Hello community, here is the log from the commit of package avogadro for openSUSE:Factory checked in at 2018-02-05 10:52:53 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/avogadro (Old) and /work/SRC/openSUSE:Factory/.avogadro.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "avogadro" Mon Feb 5 10:52:53 2018 rev:26 rq:572407 version:1.2.0 Changes: -------- --- /work/SRC/openSUSE:Factory/avogadro/avogadro.changes 2016-03-31 13:02:32.000000000 +0200 +++ /work/SRC/openSUSE:Factory/.avogadro.new/avogadro.changes 2018-02-05 10:53:44.206270474 +0100 @@ -1,0 +2,46 @@ +Sat Feb 3 21:34:03 UTC 2018 - [email protected] + +- Force python2 by passing -DPYTHON_EXECUTABLE=%{_bindir}/python2 + to cmake to fix build on Tumbleweed + +------------------------------------------------------------------- +Wed Dec 27 07:25:10 UTC 2017 - [email protected] + +- Update to 1.2.0 + * Support for the ORCA quantum chemistry package, thanks to + Dagmar Lenk, including input generation and output parsing + * Improved support for MO calculations, including orbitals with F, + G, H, and I angular momentum, thanks to Dagmar Lenk + and Albert DeFusco + * Support for exporting VRML models of atoms, bonds, surfaces, + and orbitals (e.g. for 3D printing), thanks to Ethan Pavolik + * Support for perceiving molecular symmetry on Mac and Linux using + the libmsym library1 (i.e., Properties -> Symmetry), + thanks to Marcus Johansson + * Updated links to the new Avogadro website3, manual4, + and discussion forum + * Fixed support for compiling with the Eigen3 library up to + version 3.2.8 + * Improved support for space groups through spglib1 + * Updated translations1, now including over 25 languages in + addition to English + * Fixed a bug downloading from the Protein Data Bank + * Fixed a bug fetching molecules from the network, including + the "chemical by name" + * Fixed a bug when naming molecules from the NIH chemical + resolver website + +- drop avogadro-cmake-3.2.patch, arm-qreal-vs-double.patch (upstream) + +- add 0004-don-t-use-signbit-on-non-float.patch, + 0005-Link-with-libm.patch, 0006-Fix-libmsym-libdir-for-64bit.patch + +- fix package group: Productivity/Scientific/Chemistry + +------------------------------------------------------------------- +Sat Dec 23 21:57:19 UTC 2017 - [email protected] + +- BuildRequire libboost_python-devel instead of boost-devel on + Tumbleweed to fix build + +------------------------------------------------------------------- Old: ---- arm-qreal-vs-double.patch avogadro-1.1.1.tar.bz2 avogadro-cmake-3.2.patch New: ---- 0004-don-t-use-signbit-on-non-float.patch 0005-Link-with-libm.patch 0006-Fix-libmsym-libdir-for-64bit.patch avogadro-1.2.0.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ avogadro.spec ++++++ --- /var/tmp/diff_new_pack.OPGhxB/_old 2018-02-05 10:53:45.698200700 +0100 +++ /var/tmp/diff_new_pack.OPGhxB/_new 2018-02-05 10:53:45.702200513 +0100 @@ -17,23 +17,31 @@ Name: avogadro -Version: 1.1.1 +Version: 1.2.0 Release: 0 Summary: A Molecular design tool License: GPL-2.0 -Group: Productivity/Editors/Other -Url: http://avogadro.sourceforge.net/wiki/Main_Page -Source0: http://sourceforge.net/projects/avogadro/files/avogadro/%{version}/avogadro-%{version}.tar.bz2 +Group: Productivity/Scientific/Chemistry +Url: http://avogadro.cc +Source0: http://sourceforge.net/projects/avogadro/files/avogadro/%{version}/avogadro-%{version}.tar.gz Source1: %{name}.png Source2: baselibs.conf # PATCH-FIX-UPSTREAM avogadro-1.1.0-avopkg-fix-echo.patch [email protected] Patch1: avogadro-1.1.0-avopkg-fix-echo.patch -# PATCH-FIX-UPSTREAM avogadro-cmake-3.2.patch -- [email protected] -Patch2: avogadro-cmake-3.2.patch -Patch3: arm-qreal-vs-double.patch -Patch4: avogadro-boost.patch -Patch5: avogadro-opanbabel.patch +Patch2: avogadro-boost.patch +Patch3: avogadro-opanbabel.patch +# PATCH-FIX-OPENSUSE don't use signbit() on non-float [email protected] +Patch4: 0004-don-t-use-signbit-on-non-float.patch +# PATCH-FIX-OPENSUSE link with libm [email protected] +Patch5: 0005-Link-with-libm.patch +# PATCH-FIX-OPENSUSE install libmsym in .../lib64... [email protected] +Patch6: 0006-Fix-libmsym-libdir-for-64bit.patch + +%if 0%{?suse_version} >= 1500 +BuildRequires: libboost_python-devel +%else BuildRequires: boost-devel +%endif BuildRequires: cmake BuildRequires: docbook-utils BuildRequires: fdupes @@ -105,9 +113,10 @@ %setup -q %patch1 -p1 %patch2 -p1 -%patch3 +%patch3 -p1 %patch4 -p1 %patch5 -p1 +%patch6 -p1 %build %cmake \ @@ -115,6 +124,7 @@ -DENABLE_UPDATE_CHECKER=OFF \ -DENABLE_ZMATRIX_TOOL=ON \ -DENABLE_PYTHON=ON \ + -DPYTHON_EXECUTABLE=%{_bindir}/python2 \ -DCMAKE_BUILD_TYPE=RelWithDebInfo make %{?_smp_mflags} @@ -157,24 +167,26 @@ %files %defattr(-,root,root,-) -%doc AUTHORS ChangeLog COPYING +%doc AUTHORS COPYING README %{_mandir}/man1/avogadro.1.gz %{_mandir}/man1/avopkg.1.gz %{_bindir}/avogadro %{_bindir}/avopkg +%{_bindir}/qube %dir %{_datadir}/libavogadro %{_datadir}/libavogadro/shaders/ %{_datadir}/%{name}/ %{_datadir}/pixmaps/*.png %{_datadir}/applications/%{name}.desktop #plugins not libraries +%{_libdir}/libmsym.so %dir %{_libdir}/avogadro -%dir %{_libdir}/avogadro/1_1 -%dir %{_libdir}/avogadro/1_1/colors -%dir %{_libdir}/avogadro/1_1/engines -%dir %{_libdir}/avogadro/1_1/extensions -%dir %{_libdir}/avogadro/1_1/tools -%{_libdir}/avogadro/1_1/*/*.so +%dir %{_libdir}/avogadro/1_2 +%dir %{_libdir}/avogadro/1_2/colors +%dir %{_libdir}/avogadro/1_2/engines +%dir %{_libdir}/avogadro/1_2/extensions +%dir %{_libdir}/avogadro/1_2/tools +%{_libdir}/avogadro/1_2/*/*.so %dir %{_datadir}/libavogadro/engineScripts %dir %{_datadir}/libavogadro/extensionScripts %{_datadir}/libavogadro/engineScripts/wireframe.py @@ -184,12 +196,15 @@ %defattr(-,root,root,-) %dir %{_includedir}/avogadro %{_includedir}/avogadro/*.h -%dir %{_libdir}/avogadro/1_1/cmake +%dir %{_includedir}/libmsym +%{_includedir}/libmsym/*.h +%dir %{_libdir}/cmake/libmsym +%{_libdir}/cmake/libmsym/*.cmake +%dir %{_libdir}/avogadro/1_2/cmake %{_libdir}/libavogadro.so %{_libdir}/libavogadro_OpenQube.so - -%{_libdir}/avogadro/1_1/cmake/* -%{_libdir}/avogadro/1_1/*.cmake +%{_libdir}/avogadro/1_2/cmake/* +%{_libdir}/avogadro/1_2/*.cmake %{_libdir}/avogadro/*.cmake %{_libdir}/pkgconfig/*.pc %{_datadir}/qt4/mkspecs/features/avogadro.prf ++++++ 0004-don-t-use-signbit-on-non-float.patch ++++++ >From 53e179f4dbfa5062478f02b1ae463f4ea4251f30 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Klaus=20K=C3=A4mpf?= <[email protected]> Date: Wed, 27 Dec 2017 10:00:30 +0100 Subject: [PATCH 4/4] don't use signbit on non-float --- libavogadro/src/extensions/symmetry/libmsym/src/orbital.c | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c b/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c index 143b4de03e0f..42b5979d7d94 100644 --- a/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c +++ b/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c @@ -67,13 +67,13 @@ msym_error_t orbitalFromQuantumNumbers(int n, int l, int m, msym_orbital_t *o){ } case 2 : { //o->v = dpolynomial[m+l]; - char *d = (signbit(m) == 1 ? "-" : "+"); + char *d = (m < 0) ? "-" : "+"; 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 = (m < 0) ? "-" : "+"; snprintf(o->name, sizeof(o->name), "%d%c%d%s",n,t,abs(m),d); } } -- 2.15.1 ++++++ 0005-Link-with-libm.patch ++++++ >From c697ce9f1ee152a5d163dbcbef085776c1873743 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Klaus=20K=C3=A4mpf?