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Ahmed Khalil
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[Feat/aut951] - Distributed Mode (#437)
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‎.circleci/config.yml‎

Lines changed: 7 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,7 @@ jobs:
2626
apt-get install -y libglpk-dev seqan-dev libsdl2-dev libhdf5-dev
2727
apt-get install -y graphviz doxygen python3-pip &&
2828
apt-get install -y libpango1.0-dev gnuplot
29-
apt-get install -y cppcheck &&
29+
apt-get install -y cppcheck libssl-dev &&
3030
apt-get install -y python3-sphinx python3-breathe python3-sphinx-rtd-theme sphinx-doc doxygen-latex doxygen-doc gsfonts graphviz-doc libgd-tools xapian-tools &&
3131
pip3 install exhale &&
3232
pip3 install -r tools/smartpeak/requirements.txt
@@ -71,7 +71,7 @@ jobs:
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name: Running SmartPeak Class Tests
7272
command: |
7373
cd ~/smartpeak_release_build || exit 1
74-
ctest -V
74+
ctest -V -E "(example|example|absl|dfa|exhaustive|random|re2)"
7575
ls -l ~/SmartPeak/src/tests/class_tests/smartpeak/data
7676
cd ~/SmartPeak
7777
export PYTHONPATH="${PWD}/tools"
@@ -130,7 +130,7 @@ jobs:
130130
sed -i '' 's/std::auto_ptr/std::unique_ptr/g' include/seqan/basic/test_system.h
131131
rm lib/libz.* && rm -rf lib/pkgconfig
132132
cd ~/OpenMS && mkdir openms_debug_build && cd openms_debug_build &&
133-
cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCMAKE_PREFIX_PATH="$(brew --prefix qt5)" -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build/ -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Release -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF ..
133+
cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCMAKE_PREFIX_PATH="$(brew --prefix qt5)" -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build/ -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Release -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF -DZLIB_ROOT=$(brew --prefix zlib) ..
134134
make -j4 OpenMS
135135
- run:
136136
name: Building SmartPeak (Including SuperBuild)
@@ -141,15 +141,15 @@ jobs:
141141
cd superbuild
142142
cmake -DUSE_SUPERBUILD=ON -DCMAKE_BUILD_TYPE=Release .. && make -j4
143143
cd ../smartpeak_release_build
144-
cmake -DEIGEN_USE_GPU=OFF -DUSE_SUPERBUILD=OFF -DBOOST_USE_STATIC=OFF -DCMAKE_PREFIX_PATH="~/OpenMS/openms_debug_build/;~/OpenMS/contrib_build;$(brew --prefix qt5);(brew --prefix eigen)" -DPLOG_INCLUDE_DIR=~/SmartPeak/superbuild/Dependencies/Source/plog/include -DIMGUI_DIR=~/SmartPeak/superbuild/Dependencies/Source/imgui -DIMPLOT_DIR=~/SmartPeak/superbuild/Dependencies/Source/implot -DSQLite3_INCLUDE_DIR=~/SmartPeak/superbuild/Dependencies/Source/sqlite -DSQLite3_LIBRARY=~/SmartPeak/superbuild/Dependencies/Source/sqlite -DCMAKE_BUILD_TYPE=RelWithDebInfo -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" -DOpenMP_CXX_LIB_NAMES="omp" -DOpenMP_omp_LIBRARY=/usr/local/opt/libomp/lib/libomp.dylib ~/SmartPeak
144+
cmake -DEIGEN_USE_GPU=OFF -DUSE_SUPERBUILD=OFF -DBOOST_USE_STATIC=OFF -DCMAKE_PREFIX_PATH="~/OpenMS/openms_debug_build/;~/OpenMS/contrib_build;$(brew --prefix qt5);(brew --prefix eigen);$(brew --prefix zlib);$(brew --prefix openssl)" -DOPENSSL_ROOT_DIR=/usr/local/opt/openssl -DOPENSSL_LIBRARIES=/usr/local/opt/openssl/lib -DPLOG_INCLUDE_DIR=~/SmartPeak/superbuild/Dependencies/Source/plog/include -DIMGUI_DIR=~/SmartPeak/superbuild/Dependencies/Source/imgui -DIMPLOT_DIR=~/SmartPeak/superbuild/Dependencies/Source/implot -DSQLite3_INCLUDE_DIR=~/SmartPeak/superbuild/Dependencies/Source/sqlite -DSQLite3_LIBRARY=~/SmartPeak/superbuild/Dependencies/Source/sqlite -DCMAKE_BUILD_TYPE=RelWithDebInfo -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" -DOpenMP_CXX_LIB_NAMES="omp" -DOpenMP_omp_LIBRARY=/usr/local/opt/libomp/lib/libomp.dylib -DgRPC_ZLIB_PROVIDER=package ~/SmartPeak
145145
make -j4
146146
- run:
147147
name: Running SmartPeak Class Tests
148148
no_output_timeout: 15m
149149
command: |
150150
set -e -o pipefail
151151
cd ~/SmartPeak/smartpeak_release_build
152-
ctest -VV -F --timeout 1200
152+
ctest -VV -F -E "(example|absl|dfa|exhaustive|random|re2|charclass|compile|mimics|parse_possible|regexp|required_prefix|search|set|simplify|string_generator)" --timeout 1200
153153
cd ~/SmartPeak
154154
export PYTHONPATH="${PWD}/tools"
155155
python3 -m unittest discover -s ./tools/smartpeak
@@ -293,7 +293,8 @@ jobs:
293293
msbuild src/smartpeak/SmartPeak.sln /verbosity:normal /maxcpucount /p:Configuration=Release
294294
msbuild src/examples/SmartPeak_class_examples_smartpeak.sln /maxcpucount /property:Configuration=Release
295295
refreshenv
296-
& 'C:\Program Files\cmake\bin\ctest.exe' -VV -F
296+
@("set(CMAKE_ERROR_ON_ABSOLUTE_INSTALL_DESTINATION FALSE)") + (Get-Content ".\_deps\grpc-build\third_party\abseil-cpp\absl\base\cmake_install.cmake") | Set-Content ".\_deps\grpc-build\third_party\abseil-cpp\absl\base\cmake_install.cmake"
297+
& 'C:\Program Files\cmake\bin\ctest.exe' -VV -F -E "(example|example|absl|dfa|exhaustive|random|re2|charclass|compile|mimics|parse|regexp|required_prefix|search|set|simplify|string_generator|possible)"
297298
ThrowOnFailure "CTest failed!"
298299
& 'C:\Program Files\cmake\bin\cpack.exe' -G NSIS64
299300
ThrowOnFailure "CPack failed!"

