CMakeLists.txt

cmake_minimum_required(VERSION 2.8.12...3.6.0)

project(IMP)

set_property(GLOBAL PROPERTY USE_FOLDERS ON)

if(${CMAKE_BINARY_DIR} STREQUAL ${CMAKE_SOURCE_DIR})
   message(FATAL_ERROR "Building in the source directory not supported: ${CMAKE_SOURCE_DIR} is ${CMAKE_BINARY_DIR}. If this message seems wrong, make sure to delete the CMakeFiles directory and the CMakeCache.txt file if they exist in the source dir (${CMAKE_SOURCE_DIR}).")
endif()

# Default Python3_FIND_STRATEGY to LOCATION
if(POLICY CMP0094)
cmake_policy(SET CMP0094 NEW)
endif(POLICY CMP0094)

# Use new-style variables/escapes
if(POLICY CMP0053)
cmake_policy(SET CMP0053 NEW)
endif(POLICY CMP0053)

include(${CMAKE_SOURCE_DIR}/cmake_modules/IMPFindPython.cmake)
imp_find_python()

# Check Python version early so we can use Python >= 3.6 features in other
# build scripts
execute_process(COMMAND ${PYTHON_EXECUTABLE}
                        "tools/build/check_python_version.py"
                RESULT_VARIABLE setup
                OUTPUT_VARIABLE toutput
                ERROR_VARIABLE error
                WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
                OUTPUT_STRIP_TRAILING_WHITESPACE)
if(NOT ${setup} EQUAL 0)
   message(FATAL_ERROR "Failed checking Python version: ${error}")
endif()

if(IS_DIRECTORY "${PROJECT_SOURCE_DIR}/.git")
  execute_process(COMMAND ${PYTHON_EXECUTABLE}
                          "tools/dev_tools/git/setup_git.py"
                  RESULT_VARIABLE setup
                  OUTPUT_VARIABLE toutput
                  ERROR_VARIABLE error
                  WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
                  OUTPUT_STRIP_TRAILING_WHITESPACE)
  if(NOT ${setup} EQUAL 0)
     message(FATAL_ERROR " Failed to run setup_git.py: ${setup}; ${error}")
  endif()
endif()

# Quiet warning from cmake 3.1 or later about quoted variables in if()
if(POLICY CMP0054)
cmake_policy(SET CMP0054 NEW)
endif(POLICY CMP0054)

# Honor link flags in try_compile() tests
if(POLICY CMP0056)
cmake_policy(SET CMP0056 NEW)
endif(POLICY CMP0056)

# Don't complain about our use of FindCUDA for now
if(POLICY CMP0146)
cmake_policy(SET CMP0146 OLD)
endif(POLICY CMP0146)

include(${CMAKE_SOURCE_DIR}/cmake_modules/IMPExecuteProcess.cmake)
include(${CMAKE_SOURCE_DIR}/cmake_modules/IMPAddTests.cmake)
include(${CMAKE_SOURCE_DIR}/cmake_modules/CheckCompiles.cmake)

imp_execute_process("check_common_problems" ${CMAKE_SOURCE_DIR}
                    COMMAND ${PYTHON_EXECUTABLE}
                    ${CMAKE_SOURCE_DIR}/tools/build/check_common_problems.py)

imp_execute_process("clean_build_dir" ${CMAKE_BINARY_DIR}
                    COMMAND ${PYTHON_EXECUTABLE}
                    ${CMAKE_SOURCE_DIR}/tools/build/clean_build_dir.py)

imp_execute_process("setup_cmake" ${CMAKE_SOURCE_DIR}
                    COMMAND ${PYTHON_EXECUTABLE}
                    ${CMAKE_SOURCE_DIR}/tools/build/setup_cmake.py)

set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_modules)

enable_testing()

include(${CMAKE_SOURCE_DIR}/cmake_modules/IMPFindC++11.cmake)
include(${CMAKE_SOURCE_DIR}/cmake_modules/IMPFindCompilerFlags.cmake)

if(POLICY CMP0017)
cmake_policy(SET CMP0017 NEW)
endif(POLICY CMP0017)

# Don't set MACOSX_RPATH by default
set(CMAKE_MACOSX_RPATH 0)

# Stop cmake warning about files in the build directory it didn't create
if(POLICY CMP0058)
  cmake_policy(SET CMP0058 NEW)
endif(POLICY CMP0058)

