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Merge branch 'develop' of gitlab.euclid-sgs.uk:ST-TOOLS/Elements into develop
2 parents 0c7a257 + 7ef6bf1 commit 58f3172

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Lines changed: 400 additions & 571 deletions

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‎.clang-format-ignore‎

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# Ignore SWIG interfaces files
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./ElementsExamples/ElementsExamples/NumPyExample.i
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./ElementsExamples/ElementsExamples/SwigExample.i
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./**/*.i

‎.github/workflows/dependencies.txt‎

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$NUMPY
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$PYTHON-devel
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$PYTHON-setuptools
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$PYTHON-numpy
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$PYTHON-pytest
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$PYTHON-sphinx
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$PYTHON-lxml
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CCfits-devel
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$BOOST-$PYTHON-devel
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$BOOST-devel
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doxygen
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graphviz
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log4cpp-devel
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which
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git-core

‎.pre-commit-config.yaml‎

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- id: check-added-large-files
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- id: check-merge-conflict
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- repo: https://github.com/pre-commit/mirrors-clang-format
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rev: v18.1.3
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rev: v18.1.5
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hooks:
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- id: clang-format
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exclude_types: [javascript]

‎CHANGELOG.md‎

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@@ -8,6 +8,64 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [Unreleased]
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## [6.3.1] - 2024-05-22
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This release essentially fixes problems met on the MacOS platform
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### Fixed
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- Fix the include for the `boost::filesystem`
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- Revert from find_file to find_program for executables, in CMake. This former is apparently
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not supported on the conda builds
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- Fix the include for the HOST_NAME_MAX constant. Use unistd.h.
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- Readd the sstream include for `std::basic_ostringstream`
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## [6.3.0] - 2024-04-23
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### Added
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- Add an option to configure the auxiliary files.
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- They were just installed in the past and now they are interpolated in the build directory and then installed.
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- Add a `<PROJECT>_PROJECT_VERSION` CMake cache variable
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- The `elements_install_aux_files` gets a `WITH_CONFIGURE` option to enable the configure phase
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- Add the support for `include-what-you-use` (IWYU, https://github.com/include-what-you-use/include-what-you-use)
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- A new `iwyu` gmake target has been added
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- Alernatively, the IWYU can also be run at compile time by using the `-DUSE_IWYU=ON` CMake option
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- Add a CMake option to print the test command lines
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- the option name is PRINT_TEST_COMMANDS
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- it is set to OFF by default
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- Implement the indirection for the DataSync workspace location
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- the name of the variable pointing to the name of the variable containing the location is DATASYNC_WORKDIR_VAR (e.g. export DATASYNC_WORKDIR_VAR=MY_WORKSPACE).
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- By default, if DATASYNC_WORKDIR_VAR is not set or is empty, the content the WORKSPACE (the default name) variable is used for the workspace location.
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- Add the .clang-format-ignore file to ignore the SWIG interface files recursively
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- add this file also in the createProject script
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- Add sphinx-programoutput to default [[sphinx]] extensions
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- Add the `-fno-omit-frame-pointer` compiler option for all non-optimized builds
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### Changed
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- Improve the creation of the source tarball
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- Added the `--exclude-vcs-ignores` to the Tar command
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- Update the Doxyfile template for Doxygen 1.9.6
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### Fixed
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- Fix the target of the elements_add_python_program CMake function
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- it is now `{elements_module}_{executable}`. Instead of the original
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python module name with the "." replaced by "_"
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- it allows to generate several executable with the same python module
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and different option (like NO_CONFIG_FILE)
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```cmake
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elements_add_python_program(PythonProgramExample ElementsExamples.PythonProgramExample)
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elements_add_python_program(PythonProgramExampleNoConfigFile ElementsExamples.PythonProgramExample NO_CONFIG_FILE)
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```
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- Prevent the addition of the `--config-file` option to the generated C++ executable
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- It was already done for python by passing a NO_CONFIG_FILE CMake option to the elements_add_python_program function
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- For C++, a `-DNO_CONFIG_FILE` compile option seems to be the best candidate
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- Fix a lot of warnings when the `-Wno-dev` CMake option is not passed
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- Fix the the recursive globbing of python files in Elements
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- It was also picking up the `__pycache__` directory and the CMake glob cross-check was failing
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- Fix the compilation against the Gnuastro library
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- Its behavior has changed and it requires an extra arg in the examples
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- use CMake to test the compilation
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- Fix lcov execution for lcov 2.0
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## [6.2.4] - 2024-02-12
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‎CMakeLists.txt‎

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@@ -16,7 +16,7 @@ find_package(ElementsProject)
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include(ElementsDefaults)
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# Declare project name and version
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elements_project(Elements 6.3 DESCRIPTION "A C++ base framework for the Euclid Software.")
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elements_project(Elements 6.4 DESCRIPTION "A C++ base framework for the Euclid Software.")
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# This test does not really fit in a subdirectory.
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‎ElementsExamples/CMakeLists.txt‎

