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tassefftasseff
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Essentially the initial commit. There is still much to add from previous versions of this project and refactor.
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‎.gitmodules

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[submodule "libraries/rapidjson"]
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path = libraries/rapidjson
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url = [email protected]:miloyip/rapidjson.git

‎.travis.yml

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dist: trusty
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sudo: required
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language: cpp
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compiler:
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- gcc
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addons:
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apt:
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packages:
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- cmake
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- lcov
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script:
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- mkdir build && cd build
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- cmake -DCMAKE_BUILD_TYPE=Coverage ..
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- make
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- make nuflood_coverage
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after_success:
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- bash <(curl -s https://codecov.io/bash)

‎CMakeLists.txt

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project(nuflood)
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cmake_minimum_required(VERSION 2.8)
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set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMakeModules)
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set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/output)
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set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/output)
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set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/output)
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foreach(OUTPUTCONFIG ${CMAKE_CONFIGURATION_TYPES})
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string(TOUPPER ${OUTPUTCONFIG} OUTPUTCONFIG)
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set(CMAKE_RUNTIME_OUTPUT_DIRECTORY_${OUTPUTCONFIG} ${CMAKE_BINARY_DIR}/output)
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set(CMAKE_LIBRARY_OUTPUT_DIRECTORY_${OUTPUTCONFIG} ${CMAKE_BINARY_DIR}/output)
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set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY_${OUTPUTCONFIG} ${CMAKE_BINARY_DIR}/output)
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endforeach(OUTPUTCONFIG CMAKE_CONFIGURATION_TYPES)
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include_directories("libraries/rapidjson/include")
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add_subdirectory(source)