# Use FindBoost module rather than BoostConfig.cmake (which requires
# Boost 1.70 or later)
if(POLICY CMP0167)
  cmake_policy(SET CMP0167 OLD)
endif(POLICY CMP0167)

set(timeout_factor 1)
set(IMP_SWIG_PATH CACHE STRING "List of places for swig to search")
set(SWIG_EXECUTABLE swig CACHE STRING "Swig program")
set(IMP_DISABLED_MODULES CACHE STRING "A colon-separated list of disabled modules")
set(IMP_STATIC off CACHE BOOL "Link all binaries and libraries statically; currently only supported on Linux systems with gcc.")
if (${CMAKE_BUILD_TYPE} MATCHES "Debug")
set(timeout_factor "${timeout_factor} * 2")
set(IMP_MAX_CHECKS "INTERNAL" CACHE STRING "One of NONE, USAGE, INTERNAL")
set(IMP_MAX_LOG "VERBOSE" CACHE STRING "One of SILENT, PROGRESS, TERSE, VERBOSE")
else()
set(IMP_MAX_CHECKS "USAGE" CACHE STRING "One of NONE, USAGE, INTERNAL")
set(IMP_MAX_LOG "VERBOSE" CACHE STRING "One of SILENT, PROGRESS, TERSE, VERBOSE")
endif()
set(IMP_PER_CPP_COMPILATION "" CACHE STRING "A colon-separated list of modules to build one .cpp at a time, or ALL to do this for all modules.")
set(IMP_CUDA "" CACHE STRING "A colon-separated list of modules to build with CUDA support (where available), or ALL to do this for all modules.")

if (${IMP_MAX_CHECKS} MATCHES "INTERNAL")
set(timeout_factor "${timeout_factor} * 2")
endif()

set(IMP_TIMEOUT_FACTOR ${timeout_factor} CACHE STRING "A factor to scale the test timeouts. Use this when on a slow machine, or using a slow copy of IMP (eg doing coverage). This can be a math expression on integers, but not a floating point constant.")

include(FindCurrentDoxygen)

# clear list
set(IMP_DOC_DEPENDS "" CACHE INTERNAL "")
if(${IMP_DOXYGEN_FOUND})
imp_execute_process("setup_doxygen" ${CMAKE_BINARY_DIR}
                    COMMAND ${PYTHON_EXECUTABLE}
                    ${CMAKE_SOURCE_DIR}/tools/build/setup_doxygen.py
                    "--source=${CMAKE_SOURCE_DIR}")
endif()

if(IMP_STATIC)
  SET(IMP_LIB_TYPE STATIC)
  SET(Boost_USE_STATIC_LIBS ON)
  set(CMAKE_EXE_LINKER_FLAGS "-static")
  set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
  set(CMAKE_EXE_LINK_DYNAMIC_C_FLAGS)       # remove -Wl,-Bdynamic
  set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS)
  set(CMAKE_SHARED_LIBRARY_C_FLAGS)         # remove -fPIC
  set(CMAKE_SHARED_LIBRARY_CXX_FLAGS)
  set(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS)    # remove -rdynamic
  set(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS)
else()
  SET(IMP_LIB_TYPE SHARED)
endif()

if("${IMP_PER_CPP_COMPILATION}" STREQUAL "ALL")
  message(STATUS "All modules are percpp")
  set(IMP_IS_PER_CPP 1)
else()
  string(REGEX MATCHALL "[a-zA-Z0-9_]+" percpplist "${IMP_PER_CPP_COMPILATION}")
  foreach(m ${percpplist})
    message(STATUS ${m} " is percpp")
    set(IMP_${m}_IS_PER_CPP 1)
  endforeach(m)
endif()

if("${IMP_CUDA}" STREQUAL "ALL")
  message(STATUS "All modules are cuda lib")
  set(IMP_IS_CUDA 1)
  set(IMP_CUDA_REQUESTED 1)
else()
  string(REGEX MATCHALL "[a-zA-Z0-9_]+" cudalist "${IMP_CUDA}")
  foreach(m ${cudalist})
    message(STATUS ${m} " is cuda lib")
    set(IMP_${m}_IS_CUDA 1)
    set(IMP_CUDA_REQUESTED 1)
  endforeach(m)
endif()

if(WIN32)
  set(IMP_SWIG_LIBRARIES ${PYTHON_LIBRARIES})
endif(WIN32)

