AutoFlowResearch · bertrandboudaud · Jan 6, 2022 · Sep 10, 2021 · Sep 24, 2021 · Oct 9, 2021
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -26,7 +26,7 @@ jobs:
             apt-get install -y libglpk-dev seqan-dev libsdl2-dev libhdf5-dev
             apt-get install -y graphviz doxygen python3-pip &&
             apt-get install -y libpango1.0-dev gnuplot
-            apt-get install -y cppcheck &&
+            apt-get install -y cppcheck libssl-dev &&
             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 &&
             pip3 install exhale && 
             pip3 install -r tools/smartpeak/requirements.txt
@@ -71,7 +71,7 @@ jobs:
           name: Running SmartPeak Class Tests
           command: |
             cd ~/smartpeak_release_build || exit 1
-            ctest -V
+            ctest -V -E "(example|example|absl|dfa|exhaustive|random|re2)"
             ls -l ~/SmartPeak/src/tests/class_tests/smartpeak/data
             cd ~/SmartPeak
             export PYTHONPATH="${PWD}/tools"
@@ -95,19 +95,17 @@ jobs:
 
   build_macos:
     macos:
-      xcode: "11.2.1"
+      xcode: "12.5.1"
     resource_class: medium
     working_directory: ~/SmartPeak
     steps:
       - checkout
       - run:
           name: Installing required libraries
           command: |
-            git -C /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core fetch --unshallow
-            git -C /usr/local/Homebrew/Library/Taps/homebrew/homebrew-cask fetch --unshallow
             brew update
             brew remove yarn node
-            brew install cmake qt5 sdl2
+            brew install cmake qt5 sdl2 zlib
             brew install cppcheck gnuplot
             brew install libomp
             pip3 install -r tools/smartpeak/requirements.txt
@@ -130,8 +128,9 @@ jobs:
             curl -C - -O https://abibuilder.informatik.uni-tuebingen.de/archive/openms/contrib/macOS/10.15.4/x64/appleclang-11.0.0/contrib_build.tar.gz
             tar -xzf contrib_build.tar.gz
             sed -i '' 's/std::auto_ptr/std::unique_ptr/g' include/seqan/basic/test_system.h
+            rm lib/libz.* && rm -rf lib/pkgconfig
             cd ~/OpenMS &&  mkdir openms_debug_build && cd openms_debug_build &&
-            cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCMAKE_PREFIX_PATH="$(brew --prefix qt5)" -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build/ -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Release -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF ..
+            cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCMAKE_PREFIX_PATH="$(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=$(brew --prefix zlib) ..
             make -j4 OpenMS
       - run:
           name: Building SmartPeak (Including SuperBuild)
@@ -142,15 +141,15 @@ jobs:
             cd superbuild
             cmake -DUSE_SUPERBUILD=ON -DCMAKE_BUILD_TYPE=Release .. && make -j4
             cd ../smartpeak_release_build
-            cmake -DEIGEN_USE_GPU=OFF -DUSE_SUPERBUILD=OFF -DBOOST_USE_STATIC=OFF -DCMAKE_PREFIX_PATH="~/OpenMS/openms_debug_build/;~/OpenMS/contrib_build;$(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
+            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);$(brew --prefix openssl)" -DOPENSSL_ROOT_DIR=/usr/local/opt/openssl -DOPENSSL_LIBRARIES=/usr/local/opt/openssl/lib -DPLOG_INCLUDE_DIR=~/SmartPeak/superbuild/Dependencies/Source/plog/include   -DIMGUI_DIR=~/SmartPeak/superbuild/Dependencies/Source/imgui  -DIMPLOT_DIR=~/SmartPeak/superbuild/Dependencies/Source/implot -DSQLite3_INCLUDE_DIR=~/SmartPeak/superbuild/Dependencies/Source/sqlite -DSQLite3_LIBRARY=~/SmartPeak/superbuild/Dependencies/Source/sqlite -DCMAKE_BUILD_TYPE=RelWithDebInfo -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" -DOpenMP_CXX_LIB_NAMES="omp" -DOpenMP_omp_LIBRARY=/usr/local/opt/libomp/lib/libomp.dylib -DgRPC_ZLIB_PROVIDER=package ~/SmartPeak
             make -j4
       - run:
           name: Running SmartPeak Class Tests
           no_output_timeout: 15m
           command: |
             set -e -o pipefail
             cd ~/SmartPeak/smartpeak_release_build
-            ctest -VV -F --timeout 1200
+            ctest -VV -F -E "(example|absl|dfa|exhaustive|random|re2|charclass|compile|mimics|parse_possible|regexp|required_prefix|search|set|simplify|string_generator)" --timeout 1200
             cd ~/SmartPeak
             export PYTHONPATH="${PWD}/tools"
             python3 -m unittest discover -s ./tools/smartpeak
@@ -294,7 +293,8 @@ jobs:
             msbuild src/smartpeak/SmartPeak.sln /verbosity:normal /maxcpucount /p:Configuration=Release
             msbuild src/examples/SmartPeak_class_examples_smartpeak.sln /maxcpucount /property:Configuration=Release
             refreshenv
-            & 'C:\Program Files\cmake\bin\ctest.exe' -VV -F
+            @("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"
+            & '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)"
             ThrowOnFailure "CTest failed!"
             & 'C:\Program Files\cmake\bin\cpack.exe' -G NSIS64
             ThrowOnFailure "CPack failed!"

