Accepting request 999298 from home:StefanBruens:branches:science

Needs some more work, but at least builds again.

- Update to version 2.8.0
  See https://github.com/OpenMS/OpenMS/releases/tag/Release2.8.0  
- Add compile fixes from upstream:
  * fix-compile-warnings.patch
  * fix-isnan-undeclared.patch
  * fix-libwm5core-linkage.patch
  * 0001-Fix-install-path-for-evergreen-headers.patch
- Drop obsolete patches:
  * openms-Selenocysteine.patch
  * openms-addlibs.patch
  * openms-fix-pyOpenMSbuild.patch
  * openms-fix-python_tests.patch
  * openms-remove_testflag.patch
  * openms-revert_TOPP_PeakPickerWavelet_test.patch
  * openms-setuptools.patch
- Use wildmagick5 package instead of bundling it

OBS-URL: https://build.opensuse.org/request/show/999298
OBS-URL: https://build.opensuse.org/package/show/science/openms?expand=0&rev=18

openms.changes

@@ -1,3 +1,23 @@
+-------------------------------------------------------------------
+Tue Aug 23 20:20:56 UTC 2022 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
+
+- Update to version 2.8.0
+  See https://github.com/OpenMS/OpenMS/releases/tag/Release2.8.0  
+- Add compile fixes from upstream:
+  * fix-compile-warnings.patch
+  * fix-isnan-undeclared.patch
+  * fix-libwm5core-linkage.patch
+  * 0001-Fix-install-path-for-evergreen-headers.patch
+- Drop obsolete patches:
+  * openms-Selenocysteine.patch
+  * openms-addlibs.patch
+  * openms-fix-pyOpenMSbuild.patch
+  * openms-fix-python_tests.patch
+  * openms-remove_testflag.patch
+  * openms-revert_TOPP_PeakPickerWavelet_test.patch
+  * openms-setuptools.patch
+- Use wildmagick5 package instead of bundling it
+
 -------------------------------------------------------------------
 Sun Sep  4 19:53:06 UTC 2016 - mailaender@opensuse.org
 

openms.spec

@@ -1,148 +1,108 @@
-# $Id$
-
 #
-# Copyright 2015 Antonio Trande
-# Copyright 2015 Archie L. Cobbs.
-# 
-# Licensed under the Apache License, Version 2.0 (the "License"); you may
-# not use this file except in compliance with the License. You may obtain
-# a copy of the License at
-# 
-#     http://www.apache.org/licenses/LICENSE-2.0
-# 
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
-# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
-# License for the specific language governing permissions and limitations
-# under the License.
-# 
+# spec file for package openms
+#
+# Copyright (c) 2022 SUSE LLC
+#
+# All modifications and additions to the file contributed by third parties
+# remain the property of their copyright owners, unless otherwise agreed
+# upon. The license for this file, and modifications and additions to the
+# file, is the same license as for the pristine package itself (unless the
+# license for the pristine package is not an Open Source License, in which
+# case the license is the MIT License). An "Open Source License" is a
+# license that conforms to the Open Source Definition (Version 1.9)
+# published by the Open Source Initiative.
+
+# Please submit bugfixes or comments via https://bugs.opensuse.org/
+#
 
 
-
-##This macro enables/disables pyOpenMS python bindings
-%ifarch %{arm}
-%global with_pyOpenMS 0
+# Required python-autowrap not packaged
+%bcond_with pyOpenMS
+%bcond_with documentation
+# GUI requires Qt build with Desktop OpenGL backend
+%ifarch %{arm} aarch64
+%bcond_with    gui
 %else
-## can't enabled this until we have autowrap - https://pypi.python.org/pypi/autowrap
-%global with_pyOpenMS 0
+%bcond_without gui
 %endif
 
 Name:           openms
-Version:        2.0.1
+Version:        2.8.0
 Release:        0
 License:        BSD-3-Clause
 Summary:        LC/MS data management and analysis suite
 Group:          Productivity/Scientific/Chemistry
-Source0:        http://downloads.sourceforge.net/project/open-ms/OpenMS/OpenMS-%{version}/OpenMS-%{version}-sources.tar.gz
-Source1:        http://downloads.sourceforge.net/project/open-ms/contrib/seqan-mini-1.4.1.tar.gz
-Source2:        http://downloads.sourceforge.net/project/open-ms/contrib/WildMagic5.tar.gz
-Url:            http://www.openms.de/
-BuildRoot:      %{_tmppath}/%{name}-%{version}-root
-
-##TOPPView, TOPPAS, INIFileEditor .desktop and icon files
-Source3:        TOPPView.xpm
-Source4:        TOPPAS.xpm
-Source5:        INIFileEditor.xpm
-Source6:        inifileeditor.desktop
-
-BuildRequires:  autoconf
-BuildRequires:  automake
-#BuildRequires:  autowrap
-BuildRequires:  boost-devel
-BuildRequires:  cmake
+URL:            https://www.openms.de/
+Source0:        https://github.com/OpenMS/OpenMS/archive/refs/tags/Release%{version}.tar.gz
+# PATCH-FIX-UPSTREAM
+Patch0:         https://patch-diff.githubusercontent.com/raw/OpenMS/OpenMS/pull/5916.patch#/fix-isnan-undeclared.patch
+# PATCH-FIX-UPSTREAM
+Patch1:         https://patch-diff.githubusercontent.com/raw/OpenMS/OpenMS/pull/6302.patch#/fix-libwm5core-linkage.patch
+# PATCH-FIX-UPSTREAM
+Patch2:         https://github.com/OpenMS/OpenMS/pull/5838.patch#/fix-compile-warnings.patch
+# PATCH-FIX-UPSTREAM
+Patch3:         0001-Fix-install-path-for-evergreen-headers.patch
+BuildRequires:  chrpath
+BuildRequires:  cmake >= 3.9
 BuildRequires:  desktop-file-utils
-BuildRequires:  eigen3-devel
+BuildRequires:  eigen3-devel >= 3.3.4
 BuildRequires:  gcc-c++
 BuildRequires:  glpk-devel
-BuildRequires:  gsl-devel
+BuildRequires:  hdf5-devel
+BuildRequires:  hicolor-icon-theme
 BuildRequires:  libbz2-devel
-BuildRequires:  libqt4-devel
-BuildRequires:  libqt4-devel
-BuildRequires:  libQtWebKit-devel
-BuildRequires:  libsvm2
-BuildRequires:  libsvm-devel
-BuildRequires:  libtool
-BuildRequires:  libxerces-c-devel
-BuildRequires:  make
-BuildRequires:  openmpi-devel
-BuildRequires:  patch
-BuildRequires:  qt-x11
-#BuildRequires:  seqan-devel
-#BuildRequires:  tbb-devel
-#BuildRequires:  wildmagic5-devel
-BuildRequires:  xtandem
-BuildRequires:  zlib
+BuildRequires:  libboost_date_time-devel
+BuildRequires:  libboost_headers-devel
+BuildRequires:  libboost_iostreams-devel
+BuildRequires:  libboost_math-devel
+BuildRequires:  libboost_regex-devel
+BuildRequires:  libsvm-devel >= 2.91
+BuildRequires:  wildmagic5-devel
+BuildRequires:  update-desktop-files
 BuildRequires:  zlib-devel
-
-## Build documentation
-## Doxygen useful only on SVN versions  
-## xvfb is needed to build documentation by "DefaultParamHandlerDocumenter"
-%if %{suse_version} >= 1320
-BuildRequires:  doxygen, dos2unix, graphviz
-BuildRequires:  texlive, ImageMagick, texlive-a4wide, texlive-xtab
+BuildRequires:  pkgconfig(cbc)
+BuildRequires:  pkgconfig(cgl)
+BuildRequires:  pkgconfig(sqlite3)
+BuildRequires:  pkgconfig(xerces-c)
+BuildRequires:  cmake(Qt5Concurrent)
+BuildRequires:  cmake(Qt5Core)
+BuildRequires:  cmake(Qt5Network)
+BuildRequires:  cmake(Qt5Sql)
+BuildRequires:  cmake(Qt5Svg)
+BuildRequires:  cmake(Qt5Test)
+%if %{with gui}
+BuildRequires:  cmake(Qt5Gui)
+BuildRequires:  cmake(Qt5WebEngineWidgets)
+BuildRequires:  cmake(Qt5Widgets)
+%endif
+%if %{with pyOpenMS}
+BuildRequires:  python3-Cython
+BuildRequires:  python3-autowrap
+BuildRequires:  python3-numpy
+BuildRequires:  python3-pytest
+BuildRequires:  python3-wheel
+%endif
+%if %{with documentaton}
+BuildRequires:  doxygen
+BuildRequires:  graphviz
+BuildRequires:  texlive
+BuildRequires:  texlive-a4wide
+BuildRequires:  texlive-xtab
 %endif
-
 ##Xvfb is needed to run a virtual X server used by some tests
-%if %{suse_version} >= 1320
 BuildRequires:  xvfb-run
-%endif
-BuildRequires:  gnuplot
-
-Recommends:     xtandem
-Requires:       %{name}-data = %{version}-%{release}
-
-##Fixing pyOpenMS build without contrib
-##https://github.com/OpenMS/OpenMS/commit/7e85e1ed12601e852eb0dc25e285a889304cf08e
-Patch0: %{name}-fix-pyOpenMSbuild.patch  
-
-##Use 'setuptools' instead of 'distribute' downloaded/built separately
-Patch1: %{name}-setuptools.patch  
-
-##Remove -O0 flag for tests compiling
-Patch2: %{name}-remove_testflag.patch
-
-##Fix mzML unittests
-Patch3: %{name}-fix-python_tests.patch
-
-##https://github.com/hroest/OpenMS/commit/6164699056398c043fc1bf0592ff0e9ba9a69cee
-Patch4: %{name}-revert_TOPP_PeakPickerWavelet_test.patch
-
-Patch5: %{name}-addlibs.patch
-
-Patch6: %{name}-Selenocysteine.patch
+Requires:       %{name}-data = %{version}
+Requires:       hicolor-icon-theme
 