if(${PYTHON_NUMPY_FOUND})
  set(NUMPY_INCLUDE_PATH ${PYTHON_NUMPY_INCLUDE_DIR} CACHE INTERNAL "" FORCE)
  file(WRITE "${CMAKE_BINARY_DIR}/build_info/NumPy"
       "ok=True\n"
       "includepath='${NUMPY_INCLUDE_PATH}'")
else()
  file(WRITE "${CMAKE_BINARY_DIR}/build_info/NumPy" "ok=False")
endif()

if(NOT DEFINED PATH_SEP)
  if(WIN32)
    Set(PATH_SEP ";")
  else()
    Set(PATH_SEP ":")
  endif()
endif()
if(NOT DEFINED SETUP_EXT)
  if(WIN32)
    Set(SETUP_EXT "bat")
  else()
    Set(SETUP_EXT "sh")
  endif()
endif()

if("${SETUP_EXT}" STREQUAL "sh")
  set(IMP_TEST_SETUP "${CMAKE_BINARY_DIR}/setup_environment.sh")
else()
  # On Windows the batch file is run once to set up the test environment, not
  # per test
  set(IMP_TEST_SETUP )
endif()

include(GNUInstallDirs)
# Add extra installation locations for SWIG .i files, build tools,
# cmake files, and Python code
# As per GNUInstallDirs.cmake, set empty values in the cache and store defaults
# in local variables for locations defined relative to existing CMAKE_INSTALL_*.
# This auto-updates the defaults when the existing CMAKE_INSTALL_* changes.
if(NOT DEFINED CMAKE_INSTALL_SWIGDIR)
  set(CMAKE_INSTALL_SWIGDIR "share/IMP/swig" CACHE PATH "SWIG interface files")
endif()
if(NOT CMAKE_INSTALL_BUILDINFODIR)
  set(CMAKE_INSTALL_BUILDINFODIR "" CACHE PATH "Build info files")
  set(CMAKE_INSTALL_BUILDINFODIR "${CMAKE_INSTALL_DATADIR}/IMP/build_info")
endif()
if(NOT DEFINED CMAKE_INSTALL_TOOLSDIR)
  set(CMAKE_INSTALL_TOOLSDIR "share/IMP/tools" CACHE PATH "IMP build tools")
endif()
if(NOT CMAKE_INSTALL_PYTHONDIR)
  set(CMAKE_INSTALL_PYTHONDIR "" CACHE PATH "Python modules")
  set(CMAKE_INSTALL_PYTHONDIR "${CMAKE_INSTALL_LIBDIR}/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages")
endif()
if(NOT CMAKE_INSTALL_CMAKEDIR)
  set(CMAKE_INSTALL_CMAKEDIR "" CACHE PATH "cmake modules")
  set(CMAKE_INSTALL_CMAKEDIR "${CMAKE_INSTALL_LIBDIR}/cmake/IMP")
endif()

foreach(dir SWIGDIR BUILDINFODIR TOOLSDIR PYTHONDIR CMAKEDIR)
  if(NOT IS_ABSOLUTE ${CMAKE_INSTALL_${dir}})
    set(CMAKE_INSTALL_FULL_${dir} "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_${dir}}")
  else()
    set(CMAKE_INSTALL_FULL_${dir} "${CMAKE_INSTALL_${dir}}")
  endif()
endforeach()

include(InstallDeref)

set(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib)

include_directories("${CMAKE_BINARY_DIR}/include")

# Keep track of all variables relating to dependencies
set(IMP_ALL_DEPENDS_VARS BOOST.FILESYSTEM_LIBRARIES BOOST.SYSTEM_LIBRARIES
    BOOST.THREAD_LIBRARIES BOOST.PROGRAMOPTIONS_LIBRARIES BOOST.REGEX_LIBRARIES
    BOOST.GRAPH_LIBRARIES BOOST.RANDOM_LIBRARIES
    CACHE INTERNAL "" FORCE)

imp_execute_process("setup" ${CMAKE_BINARY_DIR}
                    COMMAND ${PYTHON_EXECUTABLE}
                    ${CMAKE_SOURCE_DIR}/tools/build/setup.py
                    --source=${CMAKE_SOURCE_DIR}
                    --disabled=${IMP_DISABLED_MODULES}
                    --datapath=${IMP_DATAPATH})

imp_execute_process("setup_all" ${CMAKE_BINARY_DIR}
                    COMMAND ${PYTHON_EXECUTABLE}
                    ${CMAKE_SOURCE_DIR}/tools/build/setup_all.py
                    --source=${CMAKE_SOURCE_DIR})

imp_execute_process("making containers" ${CMAKE_BINARY_DIR}
                    COMMAND ${PYTHON_EXECUTABLE}
                    ${CMAKE_SOURCE_DIR}/tools/build/make_containers.py)

include(${PROJECT_SOURCE_DIR}/tools/build/cmake_files/MakeContainers.cmake)