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@@ -15,13 +15,7 @@ find_package(Boost REQUIRED COMPONENTS unit_test_framework)
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find_package(CppUnit)
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find_package(GMock)
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cmake_policy(PUSH)
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if(POLICY CMP0148)
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cmake_policy(SET CMP0148 OLD)
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endif()
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find_package(PythonLibs ${PYTHON_EXPLICIT_VERSION})
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cmake_policy(POP)
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find_package(Python ${PYTHON_EXPLICIT_VERSION} COMPONENTS Interpreter Development NumPy)
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#===== Libraries ===============================================================
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# Instruction for creating a C++ library
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LINK_LIBRARIES ElementsExamples ElementsOther
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NO_CONFIG_FILE)
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elements_add_executable(CppProgramExampleNoDefaultConf src/program/Program.cpp
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INCLUDE_DIRS ElementsExamples ElementsOther
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LINK_LIBRARIES ElementsExamples ElementsOther
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NO_DEFAULT_CONF)
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elements_add_executable(CppExtProgramExample src/program/ExtProgram.cpp
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INCLUDE_DIRS ElementsExamples ElementsOther
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#===== Test that the executables do run ========================================
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elements_add_test(CppProgramExampleRun COMMAND CppProgramExample)
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elements_add_test(CppProgramExampleNoConfigFileRun COMMAND CppProgramExample --config-file=toto.conf FAILS)
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elements_add_test(CppProgramExampleNoConfigFileRun COMMAND CppProgramExampleNoConfigFile --config-file=toto.conf FAILS)
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elements_add_test(CppProgramExampleNoDefaultConfRun COMMAND CppProgramExampleNoDefaultConf)
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elements_add_test(CppProgramExampleWrongArgument COMMAND CppProgramExample --toto FAILS)
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elements_add_test(CppProgramExampleWrongLevel COMMAND CppProgramExample --log-level dddsc FAILS)
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elements_add_test(CProgramExampleRun COMMAND CProgramExample)
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find_package(SWIG QUIET)
306-
if(SWIG_FOUND AND PYTHONLIBS_FOUND)
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if(SWIG_FOUND AND Python_Development_FOUND)
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elements_add_swig_binding(SwigExample ElementsExamples/SwigExample.i
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LINK_LIBRARIES ElementsExamples
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INCLUDE_DIRS ElementsExamples
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PUBLIC_HEADERS ElementsExamples)
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find_package(NumPy)
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if(NUMPY_FOUND)
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if(Python_NumPy_FOUND)
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elements_add_swig_binding(NumPyExample ElementsExamples/NumPyExample.i
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INCLUDE_DIRS NumPy
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NO_PUBLIC_HEADERS)
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endif()
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endif()
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find_package(Cython QUIET)
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if(CYTHON_FOUND AND PYTHONLIBS_FOUND)
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if(CYTHON_FOUND AND Python_Development_FOUND)
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elements_add_cython_module(src/Cython/lib/PiCalculator.pyx
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LINK_LIBRARIES ElementsExamples
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INCLUDE_DIRS ElementsExamples
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331329
endif()
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find_package(pybind11)
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if(pybind11_FOUND AND PYTHONLIBS_FOUND)
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if(pybind11_FOUND AND Python_Development_FOUND)
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elements_add_pybind11_module(testCallBack src/pybind11/callback.cpp
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INCLUDE_DIRS ElementsExamples
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LINK_LIBRARIES ElementsExamples)
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# ElementsExamples.PythonProgramExample is the source file
348346
elements_add_python_program(PythonProgramExample ElementsExamples.PythonProgramExample)
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elements_add_python_program(PythonProgramExampleNoConfigFile ElementsExamples.PythonProgramExample NO_CONFIG_FILE)
350-
if(SWIG_FOUND AND PYTHONLIBS_FOUND)
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elements_add_python_program(PythonProgramExampleNoDefaultConf ElementsExamples.PythonProgramExample NO_DEFAULT_CONF)
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if(SWIG_FOUND AND Python_Development_FOUND)
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elements_add_python_program(SwigProgramExample ElementsExamples.SwigProgramExample)
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endif()
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355354
#===== Test that the python program does run ========================================
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elements_add_test(PythonProgramExampleRun COMMAND PythonProgramExample)
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elements_add_test(PythonProgramExampleNoConfigFileRun COMMAND PythonProgramExample --config-file=toto.conf FAILS)
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if(SWIG_FOUND AND PYTHONLIBS_FOUND)
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elements_add_test(PythonProgramExampleNoConfigFileRun COMMAND PythonProgramExampleNoConfigFile --config-file=toto.conf FAILS)
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elements_add_test(PythonProgramExampleNoDefaultConfRun COMMAND PythonProgramExampleNoDefaultConf)
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if(SWIG_FOUND AND Python_Development_FOUND)
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elements_add_test(SwigProgramExampleRun COMMAND SwigProgramExample LABELS Swig Build)
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endif()
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‎ElementsExamples/src/program/SimpleProgram.cpp‎

