From db199decdcfdd34af92b7245cfb6ce095555dfda Mon Sep 17 00:00:00 2001 From: Silvan Calarco Date: Fri, 5 Jan 2024 20:43:00 +0100 Subject: [PATCH] update to 1.2.0 [release 1.2.0-1mamba;Sat May 16 2020] --- avogadro-1.2.0-eigen2.patch | 20 ++++ avogadro-1.2.0-glibc-2.23.patch | 18 +++ avogadro-1.2.0-libmsym-add-link-library.patch | 10 ++ avogadro-1.2.0-libopenbabel2-2.4.1.patch | 22 ++++ avogadro-1.2.0-libopenbabel2.patch | 14 +++ avogadro.spec | 108 ++++++++++++------ 6 files changed, 155 insertions(+), 37 deletions(-) create mode 100644 avogadro-1.2.0-eigen2.patch create mode 100644 avogadro-1.2.0-glibc-2.23.patch create mode 100644 avogadro-1.2.0-libmsym-add-link-library.patch create mode 100644 avogadro-1.2.0-libopenbabel2-2.4.1.patch create mode 100644 avogadro-1.2.0-libopenbabel2.patch diff --git a/avogadro-1.2.0-eigen2.patch b/avogadro-1.2.0-eigen2.patch new file mode 100644 index 0000000..dc68918 --- /dev/null +++ b/avogadro-1.2.0-eigen2.patch @@ -0,0 +1,20 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 1cbeb8f..e1e40d6 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -231,14 +231,7 @@ if(NOT Linguist_FOUND) + message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations") + endif() + +-find_package(Eigen3) # find and setup Eigen3 if available +-if(NOT EIGEN3_FOUND) +- message(STATUS "Cannot find Eigen3, trying Eigen2") +- find_package(Eigen2 REQUIRED) # Some version is required +-else() +-# Use Stage10 Eigen3 support +- set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE) +-endif() ++find_package(Eigen2 REQUIRED) + + find_package(ZLIB REQUIRED) + find_package(OpenBabel2 REQUIRED) # find and setup OpenBabel diff --git a/avogadro-1.2.0-glibc-2.23.patch b/avogadro-1.2.0-glibc-2.23.patch new file mode 100644 index 0000000..44506dc --- /dev/null +++ b/avogadro-1.2.0-glibc-2.23.patch @@ -0,0 +1,18 @@ +--- avogadro-1.2.0/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c.orig 2016-06-16 06:36:58.888214167 +0000 ++++ avogadro-1.2.0/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c 2016-06-16 06:37:19.091459100 +0000 +@@ -67,13 +67,13 @@ + } + case 2 : { + //o->v = dpolynomial[m+l]; +- char *d = (signbit(m) == 1 ? "-" : "+"); ++ char *d = (signbit(m*1.0) == 1 ? "-" : "+"); + snprintf(o->name, sizeof(o->name), "%dd%d%s",n,abs(m),d); + break; + } + default : { + char t = 'f' - 3 + l; +- char *d = (signbit(m) == 1 ? "-" : "+"); ++ char *d = (signbit(m*1.0) == 1 ? "-" : "+"); + snprintf(o->name, sizeof(o->name), "%d%c%d%s",n,t,abs(m),d); + } + } diff --git a/avogadro-1.2.0-libmsym-add-link-library.patch b/avogadro-1.2.0-libmsym-add-link-library.patch new file mode 100644 index 0000000..645f6a9 --- /dev/null +++ b/avogadro-1.2.0-libmsym-add-link-library.patch @@ -0,0 +1,10 @@ +--- avogadro-1.2.0/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt.orig 2020-05-16 15:58:24.829000000 +0200 ++++ avogadro-1.2.0/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt 2020-05-16 15:59:08.768000000 +0200 +@@ -28,6 +28,7 @@ + + file (GLOB source src/*.c) + add_library (msym ${source}) ++target_link_libraries(msym m) + if (BUILD_SHARED_LIBS) + set_target_properties (msym PROPERTIES + POSITION_INDEPENDENT_CODE "TRUE") diff --git a/avogadro-1.2.0-libopenbabel2-2.4.1.patch b/avogadro-1.2.0-libopenbabel2-2.4.1.patch new file mode 100644 index 0000000..05ee84c --- /dev/null +++ b/avogadro-1.2.0-libopenbabel2-2.4.1.patch @@ -0,0 +1,22 @@ +--- avogadro-1.2.0/cmake/modules/FindOpenBabel2.cmake.orig 2020-05-16 14:57:50.268000000 +0200 ++++ avogadro-1.2.0/cmake/modules/FindOpenBabel2.cmake 