BUILD_MINIMAL_LIB_RXN "build support for reactions into MinimalLib" O
 option(RDK_BUILD_MINIMAL_LIB_SUBSTRUCTLIBRARY "build support for SubstructLibrary into MinimalLib" ON )
 option(RDK_BUILD_MINIMAL_LIB_MCS "build support for MCS into MinimalLib" OFF )
 
-set(RDK_BOOST_VERSION "1.58.0")
+set(RDK_BOOST_VERSION "1.70.0")
 
 if(NOT MSVC)
   if(RDK_OPTIMIZE_POPCNT)
@@ -150,7 +150,7 @@ set(RDKit_ExternalDir "${CMAKE_CURRENT_SOURCE_DIR}/External")
 set(RDKit_DataDir "${CMAKE_CURRENT_SOURCE_DIR}/Data")
 
 #include catch
-find_package(Catch2 3)
+find_package(Catch2 3 QUIET)
 if(NOT Catch2_FOUND)
   Include(FetchContent)
 
@@ -290,59 +290,26 @@ if(RDK_BUILD_PYTHON_WRAPPERS)
 
   #-------
   # pull in python:
-  find_package(PythonInterp)
-  if (PYTHONINTERP_FOUND AND NOT Python_ADDITIONAL_VERSIONS)
-    set(Python_ADDITIONAL_VERSIONS "${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}")
-  endif (PYTHONINTERP_FOUND AND NOT Python_ADDITIONAL_VERSIONS)
-
-  if(PYTHON_VERSION_MAJOR EQUAL 2)
-    message(FATAL_ERROR "ERROR: The RDKit no longer supports Python 2.\nIf you have Python 3 installed, you can tell cmake where to find it using the -DPYTHON_EXECUTABLE argument.")
-  endif()
-
-  find_package(PythonLibs)
-  target_include_directories(rdkit_base INTERFACE ${PYTHON_INCLUDE_DIR})
+  find_package(Python3 COMPONENTS Interpreter Development NumPy)
+  target_include_directories(rdkit_base INTERFACE ${Python3_INCLUDE_DIRS})
+  target_include_directories(rdkit_base INTERFACE ${Python3_NumPy_INCLUDE_DIRS})
 
   # determine linkage of python
   execute_process(
       COMMAND
-      ${PYTHON_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var('Py_ENABLE_SHARED'))"
+      ${Python3_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var('Py_ENABLE_SHARED'))"
       OUTPUT_VARIABLE Py_ENABLE_SHARED
       OUTPUT_STRIP_TRAILING_WHITESPACE
   )
 
   if(WIN32 OR "${Py_ENABLE_SHARED}" STREQUAL "1")
-    target_link_libraries(rdkit_py_base INTERFACE ${PYTHON_LIBRARIES} )
-  endif()
-
-  find_package(NumPy REQUIRED)
-  target_include_directories(rdkit_base INTERFACE ${PYTHON_NUMPY_INCLUDE_PATH})
-
-  if(PYTHON_VERSION_MAJOR EQUAL 3)
-    # Find boost-python3 using name specified as command line option then fall back to commonly used names
-    set(RDK_BOOST_PYTHON3_NAME "python3" CACHE STRING "Name of the boost python3 library. If installed as libboost_python-xxx.so, use python-xxx.")
-    list(APPEND Boost_Python_Names "${RDK_BOOST_PYTHON3_NAME}" "python-py3${PYTHON_VERSION_MINOR}" "python3")
-  endif(PYTHON_VERSION_MAJOR EQUAL 3)
-
-  # Boost 1.67+ uses a version suffix like "python36" or "python27"
-  list(APPEND Boost_Python_Names "python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}")
-
-  # Try each potential boost-python name until one works
-  foreach(Boost_Python_LibN ${Boost_Python_Names})
-    find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS "${Boost_Python_LibN}" QUIET)
-    if(Boost_FOUND)
-      set(Boost_Python_Lib ${Boost_Python_LibN})
-      break()
-    endif()
-  endforeach()
-  # Finally just try "python" and hope it is a compatible version
-  if(NOT Boost_FOUND)
-    find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS python REQUIRED)
-    set(Boost_Python_Lib "python")
+    target_link_libraries(rdkit_py_base INTERFACE ${Python3_LIBRARY} )
   endif()
 
-  find_package(Boost COMPONENTS "numpy${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}" REQUIRED)
+
+  find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS "python${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}" "numpy${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}" REQUIRED CONFIG)
 
