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update to 1.2.0 [release 1.2.0-1mamba;Sat May 16 2020]

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This commit is contained in:
Silvan Calarco 2024-01-05 20:43:00 +01:00
parent 641cb815a5
commit db199decdc
6 changed files with 155 additions and 37 deletions
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20
avogadro-1.2.0-eigen2.patch Normal file
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@ -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

18
avogadro-1.2.0-glibc-2.23.patch Normal file
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@ -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);
}
}

10
avogadro-1.2.0-libmsym-add-link-library.patch Normal file
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@ -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")

22
avogadro-1.2.0-libopenbabel2-2.4.1.patch Normal file
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@ -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

14
avogadro-1.2.0-libopenbabel2.patch Normal file
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@ -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:

106
avogadro.spec
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@ -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 <davide.madrisan@gmail.com>
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 <silvan.calarco@mambasoft.it> 1.2.0-1mamba
- update to 1.2.0
* Sat Jun 14 2014 Silvan Calarco <silvan.calarco@mambasoft.it> 1.1.1-1mamba
- update to 1.1.1