# Don't link in libpython (that prevents the extension from being used in
# later compatible versions of Python), except on Windows where all DLL
# symbols must be defined
IF(WIN32)
  set(SWIG_PYTHON_LIBRARIES ${PYTHON_LIBRARIES} )
ELSE(WIN32)
  set(SWIG_PYTHON_LIBRARIES )
ENDIF(WIN32)

# Visual Studio always adds Release or Debug to binary directories
if (${CMAKE_GENERATOR} MATCHES "Visual Studio")
  SET(IMP_BINARY_PATH_SUFFIX ${CMAKE_BUILD_TYPE})
else()
  SET(IMP_BINARY_PATH_SUFFIX )
endif()

set(Boost_NO_BOOST_CMAKE ON)
find_package(Boost 1.53.0 COMPONENTS system filesystem thread program_options REQUIRED)
if("${Boost_SYSTEM_LIBRARY_RELEASE}" MATCHES ".*NOTFOUND.*")
  message(FATAL_ERROR "Boost is required to build IMP.")
endif()
find_package(Boost 1.53.0 QUIET COMPONENTS random regex graph)

if("${Boost_RANDOM_LIBRARY_RELEASE}" MATCHES ".*NOTFOUND.*")
set(Boost_RANDOM_LIBRARY_RELEASE "" CACHE INTERNAL "" FORCE)
set(Boost_RANDOM_LIBRARY_DEBUG "" CACHE INTERNAL "" FORCE)
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Random" "ok=False")
elseif(NOT "${Boost_RANDOM_LIBRARY_RELEASE}" STREQUAL "")
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Random" "ok=True")
else()
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Random" "ok=False")
endif()

if("${Boost_REGEX_LIBRARY_RELEASE}" MATCHES ".*NOTFOUND.*")
set(Boost_REGEX_LIBRARY_RELEASE "" CACHE INTERNAL "" FORCE)
set(Boost_REGEX_LIBRARY_DEBUG "" CACHE INTERNAL "" FORCE)
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Regex" "ok=False")
elseif(NOT "${Boost_REGEX_LIBRARY_RELEASE}" STREQUAL "")
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Regex" "ok=True")
else()
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Regex" "ok=False")
endif()

if("${Boost_GRAPH_LIBRARY_RELEASE}" MATCHES ".*NOTFOUND.*")
set(Boost_GRAPH_LIBRARY_RELEASE "" CACHE INTERNAL "" FORCE)
set(Boost_GRAPH_LIBRARY_DEBUG "" CACHE INTERNAL "" FORCE)
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Graph" "ok=False")
elseif(NOT "${Boost_GRAPH_LIBRARY_RELEASE}" STREQUAL "")
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Graph" "ok=True")
else()
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Graph" "ok=False")
endif()

include_directories(SYSTEM ${Boost_INCLUDE_DIR})
link_directories(${Boost_LIBRARY_DIRS})

set(BOOST.FILESYSTEM_LIBRARIES ${Boost_FILESYSTEM_LIBRARY_RELEASE})
set(BOOST.SYSTEM_LIBRARIES ${Boost_SYSTEM_LIBRARY_RELEASE})
set(BOOST.THREAD_LIBRARIES ${Boost_THREAD_LIBRARY_RELEASE})
set(BOOST.PROGRAMOPTIONS_LIBRARIES ${Boost_PROGRAM_OPTIONS_LIBRARY_RELEASE})
set(BOOST.REGEX_LIBRARIES ${Boost_REGEX_LIBRARY_RELEASE})
set(BOOST.GRAPH_LIBRARIES ${Boost_GRAPH_LIBRARY_RELEASE})
set(BOOST.RANDOM_LIBRARIES ${Boost_RANDOM_LIBRARY_RELEASE})

file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.FileSystem" "ok=True")
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.ProgramOptions" "ok=True")
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Serialization" "ok=True")
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.System" "ok=True")
file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Thread" "ok=True")