-  target_link_libraries(rdkit_py_base INTERFACE Boost::${Boost_Python_Lib} "Boost::numpy${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}")
+  target_link_libraries(rdkit_py_base INTERFACE "Boost::python${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}" "Boost::numpy${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}")
 
   if(RDK_INSTALL_INTREE)
     set(RDKit_PythonDir "${CMAKE_SOURCE_DIR}/rdkit")
@@ -351,7 +318,7 @@ if(RDK_BUILD_PYTHON_WRAPPERS)
       # Determine correct installation directory for Python bindings
       execute_process(
         COMMAND
-        ${PYTHON_EXECUTABLE} -c "import sys; import sysconfig; \
+        ${Python3_EXECUTABLE} -c "import sys; import sysconfig; \
           base_key = 'base' if sys.platform == 'win32' else 'platbase'; \
           schema = 'nt' if sys.platform == 'win32' else 'posix_prefix'; \
           print(sysconfig.get_path('platlib', schema, vars={base_key: '${CMAKE_INSTALL_PREFIX}'}))"
@@ -392,21 +359,20 @@ if(RDK_BUILD_PYTHON_WRAPPERS)
     # We strip off the first word though (which will be the compiler name).
     execute_process(
         COMMAND
-        ${PYTHON_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var('LDSHARED').lstrip().split(' ', 1)[1])"
+        ${Python3_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var('LDSHARED').lstrip().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()
 
+
   install(TARGETS rdkit_py_base EXPORT ${RDKit_EXPORTED_TARGETS}
           COMPONENT dev )
 
   # check to see if we can find nbval,
   execute_process(
     COMMAND
-    ${PYTHON_EXECUTABLE} -c "import nbval"
+    ${Python3_EXECUTABLE} -c "import nbval"
     ERROR_VARIABLE nbvalERR
     OUTPUT_STRIP_TRAILING_WHITESPACE)
   if(NOT nbvalERR)
@@ -416,7 +382,7 @@ if(RDK_BUILD_PYTHON_WRAPPERS)
   endif()
 
 else(RDK_BUILD_PYTHON_WRAPPERS)
-  find_package(Boost ${RDK_BOOST_VERSION} REQUIRED)
+  find_package(Boost ${RDK_BOOST_VERSION} REQUIRED CONFIG)
 endif(RDK_BUILD_PYTHON_WRAPPERS)
 
 find_package(Eigen3)
@@ -452,7 +418,7 @@ else()
 endif()
 
 if(RDK_USE_BOOST_SERIALIZATION)
-    find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS system serialization iostreams REQUIRED)
+    find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS system serialization iostreams REQUIRED CONFIG)
     target_link_libraries(rdkit_base INTERFACE ${Boost_LIBRARIES})
     target_compile_definitions(rdkit_base INTERFACE -DRDK_USE_BOOST_SERIALIZATION)
     if(NOT Boost_USE_STATIC_LIBS)
@@ -462,7 +428,7 @@ endif()
 
 if(RDK_USE_BOOST_IOSTREAMS)
     target_compile_definitions(rdkit_base INTERFACE -DRDK_USE_BOOST_IOSTREAMS)
-    find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS system iostreams REQUIRED)
+    find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS system iostreams REQUIRED CONFIG)
     target_link_libraries(rdkit_base INTERFACE ${Boost_LIBRARIES})
 
     if (NOT Boost_USE_STATIC_LIBS)
@@ -471,7 +437,7 @@ if(RDK_USE_BOOST_IOSTREAMS)
 
     # deal with zlib
     if (WIN32)
-      find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS zlib)
+      find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS zlib CONFIG)
       if(Boost_zlib_FOUND)
         set(zlib_lib Boost::zlib)
       endif()

Code/GraphMol/FilterCatalog/CMakeLists.txt

@@ -2,9 +2,8 @@ if(NOT RDK_USE_BOOST_SERIALIZATION)
     message("== Making FilterCatalog without boost Serialization support")
 endif()
 
-find_package(PythonInterp)
-if (PYTHONINTERP_FOUND)
-  if(DEFINED PYTHON_VERSION_STRING AND ${PYTHON_VERSION_STRING} VERSION_GREATER "2.6" )
+find_package(Python3 COMPONENTS Interpreter)
+if (Python3::Interpreter)
         message("== Updating Filters.cpp from pains file")
         execute_process(
           COMMAND
@@ -14,7 +13,6 @@ if (PYTHONINTERP_FOUND)
         if(NOT rc EQUAL 0)
           message(FATAL_ERROR "Failed updating Filters.cpp from wehi_pains.csv")
         endif(NOT rc EQUAL 0)
-  endif()
 endif()
 
 

Code/GraphMol/RGroupDecomposition/CMakeLists.txt

@@ -23,7 +23,7 @@ rdkit_test(testRGroupDecompInternals testRGroupInternals.cpp
 rdkit_catch_test(rgroupCatchTests catch_rgd.cpp 
 		LINK_LIBRARIES RGroupDecomposition )
 
-find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS program_options)
+find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS program_options CONFIG)
 if(RDK_BUILD_CPP_TESTS AND Boost_FOUND)
 	add_executable(gaExample GaExample.cpp)
 	if(NOT Boost_USE_STATIC_LIBS)

Code/cmake/Modules/CodeCoverage.cmake

@@ -86,6 +86,7 @@ IF ( NOT (CMAKE_BUILD_TYPE STREQUAL "Debug" OR CMAKE_BUILD_TYPE STREQUAL "Covera
   MESSAGE( WARNING "Code coverage results with an optimized (non-Debug) build may be misleading" )
 ENDIF() # NOT CMAKE_BUILD_TYPE STREQUAL "Debug"
 
+find_package(Python3 COMPONENTS Interpreter)
 
