Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package avogadrolibs for openSUSE:Factory checked in at 2021-09-01 21:36:57 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/avogadrolibs (Old) and /work/SRC/openSUSE:Factory/.avogadrolibs.new.1899 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "avogadrolibs" Wed Sep 1 21:36:57 2021 rev:4 rq:915098 version:1.95.0 Changes: -------- --- /work/SRC/openSUSE:Factory/avogadrolibs/avogadrolibs.changes 2018-06-04 13:23:22.510763740 +0200 +++ /work/SRC/openSUSE:Factory/.avogadrolibs.new.1899/avogadrolibs.changes 2021-09-01 21:37:12.612879006 +0200 @@ -1,0 +2,72 @@ +Mon Aug 30 09:00:55 UTC 2021 - Ferdinand Thiessen <r...@fthiessen.de> + +- Update to version 1.95.0 + * Update render options for Wireframe and Ball-and-Sticks + * Use MMTF downloads - more efficient than PDB format + * Add back support for importing crystals + * Add CJSON support for save/load residues and atom colors + * Detect secondary structure from residues / backbones + * Remove dependency on MoleQueue (bundled...) + * Export to SVG + * OpenMM script builder plugin + * Allow manipulate to rotate selected fragments + * Add bestFitPlane on Molecule + * Transparent support for ASE "extended XYZ" files + * Switch Open Babel calls to use CML and non-local numeric format + * Save background color across sessions and set bg alpha for export + * Add support for a JSON list of selected atoms + * Update example Avogadro RPC script + * Fix several crashes with proteins + * Fix crash in CJSON reading file without labels + * Fix bug deleting selected atoms +- Add molecules and crystals data files as source, as downloading + on build time is not possible on OBS +- Drop upstream merged avogadrolibs-spglib-includes.patch +- Split data molecules and crystals data into avogadro2-data package + and seperated plugins into plugins subpackage + +------------------------------------------------------------------- +Sat Aug 21 11:32:55 UTC 2021 - Dirk Stoecker <opens...@dstoecker.de> + +- Move non-library stuff into it's own package again + +------------------------------------------------------------------- +Wed Aug 18 12:05:15 UTC 2021 - Atri Bhattacharya <badshah...@gmail.com> + +- Add avogadrolibs-spglib-includes.patch -- Correct spglib + includes according to the location spglib headers are installed + to on openSUSE, which is directly inside %%_includedir. + +------------------------------------------------------------------- +Wed Aug 18 06:36:23 UTC 2021 - Ferdinand Thiessen <r...@fthiessen.de> + +- As Factory switched from Avagadro 1 to 2, make factory bot happy + as patches Fix-build-with-Qt-511.patch, fix-linking-issues.patch, + fix-gcc-version-check.patch, 0002-create-soversion-libs.patch, + and use-system-libjsoncpp.patch from old package are not present + in this package. + +------------------------------------------------------------------- +Wed May 26 09:49:41 UTC 2021 - Ferdinand Thiessen <r...@fthiessen.de> + +- Update to version 1.93.1 + * Add support for a JSON list of selected atoms + * Add support for only clearing selected atoms + * Fix invalid cmake files + * Fix build with HDF5 >= 1.12.0 + * Fix problems with large molecule + * Update translations +- Enable building with MoleQueue, mmtf and libmsym they are already + in Factory and science repository +- Split python into seperate package +- Add not-install-gwavi.patch +- Drop upstream fixed fix_libgwavi_linking.patch + +------------------------------------------------------------------- +Wed Feb 12 20:45:21 UTC 2020 - Stefan Br??ns <stefan.bru...