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AkantuTestsMacros.cmake
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			#===============================================================================
			# @file AkantuTestsMacros.cmake
			#
			# @author Nicolas Richart <nicolas.richart@epfl.ch>
			#
			# @date creation: Fri Sep 03 2010
			# @date last modification: Tue Jun 30 2020
			#
			# @brief macros for tests
			#
			#
			# @section LICENSE
			#
			# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
			# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
			#
			# Akantu is free software: you can redistribute it and/or modify it under the
			# terms of the GNU Lesser General Public License as published by the Free
			# Software Foundation, either version 3 of the License, or (at your option) any
			# later version.
			#
			# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
			# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
			# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
			# details.
			#
			# You should have received a copy of the GNU Lesser General Public License along
			# with Akantu. If not, see <http://www.gnu.org/licenses/>.
			#
			#===============================================================================


			#[=======================================================================[.rst:
			AkantuTestsMacros
			-----------------

			This modules provides the functions to helper to declare tests and folders
			containing tests in akantu

			.. command:: add_test_tree

			add_test_tree(<test_direcotry>)

			``<test_directory>`` is the entry direcroty of the full structure of
			subfolders containing tests

			.. command:: add_akantu_test

			add_akantu_test(<dir> <desc>)

			This function add a subdirectory ``<dir>`` of tests that will be conditionnaly
			activable and will be visible only if the parent folder as been activated An
			option ``AKANTU_BUILD_TEST_<dir>`` will appear in ccmake with the description
			``<desc>``. The compilation of all tests can be forced with the option
			``AKANTU_BUILD_ALL_TESTS``

			.. command:: register_test

			register_test(<test_name>
			SOURCES <sources>...
			PACKAGE <akantu_packages>...
			SCRIPT <scirpt>
			[FILES_TO_COPY <filenames>...]
			[DEPENDS <targets>...]
			[DIRECTORIES_TO_CREATE <directories>...]
			[COMPILE_OPTIONS <flags>...]
			[EXTRA_FILES <filnames>...]
			[LINK_LIBRARIES <libraries>...]
			[INCLUDE_DIRECTORIES <include>...]
			[UNSABLE]
			[PARALLEL]
			[PARALLEL_LEVEL <procs>...]
			)

			This function defines a test ``<test_name>_run`` this test could be of
			different nature depending on the context. If Just sources are provided the
			test consist of running the executable generated. If a file ``<test_name>.sh``
			is present the test will execute the script. And if a ``<test_name>.verified``
			exists the output of the test will be compared to this reference file

			The options are:

			``SOURCES <sources>...``
			The list of source files to compile to generate the executable of the test

			``PACKAGE <akantu_packages>...``
			The list of package to which this test belongs. The test will be activable
			only of all the packages listed are activated

			``SCRIPT <script>``
			The script to execute instead of the executable

			``FILES_TO_COPY <filenames>...``
			List of files to copy from the source directory to the build directory

			``DEPENDS <targets>...``
			List of targets the test depends on, for example if a mesh as to be generated

			``DIRECTORIES_TO_CREATE <directories>...``
			Obsolete. This specifies a list of directories that have to be created in
			the build folder

			``COMPILE_OPTIONS <flags>...``
			List of extra compilations options to pass to the compiler

			``EXTRA_FILES <filnames>...``
			Files to consider when generating a package_source

			``UNSABLE``
			If this option is specified the test can be unacitivated by the glocal option
			``AKANTU_BUILD_UNSTABLE_TESTS``, this is mainly intendeed to remove test
			under developement from the continious integration

			``PARALLEL``
			This specifies that this test should be run in parallel. It will generate a
			series of test for different number of processors. This automaticaly adds a
			dependency to the package ``AKANTU_PARALLEL``

			``PARALLEL_LEVEL``
			This defines the different processor numbers to use, if not defined the
			macro tries to determine it in a "clever" way

			]=======================================================================]

			set(AKANTU_DRIVER_SCRIPT ${AKANTU_CMAKE_DIR}/akantu_test_driver.sh)