 %description
 OpenMS is an open-source C++ library for LC/MS data management and analyses.
 It offers an infrastructure for the rapid development 
 of mass spectrometry related software.
-It comes with a vast variety ready-to-use tools for proteomics and 
-metabolomics data analysis (TOPPTools) and powerful 2D and 
-3D visualization(TOPPView).
-OpenMS offers analyses for various quantitation protocols, 
-including label-free quantitation, SILAC, iTRAQ, SRM, SWATH.
-OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data.
-
-The OpenMS Proteomics Pipeline is a pipeline for 
-the analysis of HPLC-MS data. 
-It consists of several small applications that 
-can be chained to create analysis pipelines tailored 
-for a specific problem.
-
-The TOPP tools are divided into several subgroups:
- - Graphical Tools
- - File Handling
- - Signal Processing and Preprocessing
- - Quantitation
- - Map Alignment
- - Protein/Peptide Identification
- - Protein/Peptide Processing
- - Targeted Experiments
- - Peptide Property Prediction
- - Misc
 
 %package tools
-Summary: OpenMS tools
-Requires: %{name}-data = %{version}-%{release}
+Summary:        OpenMS tools
+Requires:       %{name}-data = %{version}
+
 %description tools
 Besides TOPP, OpenMS offers a range of other tools. 
 They are not included in TOPP as they are not part of 
@@ -160,13 +120,10 @@ The UTILS tools are divided into several subgroups:
  - Metabolite identification
  - Quality control
 
-%if 0%{?with_pyOpenMS}
 %package -n python-openms
 Summary: OpenMS Python bindings
-BuildRequires: python-setuptools, python-devel, numpy 
-BuildRequires: python-nose, python-Cython
-Requires: %{name}-data = %{version}-%{release}
-Requires: %{name}%{?_isa} = %{version}-%{release}
+Requires: %{name}-data = %{version}
+
 %description -n python-openms
 This package contains Python bindings for a large part of the OpenMS library
 for mass spectrometry based proteomics.  It thus provides providing facile 
@@ -177,194 +134,139 @@ implemented in OpenMS, specifically those for file access
 (mzXML, mzML, TraML, mzIdentML among others), basic signal processing 
 (smoothing, filtering, de-isotoping and peak-picking) and complex data analysis 
 (including label-free, SILAC, iTRAQ and SWATH analysis tools).
-%endif
 
 %package devel
 Summary: OpenMS header files
+
 %description devel
 OpenMS development files.
 
-%if %{suse_version} >= 1320
+
 %package doc
 Summary: OpenMS documentation
 BuildArch: noarch
+
 %description doc
 HTML documentation and PDF tutorials of OpenMS.
-%endif
 
 %package tutorials
 Summary: OpenMS tutorials
-Requires: %{name}-data = %{version}-%{release}
+Requires: %{name}-data = %{version}
+
 %description tutorials
 OpenMS executable tutorials.
 
 %package data
 Summary: The OpenMS data files
 BuildArch: noarch
+
 %description data
 The OpenMS data files.
 
 %prep
-%setup -q -n OpenMS-%{version}
+%autosetup -n OpenMS-Release%{version} -p1
 rm -rf cmake/MacOSX
 
-mkdir contrib/archives
-cp %{SOURCE1} contrib/archives/
-cp %{SOURCE2} contrib/archives/
-
-## Strip all .png files 
-## 'iCCP: known incorrect sRGB profile' warnings
-find . -type f -name "*.png" -exec convert {} -strip {} \;
-
-%if 0%{?with_pyOpenMS}
-%patch0 -p0
-%patch1 -p0
-%endif
-
-%patch2 -p0
-
-%if 0%{?fedora} < 22
-%ifarch %{arm}
-%patch4 -p0
-%endif
-%endif
-
-%patch5 -p0
-%patch6 -p0
 