if(DEFINED IMP_CUDA_REQUESTED)
  find_package(CUDA REQUIRED)
  include(FindCUDA)
  list(APPEND CUDA_NVCC_FLAGS --compiler-options -fno-strict-aliasing -lineinfo -use_fast_math -Xptxas -dlcm=cg)
  list(APPEND CUDA_NVCC_FLAGS -lcufft)
  # Support for the Fermi architecture was removed in CUDA toolkit 9
  if (CUDA_VERSION_MAJOR LESS 9)
    list(APPEND CUDA_NVCC_FLAGS -gencode arch=compute_20,code=sm_20)
  endif()
  if (CUDA_VERSION_MAJOR LESS 11)
    list(APPEND CUDA_NVCC_FLAGS -gencode arch=compute_30,code=sm_30)
    list(APPEND CUDA_NVCC_FLAGS -gencode arch=compute_35,code=sm_35)
  endif()
  list(APPEND CUDA_NVCC_FLAGS -gencode arch=compute_52,code=sm_52)
  list(APPEND CUDA_NVCC_FLAGS -arch sm_53)
  message(STATUS "CUDA libraries: " "${CUDA_LIBRARIES}")
  message(STATUS "CUDA curand library: " "${CUDA_curand_LIBRARY}")
  message(STATUS "CUDA cufft library: " "${CUDA_cufft_LIBRARY}")
endif()

if(NOT IMP_STATIC)
  # Automatically enable OpenMP if available and at least version 3
  find_package(OpenMP3)
endif()

find_package(Eigen3 3.0 REQUIRED)
# Add Eigen3 to 'system' include path. Amongst other things, this will suppress
# many compiler warnings about Eigen code which a) clutter the output and
# b) we're not going to fix, since Eigen isn't our code.
include_directories(SYSTEM ${EIGEN3_INCLUDE_DIR})

find_package(cereal REQUIRED)
include_directories(SYSTEM ${cereal_INCLUDE_DIRS})

add_custom_target("IMP-version"
                  COMMAND ${PYTHON_EXECUTABLE}
                          ${CMAKE_SOURCE_DIR}/tools/build/make_version.py
                          --source=${CMAKE_SOURCE_DIR}
                  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
                  COMMENT "Computing version number")


# configure modules
file(STRINGS "${CMAKE_BINARY_DIR}/build_info/sorted_modules" modules)

foreach(mod ${modules})
  add_subdirectory("${CMAKE_SOURCE_DIR}/modules/${mod}/")
endforeach(mod)

# build modules
file(STRINGS "${CMAKE_BINARY_DIR}/build_info/sorted_modules" enabled_modules)

if(NOT DEFINED IMP_NO_SWIG_DEPENDENCIES)
# the make_containers.py call is needed to let swig find all headers it needs
imp_execute_process("setup_swig_dependencies" ${CMAKE_BINARY_DIR}
                    COMMAND ${PYTHON_EXECUTABLE}
                    ${CMAKE_SOURCE_DIR}/tools/build/setup_swig_deps.py
                    "--swig=${SWIG_EXECUTABLE}")
endif()

# Static builds don't include Python extensions
if(NOT IMP_STATIC)
  # Can't set up pyext until we have SWIG dependencies
  foreach(mod ${enabled_modules})
    add_subdirectory("${CMAKE_SOURCE_DIR}/modules/${mod}/pyext")
  endforeach(mod)
endif()

foreach(mod ${enabled_modules})
  add_custom_target(IMP.${mod} DEPENDS
  ${IMP_${mod}_LIBRARY}
  ${IMP_${mod}_BINS}
  ${IMP_${mod}_UTILS}
  ${IMP_${mod}_TESTS}
  ${IMP_${mod}_BENCHMARKS}
  ${IMP_${mod}_PYTHON}
  ${IMP_${mod}_EXAMPLES}
  ${IMP_${mod}_DOC})
endforeach(mod)

list(INSERT IMP_PYTHONPATH 0 "${CMAKE_BINARY_DIR}/lib")
list(INSERT IMP_LDPATH 0 "${CMAKE_BINARY_DIR}/lib")
list(INSERT IMP_PATH 0 "${CMAKE_BINARY_DIR}/bin")
set(PATH_ARGS )
foreach(path ${IMP_PYTHONPATH})
  list(APPEND PATH_ARGS "--python_path=${path}")
endforeach(path)
foreach(path ${IMP_LDPATH})
  list(APPEND PATH_ARGS "--ld_path=${path}")
endforeach(path)
foreach(path ${IMP_PATH})
  list(APPEND PATH_ARGS "--path=${path}")
endforeach(path)
imp_execute_process("setup_imppy" ${CMAKE_BINARY_DIR}
                    COMMAND ${PYTHON_EXECUTABLE}
                    ${CMAKE_SOURCE_DIR}/tools/build/setup_imppy.py
                    "--python_pathsep=${PYTHON_PATH_SEP}"
                    "--precommand="
                    "--propagate=yes"
                    "--suffix=${IMP_BINARY_PATH_SUFFIX}"
                    "--output=setup_environment.${SETUP_EXT}"
                    ${PATH_ARGS})