			# ==============================================================================
			macro(add_test_tree dir)
			if(AKANTU_TESTS)
			enable_testing()
			include(CTest)
			mark_as_advanced(BUILD_TESTING)

			set(_akantu_current_parent_test ${dir} CACHE INTERNAL "Current test folder" FORCE)
			set(_akantu_${dir}_tests_count 0 CACHE INTERNAL "" FORCE)

			string(TOUPPER ${dir} _u_dir)
			set(AKANTU_BUILD_${_u_dir} ON CACHE INTERNAL "${desc}" FORCE)

			package_get_all_test_folders(_test_dirs)

			foreach(_dir ${_test_dirs})
			add_subdirectory(${_dir})
			endforeach()
			endif()
			endmacro()


			set(_test_flags
			UNSTABLE
			PARALLEL
			PYTHON
			GTEST
			HEADER_ONLY
			)

			set(_test_one_variables
			POSTPROCESS
			SCRIPT
			)

			set(_test_multi_variables
			SOURCES
			FILES_TO_COPY
			DEPENDS
			DIRECTORIES_TO_CREATE
			COMPILE_OPTIONS
			EXTRA_FILES
			LINK_LIBRARIES
			INCLUDE_DIRECTORIES
			PACKAGE
			PARALLEL_LEVEL
			)


			# ==============================================================================
			function(add_akantu_test dir desc)
			if(NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${dir})
			return()
			endif()

			set(_my_parent_dir ${_akantu_current_parent_test})

			# initialize variables
			set(_akantu_current_parent_test ${dir} CACHE INTERNAL "Current test folder" FORCE)
			set(_akantu_${dir}_tests_count 0 CACHE INTERNAL "" FORCE)

			# set the option for this directory
			string(TOUPPER ${dir} _u_dir)
			option(AKANTU_BUILD_${_u_dir} "${desc}")
			mark_as_advanced(AKANTU_BUILD_${_u_dir})

			# add the sub-directory
			add_subdirectory(${dir})

			# if no test can be activated make the option disappear
			set(_force_deactivate_count FALSE)
			if(${_akantu_${dir}_tests_count} EQUAL 0)
			set(_force_deactivate_count TRUE)
			endif()

			# if parent off make the option disappear
			set(_force_deactivate_parent FALSE)
			string(TOUPPER ${_my_parent_dir} _u_parent_dir)
			if(NOT AKANTU_BUILD_${_u_parent_dir})
			set(_force_deactivate_parent TRUE)
			endif()

			if(_force_deactivate_parent OR _force_deactivate_count OR AKANTU_BUILD_ALL_TESTS)
			if(NOT DEFINED _AKANTU_BUILD_${_u_dir}_SAVE)
			set(_AKANTU_BUILD_${_u_dir}_SAVE ${AKANTU_BUILD_${_u_dir}} CACHE INTERNAL "" FORCE)
			endif()
			unset(AKANTU_BUILD_${_u_dir} CACHE)
			if(AKANTU_BUILD_ALL_TESTS AND NOT _force_deactivate_count)
			set(AKANTU_BUILD_${_u_dir} ON CACHE INTERNAL "${desc}" FORCE)
			else()
			set(AKANTU_BUILD_${_u_dir} OFF CACHE INTERNAL "${desc}" FORCE)
			endif()
			else()
			if(DEFINED _AKANTU_BUILD_${_u_dir}_SAVE)
			unset(AKANTU_BUILD_${_u_dir} CACHE)
			set(AKANTU_BUILD_${_u_dir} ${_AKANTU_BUILD_${_u_dir}_SAVE} CACHE BOOL "${desc}")
			unset(_AKANTU_BUILD_${_u_dir}_SAVE CACHE)
			endif()
			endif()

			# adding up to the parent count
			math(EXPR _tmp_parent_count "${_akantu_${dir}_tests_count} + ${_akantu_${_my_parent_dir}_tests_count}")
			set(_akantu_${_my_parent_dir}_tests_count ${_tmp_parent_count} CACHE INTERNAL "" FORCE)

