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Merge branch 'develop'

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jbakosi committed Mar 12, 2019
2 parents 2050312 + c9a6ac9 commit 45098581207f8b318e3865be2581021b3e9bfc57
Showing 984 changed files with 9,916 additions and 11,216 deletions.
@@ -5,7 +5,7 @@

jobs:
- job: "Quinoa"
timeoutInMinutes: 120
timeoutInMinutes: 180
pool:
vmImage: 'Ubuntu 16.04'
variables:
@@ -30,7 +30,16 @@ jobs:
BUILD: 'Release'
SHARED_LIBS: 'off'
DISTRO: 'debian-gnu-static'
DOCKERHUB: 'true'
gnu-debug-smp:
COMPILER: 'gnu'
BUILD: 'Debug'
DISTRO: 'debian-gnu-smp'
SMP: 'on'
gnu-release-smp:
COMPILER: 'gnu'
BUILD: 'Release'
DISTRO: 'debian-gnu-smp'
SMP: 'on'
clang-debug:
COMPILER: 'clang'
BUILD: 'Debug'
@@ -49,6 +58,16 @@ jobs:
BUILD: 'Release'
SHARED_LIBS: 'off'
DISTRO: 'debian-clang-static'
clang-debug-smp:
COMPILER: 'clang'
BUILD: 'Debug'
DISTRO: 'debian-clang-smp'
SMP: 'on'
clang-release-smp:
COMPILER: 'clang'
BUILD: 'Release'
DISTRO: 'debian-clang-smp'
SMP: 'on'
doc:
DOC: true
DISTRO: 'debian-doc'
@@ -61,5 +80,6 @@ jobs:
--build-arg BUILD=${BUILD} \
--build-arg DOC=${DOC} \
--build-arg SHARED_LIBS="${SHARED_LIBS}" \
--build-arg SMP=${SMP} \
--rm=false -f docker/Dockerfile.quinoa-build-azure -t ${DISTRO} .
displayName: 'Build & Test'
@@ -12,39 +12,51 @@ git:
env:
matrix:
- TARGET=unittest COMPILER=gnu BUILD=Debug
- TARGET=unittest COMPILER=gnu BUILD=Debug SMP=true
- TARGET=unittest COMPILER=gnu BUILD=Debug SHARED_LIBS=off
- TARGET=unittest COMPILER=gnu BUILD=Release
- TARGET=unittest COMPILER=gnu BUILD=Release SMP=true
- TARGET=unittest COMPILER=gnu BUILD=Release SHARED_LIBS=off DOCKERHUB=true
- TARGET=unittest COMPILER=clang BUILD=Debug
- TARGET=unittest COMPILER=clang BUILD=Debug SMP=true
- TARGET=unittest COMPILER=clang BUILD=Debug SHARED_LIBS=off
- TARGET=unittest COMPILER=clang BUILD=Release
- TARGET=unittest COMPILER=clang BUILD=Release SMP=true
- TARGET=unittest COMPILER=clang BUILD=Release SHARED_LIBS=off

- TARGET=walker COMPILER=gnu BUILD=Debug
- TARGET=walker COMPILER=gnu BUILD=Debug SHARED_LIBS=off
- TARGET=walker COMPILER=gnu BUILD=Release
- TARGET=walker COMPILER=gnu BUILD=Release SMP=true
- TARGET=walker COMPILER=gnu BUILD=Release SHARED_LIBS=off DOCKERHUB=true
- TARGET=walker COMPILER=clang BUILD=Debug
- TARGET=walker COMPILER=clang BUILD=Debug SHARED_LIBS=off
- TARGET=walker COMPILER=clang BUILD=Release
- TARGET=walker COMPILER=clang BUILD=Release SMP=true
- TARGET=walker COMPILER=clang BUILD=Release SHARED_LIBS=off

- TARGET=inciter COMPILER=gnu BUILD=Debug
- TARGET=inciter COMPILER=gnu BUILD=Debug SHARED_LIBS=off
- TARGET=inciter COMPILER=gnu BUILD=Release
- TARGET=inciter COMPILER=gnu BUILD=Release SMP=true
- TARGET=inciter COMPILER=gnu BUILD=Release SHARED_LIBS=off DOCKERHUB=true
- TARGET=inciter COMPILER=clang BUILD=Debug
- TARGET=inciter COMPILER=clang BUILD=Debug SHARED_LIBS=off
- TARGET=inciter COMPILER=clang BUILD=Release
- TARGET=inciter COMPILER=clang BUILD=Release SMP=true
- TARGET=inciter COMPILER=clang BUILD=Release SHARED_LIBS=off