if(IMP_DOXYGEN_FOUND)

 file(GLOB docs ${CMAKE_SOURCE_DIR}/doc/*/*.dox
   ${CMAKE_SOURCE_DIR}/doc/*/*.md)

  add_custom_target(IMP-doc
    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/setup_doxygen_config.py "--source=${CMAKE_SOURCE_DIR}"
    # Generate manual's tag file so we can link from the refguide to it
    COMMAND ${IMP_DOXYGEN_EXECUTABLE} doxygen/manual.xml
    COMMAND ${IMP_DOXYGEN_EXECUTABLE} doxygen/ref.xml
    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/make_cross_refs.py
    COMMAND ${IMP_DOXYGEN_EXECUTABLE} doxygen/ref.html
    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_show_warnings.py --warn=${CMAKE_BINARY_DIR}/doxygen/ref-warnings.txt
    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_fix_links.py ${CMAKE_BINARY_DIR}/doc/ref
    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_fix_php.py ${CMAKE_BINARY_DIR}/doc/ref
    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_add_ref_nav.py ${CMAKE_SOURCE_DIR}
    # Rebuild manual so that it can link to the refguide tags
    COMMAND ${IMP_DOXYGEN_EXECUTABLE} doxygen/manual.html
    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_show_warnings.py --warn=${CMAKE_BINARY_DIR}/doxygen/manual-warnings.txt
    COMMAND patch -p1 < ${CMAKE_SOURCE_DIR}/doc/doxygen/search.patch
    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_fix_php.py ${CMAKE_BINARY_DIR}/doc/manual
    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_add_nav.py ${CMAKE_SOURCE_DIR} . doc/manual tools
    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_spell_check.py doxygen/manual/xml ${CMAKE_SOURCE_DIR}/doc/standards_exceptions
    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
    DEPENDS ${IMP_DOC_DEPENDS} ${docs} ${IMP_DOXYGEN_FETCH} IMP-version
    COMMENT "Building documentation")

  add_custom_target(IMP-doc-install
    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/copy_directory_deref.py "${CMAKE_BINARY_DIR}/doc/manual" "${CMAKE_INSTALL_FULL_DOCDIR}/manual"
    COMMAND ${CMAKE_COMMAND} -E copy "${CMAKE_BINARY_DIR}/doxygen/manual-tags.xml" "${CMAKE_INSTALL_FULL_DOCDIR}"
    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/copy_directory_deref.py "${CMAKE_BINARY_DIR}/doc/ref" "${CMAKE_INSTALL_FULL_DOCDIR}/ref"
    COMMAND ${CMAKE_COMMAND} -E copy "${CMAKE_BINARY_DIR}/doxygen/ref-tags.xml" "${CMAKE_INSTALL_FULL_DOCDIR}"
    DEPENDS "IMP-doc"
    COMMENT "Installing documentation to ${CMAKE_INSTALL_FULL_DOCDIR}")
else()
  message(STATUS "Documentation disabled as doxygen not found")
endif(IMP_DOXYGEN_FOUND)

