SyneRBI · KrisThielemans · Jan 18, 2021 · Jan 15, 2021 · Jan 15, 2021
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,7 +1,8 @@
 # ChangeLog
 ## v#.#.#
 - Enabled HDF5 support for STIR by default (build C++ libraries for HDF5)
-- Add option BULD_TESTING_JSON (default OFF)
+- Fix some issues with finding Python [#472](https://github.com/SyneRBI/SIRF-SuperBuild/issues/472)
+- Add option `BUILD_TESTING_JSON` (default OFF)
 - Updated versions:
    - JSON: 3.9.1
    - SWIG: 4.0.2

diff --git a/SuperBuild.cmake b/SuperBuild.cmake
@@ -135,6 +135,21 @@ else()
       CONDA:      do nothing")
     set_property(CACHE PYTHON_STRATEGY PROPERTY STRINGS PYTHONPATH SETUP_PY CONDA)
   endif()
+
+  # set PYTHONLIBS_CMAKE_ARGS to be used in the ExternalProject_add calls
+  # note: Find_package(PythonLibs) takes PYTHON_INCLUDE_DIR and PYTHON_LIBRARY as input
+  set (PYTHONLIBS_CMAKE_ARGS -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE})
+  if (EXISTS ${PYTHON_INCLUDE_DIR})
+    set (PYTHONLIBS_CMAKE_ARGS ${PYTHONLIBS_CMAKE_ARGS}
+      -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR})
+  endif()
+  if (EXISTS ${PYTHON_LIBRARY})
+    set (PYTHONLIBS_CMAKE_ARGS ${PYTHONLIBS_CMAKE_ARGS}
+      -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY})
+  endif()
+
+
+  message(STATUS "PYTHONLIBS_CMAKE_ARGS= " "${PYTHONLIBS_CMAKE_ARGS}")
 endif()
 
 #### MATLAB support
@@ -232,8 +247,7 @@ option(BUILD_pet_rd_tools "Build pet_rd_tools" OFF)
 option(BUILD_CIL "Build CCPi CIL Modules and ASTRA engine" OFF)
 option(BUILD_CIL_LITE "Build CCPi CIL Modules" OFF)
 option(BUILD_NIFTYREG "Build NIFTYREG" ON)
-option(BUILD_SIRF_Contribs "Build SIRF-Contribs" ON)
-
+option(BUILD_SIRF_Contribs "Build SIRF-Contribs" ${BUILD_SIRF})
 option(BUILD_SIRF_Registration "Build SIRFS's registration functionality" ${BUILD_NIFTYREG})
 if (BUILD_SIRF AND BUILD_SIRF_Registration AND NOT BUILD_NIFTYREG)
   message(WARNING "Building SIRF registration is enabled, but BUILD_NIFTYREG=OFF. Reverting to BUILD_NIFTYREG=ON")
@@ -313,12 +327,8 @@ message(STATUS "")
 message(STATUS "Boost_CMAKE_ARGS= " "${Boost_CMAKE_ARGS}")
 message(STATUS "ISMRMRD_DIR = " ${ISMRMRD_DIR})
 message(STATUS "STIR_DIR = " ${STIR_DIR})
-message(STATUS "HDF5_ROOT = " ${HDF5_ROOT})
 message(STATUS "GTEST_ROOT = " ${GTEST_ROOT})
 message(STATUS "Matlab_ROOT_DIR = " ${Matlab_ROOT_DIR})
-message(STATUS "PYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}")
-message(STATUS "PYTHON_LIBRARIES=${PYTHON_LIBRARIES}")
-message(STATUS "PYTHON_INCLUDE_DIRS=${PYTHON_INCLUDE_DIRS}")
 
 #Need to configure main project here.
 #set(proj ${PRIMARY_PROJECT_NAME})

diff --git a/SuperBuild/External_CCPi-Framework.cmake b/SuperBuild/External_CCPi-Framework.cmake
@@ -56,9 +56,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
       CONFIGURE_COMMAND ${CMAKE_COMMAND} -E env CIL_VERSION=${${proj}_TAG}
         ${CMAKE_COMMAND} ${${proj}_SOURCE_DIR}
           -DCMAKE_INSTALL_PREFIX:PATH=${${proj}_INSTALL_DIR}
-          -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE}
-          -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIRS}
-          -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARIES}      
+          ${PYTHONLIBS_CMAKE_ARGS}
           -DPYTHON_DEST_DIR:PATH=${PYTHON_DEST}
           -DOPENMP_INCLUDES:PATH=${OPENMP_INCLUDES}
           -DCIL_VERSION:STRING=${${proj}_TAG}

diff --git a/SuperBuild/External_CCPi-Regularisation-Toolkit.cmake b/SuperBuild/External_CCPi-Regularisation-Toolkit.cmake
@@ -84,9 +84,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
         -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
         -DBUILD_PYTHON_WRAPPER:BOOL=ON
         -DBUILD_CUDA:BOOL=${${proj}_USE_CUDA} -DCONDA_BUILD:BOOL=OFF
-        -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE}
-        -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIRS}
-        -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARIES}
+        ${PYTHONLIBS_CMAKE_ARGS}
         -DPYTHON_DEST_DIR:PATH=${PYTHON_DEST}
 
       BUILD_COMMAND ${CMAKE_COMMAND} -E env CIL_VERSION=${${proj}_TAG} ${CMAKE_COMMAND} --build .