- TARGET=rngtest COMPILER=gnu BUILD=Debug
- TARGET=rngtest COMPILER=gnu BUILD=Debug SMP=true
- TARGET=rngtest COMPILER=gnu BUILD=Debug SHARED_LIBS=off
- TARGET=rngtest COMPILER=gnu BUILD=Release
- TARGET=rngtest COMPILER=gnu BUILD=Release SMP=true
- TARGET=rngtest COMPILER=gnu BUILD=Release SHARED_LIBS=off DOCKERHUB=true
- TARGET=rngtest COMPILER=clang BUILD=Debug
- TARGET=rngtest COMPILER=clang BUILD=Debug SMP=true
- TARGET=rngtest COMPILER=clang BUILD=Debug SHARED_LIBS=off
- TARGET=rngtest COMPILER=clang BUILD=Release
- TARGET=rngtest COMPILER=clang BUILD=Release SMP=true
- TARGET=rngtest COMPILER=clang BUILD=Release SHARED_LIBS=off

- TARGET=meshconv COMPILER=gnu BUILD=Debug
@@ -56,14 +68,15 @@ env:
- TARGET=meshconv COMPILER=clang BUILD=Release
- TARGET=meshconv COMPILER=clang BUILD=Release SHARED_LIBS=off

- TARGET=all COMPILER=gnu BUILD=Debug
- TARGET=all COMPILER=gnu BUILD=Debug SONARQUBE=ON
- TARGET=doc

script:
- if [[ ${TARGET} = doc ]]; then
export DISTRO=debian-doc;
else
export DISTRO=alpine-${COMPILER}${SHARED_LIBS:+-static}${SONARQUBE:+-sonarqube};
export DISTRO=alpine-${COMPILER}${SMP:+-smp}${SHARED_LIBS:+-static}${SONARQUBE:+-sonarqube};
fi
- rm -rf tpl
- cp -vr docker ${HOME}/docker
@@ -76,6 +89,7 @@ script:
--build-arg BUILD=${BUILD}
--build-arg TARGET=${TARGET}
--build-arg SHARED_LIBS="${SHARED_LIBS}"
--build-arg SMP=${SMP}
--build-arg SONARQUBE=${SONARQUBE}
--build-arg SONARQUBE_TOKEN=${SONARQUBE_TOKEN}
--build-arg SONARQUBE_GITHUB_TOKEN=${SONARQUBE_GITHUB_TOKEN}
45 LICENSE
@@ -1,16 +1,18 @@
Copyright (c) 2012-2015, J. Bakosi
Copyright (c) 2016-2018, Los Alamos National Security, LLC
Copyright (c) 2019, Triad National Security, LLC
All rights reserved.

Copyright 2016-2018. Los Alamos National Security, LLC. This software was
produced under U.S. Government contract DE-AC52-06NA25396 for Los Alamos
National Laboratory (LANL), which is operated by Los Alamos National Security,
LLC for the U.S. Department of Energy. The U.S. Government has rights to use,
reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR LOS ALAMOS
NATIONAL SECURITY, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY
LIABILITY FOR THE USE OF THIS SOFTWARE. If software is modified to produce
derivative works, such modified software should be clearly marked, so as not to
confuse it with the version available from LANL.
This program was produced under U.S. Government contract 89233218CNA000001 for
Los Alamos National Laboratory (LANL), which is operated by Triad National
Security, LLC for the U.S. Department of Energy/National Nuclear Security
Administration. All rights in the program are reserved by Triad National
Security, LLC, and the U.S. Department of Energy/National Nuclear Security
Administration. The Government is granted for itself and others acting on its
behalf a nonexclusive, paid-up, irrevocable worldwide license in this material
to reproduce, prepare derivative works, distribute copies to the public,
perform publicly and display publicly, and to permit others to do so.

Additionally, redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

@@ -21,19 +23,18 @@ list of conditions and the following disclaimer.
this list of conditions and the following disclaimer in the documentation and/or
other materials provided with the distribution.

3. Neither the name of Los Alamos National Security, LLC, Los Alamos National
3. Neither the name of Triad National Security, LLC, Los Alamos National
Laboratory, LANL, the U.S. Government, nor the names of its contributors may be
used to endorse or promote products derived from this software without specific
prior written permission.