			# restoring the parent current dir
			set(_akantu_current_parent_test ${_my_parent_dir} CACHE INTERNAL "Current test folder" FORCE)
			endfunction()

			function(is_test_active is_active)
			cmake_parse_arguments(_register_test
			"${_test_flags}"
			"${_test_one_variables}"
			"${_test_multi_variables}"
			${ARGN}
			)

			if(NOT _register_test_PACKAGE)
			message(FATAL_ERROR "No reference package was defined for the test"
			" ${test_name} in folder ${CMAKE_CURRENT_SOURCE_DIR}")
			endif()

			if(_register_test_PYTHON)
			list(APPEND _register_test_PACKAGE python_interface)
			endif()

			set(_test_act TRUE)
			# Activate the test anly if all packages associated to the test are activated
			foreach(_package ${_register_test_PACKAGE})
			package_is_activated(${_package} _act)
			if(NOT _act)
			set(_test_act FALSE)
			endif()
			endforeach()

			# check if the test is marked unstable and if the unstable test should be run
			if(_register_test_UNSTABLE AND NOT AKANTU_BUILD_UNSTABLE_TESTS)
			set(_test_act FALSE)
			endif()

			if(_test_act)
			# todo this should be checked for the build package_sources since the file will not be listed.
			math(EXPR _tmp_parent_count "${_akantu_${_akantu_current_parent_test}_tests_count} + 1")
			set(_akantu_${_akantu_current_parent_test}_tests_count ${_tmp_parent_count} CACHE INTERNAL "" FORCE)
			endif()

			string(TOUPPER ${_akantu_current_parent_test} _u_parent)
			if(NOT (AKANTU_BUILD_${_u_parent} OR AKANTU_BUILD_ALL_TESTS))
			set(_test_act FALSE)
			endif()

			set(${is_active} ${_test_act} PARENT_SCOPE)
			endfunction()

			# ------------------------------------------------------------------------------
			function(register_gtest_sources)
			cmake_parse_arguments(_register_test
			"${_test_flags}"
			"${_test_one_variables}"
			"${_test_multi_variables}"
			${ARGN}
			)

			is_test_active(_is_active ${ARGN})
			register_test_files_to_package(${ARGN})

			if(NOT _is_active)
			return()
			endif()

			if(_register_test_PACKAGE)
			set(_list ${_gtest_PACKAGE})
			list(APPEND _list ${_register_test_PACKAGE})
			list(REMOVE_DUPLICATES _list)
			set(_gtest_PACKAGE ${_list} PARENT_SCOPE)
			endif()

			foreach (_var ${_test_flags})
			if(_var STREQUAL "HEADER_ONLY")
			if(NOT DEFINED_register_test_${_var})
			set(_gtest_${_var} OFF PARENT_SCOPE)
			elseif(NOT DEFINED _gtest_${_var})
			set(_gtest_${_var} ON PARENT_SCOPE)
			endif()
			continue()
			endif()

			if(_register_test_${_var})
			set(_gtest_${_var} ON PARENT_SCOPE)
			else()
			if(_gtest_${_var})
			message("Another gtest file required ${_var} to be ON it will be globally set for this folder...")
			endif()
			endif()
			endforeach()

			if(_register_test_UNPARSED_ARGUMENTS)
			list(APPEND _register_test_SOURCES ${_register_test_UNPARSED_ARGUMENTS})
			endif()

			foreach (_var ${_test_multi_variables})
			if(_register_test_${_var})
			set(_list ${_gtest_${_var}})
			list(APPEND _list ${_register_test_${_var}})
			list(REMOVE_DUPLICATES _list)
			set(_gtest_${_var} ${_list} PARENT_SCOPE)
			endif()
			endforeach()
			endfunction()