diff --git a/SuperBuild/External_Gadgetron.cmake b/SuperBuild/External_Gadgetron.cmake
@@ -100,9 +100,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
       -DCMAKE_INCLUDE_PATH:PATH=${SUPERBUILD_INSTALL_DIR}/include
       -DCMAKE_INSTALL_PREFIX:PATH=${Gadgetron_INSTALL_DIR}
       ${Boost_CMAKE_ARGS}
-      -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE}
-      -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIRS}
-      -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARIES}
+      ${PYTHONLIBS_CMAKE_ARGS}
       -DGTEST_ROOT:PATH=${GTEST_ROOT}
       ${HDF5_CMAKE_ARGS}
       ${FFTW3_CMAKE_ARGS}

diff --git a/SuperBuild/External_SIRF-Contribs.cmake b/SuperBuild/External_SIRF-Contribs.cmake
@@ -1,6 +1,7 @@
 #========================================================================
 # Author: Edoardo Pasca
 # Copyright 2018, 2020 STFC
+# Copyright 2021, University College London
 #
 # This file is part of the CCP SyneRBI (formerly PETMR) Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
 #
@@ -33,30 +34,28 @@ SetExternalProjectFlags(${proj})
 if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalProjName}}" ) )
   message(STATUS "${__indent}Adding project ${proj}")
   SetGitTagAndRepo("${proj}")
+  if (BUILD_PYTHON)
+    # conda build should never get here
+    if("${PYTHON_STRATEGY}" STREQUAL "PYTHONPATH")
+      # in case of PYTHONPATH it is sufficient to copy the files to the 
+      # $PYTHONPATH directory
+      ExternalProject_Add(${proj}
+        ${${proj}_EP_ARGS}
+        ${${proj}_EP_ARGS_GIT}
+        ${${proj}_EP_ARGS_DIRS}
 
-  # conda build should never get here
-  if("${PYTHON_STRATEGY}" STREQUAL "PYTHONPATH")
-    # in case of PYTHONPATH it is sufficient to copy the files to the 
-    # $PYTHONPATH directory
-    ExternalProject_Add(${proj}
-      ${${proj}_EP_ARGS}
-      ${${proj}_EP_ARGS_GIT}
-      ${${proj}_EP_ARGS_DIRS}
-
-      CONFIGURE_COMMAND ""
-      BUILD_COMMAND ""
-      INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory ${${proj}_SOURCE_DIR}/src/Python/sirf/ ${PYTHON_DEST}/sirf
-    )
-
-  else()
-    # if SETUP_PY one can launch the conda build.sh script setting 
-    # the appropriate variables.
-    message(FATAL_ERROR "Only PYTHONPATH install method is currently supported")
+        CONFIGURE_COMMAND ""
+        BUILD_COMMAND ""
+        INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory ${${proj}_SOURCE_DIR}/src/Python/sirf/ ${PYTHON_DEST}/sirf
+      )
+    else()
+      # if SETUP_PY one can launch the conda build.sh script setting 
+      # the appropriate variables.
+      message(FATAL_ERROR "Only PYTHONPATH install method is currently supported")
+    endif()
   endif()
 
-
-  set(${proj}_ROOT        ${${proj}_SOURCE_DIR})
-  set(${proj}_INCLUDE_DIR ${${proj}_SOURCE_DIR})
+  # any non-Python stuff here    
 
 else()
   ExternalProject_Add_Empty(${proj} DEPENDS "${${proj}_DEPENDENCIES}"

diff --git a/SuperBuild/External_SIRF.cmake b/SuperBuild/External_SIRF.cmake
@@ -93,9 +93,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
       -DISMRMRD_DIR:PATH=${ISMRMRD_DIR}
       -DSWIG_EXECUTABLE:FILEPATH=${SWIG_EXECUTABLE}
       -DDISABLE_PYTHON:BOOL=${DISABLE_PYTHON}
-      -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE}
-      -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIRS}
-      -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARIES}
+      ${PYTHONLIBS_CMAKE_ARGS}
       -DPYTHON_DEST_DIR:PATH=${PYTHON_DEST_DIR}
       -DPYTHON_STRATEGY=${PYTHON_STRATEGY}
       -DNIFTYREG_DIR:PATH=${NIFTYREG_DIR}

diff --git a/SuperBuild/External_STIR.cmake b/SuperBuild/External_STIR.cmake
@@ -87,6 +87,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
     -DBUILD_EXECUTABLES:BOOL=${STIR_BUILD_EXECUTABLES}
     -DBUILD_SWIG_PYTHON:BOOL=${STIR_BUILD_SWIG_PYTHON}
     -DPYTHON_DEST:PATH=${PYTHON_DEST}
+    ${PYTHONLIBS_CMAKE_ARGS}
     -DMatlab_ROOT_DIR:PATH=${Matlab_ROOT_DIR}
     -DMATLAB_DEST:PATH=${MATLAB_DEST}
     -DBUILD_TESTING:BOOL=${BUILD_TESTING_${proj}}

diff --git a/SuperBuild/External_TomoPhantom.cmake b/SuperBuild/External_TomoPhantom.cmake
@@ -56,9 +56,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
     	-DINCLUDE_DIR:PATH=${${proj}_INSTALL_DIR}/include
     	-DCONDA_BUILD=OFF
     	-DBUILD_PYTHON_WRAPPER=ON
-    	-DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}
-    	-DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIRS}
-    	-DPYTHON_LIBRARY=${PYTHON_LIBRARIES}
+        ${PYTHONLIBS_CMAKE_ARGS}
     	-DPYTHON_DEST_DIR:PATH=${PYTHON_DEST_DIR}
     	-DPYTHON_STRATEGY=${PYTHON_STRATEGY}
       ${${proj}_EXTRA_CMAKE_ARGS_LIST}