‎CMakeLists.txt‎

Lines changed: 18 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,24 @@
11
# --------------------------------------------------------------------------
2-
# SmartPeak
2+
# SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
33
# --------------------------------------------------------------------------
4-
# TODO: license
4+
# Copyright The SmartPeak Team -- Novo Nordisk Foundation
5+
# Center for Biosustainability, Technical University of Denmark 2018-2022.
6+
#
7+
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
8+
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
9+
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
10+
# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
11+
# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
12+
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
13+
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
14+
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
15+
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
16+
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
17+
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
18+
#
519
# --------------------------------------------------------------------------
6-
# $Maintainer: Douglas McCloskey
7-
# $Author: Douglas McCloskey
20+
# $Maintainer: Douglas McCloskey, Ahmed Khalil $
21+
# $Authors: Douglas McCloskey $
822
# --------------------------------------------------------------------------
923

1024
cmake_minimum_required(VERSION 3.8.2 FATAL_ERROR)

‎cmake/add_library_macros.cmake‎

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@@ -1,4 +1,25 @@
1-
1+
# --------------------------------------------------------------------------
2+
# SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
3+
# --------------------------------------------------------------------------
4+
# Copyright The SmartPeak Team -- Novo Nordisk Foundation
5+
# Center for Biosustainability, Technical University of Denmark 2018-2022.
6+
#
7+
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
8+
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
9+
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
10+
# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
11+
# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
12+
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
13+
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
14+
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
15+
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
16+
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
17+
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
18+
#
19+
# --------------------------------------------------------------------------
20+
# $Maintainer: Douglas McCloskey, Ahmed Khalil $
21+
# $Authors: Douglas McCloskey $
22+
# --------------------------------------------------------------------------
223

324
# required modules
425
include(CMakeParseArguments)

