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-rw-r--r--src/cmake/modules/GUDHI_boost_test.cmake7
-rw-r--r--src/cmake/modules/GUDHI_compilation_flags.cmake37
-rw-r--r--src/cmake/modules/GUDHI_third_party_libraries.cmake62
-rw-r--r--src/cmake/modules/GUDHI_user_version_target.cmake11
4 files changed, 73 insertions, 44 deletions
diff --git a/src/cmake/modules/GUDHI_boost_test.cmake b/src/cmake/modules/GUDHI_boost_test.cmake
index c3b29883..4a13404b 100644
--- a/src/cmake/modules/GUDHI_boost_test.cmake
+++ b/src/cmake/modules/GUDHI_boost_test.cmake
@@ -9,7 +9,6 @@ if (WITH_GUDHI_BOOST_TEST_COVERAGE)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
endif()
set(GUDHI_UT_LOG_FORMAT "--log_format=XML")
- set(GUDHI_UT_LOG_SINK "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml")
set(GUDHI_UT_LOG_LEVEL "--log_level=test_suite")
set(GUDHI_UT_REPORT_LEVEL "--report_level=no")
else (WITH_GUDHI_BOOST_TEST_COVERAGE)
@@ -19,7 +18,11 @@ else (WITH_GUDHI_BOOST_TEST_COVERAGE)
endif(WITH_GUDHI_BOOST_TEST_COVERAGE)
function(gudhi_add_boost_test unitary_test)
- target_link_libraries(${unitary_test} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+ if (WITH_GUDHI_BOOST_TEST_COVERAGE)
+ set(GUDHI_UT_LOG_SINK "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml")
+ endif(WITH_GUDHI_BOOST_TEST_COVERAGE)
+
+ target_link_libraries(${unitary_test} Boost::unit_test_framework)
add_test(NAME ${unitary_test} COMMAND $<TARGET_FILE:${unitary_test}>
${GUDHI_UT_LOG_FORMAT} ${GUDHI_UT_LOG_SINK}
${GUDHI_UT_LOG_LEVEL} ${GUDHI_UT_REPORT_LEVEL})
diff --git a/src/cmake/modules/GUDHI_compilation_flags.cmake b/src/cmake/modules/GUDHI_compilation_flags.cmake
index 34c2e065..567fbc40 100644
--- a/src/cmake/modules/GUDHI_compilation_flags.cmake
+++ b/src/cmake/modules/GUDHI_compilation_flags.cmake
@@ -1,7 +1,6 @@
# This files manage compilation flags required by GUDHI
include(TestCXXAcceptsFlag)
-include(CheckCXXSourceCompiles)
# add a compiler flag only if it is accepted
macro(add_cxx_compiler_flag _flag)
@@ -12,32 +11,6 @@ macro(add_cxx_compiler_flag _flag)
endif()
endmacro()
-function(can_cgal_use_cxx11_thread_local)
- # This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h
- # CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac).
- # The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h
- # #if __has_feature(cxx_thread_local) || \
- # ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \
- # ( _MSC_VER >= 1900 )
- # #define CGAL_CAN_USE_CXX11_THREAD_LOCAL
- # #endif
- set(CGAL_CAN_USE_CXX11_THREAD_LOCAL "
- int main() {
- #ifndef __has_feature
- #define __has_feature(x) 0 // Compatibility with non-clang compilers.
- #endif
- #if __has_feature(cxx_thread_local) || \
- ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \
- ( _MSC_VER >= 1900 )
- bool has_feature_thread_local = true;
- #else
- // Explicit error of compilation for CMake test purpose - has_feature_thread_local is not defined
- #endif
- bool result = has_feature_thread_local;
- } ")
- check_cxx_source_compiles("${CGAL_CAN_USE_CXX11_THREAD_LOCAL}" CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
-endfunction()
-
set (CMAKE_CXX_STANDARD 14)
enable_testing()
@@ -58,16 +31,6 @@ if (DEBUG_TRACES)
add_definitions(-DDEBUG_TRACES)
endif()
-set(GUDHI_CAN_USE_CXX11_THREAD_LOCAL "
- int main() {
- thread_local int result = 0;
- return result;
- } ")
-check_cxx_source_compiles("${GUDHI_CAN_USE_CXX11_THREAD_LOCAL}" GUDHI_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
-if (GUDHI_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
- add_definitions(-DGUDHI_CAN_USE_CXX11_THREAD_LOCAL)
-endif()
-
if(CMAKE_BUILD_TYPE MATCHES Debug)
message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
else()
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 24a34150..0abe66b7 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -6,6 +6,38 @@ if(NOT Boost_FOUND)
message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
endif(NOT Boost_FOUND)
+# cf. https://cliutils.gitlab.io/modern-cmake/chapters/packages/Boost.html
+# This is needed if your Boost version is newer than your CMake version
+# or if you have an old version of CMake (<3.5)
+if(NOT TARGET Boost::program_options)
+ add_library(Boost::program_options IMPORTED INTERFACE)
+ set_property(TARGET Boost::program_options PROPERTY
+ INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
+ set_property(TARGET Boost::program_options PROPERTY
+ INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES})
+endif()
+if(NOT TARGET Boost::filesystem)
+ add_library(Boost::filesystem IMPORTED INTERFACE)
+ set_property(TARGET Boost::filesystem PROPERTY
+ INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
+ set_property(TARGET Boost::filesystem PROPERTY
+ INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES})
+endif()
+if(NOT TARGET Boost::unit_test_framework)
+ add_library(Boost::unit_test_framework IMPORTED INTERFACE)
+ set_property(TARGET Boost::unit_test_framework PROPERTY
+ INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
+ set_property(TARGET Boost::unit_test_framework PROPERTY
+ INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES})
+endif()
+if(NOT TARGET Boost::system)
+ add_library(Boost::system IMPORTED INTERFACE)
+ set_property(TARGET Boost::system PROPERTY
+ INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
+ set_property(TARGET Boost::system PROPERTY
+ INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES})
+endif()
+
find_package(GMP)
if(GMP_FOUND)
INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
@@ -35,6 +67,9 @@ if(CGAL_FOUND)
include( ${CGAL_USE_FILE} )
endif()
+# For those who dislike bundled dependencies, this indicates where to find a preinstalled Hera.