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,10 +1,24 @@
 # --------------------------------------------------------------------------
-# SmartPeak
+#   SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
 # --------------------------------------------------------------------------
-# TODO: license
+# Copyright The SmartPeak Team -- Novo Nordisk Foundation 
+# Center for Biosustainability, Technical University of Denmark 2018-2022.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 ANY OF THE AUTHORS OR THE CONTRIBUTING
+# INSTITUTIONS 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.
+#
 # --------------------------------------------------------------------------
-# $Maintainer: Douglas McCloskey
-# $Author: Douglas McCloskey
+# $Maintainer: Douglas McCloskey, Ahmed Khalil $
+# $Authors: Douglas McCloskey $
 # --------------------------------------------------------------------------
 
 cmake_minimum_required(VERSION 3.8.2 FATAL_ERROR)

diff --git a/cmake/add_library_macros.cmake b/cmake/add_library_macros.cmake
@@ -1,4 +1,25 @@
-
+# --------------------------------------------------------------------------
+#   SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
+# --------------------------------------------------------------------------
+# Copyright The SmartPeak Team -- Novo Nordisk Foundation 
+# Center for Biosustainability, Technical University of Denmark 2018-2022.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 ANY OF THE AUTHORS OR THE CONTRIBUTING
+# INSTITUTIONS 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.
+#
+# --------------------------------------------------------------------------
+# $Maintainer: Douglas McCloskey, Ahmed Khalil $
+# $Authors: Douglas McCloskey $
+# --------------------------------------------------------------------------
 