 %build
-
-# Contrib stuff
-( cd contrib && cmake -DBUILD_TYPE=SEQAN . )
-( cd contrib && cmake -DBUILD_TYPE=WILDMAGIC . )
-
-export LDFLAGS="-Wl,--as-needed"
 %cmake -Wno-dev \
- -DCMAKE_COLOR_MAKEFILE:BOOL=ON \
- -DCMAKE_CXX_FLAGS_RELEASE:STRING="-Wno-cpp $RPM_OPT_FLAGS" -DCMAKE_C_FLAGS_RELEASE:STRING="-Wno-cpp $RPM_OPT_FLAGS" \
- -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_PREFIX_PATH=%{_prefix} \
- -DENABLE_SVN=OFF -DCMAKE_BUILD_TYPE=Release -DBOOST_USE_STATIC=OFF \
- -DCMAKE_SKIP_RPATH:BOOL=TRUE -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \
- -DMT_ENABLE_OPENMP=ON -DENABLE_GCC_WERROR:BOOL=OFF \
- -DXTANDEM_BINARY=%{_bindir}/xtandem \
- -DBOOST_USE_STATIC:BOOL=OFF -DBoost_INCLUDE_DIR:PATH=%{_includedir} \
- -DBoost_IOSTREAMS_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_iostreams.so \
- -DBoost_MATH_C99_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_math_c99.so \
- -DBoost_REGEX_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_regex.so \
- -DENABLE_TUTORIALS:BOOL=ON -DENABLE_UNITYBUILD:BOOL=OFF \
+ -DBOOST_USE_STATIC=OFF \
+ -DENABLE_UPDATE_CHECK:BOOL=FALSE \
+ -DCMAKE_SKIP_RPATH:BOOL=FALSE \
+ -DCMAKE_SKIP_INSTALL_RPATH:BOOL=TRUE \
+ -DMT_ENABLE_OPENMP=ON \
+ -DENABLE_GCC_WERROR:BOOL=OFF \
+ -DENABLE_TUTORIALS:BOOL=ON \
+ -DENABLE_UNITYBUILD:BOOL=OFF \
  -DHAS_XSERVER:BOOL=ON \
- -DCMAKE_INSTALL_PREFIX=%{_prefix} \
- -DINSTALL_BIN_DIR:PATH=bin -DINSTALL_CMAKE_DIR:PATH=%{_lib}/cmake/OpenMS \
- -DINSTALL_DOC_DIR:PATH=share/doc/OpenMS -DINSTALL_INCLUDE_DIR:PATH=include \
- -DINSTALL_LIB_DIR:PATH=%{_lib}/OpenMS -DINSTALL_SHARE_DIR:PATH=share/OpenMS \
- -DPACKAGE_TYPE:STRING=none -DWITH_GUI:BOOL=ON \
- -DXercesC_INCLUDE_DIRS:PATH=%{_includedir}/xercesc \
- -DXercesC_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libxerces-c.so \
+ -DINSTALL_BIN_DIR:PATH=bin \
+ -DINSTALL_CMAKE_DIR:PATH=%{_lib}/cmake/OpenMS \
+ -DINSTALL_DOC_DIR:PATH=share/doc/packages/OpenMS \
+ -DINSTALL_INCLUDE_DIR:PATH=include \
+ -DINSTALL_LIB_DIR:PATH=%{_lib} \
+ -DINSTALL_SHARE_DIR:PATH=share/OpenMS \
+ -DPACKAGE_TYPE:STRING=none \
+ -DWITH_GUI:BOOL=%{?with_gui:ON}%{!?with_gui:OFF} \
 %if 0%{?with_pyOpenMS}
  -DPYOPENMS=ON \
- -DCYTHON_EXECUTABLE:FILEPATH=%{_bindir}/cython
 %else
- -DPYOPENMS=OFF
+ -DPYOPENMS=OFF \
 %endif
+ %{nil}
 
+%cmake_build all
 %if 0%{?with_pyOpenMS}
-######################make %{?_smp_mflags} OpenMS TOPP UTILS GUI
-make OpenMS TOPP UTILS GUI
-make pyopenms
-%else
-######################make %{?_smp_mflags} OpenMS TOPP UTILS GUI
-make OpenMS TOPP UTILS GUI
-%endif
-
-
-## Make HTML documentation (only on SVN versions)
-## Make Tutorials
-## Run a Virtual X server waiting 3 seconds before
-export LD_LIBRARY_PATH=$PWD/lib:$LD_LIBRARY_PATH
-%if %{suse_version} >= 1320
-xvfb-run -a make doc
-%else
-make doc
+%cmake_build pyopenms
 %endif
+%cmake_build doc
 
 %install
-cd build
-export LD_LIBRARY_PATH=$PWD/lib:$LD_LIBRARY_PATH
-%if %{suse_version} >= 1320
-xvfb-run -a make install DESTDIR=%{buildroot}
-%else
-make install DESTDIR=%{buildroot}
-%endif
+%cmake_install
 
 %if 0%{?with_pyOpenMS}
 ## pyOpenMS installation
 pushd pyOpenMS
-python setup.py install --skip-build --root %{buildroot}
-
-ln -s -f %{_libdir}/OpenMS/libOpenMS.so %{buildroot}%{python_sitearch}/pyopenms/libOpenMS.so
-ln -s -f %{_libdir}/OpenMS/libOpenSwathAlgo.so %{buildroot}%{python_sitearch}/pyopenms/libOpenSwathAlgo.so
-ln -s -f %{_libdir}/OpenMS/libSuperHirn.so %{buildroot}%{python_sitearch}/pyopenms/libSuperHirn.so
+python3 setup.py install --skip-build --root %{buildroot}
 
 ## Fix standard permissions 
 chmod 0755 %{buildroot}%{python_sitearch}/pyopenms/pyopenms.so
 popd
 %endif
 
-##Install TOPPAS/TOPPView .png icons
-mkdir -p %{buildroot}%{_datadir}/icons/TOPP/pixmaps
-install -pm 644 %{SOURCE3} %{buildroot}%{_datadir}/icons/TOPP/pixmaps
-install -pm 644 %{SOURCE4} %{buildroot}%{_datadir}/icons/TOPP/pixmaps
-install -pm 644 %{SOURCE5} %{buildroot}%{_datadir}/icons/TOPP/pixmaps
+%if %{with gui}
+## Install icons
+install -m 0644 -D -t %{buildroot}%{_datadir}/icons/hicolor/64x64/apps src/openms_gui/source/VISUAL/ICONS/TOPPAS.png
+install -m 0644 -D -t %{buildroot}%{_datadir}/icons/hicolor/64x64/apps src/openms_gui/source/VISUAL/ICONS/TOPPView.png
+install -m 0644 -D -t %{buildroot}%{_datadir}/icons/hicolor/64x64/apps src/openms_gui/source/VISUAL/ICONS/INIFileEditor.png
 
-##Install toppas/toppview/inifileeditor .desktop files
+## Move files to correct location
 mkdir -p %{buildroot}%{_datadir}/applications
-desktop-file-install \
- --set-key=Exec --set-value="env LD_LIBRARY_PATH=%{_libdir}/OpenMS OPENMS_DATA_PATH=%{_datadir}/OpenMS TOPPAS %U" \
- --set-icon=%{_datadir}/icons/TOPP/pixmaps/TOPPAS.xpm \
- --set-key=StartupNotify --set-value=true \
- --dir=%{buildroot}%{_datadir}/applications ../share/OpenMS/DESKTOP/TOPPAS.desktop
+mv %{buildroot}%{_datadir}/OpenMS/DESKTOP/*.desktop %{buildroot}%{_datadir}/applications
+sed -i -e 's@Icon=.*@Icon=TOPPAS@' %{buildroot}%{_datadir}/applications/TOPPAS.desktop
+sed -i -e 's@Icon=.*@Icon=TOPPView@' %{buildroot}%{_datadir}/applications/TOPPView.desktop
 
-desktop-file-install \
- --set-key=Exec --set-value="env LD_LIBRARY_PATH=%{_libdir}/OpenMS OPENMS_DATA_PATH=%{_datadir}/OpenMS TOPPView %U" \
- --set-icon=%{_datadir}/icons/TOPP/pixmaps/TOPPView.xpm \
- --set-key=StartupNotify --set-value=true \
- --dir=%{buildroot}%{_datadir}/applications ../share/OpenMS/DESKTOP/TOPPView.desktop
+mkdir -p %{buildroot}%{_datadir}/metainfo/
+mv %{buildroot}%{_datadir}/OpenMS/DESKTOP/TOPPView.appdata.xml %{buildroot}%{_datadir}/metainfo/
+mv %{buildroot}%{_datadir}/OpenMS/DESKTOP/TOPPAS.appdata.xml %{buildroot}%{_datadir}/metainfo/
+rm %{buildroot}%{_datadir}/OpenMS/DESKTOP/readme.txt
+rmdir %{buildroot}%{_datadir}/OpenMS/DESKTOP
 
-desktop-file-install \
- --set-key=Exec --set-value="env LD_LIBRARY_PATH=%{_libdir}/OpenMS OPENMS_DATA_PATH=%{_datadir}/OpenMS INIFileEditor %U" \
- --dir=%{buildroot}%{_datadir}/applications %{SOURCE6}
+## Create inifileeditor .desktop file
+%suse_update_desktop_file -c INIFileEditor INIFileEditor INIFileEditor INIFileEditor INIFileEditor
+%else
+rm -Rf %{buildroot}%{_datadir}/OpenMS/DESKTOP
+%endif
 
