AUTO UIC fixes and linux install docs

doc/doxygen/install/install-linux.doxygen

@@ -49,7 +49,7 @@
   <ul>
     <li>
       Essential are \b gcc/g++ (>= 7.0) or similar ANSI C++ compiler with full C++17 support,
-      \b CMake (>= 3.24), \b Qt5 (>= 5.6), \b patch, \b autoconf (> 2.60), \b automake (> 1.9), \b libtool (libtoolize/glibtoolize).
+      \b CMake (>= 3.24), \b Qt 6 (>= 6.2), \b patch, \b autoconf (> 2.60), \b automake (> 1.9), \b libtool (libtoolize/glibtoolize).
     </li>
     <li>
       For the complete feature set to be enabled, %OpenMS needs recent versions of
@@ -82,7 +82,7 @@
     # Update repo list for the thirdparty repository EPEL
     sudo yum repolist
     # Get REQUIRED installable contrib libraries
-    sudo yum install cmake3 qt5-qtbase-gui qt5-qtbase-devel qt5-qtsvg-devel python-devel
+    sudo yum install cmake3 qt6-qtbase-gui qt6-qtbase-devel qt6-qtsvg-devel python-devel
     # Get OPTIONAL installable contrib libraries preferably from our Contrib package in the next step.
     ## sudo yum boost-devel libsvm-devel libzip-devel zlib-devel xerces-c-devel bzip2-devel libhdf5-devel glpk-devel
     # NOTE that you might need to use cmake3 instead of cmake in the commands of the following steps.
@@ -96,7 +96,7 @@
       # tools
       sudo zypper install cmake gcc-c++ autoconf git patch automake libtool
       # REQUIRED dependencies
-      sudo zypper install libqt5-qtbase-devel libqt5-qtsvg-devel python-devel glpk-devel
+      sudo zypper install libqt6-qtbase-devel libqt6-qtsvg-devel python-devel glpk-devel
       # OPTIONAL dependencies, preferably installed with our Contrib package in the next step
       ## sudo zypper install boost-devel libzip-devel zlib-devel \
       # libxerces-c-devel libbz2-devel libsvm-devel libhdf5-10
@@ -109,7 +109,7 @@
     sudo add-apt-repository universe
     sudo apt update
     sudo apt-get install build-essential cmake autoconf patch libtool git automake
-    sudo apt-get install qtbase5-dev libqt5svg5-dev libqt5opengl5-dev
+    sudo apt-get install qtbase6-dev libqt6svg6-dev libqt6opengl6-dev
     sudo apt-get install libeigen3-dev libboost-random-dev libboost-regex-dev \
       libboost-iostreams-dev libboost-date-time-dev libboost-math-dev libxerces-c-dev \
       zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev
@@ -180,13 +180,23 @@
   \endcode
 
   Alternatively, you can build one package after the other by providing
-  <tt>-DBUILD_TYPE=...</tt> with the appropriate argument. In addition, you
-  may have to compile Qt yourself which you can get from <a
+  <tt>-DBUILD_TYPE=...</tt> with the appropriate argument. 
+
+
+  In addition, you may have to compile Qt yourself which you can get from <a
   href="http://download.qt.io/official_releases/qt">http://download.qt.io/official_releases/qt</a>
-  (use version >5.5), if it is not provided on your server or the version on
+  (use version >6.2), if it is not provided on your server or the version on
   your environment is too old. Then you can use the traditional
-  <tt>./configure --prefix=/path && make && make install</tt> sequence to compile
-  and install Qt (note that you should set the <tt>--prefix=/path</tt> to a local directory assuming
+
+  @code
+  tar xvf qt-everywhere-src-6.5.3.tar.xz
+  cd qt-everywhere-src-6.5.3
+  ./configure --prefix=.   -skip qtdoc -skip qttranslations -skip qttools
+  cmake --build . --parallel
+  cmake --install .
+
+  @endcode 
+  to compile and install Qt (note that you should set the <tt>--prefix=/path</tt> to a local directory assuming
   you don't have root privileges).
 
 
@@ -223,11 +233,11 @@
   \endcode
   to the CMake options.
 