‎CMakeModules/CodeCoverage.cmake

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# Copyright (c) 2012 - 2015, Lars Bilke
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# All rights reserved.
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#
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# Redistribution and use in source and binary forms, with or without modification,
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# are permitted provided that the following conditions are met:
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#
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# 1. Redistributions of source code must retain the above copyright notice, this
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# list of conditions and the following disclaimer.
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#
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# 2. Redistributions in binary form must reproduce the above copyright notice,
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# this list of conditions and the following disclaimer in the documentation
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# and/or other materials provided with the distribution.
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#
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# 3. Neither the name of the copyright holder nor the names of its contributors
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# may be used to endorse or promote products derived from this software without
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# specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
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# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
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# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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#
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#
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# 2012-01-31, Lars Bilke
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# - Enable Code Coverage
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#
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# 2013-09-17, Joakim Söderberg
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# - Added support for Clang.
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# - Some additional usage instructions.
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#
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# USAGE:
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# 0. (Mac only) If you use Xcode 5.1 make sure to patch geninfo as described here:
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# http://stackoverflow.com/a/22404544/80480
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#
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# 1. Copy this file into your cmake modules path.
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#
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# 2. Add the following line to your CMakeLists.txt:
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# INCLUDE(CodeCoverage)
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#
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# 3. Set compiler flags to turn off optimization and enable coverage:
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# SET(CMAKE_CXX_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
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# SET(CMAKE_C_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
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#
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# 3. Use the function SETUP_TARGET_FOR_COVERAGE to create a custom make target
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# which runs your test executable and produces a lcov code coverage report:
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# Example:
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# SETUP_TARGET_FOR_COVERAGE(
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# my_coverage_target # Name for custom target.
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# test_driver # Name of the test driver executable that runs the tests.
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# # NOTE! This should always have a ZERO as exit code
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# # otherwise the coverage generation will not complete.
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# coverage # Name of output directory.
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# )
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#
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# 4. Build a Debug build:
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# cmake -DCMAKE_BUILD_TYPE=Debug ..
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# make
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# make my_coverage_target
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#
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#
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# Check prereqs
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FIND_PROGRAM( GCOV_PATH gcov )
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FIND_PROGRAM( LCOV_PATH lcov )
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FIND_PROGRAM( GENHTML_PATH genhtml )
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FIND_PROGRAM( GCOVR_PATH gcovr PATHS ${CMAKE_SOURCE_DIR}/tests)
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IF(NOT GCOV_PATH)
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MESSAGE(FATAL_ERROR "gcov not found! Aborting...")
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ENDIF() # NOT GCOV_PATH
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IF(NOT CMAKE_COMPILER_IS_GNUCXX)
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# Clang version 3.0.0 and greater now supports gcov as well.
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MESSAGE(WARNING "Compiler is not GNU gcc! Clang Version 3.0.0 and greater supports gcov as well, but older versions don't.")
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IF(NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
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MESSAGE(FATAL_ERROR "Compiler is not GNU gcc! Aborting...")
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ENDIF()
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ENDIF() # NOT CMAKE_COMPILER_IS_GNUCXX
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SET(CMAKE_CXX_FLAGS_COVERAGE
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"-g -O0 --coverage -fprofile-arcs -ftest-coverage"
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CACHE STRING "Flags used by the C++ compiler during coverage builds."
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FORCE )
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SET(CMAKE_C_FLAGS_COVERAGE
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"-g -O0 --coverage -fprofile-arcs -ftest-coverage"
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CACHE STRING "Flags used by the C compiler during coverage builds."
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FORCE )
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SET(CMAKE_EXE_LINKER_FLAGS_COVERAGE
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""
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CACHE STRING "Flags used for linking binaries during coverage builds."
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FORCE )
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SET(CMAKE_SHARED_LINKER_FLAGS_COVERAGE
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""
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CACHE STRING "Flags used by the shared libraries linker during coverage builds."
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FORCE )
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MARK_AS_ADVANCED(
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CMAKE_CXX_FLAGS_COVERAGE
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CMAKE_C_FLAGS_COVERAGE
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CMAKE_EXE_LINKER_FLAGS_COVERAGE
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CMAKE_SHARED_LINKER_FLAGS_COVERAGE )
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IF ( NOT (CMAKE_BUILD_TYPE STREQUAL "Debug" OR CMAKE_BUILD_TYPE STREQUAL "Coverage"))
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MESSAGE( WARNING "Code coverage results with an optimized (non-Debug) build may be misleading" )
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ENDIF() # NOT CMAKE_BUILD_TYPE STREQUAL "Debug"
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# Param _targetname The name of new the custom make target
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# Param _testrunner The name of the target which runs the tests.
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# MUST return ZERO always, even on errors.
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# If not, no coverage report will be created!
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# Param _outputname lcov output is generated as _outputname.info
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# HTML report is generated in _outputname/index.html
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# Optional fourth parameter is passed as arguments to _testrunner
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# Pass them in list form, e.g.: "-j;2" for -j 2
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FUNCTION(SETUP_TARGET_FOR_COVERAGE _targetname _testrunner _outputname)
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IF(NOT LCOV_PATH)
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MESSAGE(FATAL_ERROR "lcov not found! Aborting...")
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ENDIF() # NOT LCOV_PATH
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IF(NOT GENHTML_PATH)
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MESSAGE(FATAL_ERROR "genhtml not found! Aborting...")
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ENDIF() # NOT GENHTML_PATH
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# Setup target
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ADD_CUSTOM_TARGET(${_targetname}
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# Cleanup lcov
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${LCOV_PATH} --directory . --zerocounters
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# Run tests
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COMMAND ${_testrunner} ${ARGV3}
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# Capturing lcov counters and generating report
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COMMAND ${LCOV_PATH} --directory . --capture --output-file ${_outputname}.info
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COMMAND ${LCOV_PATH} --remove ${_outputname}.info 'tests/*' '/usr/*' --output-file ${_outputname}.info.cleaned
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COMMAND ${GENHTML_PATH} -o ${_outputname} ${_outputname}.info.cleaned
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COMMAND ${CMAKE_COMMAND} -E remove ${_outputname}.info ${_outputname}.info.cleaned
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WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
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COMMENT "Resetting code coverage counters to zero.\nProcessing code coverage counters and generating report."
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)
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# Show info where to find the report
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ADD_CUSTOM_COMMAND(TARGET ${_targetname} POST_BUILD
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COMMAND ;
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COMMENT "Open ./${_outputname}/index.html in your browser to view the coverage report."
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)
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ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE
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# Param _targetname The name of new the custom make target
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# Param _testrunner The name of the target which runs the tests
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# Param _outputname cobertura output is generated as _outputname.xml
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# Optional fourth parameter is passed as arguments to _testrunner
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# Pass them in list form, e.g.: "-j;2" for -j 2
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FUNCTION(SETUP_TARGET_FOR_COVERAGE_COBERTURA _targetname _testrunner _outputname)
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IF(NOT PYTHON_EXECUTABLE)
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MESSAGE(FATAL_ERROR "Python not found! Aborting...")
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ENDIF() # NOT PYTHON_EXECUTABLE
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IF(NOT GCOVR_PATH)
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MESSAGE(FATAL_ERROR "gcovr not found! Aborting...")
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ENDIF() # NOT GCOVR_PATH
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ADD_CUSTOM_TARGET(${_targetname}
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# Run tests
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${_testrunner} ${ARGV3}
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# Running gcovr
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COMMAND ${GCOVR_PATH} -x -r ${CMAKE_SOURCE_DIR} -e '${CMAKE_SOURCE_DIR}/tests/' -o ${_outputname}.xml
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WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
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COMMENT "Running gcovr to produce Cobertura code coverage report."
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)
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# Show info where to find the report
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ADD_CUSTOM_COMMAND(TARGET ${_targetname} POST_BUILD
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COMMAND ;
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COMMENT "Cobertura code coverage report saved in ${_outputname}.xml."
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)
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ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE_COBERTURA

‎Dockerfile

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FROM ubuntu:14.04
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MAINTAINER Byron Tasseff <[email protected]>
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ENV HOME /root
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WORKDIR $HOME/
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ADD . nuflood/
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RUN apt-get update && apt-get -y upgrade
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RUN apt-get -y install gcc g++ make cmake
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RUN cd /root/nuflood/ && mkdir build && cd build/ && cmake .. && make
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RUN mv nuflood/build/output/kurganov_petrova /usr/bin/kurganov_petrova
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RUN rm -r nuflood/