+set(HERA_WASSERSTEIN_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include CACHE PATH "Directory where one can find Hera's wasserstein.h")
+
option(WITH_GUDHI_USE_TBB "Build with Intel TBB parallelization" ON)
# Find TBB package for parallel sort - not mandatory, just optional.
@@ -82,9 +117,6 @@ add_definitions( -DBOOST_ALL_DYN_LINK )
# problem on Mac with boost_system and boost_thread
add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED )
-INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
-LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
-
message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
@@ -118,6 +150,25 @@ function( find_python_module PYTHON_MODULE_NAME )
endif()
endfunction( find_python_module )
+# For modules that do not define module.__version__
+function( find_python_module_no_version PYTHON_MODULE_NAME )
+ string(TOUPPER ${PYTHON_MODULE_NAME} PYTHON_MODULE_NAME_UP)
+ execute_process(
+ COMMAND ${PYTHON_EXECUTABLE} -c "import ${PYTHON_MODULE_NAME}"
+ RESULT_VARIABLE PYTHON_MODULE_RESULT
+ ERROR_VARIABLE PYTHON_MODULE_ERROR)
+ if(PYTHON_MODULE_RESULT EQUAL 0)
+ # Remove carriage return
+ message ("++ Python module ${PYTHON_MODULE_NAME} found")
+ set(${PYTHON_MODULE_NAME_UP}_FOUND TRUE PARENT_SCOPE)
+ else()
+ message ("PYTHON_MODULE_NAME = ${PYTHON_MODULE_NAME}
+ - PYTHON_MODULE_RESULT = ${PYTHON_MODULE_RESULT}
+ - PYTHON_MODULE_ERROR = ${PYTHON_MODULE_ERROR}")
+ set(${PYTHON_MODULE_NAME_UP}_FOUND FALSE PARENT_SCOPE)
+ endif()
+endfunction( find_python_module_no_version )
+
if( PYTHONINTERP_FOUND )
find_python_module("cython")
find_python_module("pytest")
@@ -127,6 +178,11 @@ if( PYTHONINTERP_FOUND )
find_python_module("sphinx")
find_python_module("sklearn")
find_python_module("ot")
+ find_python_module("pybind11")
+ find_python_module("torch")
+ find_python_module("pykeops")
+ find_python_module("eagerpy")
+ find_python_module_no_version("hnswlib")
endif()
if(NOT GUDHI_PYTHON_PATH)
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 0b361a0f..9cf648e3 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -26,8 +26,12 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
# Generate bib files for Doxygen - cf. root CMakeLists.txt for explanation
string(TIMESTAMP GUDHI_VERSION_YEAR "%Y")
configure_file(${CMAKE_SOURCE_DIR}/biblio/how_to_cite_gudhi.bib.in "${CMAKE_CURRENT_BINARY_DIR}/biblio/how_to_cite_gudhi.bib" @ONLY)
-file(COPY "${CMAKE_SOURCE_DIR}/biblio/how_to_cite_cgal.bib" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/biblio/")
file(COPY "${CMAKE_SOURCE_DIR}/biblio/bibliography.bib" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/biblio/")
+
+# append cgal citation inside bibliography - sphinx cannot deal with more than one bib file
+file(READ "${CMAKE_SOURCE_DIR}/biblio/how_to_cite_cgal.bib" CGAL_CITATION_CONTENT)
+file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/biblio/bibliography.bib" "${CGAL_CITATION_CONTENT}")
+
# Copy biblio directory for user version
add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
copy_directory ${CMAKE_CURRENT_BINARY_DIR}/biblio ${GUDHI_USER_VERSION_DIR}/biblio)
@@ -54,6 +58,9 @@ 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}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+ copy_directory ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include ${GUDHI_USER_VERSION_DIR}/ext/hera/wasserstein/include)
+
set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi")
@@ -93,4 +100,4 @@ foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
endforeach()
endforeach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
-endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST}) \ No newline at end of file
+endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-17 22:13:30 +0000