 ##Install Tutorials executable
 mkdir -p %{buildroot}%{_bindir}
-cp -a bin/Tutorial_* %{buildroot}%{_bindir}
+cp -a %{__builddir}/bin/Tutorial_* %{buildroot}%{_bindir}
+chrpath -d %{buildroot}%{_bindir}/Tutorial_*
 
-##Install ldconfig include file
-mkdir -p %{buildroot}%{_sysconfdir}/ld.so.conf.d/
-printf '# %%s\n%%s\n' '%{name}-%{version}-%{release}' '%{_libdir}/OpenMS' \
-  > %{buildroot}%{_sysconfdir}/ld.so.conf.d/%{name}.conf
-
-mkdir -p %{buildroot}%{_datadir}/appdata/
-cp -a ../share/OpenMS/DESKTOP/TOPPView.appdata.xml %{buildroot}%{_datadir}/appdata/
-cp -a ../share/OpenMS/DESKTOP/TOPPAS.appdata.xml %{buildroot}%{_datadir}/appdata/
-
-%post
-/sbin/ldconfig
-%desktop_database_post
-
-%postun
-/sbin/ldconfig
-%desktop_database_postun
+%post -p /sbin/ldconfig
+%postun -p /sbin/ldconfig
 
 %check
 ## Make all test
-export LD_LIBRARY_PATH=$PWD/lib:$LD_LIBRARY_PATH
-export PATH=$PWD/bin:$PATH
+export PATH=$PWD/%{__builddir}/bin:$PATH
 export OPENMS_DATA_PATH=$PWD/share/OpenMS:$OPENMS_DATA_PATH
+pushd %{__builddir}
 ## Run a Virtual X server waiting 3 seconds before
-## starting tests
-%if %{suse_version} >= 1320
-xvfb-run -a ctest -V -R TOPP -E TOPP_XTandemAdapter_ --force-new-ctest-process %{?_smp_mflags}
-xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags}
+# TOPP_DatabaseSuitability_* depends on Comet (https://github.com/UWPR/Comet)
+# Some tests known to fail, see https://github.com/OpenMS/OpenMS/issues/5541:
+# - PrecursorIonSelectionPreprocessing_test
+# - DetectabilitySimulation_test
+# - MRMAssay_test
+# - MRMFeatureSelector_test
+# - TOPP_OpenPepXL_1_out_2
+# - TOPP_OpenPepXLLF_1_out_2
+# Several tests depent on the GUI (https://github.com/OpenMS/OpenMS/issues/5781)
+# Numeric problems on ix86
+%if %{with gui}
+%ifnarch %{ix86}
+xvfb-run -a ctest --output-on-failure --force-new-ctest-process %{?_smp_mflags} \
+  --exclude-regex 'TOPP_DatabaseSuitability_.*|PrecursorIonSelectionPreprocessing_test|DetectabilitySimulation_test|MRMAssay_test|MRMFeatureSelector_test|TOPP_OpenPepXL.*_1_out_2'
+popd
+%endif
 %endif
 
 ##pyOpenMS tests including mem leak
@@ -376,9 +278,23 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags}
 #%%endif
 
 %files
+%doc CHANGELOG AUTHORS README.md
+%license License.txt
+%if %{with gui}
 %{_bindir}/TOPPView
 %{_bindir}/TOPPAS
 %{_bindir}/INIFileEditor
+%{_bindir}/Resampler
+%{_bindir}/ExecutePipeline
+%{_bindir}/SwathWizard
+%{_datadir}/applications/TOPPAS.desktop
+%{_datadir}/applications/TOPPView.desktop
+%{_datadir}/applications/INIFileEditor.desktop
+%dir %{_datadir}/metainfo/
+%{_datadir}/metainfo/TOPPView.appdata.xml
+%{_datadir}/metainfo/TOPPAS.appdata.xml
+%{_datadir}/icons/hicolor/64x64/apps/*png
+%endif
 %{_bindir}/DTAExtractor
 %{_bindir}/FileConverter
 %{_bindir}/FileInfo
@@ -400,7 +316,6 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags}
 %{_bindir}/PeakPickerWavelet
 %{_bindir}/PrecursorMassCorrector
 %{_bindir}/HighResPrecursorMassCorrector
-%{_bindir}/Resampler
 %{_bindir}/SpectraFilterBernNorm
 %{_bindir}/SpectraFilterMarkerMower
 %{_bindir}/SpectraFilterNLargest
@@ -411,7 +326,6 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags}
 %{_bindir}/SpectraFilterThresholdMower
 %{_bindir}/SpectraFilterWindowMower
 %{_bindir}/TOFCalibration
-%{_bindir}/AdditiveSeries
 %{_bindir}/Decharger
 %{_bindir}/EICExtractor
 %{_bindir}/FeatureFinderCentroided
@@ -419,11 +333,9 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags}
 %{_bindir}/FeatureFinderMetabo
 %{_bindir}/FeatureFinderMRM 
 %{_bindir}/IsobaricAnalyzer
-%{_bindir}/ITRAQAnalyzer
 %{_bindir}/ProteinQuantifier 
 %{_bindir}/ProteinResolver
 %{_bindir}/SeedListGenerator
-%{_bindir}/TMTAnalyzer
 %{_bindir}/ConsensusMapNormalizer
 %{_bindir}/MapAlignerIdentification
 %{_bindir}/MapAlignerPoseClustering
@@ -434,7 +346,6 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags}
 %{_bindir}/FeatureLinkerUnlabeledQT
 %{_bindir}/CompNovo
 %{_bindir}/CompNovoCID
-%{_bindir}/InspectAdapter
 %{_bindir}/MascotAdapter
 %{_bindir}/MascotAdapterOnline
 %{_bindir}/MyriMatchAdapter
@@ -470,49 +381,73 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags}
 %{_bindir}/RTModel
 %{_bindir}/RTPredict
 %{_bindir}/GenericWrapper
-%{_bindir}/ExecutePipeline
 %{_bindir}/FeatureFinderIdentification
 %{_bindir}/FeatureFinderMultiplex
 %{_bindir}/FidoAdapter
-%{_bindir}/LowMemPeakPickerHiRes
-%{_bindir}/LowMemPeakPickerHiRes_RandomAccess
 %{_bindir}/MRMTransitionGroupPicker
 %{_bindir}/MSGFPlusAdapter
 %{_bindir}/MetaboliteSpectralMatcher
 %{_bindir}/OpenSwathWorkflow
 %{_bindir}/PeakPickerIterative
 %{_bindir}/SimpleSearchEngine
-%{_bindir}/TopPerc
-%{_datadir}/applications/TOPPAS.desktop
-%{_datadir}/applications/TOPPView.desktop
-%{_datadir}/applications/inifileeditor.desktop
-%dir %{_datadir}/appdata/
-%{_datadir}/appdata/TOPPView.appdata.xml
-%{_datadir}/appdata/TOPPAS.appdata.xml
-%{_datadir}/icons/TOPP/
-%{_libdir}/OpenMS/
-%attr(0644,root,root) %{_sysconfdir}/ld.so.conf.d/%{name}.conf
+%{_bindir}/AssayGeneratorMetabo
+%{_bindir}/ClusterMassTraces
+%{_bindir}/ClusterMassTracesByPrecursor
+%{_bindir}/CometAdapter
+%{_bindir}/CruxAdapter
+%{_bindir}/DatabaseFilter
+%{_bindir}/DatabaseSuitability
+%{_bindir}/Epifany
+%{_bindir}/ExternalCalibration
+%{_bindir}/FeatureFinderMetaboIdent
+%{_bindir}/FeatureLinkerUnlabeledKD
+%{_bindir}/GNPSExport
+%{_bindir}/MSFraggerAdapter
+%{_bindir}/MSstatsConverter
+%{_bindir}/MaRaClusterAdapter
+%{_bindir}/MapAlignerTreeGuided
+%{_bindir}/MetaboliteAdductDecharger
+%{_bindir}/MultiplexResolver
+%{_bindir}/NovorAdapter
+%{_bindir}/NucleicAcidSearchEngine
+%{_bindir}/OpenMSDatabasesInfo
+%{_bindir}/OpenPepXL
+%{_bindir}/OpenPepXLLF
+%{_bindir}/OpenSwathFileSplitter
+%{_bindir}/PSMFeatureExtractor
+%{_bindir}/PercolatorAdapter
+%{_bindir}/ProteomicsLFQ
+%{_bindir}/QualityControl
+%{_bindir}/RNADigestor
+%{_bindir}/RNAMassCalculator
+%{_bindir}/RNPxlSearch
+%{_bindir}/SiriusAdapter
+%{_bindir}/SpectraSTSearchAdapter
+%{_bindir}/StaticModification
+%{_bindir}/TICCalculator
+%{_bindir}/TargetedFileConverter
+%{_bindir}/TriqlerConverter
+%{_bindir}/XFDR
+%{_libdir}/lib*.so
 