‎libraries/rapidjson

Submodule rapidjson added at ab791ae

‎source/CMakeLists.txt

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add_definitions(-DUSE_DOUBLE=1)
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add_definitions(-DBIG_GRID=0)
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find_program (INTEL_COMPILER icc)
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if(INTEL_COMPILER)
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11; -O3; -parallel; -openmp;
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-lpthread; -Wall; -g; -shared-intel; -debug inline-debug-info")
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if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
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set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fPIC")
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set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fPIC")
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endif()
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elseif(CMAKE_COMPILER_IS_GNUCXX)
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IF(NOT(CMAKE_BUILD_TYPE STREQUAL "Debug" OR CMAKE_BUILD_TYPE STREQUAL "Coverage"))
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Ofast -fopenmp -Wall")
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if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
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set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fPIC")
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set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fPIC")
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endif()
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ELSE()
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include(CodeCoverage)
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setup_target_for_coverage(${PROJECT_NAME}_coverage kurganov_petrova coverage "../test/coverage.json")
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set(CMAKE_CXX_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage -std=c++11")
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SET(CMAKE_C_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
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ENDIF()
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endif()
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if(APPLE)
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set(CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LANGUAGE_STANDARD "c++11")
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set(CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LIBRARY "libc++")
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set(CMAKE_XCODE_ATTRIBUTE_GCC_VERSION "com.apple.compilers.llvm.clang.1_0")
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endif()
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if(WIN32)
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add_definitions(-DUNICODE -D_UNICODE)
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set(TARGET_ARCHITECTURE "x86")
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endif()
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find_package(CUDA)
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if(CUDA_FOUND)
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#add_definitions(-DCUDA)
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include_directories(${CUDA_INCLUDE_DIRS})
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link_directories(${CUDA_LIBRARIES})
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list(APPEND LIBS ${CUDA_LIBRARIES})
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set(CUDA_PROPAGATE_HOST_FLAGS OFF)
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set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS} -std=c++11; -O3; -use_fast_math;
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-ftz=true; -prec-div=false; -prec-sqrt=false; -Xptxas -dlcm=ca;
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-lineinfo; -Wno-deprecated-gpu-targets")
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endif()
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include_directories("${CMAKE_CURRENT_SOURCE_DIR}")
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add_subdirectory(common)
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add_subdirectory(models)

‎source/common/CMakeLists.txt

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set(SOURCE_FILES
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iconstants.cpp document.cpp error.cpp file.cpp gpu_error.cpp folder.cpp
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isinks.cpp isources.cpp index_table.cpp itime.cpp name_list.cpp
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timer.cpp itopography.cpp ioutput.cpp)
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set(HEADER_FILES
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iconstants.h document.h error.h file.h folder.h gpu_error.h gpu_grid.h
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gpu_vector.h grid.h isinks.h isources.h index_table.h itime.h
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name_list.h parameter.h point_sink.h point_source.h point_source_list.h
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time_series.h timer.h itopography.h ioutput.h)
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include_directories(${CMAKE_CURRENT_BINARY_DIR})
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include_directories(${CMAKE_CURRENT_SOURCE_DIR})
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add_library(Common STATIC ${SOURCE_FILES} ${HEADER_FILES})
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INSTALL(FILES ${HEADER_FILES} DESTINATION "include/nuflood/common")

‎source/common/document.cpp

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#include "document.h"
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#include "error.h"
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#include "file.h"
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Document::Document(const File& file) {
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FILE* p_file = fopen(file.path().c_str(), "r");
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char buffer[65536];
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rapidjson::FileReadStream file_read_stream(p_file, buffer, sizeof(buffer));
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root.ParseStream<0>(file_read_stream);
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fclose(p_file);
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if (!root.IsObject()) {
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PrintErrorAndExit("File '" + file.path() + "' is not a valid JSON document.");
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}
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}

‎source/common/document.h

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#pragma once
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#include <rapidjson/document.h>
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#include <rapidjson/writer.h>
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#include <rapidjson/stringbuffer.h>
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#include <rapidjson/filereadstream.h>
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#include "file.h"
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class Document {
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public:
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Document(const File& file);
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rapidjson::Document root;
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};

‎source/common/error.cpp

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#include <iostream>
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#include <fstream>
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#include <cstdlib>
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#include "error.h"
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void PrintErrorAndExit(const std::string& error_message, int exit_code) {
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std::cerr << "Error: " << error_message << std::endl;
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std::exit(exit_code);
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}
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void PrintWarning(const std::string& warning_message) {
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std::cerr << "Warning: " << warning_message << std::endl;
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}

‎source/common/error.h

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#pragma once
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#include <string>
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void PrintErrorAndExit(const std::string& error_message, int error_code = 1);
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void PrintWarning(const std::string& warning_message);

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