2020-05-16 14:57:56.301000000 +0200 +@@ -48,7 +48,7 @@ + endif(NOT OPENBABEL2_INCLUDE_DIR) + endif() + +- find_library(OPENBABEL2_LIBRARIES NAMES openbabel openbabel-2 ++ find_library(OPENBABEL2_LIBRARIES NAMES openbabel-2 + PATHS + ${_obLinkDir} + ${GNUWIN32_DIR}/lib +--- avogadro-1.2.0/avogadro.prf.in.orig 2020-05-16 15:16:17.226000000 +0200 ++++ avogadro-1.2.0/avogadro.prf.in 2020-05-16 15:16:23.884000000 +0200 +@@ -5,7 +5,7 @@ + "@OPENBABEL2_INCLUDE_DIR@ \ + "@EIGEN2_INCLUDE_DIR@" + LIBS += -L"$$AVOGADRO_PREFIX/lib" -lavogadro \ +- -L"$$OPENBABEL_PREFIX/lib" -lopenbabel ++ -L"$$OPENBABEL_PREFIX/lib" -lopenbabel-2 + + unix { + manifest_.target = $$eval(TARGET).mf diff --git a/avogadro-1.2.0-libopenbabel2.patch b/avogadro-1.2.0-libopenbabel2.patch new file mode 100644 index 0000000..c819b08 --- /dev/null +++ b/avogadro-1.2.0-libopenbabel2.patch @@ -0,0 +1,14 @@ +diff -up avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt.openbabel avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt +--- avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt.openbabel 2013-12-06 09:50:04.000000000 -0600 ++++ avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt 2016-01-25 13:50:10.469758655 -0600 +@@ -20,8 +20,8 @@ if (WIN32) + set_target_properties(python-module PROPERTIES SUFFIX ".pyd") + target_link_libraries(python-module avogadro ${PYTHON_LIBRARIES}) + else() +- target_link_libraries(python-module stdc++ avogadro +- ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${Boost_LIBRARIES}) ++ target_link_libraries(python-module stdc++ avogadro ++ ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${OPENBABEL2_LIBRARIES} ${Boost_LIBRARIES}) + endif() + + # Let's try to use this instead: diff --git a/avogadro.spec b/avogadro.spec index 8af57d0..116550a 100644 --- a/avogadro.spec +++ b/avogadro.spec @@ -1,14 +1,20 @@ Name: avogadro -Version: 1.1.1 +Version: 1.2.0 Release: 1mamba Summary: An advanced molecule editor and visualizer Group: Graphical Desktop/Applications/Scientific Vendor: openmamba Distribution: openmamba Packager: Davide Madrisan -URL: http://avogadro.openmolecules.net -Source: http://downloads.sourceforge.net/project/%{name}/%{name}/%{version}/%{name}-%{version}.tar.gz +URL: http://avogadro.cc +Source: https://github.com/cryos/avogadro.git/%{version}/avogadro-%{version}.tar.bz2 +#Source: http://downloads.sourceforge.net/project/%{name}/%{name}/%{version}/%{name}-%{version}.tar.gz Patch0: avogadro-1.1.1-boost-1.5.5.patch +Patch1: avogadro-1.2.0-eigen2.patch +Patch2: avogadro-1.2.0-glibc-2.23.patch +Patch3: avogadro-1.2.0-libopenbabel2.patch +Patch4: avogadro-1.2.0-libopenbabel2-2.4.1.patch +Patch5: avogadro-1.2.0-libmsym-add-link-library.patch License: GPL ## AUTOBUILDREQ-BEGIN BuildRequires: glibc-devel @@ -25,9 +31,9 @@ BuildRequires: libpython27-devel BuildRequires: libqt4-devel BuildRequires: libstdc++6-devel BuildRequires: libz-devel -BuildRequires: openbabel-devel BuildRequires: python-boost-devel ## AUTOBUILDREQ-END +BuildRequires: libopenbabel2-devel BuildRequires: python-sip-devel BuildRequires: libeigen2-devel BuildRequires: eigen3-devel @@ -39,37 +45,51 @@ BuildRoot: %{_tmppath}/%{name}-%{version}-root Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. -%package devel -Summary: Development files for %{name} -Group: Development/Libraries -Requires: %{name} = %{?epoch:%epoch:}%{version}-%{release} - -%description devel -%{summary}. - -%package -n libavogadro +%package -n lib%{name} Summary: Runtime files for %{name} Group: System/Libraries -%description -n libavogadro +%description -n lib%{name} %{summary}. +%package -n lib%{name}-devel +Summary: Development files for %{name} +Group: Development/Libraries +Requires: %{name} = %{?epoch:%epoch:}%{version}-%{release} +Requires: lib%{name} = %{?epoch:%epoch:}%{version}-%{release} +Provides: avogadro-devel +Obsoletes: avogadro-devel + +%description -n lib%{name}-devel +%{summary}. + + +%debug_package + %prep %setup -q %patch0 -p1 +%patch1 -p1 +%patch2 -p1 +%patch3 -p1 +%patch4 -p1 +%patch5 -p1 + ## use working version included in cmake #rm -f cmake/modules/FindPythonLibs.cmake %build %cmake -d build \ - -DENABLE_GLSL:BOOL=ON \ -DENABLE_PYTHON:BOOL=ON \ -DEIGEN2_INCLUDE_DIR=%{_includedir}/eigen2 \ - -DEIGEN3_INCLUDE_DIR=%{_includedir}/eigen3 - + -DEIGEN3_INCLUDE_DIR=%{_includedir}/eigen3 \ + -Dpkgcfg_lib_OPENBABEL2_openbabel=%{_libdir}/libopenbabel-2.so \ + -DSIP_INCLUDE_DIR=%{_includedir}/python%{python_version} + +# -DENABLE_GLSL:BOOL=ON \ + # -DPYTHON_LIBRARY:FILEPATH=%{_libdir}/libpython%{python_version}.so \ # -DPYTHON_INCLUDE_DIR:PATH=%{_includedir}/python%{python_version} \ -# -DSIP_INCLUDE_DIR=%{_includedir}/python%{python_version} %make @@ -81,16 +101,22 @@ install -d %{buildroot}%{_qt4_prefix}/mkspecs/features mv %{buildroot}%{_prefix}/features/avogadro.prf \ %{buildroot}%{_qt4_prefix}/mkspecs/features/avogadro.prf +%ifarch x86_64 +mv %{buildroot}%{_prefix}/lib/cmake %{buildroot}%{_libdir} +mv %{buildroot}%{_prefix}/lib/libmsym.so %{buildroot}%{_libdir} +%endif + %clean [ "%{buildroot}" != / ] && rm -rf "%{buildroot}" -%post -n libavogadro -p /sbin/ldconfig -%postun -n libavogadro -p /sbin/ldconfig +%post -n lib%{name} -p /sbin/ldconfig +%postun -n lib%{name} -p /sbin/ldconfig %files %defattr(-,root,root) %{_bindir}/avogadro %{_bindir}/avopkg +%{_bindir}/qube %{_datadir}/applications/avogadro.desktop %dir %{_datadir}/avogadro/builder %{_datadir}/avogadro/builder/* @@ -103,8 +129,26 @@ mv %{buildroot}%{_prefix}/features/avogadro.prf \ %{_mandir}/man1/avogadro.* %{_mandir}/man1/avopkg.* -%files devel +%files -n lib%{name} %defattr(-,root,root,-) +%{_datadir}/avogadro/i18n/libavogadro*.qm +#%dir %{_datadir}/libavogadro +#%{_datadir}/libavogadro/* +%{_libdir}/libavogadro.so.* +%{_libdir}/libavogadro_OpenQube.so.* +%{_libdir}/libmsym.so +%dir %{_libdir}/avogadro +%{_libdir}/avogadro/*/colors/ +%{_libdir}/avogadro/*/extensions/ +%{_libdir}/avogadro/*/engines/ +%{_libdir}/avogadro/*/tools/ +#%{python_sitearch}/Avogadro.so +%doc AUTHORS COPYING + +%files -n lib%{name}-devel +%defattr(-,root,root,-) +%dir %{_includedir}/libmsym +%{_includedir}/libmsym/*.h %dir %{_includedir}/avogadro/ %{_includedir}/avogadro/* %{_libdir}/libavogadro.so @@ -114,24 +158,14 @@ mv %{buildroot}%{_prefix}/features/avogadro.prf \ %{_libdir}/avogadro/*/cmake/ %{_libdir}/pkgconfig/avogadro.pc %{_qt4_prefix}/mkspecs/features/avogadro.prf -%doc ChangeLog README - -%files -n libavogadro -%defattr(-,root,root,-) -%{_datadir}/avogadro/i18n/libavogadro*.qm -%dir %{_datadir}/libavogadro -%{_datadir}/libavogadro/* -%{_libdir}/libavogadro.so.* -%{_libdir}/libavogadro_OpenQube.so.* -%dir %{_libdir}/avogadro -%{_libdir}/avogadro/*/colors/ -%{_libdir}/avogadro/*/extensions/ -%{_libdir}/avogadro/*/engines/ -%{_libdir}/avogadro/*/tools/ -%{python_sitearch}/Avogadro.so -#%doc AUTHORS COPYING +%dir %{_libdir}/cmake/libmsym +%{_libdir}/cmake/libmsym/*.cmake +%doc README %changelog +* Sat May 16 2020 Silvan Calarco 1.2.0-1mamba +- update to 1.2.0 + * Sat Jun 14 2014 Silvan Calarco 1.1.1-1mamba - update to 1.1.1