			# ==============================================================================
			function(akantu_pybind11_add_module target)
			package_is_activated(pybind11 _pybind11_act)
			if(_pybind11_act)
			package_get_all_external_informations(
			INTERFACE_INCLUDE AKANTU_INTERFACE_EXTERNAL_INCLUDE_DIR
			)

			pybind11_add_module(${target} ${ARGN})
			target_link_libraries(${target} PRIVATE akantu)
			target_include_directories(${target} SYSTEM PRIVATE ${PYBIND11_INCLUDE_DIR} ${PROJECT_SOURCE_DIR}/python)
			set_property(TARGET ${target} PROPERTY DEBUG_POSTFIX "")
			endif()
			endfunction()

			# ==============================================================================
			function(register_gtest_test test_name)
			if(NOT _gtest_PACKAGE)
			return()
			endif()

			set(_argn ${test_name}_gtest)

			set(_link_libraries GTest::GTest GTest::Main)

			list(FIND _gtest_PACKAGE python_interface _pos)
			package_is_activated(python_interface _python_interface_act)

			if(_python_interface_act AND (NOT _pos EQUAL -1))
			list(APPEND _link_libraries pybind11::embed)
			set(_compile_flags COMPILE_OPTIONS "AKANTU_TEST_USE_PYBIND11")
			endif()

			is_test_active(_is_active ${ARGN} PACKAGE ${_gtest_PACKAGE})
			if(NOT _is_active)
			return()
			endif()

			register_gtest_sources(${ARGN}
			SOURCES ${PROJECT_SOURCE_DIR}/test/test_gtest_main.cc
			LINK_LIBRARIES ${_link_libraries}
			PACKAGE ${_gtest_PACKAGE}
			${_compile_flags}
			)

			foreach (_var ${_test_flags})
			if(_gtest_${_var})
			list(APPEND _argn ${_var})
			unset(_gtest_${_var})
			endif()
			endforeach()

			foreach (_var ${_test_multi_variables})
			if(_gtest_${_var})
			list(APPEND _argn ${_var} ${_gtest_${_var}})
			unset(_gtest_${_var})
			endif()
			endforeach()

			register_test(${_argn} GTEST)
			target_include_directories(${test_name}_gtest PRIVATE ${PROJECT_SOURCE_DIR}/test)
			endfunction()

			# ==============================================================================
			function(register_test test_name)
			cmake_parse_arguments(_register_test
			"${_test_flags}"
			"${_test_one_variables}"
			"${_test_multi_variables}"
			${ARGN}
			)

			register_test_files_to_package(${ARGN})
			is_test_active(_test_act ${ARGN})
			if(NOT _test_act)
			return()
			endif()

			set(_extra_args)

			# check that the sources are files that need to be compiled
			if(_register_test_SOURCES} OR _register_test_UNPARSED_ARGUMENTS)
			set(_need_to_compile TRUE)
			else()
			set(_need_to_compile FALSE)
			endif()

			set(_compile_source)
			foreach(_file ${_register_test_SOURCES} ${_register_test_UNPARSED_ARGUMENTS})
			if(_file MATCHES "\\.cc$" OR _file MATCHES "\\.hh$")
			list(APPEND _compile_source ${_file})
			endif()
			endforeach()

			if(_compile_source)
			# get the include directories for sources in activated directories
			package_get_all_include_directories(
			AKANTU_LIBRARY_INCLUDE_DIRS
			)

			# get the external packages compilation and linking informations
			package_get_all_external_informations(
			INTERFACE_INCLUDE AKANTU_EXTERNAL_INCLUDE_DIR
			)

			foreach(_pkg ${_register_test_PACKAGE})
			package_get_nature(${_pkg} _nature)
			if(_nature MATCHES "^external.*")
			package_get_include_dir(${_pkg} _incl)
			package_get_libraries(${_pkg} _libs)

			list(APPEND _register_test_INCLUDE_DIRECTORIES ${_incl})
			list(APPEND _register_test_LINK_LIBRARIES ${_libs})
			endif()
			endforeach()