‎cmake/fetch_grpc.cmake‎

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@@ -0,0 +1,62 @@
1+
# --------------------------------------------------------------------------
2+
# SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
3+
# --------------------------------------------------------------------------
4+
# Copyright The SmartPeak Team -- Novo Nordisk Foundation
5+
# Center for Biosustainability, Technical University of Denmark 2018-2022.
6+
#
7+
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
8+
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
9+
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
10+
# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
11+
# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
12+
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
13+
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
14+
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
15+
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
16+
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
17+
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
18+
#
19+
# --------------------------------------------------------------------------
20+
# $Maintainer: Ahmed Khalil, Bertrand Boudaud $
21+
# $Authors: Douglas McCloskey $
22+
# --------------------------------------------------------------------------
23+
# --------------------------------------------------------------------------
24+
# gRPC
25+
# --------------------------------------------------------------------------
26+
option(FETCHCONTENT_QUIET OFF)
27+
option(abseil-cpp_BUILD_TESTS OFF)
28+
option(gRPC_BUILD_TESTS OFF)
29+
option(ABSL_BUILD_TESTING OFF)
30+
option(ABSL_RUN_TESTS OFF)
31+
option(protobuf_BUILD_TESTS OFF)
32+
option(gRPC_BUILD_CSHARP_EXT OFF)
33+
option(gRPC_BUILD_GRPC_CSHARP_PLUGIN OFF)
34+
option(gRPC_BUILD_GRPC_NODE_PLUGIN OFF)
35+
option(gRPC_BUILD_GRPC_JAVA_PLUGIN OFF)
36+
option(gRPC_BUILD_GRPC_OBJECTIVE_C_PLUGIN OFF)
37+
option(gRPC_BUILD_GRPC_PHP_PLUGIN OFF)
38+
option(gRPC_BUILD_GRPC_PYTHON_PLUGIN OFF)
39+
option(gRPC_BUILD_GRPC_RUBY_PLUGIN OFF)
40+
option(ABSL_USE_GOOGLETEST_HEAD ON)
41+
option(ABSL_USE_EXTERNAL_GOOGLETEST ON)
42+
# set(ABSL_LOCAL_GOOGLETEST_DIR ${googletest-distribution_SOURCE_DIR})
43+
set(absl_gtest_download_url "https://github.com/google/googletest/archive/refs/tags/release-1.11.0.zip")
44+
include(FetchContent)
45+
FetchContent_Declare(
46+
gRPC
47+
GIT_REPOSITORY https://github.com/grpc/grpc.git
48+
GIT_TAG v1.41.0
49+
GIT_PROGRESS TRUE
50+
)
51+
FetchContent_MakeAvailable(gRPC)
52+
53+
set(grpc_required_libs
54+
libprotobuf grpc++
55+
grpc++_reflection
56+
grpc++_unsecure grpc_unsecure
57+
grpc++_error_details
58+
grpc gpr
59+
absl_flags
60+
crypto
61+
address_sorting
62+
grpc_plugin_support grpcpp_channelz)

‎cmake/package_general.cmake‎

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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,26 @@
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# --------------------------------------------------------------------------
2+
# SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
3+
# --------------------------------------------------------------------------
4+
# Copyright The SmartPeak Team -- Novo Nordisk Foundation
5+
# Center for Biosustainability, Technical University of Denmark 2018-2022.
6+
#
7+
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
8+
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
9+
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
10+
# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
11+
# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
12+
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
13+
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
14+
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
15+
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
16+
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
17+
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
18+
#
19+
# --------------------------------------------------------------------------
20+
# $Maintainer: Douglas McCloskey, Ahmed Khalil $
21+
# $Authors: Douglas McCloskey, Ahmed Khalil $
22+
# --------------------------------------------------------------------------
23+
# --------------------------------------------------------------------------
224
# Packaging for macOS, Linux and Windows
325
# --------------------------------------------------------------------------
426

‎cmake/package_nsis.cmake‎

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,27 @@
1-
## Windows installer
1+
# --------------------------------------------------------------------------
2+
# SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
3+
# --------------------------------------------------------------------------
4+
# Copyright The SmartPeak Team -- Novo Nordisk Foundation
5+
# Center for Biosustainability, Technical University of Denmark 2018-2022.
6+
#
7+
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
8+
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
9+
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
10+
# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
11+
# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
12+
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
13+
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
14+
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
15+
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
16+
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
17+
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
18+
#
19+
# --------------------------------------------------------------------------
20+
# $Maintainer: Douglas McCloskey, Ahmed Khalil $
21+
# $Authors: Douglas McCloskey, Ahmed Khalil $
22+
# --------------------------------------------------------------------------
223

24+
## Windows installer
325
## With VS2019 the architecture HAS TO BE specified with the "–A" option or CMAKE_GENERATOR_PLATFORM var.
426
## Therefore the legacy way of adding a suffix to the Generator is not valid anymore.
527
## Read value of CMAKE_VS_PLATFORM_NAME instead

‎docs/CMakeLists.txt‎

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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,27 @@
1-
#
1+
# --------------------------------------------------------------------------
2+
# SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
3+
# --------------------------------------------------------------------------
4+
# Copyright The SmartPeak Team -- Novo Nordisk Foundation
5+
# Center for Biosustainability, Technical University of Denmark 2018-2022.
6+
#
7+
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
8+
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
9+
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
10+
# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
11+
# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
12+
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
13+
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
14+
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
15+
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
16+
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
17+
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
18+
#
19+
# --------------------------------------------------------------------------
20+
# $Maintainer: Ahmed Khalil, Douglas McCloskey $
21+
# $Authors: Ahmed Khalil $
22+
# --------------------------------------------------------------------------
223
# doc generation for SmartPeak lib
324
# with doxygen (XML) and sphinx for (RtD)
4-
# Author : Ahmed Khalil
5-
#
625

726
# doxygen
827
find_package(Doxygen REQUIRED)

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