 %files tools
+%if %{with gui}
+%{_bindir}/INIUpdater
+%{_bindir}/ImageCreator
+%endif
 %{_bindir}/FileFilter
 %{_bindir}/IDDecoyProbability
-%{_bindir}/IDEvaluatorGUI
 %{_bindir}/OpenMSInfo
 %{_bindir}/PhosphoScoring
-%{_bindir}/INIUpdater
 %{_bindir}/RNPxlXICFilter
 %{_bindir}/FuzzyDiff
 %{_bindir}/XMLValidator
 %{_bindir}/SemanticValidator
 %{_bindir}/CVInspector
 %{_bindir}/IDSplitter
-%{_bindir}/ConvertTSVToTraML 
-%{_bindir}/ConvertTraMLToTSV
 %{_bindir}/OpenSwathMzMLFileCacher
 %{_bindir}/FFEval
-%{_bindir}/IDEvaluator
 %{_bindir}/LabeledEval
-%{_bindir}/MapAlignmentEvaluation
 %{_bindir}/RTEvaluation
 %{_bindir}/TransformationEvaluation
 %{_bindir}/Digestor
@@ -522,11 +457,8 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags}
 %{_bindir}/IDExtractor
 %{_bindir}/IDMassAccuracy 
 %{_bindir}/SpecLibCreator
-%{_bindir}/RNPxl
 %{_bindir}/ERPairFinder
 %{_bindir}/MRMPairFinder
-%{_bindir}/FeatureFinderSuperHirn
-%{_bindir}/ImageCreator
 %{_bindir}/MassCalculator
 %{_bindir}/MSSimulator
 %{_bindir}/SvmTheoreticalSpectrumGeneratorTrainer
@@ -543,23 +475,24 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags}
 %{_bindir}/QCShrinker
 
 %files data
-%doc CHANGELOG AUTHORS README LICENSE
 %{_datadir}/OpenMS/
+%exclude %{_datadir}/OpenMS/examples
 
 %files tutorials
 %{_bindir}/Tutorial_*
+%{_datadir}/OpenMS/examples
 
 %files devel
-%doc CHANGELOG AUTHORS README LICENSE
 %{_includedir}/OpenMS/
+%dir %{_libdir}/cmake
+%{_libdir}/cmake/OpenMS
 
-%if %{suse_version} >= 1320
+%if %{with documentation}
 %files doc
-%doc CHANGELOG AUTHORS README LICENSE
 %{_datadir}/doc/OpenMS/
 %endif
 
-%if 0%{?with_pyOpenMS}
+%if %{with pyOpenMS}
 %files -n python-openms
 %license src/pyOpenMS/License.txt
 %{python_sitearch}/pyopenms/

.gitattributes

@@ -21,5 +21,3 @@
 *.xz filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
-## Specific LFS patterns
-TOPPView.xpm filter=lfs diff=lfs merge=lfs -text

0001-Fix-install-path-for-evergreen-headers.patch

@@ -0,0 +1,47 @@
+From f2ced768ed33ed0f54f6b60198e34f40da7f6bd6 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Stefan=20Br=C3=BCns?= <stefan.bruens@rwth-aachen.de>
+Date: Wed, 24 Aug 2022 02:41:38 +0200
+Subject: [PATCH] Fix install path for evergreen headers
+
+Also exclude demos from installation.
+
+Fixes #6314, #6315
+---
+ src/openms/thirdparty/evergreen/src/CMakeLists.txt | 14 ++++++++------
+ 1 file changed, 8 insertions(+), 6 deletions(-)
+
+diff --git a/src/openms/thirdparty/evergreen/src/CMakeLists.txt b/src/openms/thirdparty/evergreen/src/CMakeLists.txt
+index 52bc2f8..afd6453 100644
+--- a/src/openms/thirdparty/evergreen/src/CMakeLists.txt
++++ b/src/openms/thirdparty/evergreen/src/CMakeLists.txt
+@@ -39,7 +39,7 @@ cmake_minimum_required(VERSION 3.0 FATAL_ERROR)
+ add_library(Evergreen INTERFACE)
+ target_include_directories(Evergreen SYSTEM INTERFACE 
+                             "$<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}>"
+-                            "$<INSTALL_INTERFACE:${INSTALL_INCLUDE_DIR}/thirdparty/evergreen/src>")
++                            "$<INSTALL_INTERFACE:${INSTALL_INCLUDE_DIR}/OpenMS/evergreen>")
+ 
+ # Export it under OpenMSTargets.cmake instead of a separate EvergreenTargets file
+ #install(EXPORT EvergreenTargets DESTINATION lib/cmake/evergreen)
+@@ -48,11 +48,13 @@ target_include_directories(Evergreen SYSTEM INTERFACE
+ install_library(Evergreen)
+ openms_register_export_target(Evergreen)
+ 
+-get_filename_component(EVERGREEN_HEADERS "${CMAKE_CURRENT_LIST_FILE}" PATH)
+-get_filename_component(EVERGREEN_HEADERS "${EVERGREEN_HEADERS}" PATH)
++get_filename_component(EVERGREEN_HEADERS "${CMAKE_CURRENT_LIST_DIR}" PATH)
+ 
+ # Install headers
+-install_directory(${EVERGREEN_HEADERS} ${INSTALL_INCLUDE_DIR}/thirdparty thirdparty_headers)
+-
+-
++install(DIRECTORY ${EVERGREEN_HEADERS}
++        DESTINATION ${INSTALL_INCLUDE_DIR}/OpenMS/evergreen
++        COMPONENT thirdparty_headers
++        PATTERN demos EXCLUDE
++        PATTERN CMakeLists.txt EXCLUDE
++)
+ 
+-- 
+2.37.1
+

INIFileEditor.xpm

@@ -1,203 +0,0 @@
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-"32 32 165 2 ",
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OpenMS-2.0.1-sources.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:75aee1829941e9455849da4087b890b874abd649c9d2be2c673059f62fb65d57
-size 380969084

Release2.8.0.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c73f2e966246cafc9f1766db4c2df0d00b123e852e0c6e00630eb8189dd5ed9a
+size 228006843

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@@ -1,260 +0,0 @@
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-};

TOPPView.xpm

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:911d8288018e27037ef0e0b946668fbefda7db06c6ceb05cc796e123d48743c8
-size 6494