THIS SOFTWARE IS PROVIDED BY LOS ALAMOS NATIONAL SECURITY, LLC AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL LOS ALAMOS NATIONAL SECURITY, LLC OR
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
OF SUCH DAMAGE.
THIS SOFTWARE IS PROVIDED BY TRIAD NATIONAL SECURITY, LLC AND CONTRIBUTORS "AS
IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL TRIAD NATIONAL SECURITY, LLC OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
@@ -78,7 +78,7 @@ FUNCTION(SETUP_TARGET_FOR_COVERAGE suite path targetname testrunner)
# Combine trace files
COMMAND ${LCOV} --gcov-tool ${GCOV} --rc lcov_branch_coverage=1 --add-tracefile ${OUTPUT}.base.info --add-tracefile ${OUTPUT}.test.info --output-file ${OUTPUT}.total.info
# Filter out unwanted files
COMMAND ${LCOV} --gcov-tool ${GCOV} --rc lcov_branch_coverage=1 --remove ${OUTPUT}.total.info 'UnitTest/tests/*' '*/c++/*' '*/include/*' '*/boost/*' '*/charm/*' '*.decl.h' '*.def.h' '*/STDIN' '*/openmpi/*' '*/pstreams/*' '*/Random123/*' '*/pegtl/*' '*/tut/*' '*/highwayhash/*' '*/moduleinit*' --output-file ${OUTPUT}.filtered.info
COMMAND ${LCOV} --gcov-tool ${GCOV} --rc lcov_branch_coverage=1 --remove ${OUTPUT}.total.info "UnitTest/tests/*" "*/c++/*" "*/include/*" "*/boost/*" "*/charm/*" "*.decl.h" "*.def.h" "*/STDIN" "*/openmpi/*" "*/pstreams/*" "*/Random123/*" "*/pegtl/*" "*/tut/*" "*/highwayhash/*" "*/moduleinit*" --output-file ${OUTPUT}.filtered.info
# Copy over report customization files for genhtml
COMMAND ${CMAKE_COMMAND} -E copy
${CMAKE_SOURCE_DIR}/../doc/quinoa.gcov.css
@@ -87,17 +87,18 @@ FUNCTION(SETUP_TARGET_FOR_COVERAGE suite path targetname testrunner)
${CMAKE_SOURCE_DIR}/../doc/quinoa.lcov.prolog
${CMAKE_BINARY_DIR}
# Generate HTML report
COMMAND ${GENHTML} --legend --branch-coverage --demangle-cpp --css-file quinoa.gcov.css --html-prolog quinoa.lcov.prolog --title "${GIT_SHA1}" -o ${OUTPUT} ${OUTPUT}.filtered.info
COMMAND ${GENHTML} --legend --branch-coverage --demangle-cpp --css-file quinoa.gcov.css --ignore-errors source --html-prolog quinoa.lcov.prolog --title "${GIT_SHA1}" -o ${OUTPUT} ${OUTPUT}.filtered.info
# Customize page headers in generated html to own
COMMAND find ${OUTPUT} -type f -print | xargs file | grep text | cut -f1 -d: | xargs ${SED} -i 's/LCOV - code coverage report/Quinoa ${suite} test code coverage report/g'
COMMAND find ${OUTPUT} -type f -print | xargs file | grep text | cut -f1 -d: | xargs ${SED} -i 's/<td class="headerItem">Test:<\\/td>/<td class="headerItem">Commit:<\\/td>/g'
COMMAND find ${OUTPUT} -type f -print | xargs file | grep text | cut -f1 -d: | xargs ${SED} -i 's/Quinoa_v\\\(.*\\\)-\\\(.*\\\)-g\\\(.*\\\)<\\/td>/<a href="https:\\/\\/github.com\\/quinoacomputing\\/quinoa\\/commit\\/\\3">Quinoa_v\\1-\\2-g\\3<\\/a><\\/td>/g'
COMMAND find ${OUTPUT} -type f -exec ${SED} -i "s/LCOV - code coverage report/Quinoa ${suite} test code coverage report/g" {} +
COMMAND find ${OUTPUT} -type f -exec ${SED} -i "s/<td class=\"headerItem\">Test:<\\/td>/<td class=\"headerItem\">Commit:<\\/td>/g" {} +
COMMAND find ${OUTPUT} -type f -exec ${SED} -i "s/Quinoa_v\\\(.*\\\)-\\\(.*\\\)-g\\\(.*\\\)<\\/td>/<a href=\"https:\\/\\/github.com\\/quinoacomputing\\/quinoa\\/commit\\/\\3\">Quinoa_v\\1-\\2-g\\3<\\/a><\\/td>/g" {} +
# Cleanup intermediate data
COMMAND ${CMAKE_COMMAND} -E remove ${OUTPUT}.base.info ${OUTPUT}.test.info ${OUTPUT}.total.info ${OUTPUT}.filtered.info
# Set work directory for target
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
# Echo what is being done
COMMENT "Quinoa ${suite} test code coverage report"
VERBATIM USES_TERMINAL
)