-  If CMake has problems finding Qt5 (Qt5SvgConfig.cmake is usually the first to fail), you might consider adding:
+  If CMake has problems finding Qt6, you might consider adding:
   \code
-  -DQt5_DIR=/PATH/TO/qt/5.9.7/gcc_64/lib/cmake/Qt5
+  -D Qt6_DIR=/PATH/TO/qt/lib/cmake/Qt6/
   \endcode
-  to the CMake options, where <tt>/PATH/TO/qt/5.9.7/gcc_64</tt> depends on your system settings and Qt version.
+  to the CMake options, where <tt>/PATH/TO/qt/lib/cmake/Qt6/</tt> depends on your system settings and Qt version.
 
   When configuring %OpenMS, consider setting <tt>WITH_GUI=Off</tt> and
   <tt>HAS_XSERVER=Off</tt>, especially as you may not have compiled Qt with
@@ -244,17 +254,19 @@
   This works only after having executed <tt>cmake</tt> once (see @ref install_linux_openms)
 
   In order to <i>build</i> the %OpenMS library, the TOPP tools, tests, and this
-  documentation, execute the following command:
+  documentation, execute the following command (for Makefile generator, which is the default in CMake):
 
   \code
   make
   \endcode
+
 
   Advanced users can list the separate make targets by calling:
   \code
   make targets
   \endcode
 
+  @note If you use another generator, such as Ninja (`cmake -G Ninja ...`), then swap `make` for the new command, such as `ninja`.
 
   @subsection linux_openms_environment Getting your environment ready to use OpenMS
 

src/openms/include/OpenMS/MATH/MathFunctions.h

@@ -17,6 +17,7 @@
 #include <boost/random/uniform_int.hpp>
 #include <cmath>
 #include <utility> // for std::pair
+#include <vector>
 
 namespace OpenMS
 {

src/openms_gui/CMakeLists.txt

@@ -70,6 +70,19 @@ if (MSVC)
   set_property(TARGET OpenMS_GUI APPEND PROPERTY LINK_FLAGS ${GUI_lnk_flags}) ## allow multiple definitions of symbols (e.g. from template instanciations or STL-derived classes)
 endif()
 
+
+# --------------------------------------------------------------------------
+# some targets using OpenMS_GUI (e.g. in the GUI tests) need the ui_..h files, so add them to OpenMS_GUI's interface.
+get_property(_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
+if(_isMultiConfig)
+  set(AUTOGEN_INCLUDE_DIR ${CMAKE_CURRENT_BINARY_DIR}/OpenMS_GUI_autogen/include_$<CONFIG>)
+else()
+  set(AUTOGEN_INCLUDE_DIR ${CMAKE_CURRENT_BINARY_DIR}/OpenMS_GUI_autogen/include)
+endif()
+# add include-directories for UIC'd files (CMake does not do that automatically)
+target_include_directories(OpenMS_GUI INTERFACE $<BUILD_INTERFACE:${AUTOGEN_INCLUDE_DIR}>)
+
+
 #------------------------------------------------------------------------------
 # register relevant paths for the doxygen doc generation
 openms_doc_path("${PROJECT_SOURCE_DIR}/include")

src/tests/class_tests/openms_gui/source/GUI/TSGDialog_test.cpp

@@ -108,7 +108,7 @@ void OpenMS::TestTSGDialog::testIonsIntensities_()
       QRect rect = UI->ion_types->visualItemRect(item);
 
       // imitate the click on check box c
-      QTest::mouseClick(UI->ion_types->viewport(), Qt::LeftButton, 0, rect.center());
+      QTest::mouseClick(UI->ion_types->viewport(), Qt::LeftButton, Qt::NoModifier, rect.center());
       QTest::qWait(DELAY);
 
       // verfiy the check state changed
@@ -432,4 +432,4 @@ QTEST_MAIN(TestTSGDialog)
 //  QWidget* activeWidget = dropDownList->viewport();
 //  QTest::mouseClick(activeWidget, Qt::LeftButton, Qt::NoModifier, foundDropDownItemPosition);
 //  QTest::qWait(DELAY);
-//}
+//}

src/topp/DatabaseFilter.cpp

@@ -83,7 +83,7 @@ class TOPPDatabaseFilter :
 
     OPENMS_LOG_INFO << "Number of Protein IDs: " << id_accessions.size() << endl;
 
-    for (const auto entry : db)
+    for (const auto& entry : db)
     {
       const String& fasta_accession = entry.identifier;
       const bool found = id_accessions.find(fasta_accession) != id_accessions.end();