WildMagic5.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:cbdc9fa23880070b46b63764eb34795e25d099d2d06c259ad58c21d7bea45772
-size 567424

fix-compile-warnings.patch

@@ -0,0 +1,143 @@
+From 71ab0a79a6d43a8098322dfc11cb6ddb577687a4 Mon Sep 17 00:00:00 2001
+From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
+Date: Tue, 22 Feb 2022 07:22:14 +0000
+Subject: [PATCH 1/3] fix some compile warnings
+
+---
+ .../OpenMS/MATH/STATISTICS/StatisticFunctions.h       | 11 ++++-------
+ .../source/VISUAL/APPLICATIONS/TOPPViewBase.cpp       |  4 ++--
+ src/openms_gui/source/VISUAL/SpectraIDViewTab.cpp     |  8 ++++----
+ 3 files changed, 10 insertions(+), 13 deletions(-)
+
+diff --git a/src/openms/include/OpenMS/MATH/STATISTICS/StatisticFunctions.h b/src/openms/include/OpenMS/MATH/STATISTICS/StatisticFunctions.h
+index cac8c83c465..d0b116092a6 100644
+--- a/src/openms/include/OpenMS/MATH/STATISTICS/StatisticFunctions.h
++++ b/src/openms/include/OpenMS/MATH/STATISTICS/StatisticFunctions.h
+@@ -671,10 +671,7 @@ namespace OpenMS
+     template<typename T>
+     struct SummaryStatistics
+     {
+-      SummaryStatistics()
+-        :mean(0), variance(0), min(0), lowerq(0), median(0), upperq(0), max(0)
+-      {
+-      }
++      SummaryStatistics() = default;
+ 
+       // Ctor with data
+       SummaryStatistics(T& data)
+@@ -698,9 +695,9 @@ namespace OpenMS
+         }
+       }
+ 
+-      double mean, variance, lowerq, median, upperq;
+-      typename T::value_type min, max;
+-      size_t count;
++      double mean = 0, variance = 0 , lowerq = 0, median = 0, upperq = 0;
++      typename T::value_type min = 0, max = 0;
++      size_t count = 0;
+     };
+ 
+   }   // namespace Math
+diff --git a/src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp b/src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp
+index cb9ebae2612..41656c98863 100644
+--- a/src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp
++++ b/src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp
+@@ -1489,8 +1489,8 @@ namespace OpenMS
+     if (!ws_.currentSubWindow())
+     {
+       // TODO think about using lastActivatedSubwindow_
+-      const auto id = tab_bar_.currentIndex();
+-      if (id < (Size) ws_.subWindowList().size())
++      const int id = tab_bar_.currentIndex(); 
++      if (id < ws_.subWindowList().size())
+       {
+         return qobject_cast<PlotWidget*>(ws_.subWindowList()[id]->widget());
+       }
+diff --git a/src/openms_gui/source/VISUAL/SpectraIDViewTab.cpp b/src/openms_gui/source/VISUAL/SpectraIDViewTab.cpp
+index 4902e00e8bd..568fe1bc53d 100644
+--- a/src/openms_gui/source/VISUAL/SpectraIDViewTab.cpp
++++ b/src/openms_gui/source/VISUAL/SpectraIDViewTab.cpp
+@@ -251,6 +251,7 @@ namespace OpenMS
+         }
+       }
+     }
++    return {};
+   }
+ 
+   void SpectraIDViewTab::openUniProtSiteWithAccession_(const QString& accession)
+@@ -397,7 +398,7 @@ namespace OpenMS
+     if (table_widget_->selectionModel()->selectedRows().empty())
+     {
+       // deselect whatever is currently shown
+-      int last_spectrum_index = int(layer_->getCurrentSpectrumIndex());
++      layer_->getCurrentSpectrumIndex();
+       // Deselecting spectrum does not do what you think it does. It still paints stuff. Without annotations..
+       // so just leave it for now.
+       //
+@@ -1016,9 +1017,8 @@ namespace OpenMS
+     }
+   }
+ 
+-  void SpectraIDViewTab::updatedSingleProteinCell_(QTableWidgetItem* item)
+-  {
+-    
++  void SpectraIDViewTab::updatedSingleProteinCell_(QTableWidgetItem* /*item*/)
++  {    
+   }
+ 
+   // Upon changes in the table data (only possible by checking or unchecking a checkbox right now),
+
+From bd41ade6f196d625f76a6e3aaaee5222c0a1e5e8 Mon Sep 17 00:00:00 2001
+From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
+Date: Tue, 22 Feb 2022 08:13:29 +0000
+Subject: [PATCH 2/3] remove from header as well
+
+---
+ src/openms_gui/include/OpenMS/VISUAL/SpectraIDViewTab.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/openms_gui/include/OpenMS/VISUAL/SpectraIDViewTab.h b/src/openms_gui/include/OpenMS/VISUAL/SpectraIDViewTab.h
+index b0edfcea74d..4166878daa1 100644
+--- a/src/openms_gui/include/OpenMS/VISUAL/SpectraIDViewTab.h
++++ b/src/openms_gui/include/OpenMS/VISUAL/SpectraIDViewTab.h
+@@ -135,7 +135,7 @@ namespace OpenMS
+     void currentSpectraSelectionChanged_();
+ 
+     /// update ProteinHits, when data in the table changes (status of checkboxes)
+-    void updatedSingleProteinCell_(QTableWidgetItem* item);
++    void updatedSingleProteinCell_(QTableWidgetItem* /*item*/);
+     /// Protein Cell clicked in protein_table_widget; emits which protein (row) was clicked, and may show additional data
+     void proteinCellClicked_(int row, int column);
+   };
+
+From 4945e8860ff8729dc1bb2e2fd0704a82f8282af8 Mon Sep 17 00:00:00 2001
+From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
+Date: Tue, 22 Feb 2022 11:53:39 +0100
+Subject: [PATCH 3/3] Update TOPPViewBase.cpp
+
+---
+ .../source/VISUAL/APPLICATIONS/TOPPViewBase.cpp       | 11 +++++------
+ 1 file changed, 5 insertions(+), 6 deletions(-)
+
+diff --git a/src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp b/src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp
+index 41656c98863..25e40bcbd4a 100644
+--- a/src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp
++++ b/src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp
+@@ -1489,12 +1489,11 @@ namespace OpenMS
+     if (!ws_.currentSubWindow())
+     {
+       // TODO think about using lastActivatedSubwindow_
+-      const int id = tab_bar_.currentIndex(); 
+-      if (id < ws_.subWindowList().size())
+-      {
+-        return qobject_cast<PlotWidget*>(ws_.subWindowList()[id]->widget());
+-      }
+-      return nullptr;
++      const int id = tab_bar_.currentIndex();
++
++      if (id < 0 || id >= ws_.subWindowList().size()) return nullptr;
++      
++      return qobject_cast<PlotWidget*>(ws_.subWindowList()[id]->widget());
+     }
+     return qobject_cast<PlotWidget*>(ws_.currentSubWindow()->widget());
+   }