# Make test coverage target dependent on optional dependencies passed in using
@@ -183,7 +184,7 @@ FUNCTION(SETUP_TARGET_FOR_ALL_COVERAGE suite path targetname unittestrunner
# Combine trace files
COMMAND ${LCOV} --gcov-tool ${GCOV} --rc lcov_branch_coverage=1 --add-tracefile ${OUTPUT}.base.info --add-tracefile ${OUTPUT}.test.info --output-file ${OUTPUT}.total.info
# Filter out unwanted files
COMMAND ${LCOV} --gcov-tool ${GCOV} --rc lcov_branch_coverage=1 --remove ${OUTPUT}.total.info 'UnitTest/tests/*' '*/c++/*' '*/include/*' '*/boost/*' '*/charm/*' '*.decl.h' '*.def.h' '*/STDIN' '*/openmpi/*' '*/pstreams/*' '*/Random123/*' '*/pegtl/*' '*/tut/*' '*/highwayhash/*' '*/moduleinit*' --output-file ${OUTPUT}.filtered.info
COMMAND ${LCOV} --gcov-tool ${GCOV} --rc lcov_branch_coverage=1 --remove ${OUTPUT}.total.info "UnitTest/tests/*" "*/c++/*" "*/include/*" "*/boost/*" "*/charm/*" "*.decl.h" "*.def.h" "*/STDIN" "*/openmpi/*" "*/pstreams/*" "*/Random123/*" "*/pegtl/*" "*/tut/*" "*/highwayhash/*" "*/moduleinit*" --output-file ${OUTPUT}.filtered.info
# Copy over report customization files for genhtml
COMMAND ${CMAKE_COMMAND} -E copy
${CMAKE_SOURCE_DIR}/../doc/quinoa.gcov.css
@@ -192,17 +193,18 @@ FUNCTION(SETUP_TARGET_FOR_ALL_COVERAGE suite path targetname unittestrunner
${CMAKE_SOURCE_DIR}/../doc/quinoa.lcov.prolog
${CMAKE_BINARY_DIR}
# Generate HTML report
COMMAND ${GENHTML} --legend --branch-coverage --demangle-cpp --css-file quinoa.gcov.css --html-prolog quinoa.lcov.prolog --title "${GIT_SHA1}" -o ${OUTPUT} ${OUTPUT}.filtered.info
COMMAND ${GENHTML} --legend --branch-coverage --demangle-cpp --css-file quinoa.gcov.css --ignore-errors source --html-prolog quinoa.lcov.prolog --title "${GIT_SHA1}" -o ${OUTPUT} ${OUTPUT}.filtered.info
# Customize page headers in generated html to own
COMMAND find ${OUTPUT} -type f -print | xargs file | grep text | cut -f1 -d: | xargs ${SED} -i 's/LCOV - code coverage report/Quinoa ${suite} test code coverage report/g'
COMMAND find ${OUTPUT} -type f -print | xargs file | grep text | cut -f1 -d: | xargs ${SED} -i 's/<td class="headerItem">Test:<\\/td>/<td class="headerItem">Commit:<\\/td>/g'
COMMAND find ${OUTPUT} -type f -print | xargs file | grep text | cut -f1 -d: | xargs ${SED} -i 's/Quinoa_v\\\(.*\\\)-\\\(.*\\\)-g\\\(.*\\\)<\\/td>/<a href="https:\\/\\/github.com\\/quinoacomputing\\/quinoa\\/commit\\/\\3">Quinoa_v\\1-\\2-g\\3<\\/a><\\/td>/g'
COMMAND find ${OUTPUT} -type f -exec ${SED} -i "s/LCOV - code coverage report/Quinoa ${suite} test code coverage report/g" {} +
COMMAND find ${OUTPUT} -type f -exec ${SED} -i "s/<td class=\"headerItem\">Test:<\\/td>/<td class=\"headerItem\">Commit:<\\/td>/g" {} +
COMMAND find ${OUTPUT} -type f -exec ${SED} -i "s/Quinoa_v\\\(.*\\\)-\\\(.*\\\)-g\\\(.*\\\)<\\/td>/<a href=\"https:\\/\\/github.com\\/quinoacomputing\\/quinoa\\/commit\\/\\3\">Quinoa_v\\1-\\2-g\\3<\\/a><\\/td>/g" {} +
# Cleanup intermediate data
COMMAND ${CMAKE_COMMAND} -E remove ${OUTPUT}.base.info ${OUTPUT}.test.info ${OUTPUT}.total.info ${OUTPUT}.filtered.info
# Set work directory for target
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
# Echo what is being done
COMMENT "Quinoa ${suite} test code coverage report"
VERBATIM USES_TERMINAL
)