# Write configuration to a cmake file so that we can use IMP in other projects
file(WRITE ${CMAKE_BINARY_DIR}/IMPConfig.cmake
     "set(IMP_INSTALL_PREFIX \"${CMAKE_BINARY_DIR}\" )\n"
     "set(IMP_TOOLS_DIR \"${CMAKE_SOURCE_DIR}/tools\" )\n"
     "set(IMP_USE_DIR \"${CMAKE_SOURCE_DIR}/tools/cmake\" )\n"
     "set(IMP_BUILD_INFO_DIR \"${CMAKE_BINARY_DIR}/build_info\" )\n"
     "set(IMP_INCLUDE_DIR \"${CMAKE_BINARY_DIR}/include\" )\n"
     "set(IMP_BIN_DIR \"${CMAKE_BINARY_DIR}/bin\" )\n"
     "set(IMP_LIB_DIR \"${CMAKE_BINARY_DIR}/lib\" )\n"
     "set(IMP_PYTHON_DIR \"${CMAKE_BINARY_DIR}/lib\" )\n"
     "set(IMP_DATA_DIR \"${CMAKE_BINARY_DIR}/data\" )\n"
     "set(IMP_SWIG_DIR \"${CMAKE_BINARY_DIR}/swig\" )\n"
     "set(RMF_SWIG_DIR \"${CMAKE_SOURCE_DIR}/modules/rmf/dependency/RMF/swig\" )\n"
     "set(IMP_MODULES_DIR \"${CMAKE_SOURCE_DIR}/cmake_modules\" )\n"
     "set(IMP_CXX_COMPILER \"${CMAKE_CXX_COMPILER}\" )\n"
     "set(IMP_CXX_FLAGS \"${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}\" )\n"
     "set(IMP_OSX_SYSROOT \"${CMAKE_OSX_SYSROOT}\" )\n"
     "set(RMF_INCLUDE_PATH \"${RMF_INCLUDE_PATH}\" )\n"
     "set(IMP_USE_FILE \"\${IMP_USE_DIR}/UseIMP.cmake\" )\n")
# Installed locations
file(WRITE ${CMAKE_BINARY_DIR}/cmake/IMPConfig.cmake
     "set(IMP_INSTALL_PREFIX \"${CMAKE_INSTALL_PREFIX}\" )\n"
     "set(IMP_TOOLS_DIR \"${CMAKE_INSTALL_FULL_TOOLSDIR}\" )\n"
     "set(IMP_USE_DIR \"${CMAKE_INSTALL_FULL_CMAKEDIR}\" )\n"
     "set(IMP_BUILD_INFO_DIR \"${CMAKE_INSTALL_FULL_BUILDINFODIR}\" )\n"
     "set(IMP_INCLUDE_DIR \"${CMAKE_INSTALL_FULL_INCLUDEDIR}\" )\n"
     "set(IMP_BIN_DIR \"${CMAKE_INSTALL_FULL_BINDIR}\" )\n"
     "set(IMP_LIB_DIR \"${CMAKE_INSTALL_FULL_LIBDIR}\" )\n"
     "set(IMP_PYTHON_DIR \"${CMAKE_INSTALL_FULL_PYTHONDIR}\" )\n"
     "set(IMP_DATA_DIR \"${CMAKE_INSTALL_FULL_DATADIR}/IMP\" )\n"
     "set(IMP_SWIG_DIR \"${CMAKE_INSTALL_FULL_SWIGDIR}\" )\n"
     "set(RMF_SWIG_DIR \"${CMAKE_INSTALL_FULL_SWIGDIR}\" )\n"
     "set(IMP_MODULES_DIR \"${CMAKE_INSTALL_FULL_CMAKEDIR}\" )\n"
     "set(RMF_INCLUDE_PATH \"${CMAKE_INSTALL_FULL_INCLUDEDIR}\" )\n"
     "set(IMP_CXX_COMPILER \"${CMAKE_CXX_COMPILER}\" )\n"
     "set(IMP_CXX_FLAGS \"${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}\" )\n"
     "set(IMP_OSX_SYSROOT \"${CMAKE_OSX_SYSROOT}\" )\n"
     "set(IMP_USE_FILE \"\${IMP_USE_DIR}/UseIMP.cmake\" )\n")
list(REMOVE_DUPLICATES IMP_ALL_DEPENDS_VARS)
foreach(cmakefile ${CMAKE_BINARY_DIR}/IMPConfig.cmake
                  ${CMAKE_BINARY_DIR}/cmake/IMPConfig.cmake)
  foreach(var IMP_LIB_TYPE IMP_NO_SWIG_DEPENDENCIES IMP_STATIC IMP_MAX_CHECKS
              IMP_MAX_LOG IMP_SWIG_LIBRARIES EIGEN3_INCLUDE_DIR
              cereal_INCLUDE_DIRS Boost_INCLUDE_DIR ${IMP_ALL_DEPENDS_VARS})
    file(APPEND "${cmakefile}"
         "SET(${var} \"${${var}}\" CACHE INTERNAL \"\" FORCE)\n")
  endforeach()
endforeach()
file(APPEND ${CMAKE_BINARY_DIR}/IMPConfig.cmake
     "set(RMF_LIBRARIES \"\${IMP_LIB_DIR}/libRMF${CMAKE_SHARED_LIBRARY_SUFFIX}\" )\n")
file(APPEND ${CMAKE_BINARY_DIR}/cmake/IMPConfig.cmake
     "set(RMF_LIBRARIES \"\${IMP_LIB_DIR}/libRMF${CMAKE_SHARED_LIBRARY_SUFFIX}\" )\n")
foreach(mod ${enabled_modules})
  # No library for python-only modules
  if (NOT TARGET "IMP.${mod}-lib")
    file(APPEND ${CMAKE_BINARY_DIR}/IMPConfig.cmake
         "set(IMP_${mod}_LIBRARY \"\")\n")
  else()
    get_target_property(modver "IMP.${mod}-lib" VERSION)
    if (APPLE)
      file(APPEND ${CMAKE_BINARY_DIR}/IMPConfig.cmake
           "set(IMP_${mod}_LIBRARY \"\${IMP_LIB_DIR}/libimp_${mod}.${modver}.dylib\" )\n")
      file(APPEND ${CMAKE_BINARY_DIR}/cmake/IMPConfig.cmake
           "set(IMP_${mod}_LIBRARY \"\${IMP_LIB_DIR}/libimp_${mod}.${modver}.dylib\" )\n")
    elseif (WIN32)
      file(APPEND ${CMAKE_BINARY_DIR}/IMPConfig.cmake
           "set(IMP_${mod}_LIBRARY \"\${IMP_LIB_DIR}/imp_${mod}.dll\" )\n")
      file(APPEND ${CMAKE_BINARY_DIR}/cmake/IMPConfig.cmake
           "set(IMP_${mod}_LIBRARY \"\${IMP_LIB_DIR}/imp_${mod}.dll\" )\n")
    else()
      file(APPEND ${CMAKE_BINARY_DIR}/IMPConfig.cmake
          "set(IMP_${mod}_LIBRARY \"\${IMP_LIB_DIR}/libimp_${mod}.so.${modver}\" )\n")
      file(APPEND ${CMAKE_BINARY_DIR}/cmake/IMPConfig.cmake
           "set(IMP_${mod}_LIBRARY \"\${IMP_LIB_DIR}/libimp_${mod}.so.${modver}\" )\n")
    endif()
  endif()
endforeach()