			# Register the executable to compile
			add_executable(${test_name} ${_compile_source})

			# set the proper includes to build most of the tests
			target_include_directories(${test_name}
			PRIVATE ${AKANTU_LIBRARY_INCLUDE_DIRS}
			${AKANTU_EXTERNAL_INCLUDE_DIR}
			${PROJECT_BINARY_DIR}/src
			${_register_test_INCLUDE_DIRECTORIES})

			if(NOT _register_test_HEADER_ONLY)
			target_link_libraries(${test_name} PRIVATE akantu ${_register_test_LINK_LIBRARIES})
			else()
			get_target_property(_features akantu INTERFACE_COMPILE_FEATURES)
			target_link_libraries(${test_name} ${_register_test_LINK_LIBRARIES})
			target_compile_features(${test_name} PRIVATE ${_features})
			endif()

			# add the extra compilation options
			if(_register_test_COMPILE_OPTIONS)
			set_target_properties(${test_name}
			PROPERTIES COMPILE_DEFINITIONS "${_register_test_COMPILE_OPTIONS}")
			endif()

			if(AKANTU_EXTRA_CXX_FLAGS)
			set_target_properties(${test_name}
			PROPERTIES COMPILE_FLAGS "${AKANTU_EXTRA_CXX_FLAGS}")
			endif()
			else()
			add_custom_target(${test_name} ALL)
			if(_register_test_UNPARSED_ARGUMENTS AND NOT _register_test_SCRIPT)
			set(_register_test_SCRIPT ${_register_test_UNPARSED_ARGUMENTS})
			endif()
			endif()

			if(_register_test_DEPENDS)
			add_dependencies(${test_name} ${_register_test_DEPENDS})
			endif()

			# copy the needed files to the build folder
			if(_register_test_FILES_TO_COPY)
			foreach(_file ${_register_test_FILES_TO_COPY})
			_add_file_to_copy(${test_name} "${_file}")
			endforeach()
			endif()

			# create the needed folders in the build folder
			if(_register_test_DIRECTORIES_TO_CREATE)
			foreach(_dir ${_register_test_DIRECTORIES_TO_CREATE})
			if(IS_ABSOLUTE ${dir})
			file(MAKE_DIRECTORY "${_dir}")
			else()
			file(MAKE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/${_dir}")
			endif()
			endforeach()
			endif()

			# register the test for ctest
			set(_arguments -n "${test_name}")
			if(_register_test_SCRIPT)
			_add_file_to_copy(${test_name} ${_register_test_SCRIPT})
			if(_register_test_PYTHON)
			if(NOT PYTHONINTERP_FOUND)
			find_package(PythonInterp ${AKANTU_PREFERRED_PYTHON_VERSION} REQUIRED)
			endif()
			list(APPEND _arguments -e "${PYTHON_EXECUTABLE}")
			list(APPEND _extra_args "${_register_test_SCRIPT}")
			add_dependencies(${test_name} py11_akantu)
			else()
			list(APPEND _arguments -e "./${_register_test_SCRIPT}")
			endif()
			elseif(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.sh")
			_add_file_to_copy(${test_name} ${test_name}.sh)
			list(APPEND _arguments -e "./${test_name}.sh")
			else()
			list(APPEND _arguments -e "./${test_name}")
			endif()

			if(_register_test_GTEST)
			list(APPEND _extra_args "--" "--gtest_output=xml:${PROJECT_BINARY_DIR}/gtest_reports/${test_name}.xml")
			endif()

			list(APPEND _arguments -E "${PROJECT_BINARY_DIR}/akantu_environement.sh")

			package_is_activated(parallel _is_parallel)
			if(_is_parallel AND AKANTU_TESTS_ALWAYS_USE_MPI AND NOT _register_test_PARALLEL)
			set(_register_test_PARALLEL TRUE)
			set(_register_test_PARALLEL_LEVEL 1)
			endif()

			if(_register_test_PARALLEL AND _is_parallel)
			set(_exe ${MPIEXEC})
			if(NOT _exe)
			set(_exe ${MPIEXEC_EXECUTABLE})
			endif()
			list(APPEND _arguments -p "${_exe} ${MPIEXEC_PREFLAGS} ${MPIEXEC_NUMPROC_FLAG}")
			if(_register_test_PARALLEL_LEVEL)
			set(_procs "${_register_test_PARALLEL_LEVEL}")
			elseif(CMAKE_VERSION VERSION_GREATER "3.0")
			set(_procs)
			if(MPIEXEC_MAX_NUMPROCS)
			set(N MPIEXEC_MAX_NUMPROCS)
			else()
			include(ProcessorCount)
			ProcessorCount(N)
			endif()