 # required modules
 include(CMakeParseArguments)

diff --git a/cmake/fetch_grpc.cmake b/cmake/fetch_grpc.cmake
@@ -0,0 +1,62 @@
+# --------------------------------------------------------------------------
+#   SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
+# --------------------------------------------------------------------------
+# Copyright The SmartPeak Team -- Novo Nordisk Foundation 
+# Center for Biosustainability, Technical University of Denmark 2018-2022.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 ANY OF THE AUTHORS OR THE CONTRIBUTING
+# INSTITUTIONS 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.
+#
+# --------------------------------------------------------------------------
+# $Maintainer: Ahmed Khalil, Bertrand Boudaud $
+# $Authors: Douglas McCloskey $
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+# gRPC
+# --------------------------------------------------------------------------
+option(FETCHCONTENT_QUIET OFF)
+option(abseil-cpp_BUILD_TESTS OFF)
+option(gRPC_BUILD_TESTS OFF)
+option(ABSL_BUILD_TESTING OFF)
+option(ABSL_RUN_TESTS OFF) 
+option(protobuf_BUILD_TESTS OFF)
+option(gRPC_BUILD_CSHARP_EXT OFF)
+option(gRPC_BUILD_GRPC_CSHARP_PLUGIN OFF)
+option(gRPC_BUILD_GRPC_NODE_PLUGIN OFF)
+option(gRPC_BUILD_GRPC_JAVA_PLUGIN OFF)
+option(gRPC_BUILD_GRPC_OBJECTIVE_C_PLUGIN OFF)
+option(gRPC_BUILD_GRPC_PHP_PLUGIN OFF)
+option(gRPC_BUILD_GRPC_PYTHON_PLUGIN OFF)
+option(gRPC_BUILD_GRPC_RUBY_PLUGIN OFF)
+option(ABSL_USE_GOOGLETEST_HEAD ON)
+option(ABSL_USE_EXTERNAL_GOOGLETEST ON)
+# set(ABSL_LOCAL_GOOGLETEST_DIR ${googletest-distribution_SOURCE_DIR})
+set(absl_gtest_download_url "https://github.com/google/googletest/archive/refs/tags/release-1.11.0.zip")
+include(FetchContent)
+FetchContent_Declare(
+  gRPC
+  GIT_REPOSITORY https://github.com/grpc/grpc.git
+  GIT_TAG        v1.41.0
+  GIT_PROGRESS   TRUE
+)
+FetchContent_MakeAvailable(gRPC)
+
+set(grpc_required_libs 
+    libprotobuf grpc++ 
+    grpc++_reflection 
+    grpc++_unsecure grpc_unsecure
+    grpc++_error_details
+    grpc gpr
+    absl_flags
+    crypto
+    address_sorting
+    grpc_plugin_support grpcpp_channelz)
diff --git a/cmake/package_general.cmake b/cmake/package_general.cmake
@@ -1,4 +1,26 @@
 # --------------------------------------------------------------------------
+#   SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
+# --------------------------------------------------------------------------
+# Copyright The SmartPeak Team -- Novo Nordisk Foundation 
+# Center for Biosustainability, Technical University of Denmark 2018-2022.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 ANY OF THE AUTHORS OR THE CONTRIBUTING
+# INSTITUTIONS 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.
+#
+# --------------------------------------------------------------------------
+# $Maintainer: Douglas McCloskey, Ahmed Khalil $
+# $Authors: Douglas McCloskey, Ahmed Khalil $
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
 # Packaging for macOS, Linux and Windows
 # --------------------------------------------------------------------------
 

diff --git a/cmake/package_nsis.cmake b/cmake/package_nsis.cmake
@@ -1,5 +1,27 @@
-## Windows installer
+# --------------------------------------------------------------------------
+#   SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
+# --------------------------------------------------------------------------
+# Copyright The SmartPeak Team -- Novo Nordisk Foundation 
+# Center for Biosustainability, Technical University of Denmark 2018-2022.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 ANY OF THE AUTHORS OR THE CONTRIBUTING
+# INSTITUTIONS 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.
+#
+# --------------------------------------------------------------------------
+# $Maintainer: Douglas McCloskey, Ahmed Khalil $
+# $Authors: Douglas McCloskey, Ahmed Khalil $
+# --------------------------------------------------------------------------
 
+## Windows installer
 ## With VS2019 the architecture HAS TO BE specified with the "–A" option or CMAKE_GENERATOR_PLATFORM var.
 ## Therefore the legacy way of adding a suffix to the Generator is not valid anymore.
 ## Read value of CMAKE_VS_PLATFORM_NAME instead

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
@@ -1,8 +1,27 @@
-# 
+# --------------------------------------------------------------------------
+#   SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
+# --------------------------------------------------------------------------
+# Copyright The SmartPeak Team -- Novo Nordisk Foundation 
+# Center for Biosustainability, Technical University of Denmark 2018-2022.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 ANY OF THE AUTHORS OR THE CONTRIBUTING
+# INSTITUTIONS 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.
+#
+# --------------------------------------------------------------------------
+# $Maintainer: Ahmed Khalil, Douglas McCloskey $
+# $Authors: Ahmed Khalil $
+# --------------------------------------------------------------------------
 # doc generation for SmartPeak lib
 # with doxygen (XML) and sphinx for (RtD)
-# Author : Ahmed Khalil
-#
 
 # doxygen
 find_package(Doxygen REQUIRED)