# Install headers
install(FILES ${CMAKE_BINARY_DIR}/include/IMP.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
install_deref(${CMAKE_BINARY_DIR}/include/IMP * ${CMAKE_INSTALL_INCLUDEDIR}/IMP)

# Install Python modules
install_deref(${CMAKE_BINARY_DIR}/lib/IMP * ${CMAKE_INSTALL_PYTHONDIR}/IMP)

# Install data
install_deref(${CMAKE_BINARY_DIR}/data * ${CMAKE_INSTALL_DATADIR}/IMP)

# Install build_info
install(DIRECTORY ${CMAKE_BINARY_DIR}/build_info/
        DESTINATION ${CMAKE_INSTALL_BUILDINFODIR})

# Install SWIG .i files
install_deref(${CMAKE_BINARY_DIR}/swig *.i ${CMAKE_INSTALL_SWIGDIR})

# Install build tools
# dev_tools is a symlink, so we need to deref it first
get_filename_component(dev_tools_dir "${CMAKE_SOURCE_DIR}/tools/dev_tools"
                       REALPATH)
install(DIRECTORY ${dev_tools_dir}
        ${CMAKE_SOURCE_DIR}/tools/build DESTINATION ${CMAKE_INSTALL_TOOLSDIR}
        PATTERN "*.py" PERMISSIONS OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE
                                   OWNER_READ GROUP_READ WORLD_READ
                                   OWNER_WRITE)

# Install cmake scripts and configuration
install(DIRECTORY ${CMAKE_SOURCE_DIR}/cmake_modules/
                  ${CMAKE_SOURCE_DIR}/tools/cmake/
                  ${CMAKE_BINARY_DIR}/cmake/
        DESTINATION ${CMAKE_INSTALL_CMAKEDIR})

# Install examples
install_deref(${CMAKE_BINARY_DIR}/doc/examples *
              ${CMAKE_INSTALL_DOCDIR}/examples)

# Try to ensure that ctest doesn't truncate benchmark output
file(WRITE "${CMAKE_BINARY_DIR}/CTestCustom.cmake"
"SET(CTEST_CUSTOM_MAXIMUM_PASSED_TEST_OUTPUT_SIZE 4096)
")