= <[email protected]> Date: Wed, 27 Dec 2017 10:23:04 +0100 Subject: [PATCH 5/5] Link with libm --- cmake/modules/AvogadroUse.cmake | 2 +- libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/cmake/modules/AvogadroUse.cmake b/cmake/modules/AvogadroUse.cmake index 7c3fc61853c9..2e6b96c6c086 100644 --- a/cmake/modules/AvogadroUse.cmake +++ b/cmake/modules/AvogadroUse.cmake @@ -49,7 +49,7 @@ function(avogadro_plugin plugin_name src_list) endif(NOT "${ARGV3}" STREQUAL "") add_library(${plugin_name} SHARED ${src_list} ${plugin_UIS_H} ${plugin_RC_SRCS}) - target_link_libraries(${plugin_name} avogadro) + target_link_libraries(${plugin_name} avogadro m) if(UNIX) add_custom_target("${plugin_name}.mf" diff --git a/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt b/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt index 1cf00c6387a3..653b4eddff21 100644 --- a/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt +++ b/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt @@ -32,6 +32,7 @@ if (BUILD_SHARED_LIBS) set_target_properties (msym PROPERTIES POSITION_INDEPENDENT_CODE "TRUE") endif () +target_link_libraries(msym m) set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99") #set_target_properties (msym PROPERTIES # C_STANDARD 99 -- 2.15.1 ++++++ 0006-Fix-libmsym-libdir-for-64bit.patch ++++++ >From 3a2e3f5c7510c05abcf1149491b52dc6945806ec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Klaus=20K=C3=A4mpf?= <[email protected]> Date: Wed, 27 Dec 2017 10:40:21 +0100 Subject: [PATCH 6/6] Fix libmsym libdir for 64bit --- libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt b/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt index 653b4eddff21..bf7d3bb78a87 100644 --- a/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt +++ b/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt @@ -7,13 +7,19 @@ set(LIBMSYM_MINOR_VERSION 1) set(LIBMSYM_PATCH_VERSION 0) set(LIBMSYM_VERSION ${LIBMSYM_MAJOR_VERSION}.${LIBMSYM_MINOR_VERSION}.${LIBMSYM_PATCH_VERSION}) -set(INSTALL_LIB_DIR lib CACHE PATH "Installation directory for msym library") +IF (CMAKE_SIZEOF_VOID_P MATCHES "8") + SET( LIB_SUFFIX "64" ) +ELSE(CMAKE_SIZEOF_VOID_P MATCHES "8") + SET( LIB_SUFFIX "" ) +ENDIF(CMAKE_SIZEOF_VOID_P MATCHES "8") + +set(INSTALL_LIB_DIR lib${LIB_SUFFIX} CACHE PATH "Installation directory for msym library") set(INSTALL_INCLUDE_DIR include CACHE PATH "Installation directory for header files") if(WIN32 AND NOT CYGWIN) set(DEF_INSTALL_CMAKE_DIR CMake) else() - set(DEF_INSTALL_CMAKE_DIR lib/cmake/libmsym) + set(DEF_INSTALL_CMAKE_DIR lib${LIB_SUFFIX}/cmake/libmsym) endif() set(INSTALL_CMAKE_DIR ${DEF_INSTALL_CMAKE_DIR} CACHE PATH "Installation directory for CMake files") -- 2.15.1 ++++++ avogadro-boost.patch ++++++ --- /var/tmp/diff_new_pack.OPGhxB/_old 2018-02-05 10:53:45.750198268 +0100 +++ /var/tmp/diff_new_pack.OPGhxB/_new 2018-02-05 10:53:45.754198082 +0100 @@ -1,8 +1,7 @@ -Index: avogadro-1.1.1/libavogadro/src/pythonengine_p.h -=================================================================== ---- avogadro-1.1.1.orig/libavogadro/src/pythonengine_p.h -+++ avogadro-1.1.1/libavogadro/src/pythonengine_p.h -@@ -27,7 +27,9 @@ +diff -ruN -x '*~' -x '*.o' -x '*.a' -x '*.so' -x '*.so.