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#include "ElementsKernel/Sleep.h" // for nanoSleep
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#include "ElementsKernel/Unused.h" // for ELEMENTS_UNUSED
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#include "ElementsExamples/TemplateFunction.h" // for templateFunction
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using std::map;
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using std::string;
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6870
std::cout << "This Works too!" << std::endl;
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72+
templateFunction<int>();
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templateFunction<double>();
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return ExitCode::OK;
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}
7277
};

‎ElementsKernel/CMakeLists.txt‎

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253253
if(NOT "${CMAKE_BUILD_TYPE}" STREQUAL "Coverage")
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elements_add_test(SqueezedInstall COMMAND squeezedInstall_test
255255
ENVIRONMENT ELEMENTS_SOURCE_DIR=${CMAKE_SOURCE_DIR}
256-
LABELS Creation Meta)
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LABELS Creation Meta Squeezed)
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258+
find_package(Ninja)
259+
if(NINJA_FOUND)
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elements_add_test(SqueezedInstallWithNinja COMMAND squeezedInstall_test
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ENVIRONMENT ELEMENTS_SOURCE_DIR=${CMAKE_SOURCE_DIR} CMAKE_GENERATOR=Ninja
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LABELS Creation Meta Ninja Squeezed)
263+
endif()
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elements_add_test(CMakeIncludeGuards COMMAND squeezedInstall_test
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ENVIRONMENT ELEMENTS_SOURCE_DIR=${CMAKE_SOURCE_DIR} TESTCMAKEFLAGS=-DUSE_DEBUG_PRINT=ON
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LABELS Creation Meta Squeezed)
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endif()

‎ElementsKernel/ElementsKernel/Main.h‎

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#define ELEMENTS_DEFAULT_LOGLEVEL DEBUG
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#endif
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#ifdef NO_CONFIG_FILE
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#define HAS_NO_CONFIG_FILE true
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#else
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#define HAS_NO_CONFIG_FILE false
48+
#endif
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#ifdef NO_DEFAULT_CONF
51+
#define HAS_NO_DEFAULT_CONF true
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#else
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#define HAS_NO_DEFAULT_CONF false
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#endif
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/**
4557
* @def CREATE_MANAGER_WITH_ARGS(ELEMENTS_PROGRAM, MANAGER)
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* Macro that declares a program manager with custom constructor arguments. It is
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4961
* the class Elements::Program class.
5062
* @param MANAGER name of the manager variable to be created.
5163
*/
52-
#ifndef NO_CONFIG_FILE
53-
#define CREATE_MANAGER_WITH_ARGS(MANAGER, ELEMENTS_PROGRAM, ...) \
54-
Elements::ProgramManager MANAGER { \
55-
std::unique_ptr<Elements::Program>{new ELEMENTS_PROGRAM{__VA_ARGS__}}, Elements::Project::versionString(), \
56-
Elements::Project::name(), Elements::Project::vcsVersion(), Elements::Module::versionString(), \
57-
Elements::Module::name(), Elements::Project::searchDirectories(), log4cpp::Priority::ELEMENTS_DEFAULT_LOGLEVEL \
58-
}
59-
#else
6064
#define CREATE_MANAGER_WITH_ARGS(MANAGER, ELEMENTS_PROGRAM, ...) \
6165
Elements::ProgramManager MANAGER { \
6266
std::unique_ptr<Elements::Program>{new ELEMENTS_PROGRAM{__VA_ARGS__}}, Elements::Project::versionString(), \
6367
Elements::Project::name(), Elements::Project::vcsVersion(), Elements::Module::versionString(), \
6468
Elements::Module::name(), Elements::Project::searchDirectories(), \
65-
log4cpp::Priority::ELEMENTS_DEFAULT_LOGLEVEL, true \
69+
log4cpp::Priority::ELEMENTS_DEFAULT_LOGLEVEL, HAS_NO_CONFIG_FILE, HAS_NO_DEFAULT_CONF \
6670
}
67-
#endif
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/**
7073
* @def CREATE_MANAGER(ELEMENTS_PROGRAM_NAME, MANAGER)

‎ElementsKernel/ElementsKernel/ProgramManager.h‎

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6969
const std::string& parent_module_version = "", const std::string& parent_module_name = "",
7070
const std::vector<std::string>& search_dirs = {},
7171
const log4cpp::Priority::Value& elements_loglevel = log4cpp::Priority::DEBUG,
72-
bool no_config_file = false);
72+
bool no_config_file = false, bool no_default_conf = false);
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7474
/**
7575
* @brief Destructor
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281281
* prevent the --config-file option to be added
282282
*/
283283
bool m_no_config_file;
284+
285+
/**
286+
* prevent the location of default configuration files
287+
*/
288+
bool m_no_default_conf;
284289
};
285290

286291
} // namespace Elements

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