			while(N GREATER 1)
			list(APPEND _procs ${N})
			math(EXPR N "${N} / 2")
			endwhile()
			list(APPEND _procs 1)
			endif()

			if(NOT _procs)
			set(_procs 2)
			endif()
			endif()

			if(_register_test_POSTPROCESS)
			list(APPEND _arguments -s "${_register_test_POSTPROCESS}")
			file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/${_register_test_POSTPROCESS}
			FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
			DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
			endif()

			list(APPEND _arguments -w "${CMAKE_CURRENT_BINARY_DIR}")

			if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.verified")
			list(APPEND _arguments -r "${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.verified")
			endif()

			string(REPLACE ";" " " _command "${_arguments}")

			# register them test
			if(_procs)
			foreach(p ${_procs})
			add_test(NAME ${test_name}_${p} COMMAND ${AKANTU_DRIVER_SCRIPT} ${_arguments} -N ${p} ${_extra_args})
			set_property(TEST ${test_name}_${p} PROPERTY PROCESSORS ${p})
			endforeach()
			else()
			add_test(NAME ${test_name} COMMAND ${AKANTU_DRIVER_SCRIPT} ${_arguments} ${_extra_args})
			set_property(TEST ${test_name} PROPERTY PROCESSORS 1)
			endif()
			endfunction()


			function(register_test_files_to_package)
			cmake_parse_arguments(_register_test
			"${_test_flags}"
			"${_test_one_variables}"
			"${_test_multi_variables}"
			${ARGN}
			)

			if(_register_test_PYTHON)
			list(APPEND _register_test_PACKAGE python_interface)
			endif()

			set(_test_all_files)
			# add the source files in the list of all files
			foreach(_file ${_register_test_SOURCES} ${_register_test_UNPARSED_ARGUMENTS}
			${_register_test_EXTRA_FILES} ${_register_test_SOURCES} ${_register_test_SCRIPT}
			${_register_test_POSTPROCESS} ${_register_test_FILES_TO_COPY})
			if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${_file} OR EXISTS ${_file})
			list(APPEND _test_all_files "${_file}")
			else()
			message("The file \"${_file}\" registred by the test \"${test_name}\" does not exists")
			endif()
			endforeach()

			# add the different dependencies files (meshes, local libraries, ...)
			foreach(_dep ${_register_test_DEPENDS})
			get_target_list_of_associated_files(${_dep} _dep_ressources)
			if(_dep_ressources)
			list(APPEND _test_all_files "${_dep_ressources}")
			endif()
			endforeach()

			# add extra files to the list of files referenced by a given test
			if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.sh")
			list(APPEND _test_all_files "${test_name}.sh")
			endif()
			if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.verified")
			list(APPEND _test_all_files "${test_name}.verified")
			endif()
			if(_register_test_SCRIPT)
			list(APPEND _test_all_files "${_register_test_SCRIPT}")
			endif()

			# clean the list of all files for this test and add them in the total list
			foreach(_file ${_test_all_files})
			get_filename_component(_full ${_file} ABSOLUTE)
			file(RELATIVE_PATH __file ${PROJECT_SOURCE_DIR} ${_full})
			list(APPEND _tmp "${__file}")
			endforeach()

			foreach(_pkg ${_register_test_PACKAGE})
			package_get_name(${_pkg} _pkg_name)
			_package_add_to_variable(TESTS_FILES ${_pkg_name} ${_tmp})
			endforeach()
			endfunction()

rAKA/cmake/AkantuTestsMacros.cmakea23d4b76944ebugfixes/access_PBC_sla…

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rAKA/cmake/AkantuTestsMacros.cmake
a23d4b76944ebugfixes/access_PBC_sla…

AkantuTestsMacros.cmake
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