fix-isnan-undeclared.patch

@@ -0,0 +1,77 @@
+From 9264cfd89cd55dd58898f29b0ea83e1235e43490 Mon Sep 17 00:00:00 2001
+From: amit0617 <71893015+Amit0617@users.noreply.github.com>
+Date: Sat, 12 Mar 2022 22:20:50 +0530
+Subject: [PATCH 1/2] fix: 5864, isnan error
+
+---
+ src/openms/source/QC/MQEvidenceExporter.cpp | 10 +++++-----
+ 1 file changed, 5 insertions(+), 5 deletions(-)
+
+diff --git a/src/openms/source/QC/MQEvidenceExporter.cpp b/src/openms/source/QC/MQEvidenceExporter.cpp
+index f7a970908ec..6b85c71f6e3 100644
+--- a/src/openms/source/QC/MQEvidenceExporter.cpp
++++ b/src/openms/source/QC/MQEvidenceExporter.cpp
+@@ -41,10 +41,10 @@
+ #include <OpenMS/SYSTEM/File.h>
+ 
+ #include <QtCore/QDir>
+-#include <boost/math/special_functions/fpclassify.hpp> // isnan
++#include <cmath> // isnan
+ #include <fstream>
+ 
+-#include <boost/math/special_functions/fpclassify.hpp> // isnan
++#include <cmath> // isnan
+ #include <fstream>
+ 
+ using namespace OpenMS;
+@@ -315,7 +315,7 @@ void MQEvidence::exportRowFromFeature_(
+   const double& uncalibrated_mz_error_ppm = ptr_best_hit->getMetaValue("uncalibrated_mz_error_ppm", NAN);
+   const double& calibrated_mz_error_ppm = ptr_best_hit->getMetaValue("calibrated_mz_error_ppm", NAN);
+ 
+-  if (isnan(uncalibrated_mz_error_ppm) && isnan(calibrated_mz_error_ppm))
++  if (std::isnan(uncalibrated_mz_error_ppm) && std::isnan(calibrated_mz_error_ppm))
+   {
+     file_ << "NA" << "\t"; // Mass error [ppm]
+     file_ << "NA" << "\t"; // Uncalibrated Mass error [ppm]
+@@ -324,7 +324,7 @@ void MQEvidence::exportRowFromFeature_(
+     file_ << "NA" << "\t"; // Uncalibrated - Calibrated m/z [ppm]
+     file_ << "NA" << "\t"; // Uncalibrated - Calibrated m/z [mDa]
+   }
+-  else if (isnan(calibrated_mz_error_ppm))
++  else if (std::isnan(calibrated_mz_error_ppm))
+     {
+       file_ << "NA" << "\t"; // Mass error [ppm]
+       file_ << uncalibrated_mz_error_ppm << "\t"; // Uncalibrated Mass error [ppm]
+@@ -333,7 +333,7 @@ void MQEvidence::exportRowFromFeature_(
+       file_ << "NA" << "\t"; // Uncalibrated - Calibrated m/z [ppm]
+       file_ << "NA" << "\t"; // Uncalibrated - Calibrated m/z [mDa]
+     }
+-    else if (isnan(uncalibrated_mz_error_ppm))
++    else if (std::isnan(uncalibrated_mz_error_ppm))
+       {
+         file_ << calibrated_mz_error_ppm << "\t"; // Mass error [ppm]
+         file_ << "NA" << "\t"; // Uncalibrated Mass error [ppm]
+
+From 8bd42e7d799e4c1f8c0dfb1d79c60254384a17fd Mon Sep 17 00:00:00 2001
+From: AMIT KUMAR MISHRA <71893015+Amit0617@users.noreply.github.com>
+Date: Mon, 14 Mar 2022 12:45:00 +0530
+Subject: [PATCH 2/2] Update MQEvidenceExporter.cpp
+
+removed include duplicates
+---
+ src/openms/source/QC/MQEvidenceExporter.cpp | 2 --
+ 1 file changed, 2 deletions(-)
+
+diff --git a/src/openms/source/QC/MQEvidenceExporter.cpp b/src/openms/source/QC/MQEvidenceExporter.cpp
+index 6b85c71f6e3..c3889026409 100644
+--- a/src/openms/source/QC/MQEvidenceExporter.cpp
++++ b/src/openms/source/QC/MQEvidenceExporter.cpp
+@@ -44,8 +44,6 @@
+ #include <cmath> // isnan
+ #include <fstream>
+ 
+-#include <cmath> // isnan
+-#include <fstream>
+ 
+ using namespace OpenMS;
+ 

fix-libwm5core-linkage.patch

@@ -0,0 +1,27 @@
+From c6ae4a42311fc57e1bcb8b00b98b7289b90efb73 Mon Sep 17 00:00:00 2001
+From: StefanBruens <stefan.bruens@rwth-aachen.de>
+Date: Thu, 18 Aug 2022 05:19:07 +0200
+Subject: [PATCH] Correct libOpenMS linkage to libWm5Core
+
+The typo caused libOpenMS not being linked to libWm5Core, but only to
+libWm5Mathmatics (twice), causing linker failures later with
+`-Wl,--no-undefined`.
+
+Fixes #6301
+---
+ cmake/Modules/FindWM5.cmake | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/cmake/Modules/FindWM5.cmake b/cmake/Modules/FindWM5.cmake
+index 0b0a2455dd1..191b4ae27b5 100644
+--- a/cmake/Modules/FindWM5.cmake
++++ b/cmake/Modules/FindWM5.cmake
+@@ -134,7 +134,7 @@ if(WM5_FOUND)
+ 
+   if(NOT TARGET WM5::Core)
+     add_library(WM5::Core UNKNOWN IMPORTED) # TODO we could try to infer shared/static
+-    set_property(TARGET WM5::Core PROPERTY IMPORTED_LOCATION "${WM5_Wm5Mathematics_LIBRARY_RELEASE}")
++    set_property(TARGET WM5::Core PROPERTY IMPORTED_LOCATION "${WM5_Wm5Core_LIBRARY_RELEASE}")
+     set_property(TARGET WM5::Core PROPERTY IMPORTED_LOCATION_RELEASE "${WM5_Wm5Core_LIBRARY_RELEASE}")
+     set_property(TARGET WM5::Core PROPERTY IMPORTED_LOCATION_DEBUG "${WM5_Wm5Core_LIBRARY_DEBUG}")
+     set_property(TARGET WM5::Core PROPERTY INCLUDE_DIRECTORIES "${WM5_INCLUDE_DIR}")

inifileeditor.desktop

@@ -1,9 +0,0 @@
-[Desktop Entry]
-Name=INIFileEditor
-Categories=Science;Biology;Chemistry;
-Comment=An editor for OpenMS configuration files.
-Exec=env OPENMS_DATA_PATH=/usr/share/OpenMS INIFileEditor %U
-Icon=/usr/share/icons/TOPP/pixmaps/INIFileEditor.xpm
-Terminal=false
-Type=Application
-StartupNotify=true

openms-Selenocysteine.patch

@@ -1,26 +0,0 @@
---- share/OpenMS/CHEMISTRY/unimod.xml	2015-04-21 04:57:18.000000000 -0500
-+++ share/OpenMS/CHEMISTRY/unimod.xml	2015-09-12 13:02:40.267253395 -0500
-@@ -404,6 +404,8 @@
-                            spec_group="8"/>
-          <umod:specificity hidden="1" site="Y" position="Anywhere" classification="Artefact"
-                            spec_group="9"/>
-+         <umod:specificity hidden="0" site="U" position="Anywhere" classification="Chemical derivative"
-+                           spec_group="10"/>
-          <umod:delta mono_mass="57.021464" avge_mass="57.0513" composition="H(3) C(2) N O">
-             <umod:element symbol="H" number="3"/>
-             <umod:element symbol="C" number="2"/>
-@@ -24341,6 +24343,14 @@
-          <umod:element symbol="O" number="1"/>
-          <umod:element symbol="S" number="1"/>
-       </umod:aa>
-+      <umod:aa title="U" three_letter="Sec" full_name="Selenocysteine" mono_mass="150.953636"
-+               avge_mass="150.0388">
-+         <umod:element symbol="H" number="7"/>
-+         <umod:element symbol="C" number="3"/>
-+         <umod:element symbol="N" number="1"/>
-+         <umod:element symbol="O" number="2"/>
-+         <umod:element symbol="Se" number="1"/>
-+      </umod:aa>
-       <umod:aa title="E" three_letter="Glu" full_name="Glutamic acid" mono_mass="129.042593"
-                avge_mass="129.114">
-          <umod:element symbol="H" number="7"/>