[0-9]' -x autom4te.cache -x .deps -x .libs ../orig-avogadro-1.2.0/libavogadro/src/pythonengine_p.h ./libavogadro/src/pythonengine_p.h +--- ../orig-avogadro-1.2.0/libavogadro/src/pythonengine_p.h 2016-06-08 16:19:45.000000000 +0200 ++++ ./libavogadro/src/pythonengine_p.h 2017-12-27 09:38:45.897406404 +0100 +@@ -31,7 +31,9 @@ #include <avogadro/global.h> #include <avogadro/engine.h> @@ -12,11 +11,10 @@ namespace Avogadro { -Index: avogadro-1.1.1/libavogadro/src/pythonextension_p.h -=================================================================== ---- avogadro-1.1.1.orig/libavogadro/src/pythonextension_p.h -+++ avogadro-1.1.1/libavogadro/src/pythonextension_p.h -@@ -29,7 +29,9 @@ +diff -ruN -x '*~' -x '*.o' -x '*.a' -x '*.so' -x '*.so.[0-9]' -x autom4te.cache -x .deps -x .libs ../orig-avogadro-1.2.0/libavogadro/src/pythonextension_p.h ./libavogadro/src/pythonextension_p.h +--- ../orig-avogadro-1.2.0/libavogadro/src/pythonextension_p.h 2016-06-08 16:19:45.000000000 +0200 ++++ ./libavogadro/src/pythonextension_p.h 2017-12-27 09:38:45.897406404 +0100 +@@ -33,7 +33,9 @@ #include <avogadro/extension.h> #include <avogadro/primitive.h> #include <avogadro/glwidget.h> @@ -26,24 +24,9 @@ #include <QWidget> #include <QList> -Index: avogadro-1.1.1/libavogadro/src/pythontool_p.h -=================================================================== ---- avogadro-1.1.1.orig/libavogadro/src/pythontool_p.h -+++ avogadro-1.1.1/libavogadro/src/pythontool_p.h -@@ -27,7 +27,9 @@ - - #include <avogadro/global.h> - #include <avogadro/tool.h> -+#ifndef Q_MOC_RUN - #include <boost/python.hpp> -+#endif - - #include <QObject> - #include <QAction> -Index: avogadro-1.1.1/libavogadro/src/pythoninterpreter.h -=================================================================== ---- avogadro-1.1.1.orig/libavogadro/src/pythoninterpreter.h -+++ avogadro-1.1.1/libavogadro/src/pythoninterpreter.h +diff -ruN -x '*~' -x '*.o' -x '*.a' -x '*.so' -x '*.so.[0-9]' -x autom4te.cache -x .deps -x .libs ../orig-avogadro-1.2.0/libavogadro/src/pythoninterpreter.h ./libavogadro/src/pythoninterpreter.h +--- ../orig-avogadro-1.2.0/libavogadro/src/pythoninterpreter.h 2016-06-08 16:19:45.000000000 +0200 ++++ ./libavogadro/src/pythoninterpreter.h 2017-12-27 09:38:45.901406483 +0100 @@ -26,7 +26,9 @@ #define PYTHONINTERPRETER_H @@ -54,10 +37,9 @@ #include <avogadro/primitive.h> #include <QString> -Index: avogadro-1.1.1/libavogadro/src/pythonscript.h -=================================================================== ---- avogadro-1.1.1.orig/libavogadro/src/pythonscript.h -+++ avogadro-1.1.1/libavogadro/src/pythonscript.h +diff -ruN -x '*~' -x '*.o' -x '*.a' -x '*.so' -x '*.so.[0-9]' -x autom4te.cache -x .deps -x .libs ../orig-avogadro-1.2.0/libavogadro/src/pythonscript.h ./libavogadro/src/pythonscript.h +--- ../orig-avogadro-1.2.0/libavogadro/src/pythonscript.h 2016-06-08 16:19:45.000000000 +0200 ++++ ./libavogadro/src/pythonscript.h 2017-12-27 09:38:45.901406483 +0100 @@ -27,7 +27,9 @@ #define PYTHONSCRIPT_H @@ -68,3 +50,16 @@ #include "pythonerror.h" +diff -ruN -x '*~' -x '*.o' -x '*.a' -x '*.so' -x '*.so.[0-9]' -x autom4te.cache -x .deps -x .libs ../orig-avogadro-1.2.0/libavogadro/src/pythontool_p.h ./libavogadro/src/pythontool_p.h +--- ../orig-avogadro-1.2.0/libavogadro/src/pythontool_p.h 2016-06-08 16:19:45.000000000 +0200 ++++ ./libavogadro/src/pythontool_p.h 2017-12-27 09:38:45.901406483 +0100 +@@ -31,7 +31,9 @@ + + #include <avogadro/global.h> + #include <avogadro/tool.h> ++#ifndef Q_MOC_RUN + #include <boost/python.hpp> ++#endif + + #include <QObject> + #include <QAction>