 # Param _targetname     The name of new the custom make target
 # Param _testrunner     The name of the target which runs the tests.
@@ -118,7 +119,7 @@ FUNCTION(SETUP_TARGET_FOR_COVERAGE _targetname _testrunner _outputname)
 		# Capturing lcov counters and generating report
 		COMMAND ${LCOV_PATH} --directory . --capture --output-file ${_outputname}.info
 		COMMAND ${LCOV_PATH} --remove ${_outputname}.info 'tests/*' '/usr/*' '*.ll' '*.yy' --output-file ${_outputname}.info.cleaned
-                COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/Code/cmake/Modules/fixup_coverage.py ${CMAKE_SOURCE_DIR} ${_outputname}.info.cleaned
+                COMMAND ${Python3_EXECUTABLE} ${CMAKE_SOURCE_DIR}/Code/cmake/Modules/fixup_coverage.py ${CMAKE_SOURCE_DIR} ${_outputname}.info.cleaned
 
 		COMMAND ${GENHTML_PATH} -o ${_outputname} ${_outputname}.info.cleaned
 		COMMAND ${CMAKE_COMMAND} -E remove ${_outputname}.info ${_outputname}.info.cleaned
@@ -142,7 +143,7 @@ ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE
 #   Pass them in list form, e.g.: "-j;2" for -j 2
 FUNCTION(SETUP_TARGET_FOR_COVERAGE_COBERTURA _targetname _testrunner _outputname)
 
-	IF(NOT PYTHON_EXECUTABLE)
+	IF(NOT Python3_EXECUTABLE)
 		MESSAGE(FATAL_ERROR "Python not found! Aborting...")
 	ENDIF() # NOT PYTHON_EXECUTABLE
 

Code/cmake/Modules/RDKitUtils.cmake

@@ -145,7 +145,7 @@ macro(rdkit_python_extension)
   CAR(RDKPY_NAME ${RDKPY_DEFAULT_ARGS})
   CDR(RDKPY_SOURCES ${RDKPY_DEFAULT_ARGS})
   if(RDK_BUILD_PYTHON_WRAPPERS)
-    PYTHON_ADD_MODULE(${RDKPY_NAME} ${RDKPY_SOURCES})
+    Python3_add_library(${RDKPY_NAME} MODULE ${RDKPY_SOURCES})
     set_target_properties(${RDKPY_NAME} PROPERTIES PREFIX "")
 
     if(WIN32)
@@ -158,7 +158,7 @@ macro(rdkit_python_extension)
                               ${RDK_PYTHON_OUTPUT_DIRECTORY}/${RDKPY_DEST})
     endif(WIN32)
 
-    target_link_libraries(${RDKPY_NAME} ${RDKPY_LINK_LIBRARIES}
+    target_link_libraries(${RDKPY_NAME} PUBLIC ${RDKPY_LINK_LIBRARIES}
                           RDBoost rdkit_py_base rdkit_base )
     if("${PYTHON_LDSHARED}" STREQUAL "")
     else()
@@ -206,23 +206,23 @@ macro(add_pytest)
   CAR(PYTEST_NAME ${PYTEST_DEFAULT_ARGS})
   CDR(PYTEST_SOURCES ${PYTEST_DEFAULT_ARGS})
   if(RDK_BUILD_PYTHON_WRAPPERS)
-    add_test(${PYTEST_NAME}  ${PYTHON_EXECUTABLE}
+    add_test(${PYTEST_NAME}  ${Python3_EXECUTABLE}
              ${PYTEST_SOURCES})
     SET(RDKIT_PYTEST_CACHE "${PYTEST_NAME};${RDKIT_PYTEST_CACHE}" CACHE INTERNAL "Global list of python tests")
   endif(RDK_BUILD_PYTHON_WRAPPERS)
 endmacro(add_pytest)
 
 function(add_jupytertest testname workingdir notebook)
   if(RDK_BUILD_PYTHON_WRAPPERS AND RDK_NBVAL_AVAILABLE)
-    add_test(NAME ${testname}  COMMAND ${PYTHON_EXECUTABLE} -m pytest --nbval ${notebook}
+    add_test(NAME ${testname}  COMMAND ${Python3_EXECUTABLE} -m pytest --nbval ${notebook}
        WORKING_DIRECTORY ${workingdir} )
     SET(RDKIT_JUPYTERTEST_CACHE "${testname};${RDKIT_JUPYTERTEST_CACHE}" CACHE INTERNAL "Global list of jupyter tests")
   endif()
 endfunction(add_jupytertest)
 
 function(add_pythonpytest testname workingdir)
   if(RDK_BUILD_PYTHON_WRAPPERS)
-    add_test(NAME ${testname}  COMMAND ${PYTHON_EXECUTABLE} -m pytest 
+    add_test(NAME ${testname}  COMMAND ${Python3_EXECUTABLE} -m pytest 
        WORKING_DIRECTORY ${workingdir} )
     SET(RDKIT_PYTHONTEST_CACHE "${testname};${RDKIT_PYTHONTEST_CACHE}" CACHE INTERNAL "Global list of pytest tests")
   endif()