openms-addlibs.patch

@@ -1,12 +0,0 @@
---- src/openms/CMakeLists.txt	2015-04-21 04:57:19.000000000 -0500
-+++ src/openms/CMakeLists.txt	2015-05-28 18:33:59.809851316 -0500
-@@ -87,7 +87,8 @@
-                           ${WM5_LIBRARIES}
-                           ${BZIP2_LIBRARIES}
-                           ${ZLIB_LIBRARIES}
--                          ${GLPK_LIBRARIES})
-+                          ${GLPK_LIBRARIES}
-+                          -lrt -lGL)
- 
- # xerces requires linking against CoreFoundation&CoreServices
- if(APPLE)

openms-fix-pyOpenMSbuild.patch

@@ -1,12 +0,0 @@
---- src/pyOpenMS/setup.py	2014-05-31 17:33:27.924655744 +0200
-+++ src/pyOpenMS/setup.orig.py	2013-11-13 15:35:16.000000000 +0100
-@@ -109,7 +109,7 @@
- if iswin:
-     extra_compile_args = ["/EHs", "/bigobj"]
- elif sys.platform == "linux2":
--    extra_link_args = ["-Wl,-s"]
-+    extra_link_args = [ ]
- elif sys.platform == "darwin":
-     # we need to manually link to the Qt Frameworks
-     extra_compile_args = ["-Qunused-arguments"]
-

openms-fix-python_tests.patch

@@ -1,37 +0,0 @@
---- src/pyOpenMS/tests/unittests/test.indexed.orig.mzML	2015-04-09 17:57:04.000000000 +0200
-+++ src/pyOpenMS/tests/unittests/test.indexed.mzML	2015-05-01 21:50:40.523915224 +0200
-@@ -28,7 +28,7 @@
- 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
- 		</software>
- 		<software id="so_dp_sp_0_pm_0" version="1.4.0" >
--			<cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard" />
-+			<cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" />
- 		</software>
- 		<software id="so_dp_sp_0_pm_1" version="1.11.0" >
- 			<cvParam cvRef="MS" accession="MS:1000757" name="FileFilter" />
-@@ -274,4 +274,4 @@
-   </indexList>
-   <indexListOffset>655460</indexListOffset>
- <fileChecksum>0</fileChecksum>
--</indexedmzML>
-\ No newline at end of file
-+</indexedmzML>
---- src/pyOpenMS/tests/unittests/test2.orig.mzML	2015-04-09 17:57:04.000000000 +0200
-+++ src/pyOpenMS/tests/unittests/test2.mzML	2015-05-01 21:49:41.658250791 +0200
-@@ -11,7 +11,7 @@
- 		<sourceFileList count="1">
- 			<sourceFile id="sf_ru_0" name="file://IBT-RABEAM/Data/andersm/B08-08318.RAW" location="">
- 				<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8050207fea87c7c97555c6bb83fa50312b24fbbe" />
--				<cvParam cvRef="MS" accession="MS:1000564" name="PSI mzData file" />
-+				<cvParam cvRef="MS" accession="MS:1000564" name="PSI mzData format" />
- 				<cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />
- 			</sourceFile>
- 		</sourceFileList>
-@@ -304,4 +304,4 @@
- 			</spectrum>
- 		</spectrumList>
- 	</run>
--</mzML>
-\ No newline at end of file
-+</mzML>
-

openms-remove_testflag.patch

@@ -1,12 +0,0 @@
---- src/tests/class_tests/openms/CMakeLists.orig.txt	2015-04-09 17:57:04.000000000 +0200
-+++ src/tests/class_tests/openms/CMakeLists.txt	2015-04-14 11:12:48.620239096 +0200
-@@ -65,7 +65,7 @@
- # disable optimization for tests for gcc like compilers
- if (CMAKE_COMPILER_IS_INTELCXX OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
-   set(_TMP_CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
--  set(CMAKE_CXX_FLAGS_RELEASE "-O0")
-+  set(CMAKE_CXX_FLAGS_RELEASE " ")
- endif()
- 
- #------------------------------------------------------------------------------
-

openms-revert_TOPP_PeakPickerWavelet_test.patch

@@ -1,14 +0,0 @@
---- src/tests/topp/CMakeLists.orig.txt	2015-04-09 17:57:04.000000000 +0200
-+++ src/tests/topp/CMakeLists.txt	2015-05-13 10:48:06.645814337 +0200
-@@ -983,8 +983,8 @@
- # 3bAxk01KjUAAAACgmVGNQIvf6JpEWo1Ah string, they will be ignore.
- # Note that this string occurs twice in the file.
- #
--add_test("TOPP_PeakPickerWavelet_3_out1" ${DIFF} -in1 PeakPickerWavelet_3.tmp -in2 ${DATA_DIR_TOPP}/PeakPickerWavelet_2Dopt_output.mzML -whitelist "3bAxk01KjUAAAACgmVGNQIvf6JpEWo1Ah")
--set_tests_properties("TOPP_PeakPickerWavelet_3_out1" PROPERTIES DEPENDS "TOPP_PeakPickerWavelet_3")
-+#add_test("TOPP_PeakPickerWavelet_3_out1" ${DIFF} -in1 PeakPickerWavelet_3.tmp -in2 ${DATA_DIR_TOPP}/PeakPickerWavelet_2Dopt_output.mzML -whitelist "3bAxk01KjUAAAACgmVGNQIvf6JpEWo1Ah")
-+#set_tests_properties("TOPP_PeakPickerWavelet_3_out1" PROPERTIES DEPENDS "TOPP_PeakPickerWavelet_3")
- add_test("TOPP_PeakPickerWavelet_4" ${TOPP_BIN_PATH}/PeakPickerWavelet  -test -ini ${DATA_DIR_TOPP}/PeakPickerWavelet_parameters.ini -in ${DATA_DIR_TOPP}/PeakPickerWavelet_input.mzML -out PeakPickerWavelet_4.tmp -threads 2)
- add_test("TOPP_PeakPickerWavelet_4_out1" ${DIFF} -in1 PeakPickerWavelet_4.tmp -in2 ${DATA_DIR_TOPP}/PeakPickerWavelet_output.mzML)
- set_tests_properties("TOPP_PeakPickerWavelet_4_out1" PROPERTIES DEPENDS "TOPP_PeakPickerWavelet_4")
-

openms-setuptools.patch

@@ -1,31 +0,0 @@
---- src/pyOpenMS/setup.orig.py	2013-11-13 15:35:16.000000000 +0100
-+++ src/pyOpenMS/setup.py	2014-06-19 14:14:54.653917304 +0200
-@@ -1,9 +1,6 @@
- # input-encoding: latin-1
- from __future__ import print_function
- 
--import distribute_setup
--distribute_setup.use_setuptools()
--
- # windows ?
- import sys
- iswin = sys.platform == "win32"
-@@ -25,6 +22,9 @@
- import glob
- import shutil
- 
-+# Import setuptools from system 
-+import setuptools 
-+
- j = os.path.join
- 
- src_pyopenms = j(OPEN_MS_SRC, "src/pyOpenMS")
-@@ -150,7 +150,7 @@
-     packages=["pyopenms"],
-     ext_package="pyopenms",
- 
--    version=version + "-" + timestamp,
-+    version="2.0",
- 
-     maintainer="Uwe Schmitt",
-     maintainer_email="uschmitt@mineway.de",

seqan-mini-1.4.1.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:f1b96b176166b48dc20f09b5eb07183ef1f27d26497393e5167d73120d870a45
-size 7059668