@rwth-aachen.de> + +- initial version of Avogadro 2 libs +- Fix linking when using BUILD_STATIC_PLUGINS=OFF + fix_libgwavi_linking.patch + +------------------------------------------------------------------- @@ -36 +107,0 @@ - @@ -41 +111,0 @@ - Old: ---- 0002-create-soversion-libs.patch Fix-build-with-Qt-511.patch avogadrolibs-0.9.0.tar.gz fix-gcc-version-check.patch fix-linking-issues.patch use-system-libjsoncpp.patch New: ---- avogadrolibs-1.95.0.tar.gz crystals-c3e2468fa42360499f0e73d215bddfe2245258aa.tar.gz molecules-b1e16c5dc6d15e72d30dd6c4fca31b2c12025efc.tar.gz not-install-gwavi.patch ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ avogadrolibs.spec ++++++ --- /var/tmp/diff_new_pack.wA8yN0/_old 2021-09-01 21:37:14.728881552 +0200 +++ /var/tmp/diff_new_pack.wA8yN0/_new 2021-09-01 21:37:14.732881557 +0200 @@ -1,7 +1,7 @@ # # spec file for package avogadrolibs # -# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany. +# Copyright (c) 2021 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -12,124 +12,190 @@ # license that conforms to the Open Source Definition (Version 1.9) # published by the Open Source Initiative. -# Please submit bugfixes or comments via http://bugs.opensuse.org/ +# Please submit bugfixes or comments via https://bugs.opensuse.org/ # +%if 0%{suse_version} >= 1550 +%bcond_without spglib +%bcond_without python +%else +%bcond_with spglib +%bcond_with python +%endif + +# Requires genXrdPattern +%bcond_with vtk + +%define sonum 1 +%define libname libAvogadro%{sonum} +%define molecules_rev b1e16c5dc6d15e72d30dd6c4fca31b2c12025efc +%define crystals_rev c3e2468fa42360499f0e73d215bddfe2245258aa Name: avogadrolibs -Version: 0.9.0 +Version: 1.95.0 Release: 0 -Summary: Molecular simulation and visualization environment -# License note: There are GPL plugins in the source, but they are neither built nor installed by the package +Summary: Avogadro libraries for computational chemistry License: BSD-3-Clause -Group: Productivity/Scientific/Other -URL: http://www.openchemistry.org/projects/avogadro2 -Source: https://sourceforge.net/projects/avogadro/files/avogadro2/%{version}/%{name}-%{version}.tar.gz -#PATCH-FIX-OPENSUSE -- 0002-create-soversion-libs.patch tittiatc...@gmail.com -- Make the libs versioned -Patch0: 0002-create-soversion-libs.patch -#PATCH-FIX-OPENSUSE -- fix-linking-issues.patch tittiatc...@gmail.com -- Ensure that the qtplugins are linked properly -Patch1: fix-linking-issues.patch -#PATCH-FIX-OPENSUSE -- use-system-libjsoncpp.patch tittiatc...@gmail.com -- Use the system libjsoncpp -Patch2: use-system-libjsoncpp.patch -#PATCH-FIX-UPSTREAM fix-gcc-version-check.patch -Patch3: fix-gcc-version-check.patch -# PATCH-FIX-UPSTREAM -- Fix-build-with-Qt-511.patch -Patch4: Fix-build-with-Qt-511.patch -BuildRequires: cmake +Url: https://two.avogadro.cc/ +Source0: https://github.com/OpenChemistry/avogadrolibs/archive/%{version}.tar.gz#/%{name}-%{version}.tar.gz +Source1: https://github.com/OpenChemistry/molecules/archive/%{molecules_rev}.tar.gz#/molecules-%{molecules_rev}.tar.gz +Source2: https://github.com/OpenChemistry/crystals/archive/%{crystals_rev}.tar.gz#/crystals-%{crystals_rev}.tar.gz +# PATCH-FIX-UPSTREAM not-install-gwavi.patch -- Library only used locally so no need to install this helper +Patch0: not-install-gwavi.patch +BuildRequires: cmake >= 3.3 BuildRequires: eigen3-devel BuildRequires: fdupes -BuildRequires: freetype2-devel BuildRequires: gcc-c++ -BuildRequires: glew-devel -BuildRequires: glu-devel -BuildRequires: jsoncpp-devel -BuildRequires: libSM-devel -BuildRequires: libXt-devel -BuildRequires: pkgconfig -BuildRequires: python-devel -BuildRequires: pkgconfig(Qt5Concurrent) -BuildRequires: pkgconfig(Qt5Network) -BuildRequires: pkgconfig(Qt5OpenGL) -BuildRequires: pkgconfig(Qt5Widgets) +BuildRequires: hdf5-devel +BuildRequires: libqt5-linguist-devel +BuildRequires: mmtf-cpp-devel +BuildRequires: cmake(Qt5Concurrent) +BuildRequires: cmake(Qt5Network) +BuildRequires: cmake(Qt5Svg) +BuildRequires: cmake(Qt5Widgets) +BuildRequires: cmake(libmsym) +BuildRequires: pkgconfig(gl) +BuildRequires: pkgconfig(glew) +BuildRequires: pkgconfig(libarchive) +BuildRequires: pkgconfig(zlib) +%if %{with python} +BuildRequires: python3-devel +BuildRequires: python3-pybind11-devel +%endif +%if %{with spglib} +BuildRequires: spglib-devel +%endif +%if 0%{?suse_version} <= 1500 +BuildRequires: pkgconfig(glu) +%endif +%if %{with vtk} +BuildRequires: genXrdPattern +BuildRequires: cmake(vtk) +%endif %description -In order to tackle molecular simulation and visualization challenges in key areas of materials -science, chemistry and biology it is necessary to move beyond fixed software applications. The -Avogadro project is in the final stages of an ambitious rewrite of its core data structures, -algorithms and visualization capabilities. The project began as a grass roots effort to address -deficiencies observed by many of the early contributors in existing commercial and open source -solutions. Avogadro is now a robust, flexible solution that can tie in to and harness the power of -VTK for additional analysis and visualization capabilities. - -%package -n libavogadrolibs-suse0 -Summary: Main libraries for Avogadro -Group: System/Libraries -Requires: %{name} - -%description -n libavogadrolibs-suse0 -This package contains the main Avogadros libraries. +Avogadro libraries provide 3D rendering, visualization, analysis +and data processing useful in computational chemistry, molecular +modeling, bioinformatics, materials science, and related areas. + +%package -n %{libname} +Summary: Avogadro libraries for computational chemistry +Recommends: avogadro2-data >= %{version} +Recommends: %{name}-plugins >= %{version} + +%description -n %{libname} +Avogadro libraries provide 3D rendering, visualization, analysis +and data processing useful in computational chemistry, molecular +modeling, bioinformatics, materials science, and related areas. + +%package plugins +Summary: Plugins for Avogadro2libs + +%description plugins +This package contains the vendor provided plugins for Avogadro2 + +%package -n avogadro2-data +Summary: Data files for Avogadro2 and Avogadro2libs +BuildArch: noarch + +%description -n avogadro2-data +This package contains: + * Crystallographic files of common materials, elements, oxides, for visualization in Avogadro. + * Common molecule fragments for visualization in Avogadro %package devel -Summary: Development files for Avogadro -Group: Development/Libraries/C and C++ -Requires: libavogadrolibs-suse0 = %{version} +Summary: Header files for Avogadro libraries +Requires: %{libname} = %{version} +Requires: %{name}-plugins = %{version} +Requires: cmake(MoleQueue) +Requires: cmake(Qt5Network) +Requires: cmake(Qt5Widgets) +Requires: pkgconfig(gl) +Requires: pkgconfig(glew) +%if 0%{?suse_version} <= 1500 +Requires: pkgconfig(glu) +%endif %description devel -This package contains files to develop applications using -Avogadros libraries. +Header files for Avogadro libraries. -%prep -%autosetup -p1 +%if %{with python} +%package -n python3-avogadro +Summary: Python bindings for Avogadro libraries + +%description -n python3-avogadro +Avogadro libraries provide 3D rendering, visualization, analysis +and data processing useful in computational chemistry, molecular +modeling, bioinformatics, materials science, and related areas. +%endif -# Remove unnecessary bits -# This file is part of the standard cmake install -rm cmake/GenerateExportHeader.cmake -# No longer needed when building against system libjsoncpp -rm -rf thirdparty/jsoncpp -rm thirdparty/CMakeLists.txt +%prep +%setup -q -b 1 -b 2 +%autopatch -p1 +[ -e ../crystals ] && rm -rfv ../crystals; mv ../crystals-%{crystals_rev} ../crystals +[ -e ../molecules ] && rm -rfv ../molecules; mv ../molecules-%{molecules_rev} ../molecules %build -mkdir -p build -pushd build -# FIXME: you should use %%cmake macros -cmake ../ -DCMAKE_INSTALL_PREFIX=%{_prefix} -DCMAKE_SKIP_RPATH=YES -DBUILD_GPL_PLUGINS=OFF \ - -DCMAKE_C_FLAGS="%{optflags} -DNDEBUG" \ - -DCMAKE_CXX_FLAGS="%{optflags} -DNDEBUG" \ - -DCMAKE_EXE_LINKER_FLAGS="-Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions" \ - -DCMAKE_MODULE_LINKER_FLAGS="-Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions" \ - -DCMAKE_SHARED_LINKER_FLAGS="-Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions" \ - -DCMAKE_VERBOSE_MAKEFILE=ON \ - -DINSTALL_DOC_DIR=%{_defaultdocdir} \ - -DBUILD_STATIC_PLUGINS=OFF -DUSE_QT=ON -DUSE_OPENGL=ON -DUSE_MOLEQUEUE=OFF -popd - -pushd build -make %{?_smp_mflags} -popd +%cmake \ +%if (0%{?sle_version} && 0%{?sle_version} <= 150200) + -DINSTALL_LIBRARY_DIR:PATH=%{_lib} \ +%endif + -DINSTALL_DOC_DIR:PATH=%{_defaultdocdir} \ + -DBUILD_STATIC_PLUGINS:BOOL=OFF \ + -DENABLE_TRANSLATIONS:BOOL=ON \ + -DUSE_MOLEQUEUE:BOOL=ON \ + -DUSE_LIBMSYM:BOOL=ON \ + -DUSE_MMTF:BOOL=ON \ + -DUSE_HDF5:BOOL=ON \ + -DUSE_QT:BOOL=ON \ + -DUSE_VTK:BOOL=%{?with_vtk:ON}%{!?with_vtk:OFF} \ + -DUSE_PYTHON:BOOL=%{?with_python:ON}%{!?with_python:OFF} \ + -DUSE_SPGLIB:BOOL=%{?with_spglib:ON}%{!?with_spglib:OFF} \ + %{nil} +%make_build %install -pushd build -%make_install -popd -%fdupes %{buildroot} - -%post -n libavogadrolibs-suse0 -p /sbin/ldconfig -%postun -n libavogadrolibs-suse0 -p /sbin/ldconfig - -%files -%doc %{_defaultdocdir}/%{name} -%license COPYING -%doc README.md -%{_libdir}/avogadro2/ - -%files -n libavogadrolibs-suse0 -%license COPYING -%{_libdir}/libAvogadro*.so.suse0* +%cmake_install +rm %{buildroot}%{_defaultdocdir}/avogadrolibs/LICENSE +%fdupes %{buildroot}%{_datadir} + +%if %{with python} +# Fixup install location +mkdir -p %{buildroot}%{python3_sitearch} +mv %{buildroot}%{_libdir}/avogadro %{buildroot}%{python3_sitearch}/avogadro +%endif + +sed -i -e '1 s@^@#!/usr/bin/python3\n@' \ + %{buildroot}%{_libdir}/avogadro2/scripts/commands/scale.py \ + %{buildroot}%{_libdir}/avogadro2/scripts/formatScripts/zyx.py + +%post -n %{libname} -p /sbin/ldconfig + +%postun -n %{libname} -p /sbin/ldconfig + +%files -n %{libname} +%license LICENSE +%{_libdir}/libAvogadro*.so.%{sonum}* + +%files plugins +%dir %{_libdir}/avogadro2 +%{_libdir}/avogadro2/{plugins,scripts} %files devel -%license COPYING +%dir %{_defaultdocdir}/avogadrolibs +%doc %{_defaultdocdir}/avogadrolibs/*.md %{_includedir}/avogadro/ -%{_libdir}/cmake/avogadrolibs/ %{_libdir}/libAvogadro*.so +%{_libdir}/cmake/* + +%files -n avogadro2-data +%dir %{_datadir}/avogadro2 +%{_datadir}/avogadro2/crystals +%{_datadir}/avogadro2/molecules + +%if %{with python} +%files -n python3-avogadro +%{python3_sitearch}/avogadro +%endif %changelog ++++++ avogadrolibs-0.9.0.tar.gz -> avogadrolibs-1.95.0.tar.gz ++++++ /work/SRC/openSUSE:Factory/avogadrolibs/avogadrolibs-0.9.0.tar.gz /work/SRC/openSUSE:Factory/.avogadrolibs.new.1899/avogadrolibs-1.95.0.tar.gz differ: char 5, line 1 ++++++ not-install-gwavi.patch ++++++ diff -Nur avogadrolibs-1.93.1/thirdparty/libgwavi/CMakeLists.txt new/thirdparty/libgwavi/CMakeLists.txt --- avogadrolibs-1.93.1/thirdparty/libgwavi/CMakeLists.txt 2021-02-18 17:15:04.000000000 +0100 +++ new/thirdparty/libgwavi/CMakeLists.txt 2021-05-26 16:22:06.235022443 +0200 @@ -1,8 +1,9 @@ add_library(gwavi STATIC gwavi.c fileio.c avi-utils.c) set_target_properties(gwavi PROPERTIES POSITION_INDEPENDENT_CODE TRUE) -install(TARGETS gwavi - EXPORT "AvogadroLibsTargets" - RUNTIME DESTINATION "${INSTALL_RUNTIME_DIR}/avogadro2" - LIBRARY DESTINATION "${INSTALL_LIBRARY_DIR}/avogadro2" - ARCHIVE DESTINATION "${INSTALL_ARCHIVE_DIR}/avogadro2") +# linked static, not used in headers, no need to install it +#install(TARGETS gwavi +# EXPORT "AvogadroLibsTargets" +# RUNTIME DESTINATION "${INSTALL_RUNTIME_DIR}/avogadro2" +# LIBRARY DESTINATION "${INSTALL_LIBRARY_DIR}/avogadro2" +# ARCHIVE DESTINATION "${INSTALL_ARCHIVE_DIR}/avogadro2")