# Make test coverage target dependent on optional dependencies passed in using
@@ -6,34 +6,58 @@
#
################################################################################

find_program( SED sed )
find_program( CPPCHECK cppcheck )
find_program( CPPCHECK_HTMLREPORT cppcheck-htmlreport )

if(SED AND CPPCHECK AND CPPCHECK_HTMLREPORT)
if(CPPCHECK AND CPPCHECK_HTMLREPORT)

file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/doc/cppcheck)

string(REGEX REPLACE "Quinoa_v(.*)-(.*)-g(.*)" "\\3" SHA1 ${GIT_SHA1})

# Setup cppcheck static analysis target
ADD_CUSTOM_TARGET(cppcheck
# Run cppcheck static analysis
COMMAND ${CPPCHECK} --xml --xml-version=2 --enable=all
${CMAKE_CURRENT_SOURCE_DIR} 2> doc/cppcheck/cppcheck-report.xml
# Generate html output
COMMAND ${CPPCHECK_HTMLREPORT} --file=doc/cppcheck/cppcheck-report.xml
--report-dir=doc/cppcheck --source-dir=.
# Customize page headers in generated html
COMMAND find . -type f -print | xargs file | cut -f1 -d: | xargs ${SED} -i 's/project name/<a href="https:\\/\\/github.com\\/quinoacomputing\\/quinoa\\/commit\\/${SHA1}">${GIT_SHA1}<\\/a>/g'
COMMAND ${CPPCHECK} --inline-suppr --enable=all --force
--error-exitcode=1 -j${PROCESSOR_COUNT}
-I${QUINOA_SOURCE_DIR}/Base
-I${QUINOA_SOURCE_DIR}/Control
-I${QUINOA_SOURCE_DIR}/NoWarning
-I${PROJECT_BINARY_DIR}/Main
${CMAKE_CURRENT_SOURCE_DIR}
# Set work directory for target
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
# Echo what is being done
COMMENT "Quinoa cppcheck static analysis report"
VERBATIM USES_TERMINAL
)

# Output code coverage target enabled
string(REPLACE ";" " " ARGUMENTS "${ARG_TESTRUNNER_ARGS}")
message(STATUS "Enabling cppcheck static analysis target 'cppcheck', report at ${CMAKE_BINARY_DIR}/doc/cppcheck/index.html")
message(STATUS "Enabling cppcheck static analysis target 'cppcheck'")

find_program( FILEFIND find )
find_program( SED sed )

if(FILEFIND AND SED)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/doc/cppcheck)
string(REGEX REPLACE "Quinoa_v(.*)-(.*)-g(.*)" "\\3" SHA1 ${GIT_SHA1})
ADD_CUSTOM_TARGET(cppcheck-xml
# Run cppcheck static analysis
COMMAND ${CPPCHECK} --inline-suppr --enable=all --force
--xml --xml-version=2 -j${PROCESSOR_COUNT}
-I${QUINOA_SOURCE_DIR}/Base
-I${QUINOA_SOURCE_DIR}/Control
-I${QUINOA_SOURCE_DIR}/NoWarning
-I${PROJECT_BINARY_DIR}/Main
${CMAKE_CURRENT_SOURCE_DIR}
2> doc/cppcheck/cppcheck-report.xml
# Generate html output
COMMAND ${CPPCHECK_HTMLREPORT} --file=doc/cppcheck/cppcheck-report.xml
--report-dir=doc/cppcheck --source-dir=.
# Customize page headers in generated html
COMMAND ${FILEFIND} doc/cppcheck -type f -exec ${SED} -i "s/project name/<a href=https:\\/\\/github.com\\/quinoacomputing\\/quinoa\\/commit\\/${SHA1}>${GIT_SHA1}<\\/a>/g" {} +
# Set work directory for target
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
# Echo what is being done
COMMENT "Quinoa cppcheck-xml static analysis report"
VERBATIM USES_TERMINAL
)
# Output code coverage target enabled
message(STATUS "Enabling cppcheck static analysis target 'cppcheck-xml', report at ${CMAKE_BINARY_DIR}/doc/cppcheck/index.html")
endif()

endif()
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