sci-chemistry/avogadro: Version Bump & fix linking problems with openbabel

Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=569896

Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher <jlec@gentoo.org>

8 files changed, 175 insertions, 0 deletions

diff --git a/sci-chemistry/avogadro/Manifest b/sci-chemistry/avogadro/Manifest
index b9a9c4d47e3a..9dbb71c30de7 100644
--- a/sci-chemistry/avogadro/Manifest
+++ b/sci-chemistry/avogadro/Manifest
@@ -1 +1,2 @@
 DIST avogadro-1.1.0.tar.bz2 10741835 SHA256 6b4eaf57ae52bf43df9b103c77e6abae71e067053d5c99f82acbce9855ecceb0 SHA512 d621dd3ea9e9223d3a29c6b0c0eec89a935837d0c587fcaaa549f91274a76f78a8c60c2a68a67d2f3aa2e107826befb6658be601c46c5bc0760c95bf7284540a WHIRLPOOL c81e866e60b3383a58de515317c754e3982e716c27974ce43ca0c1209d24544949361a7f2f93a4a940d73fd7a18b184f68c7a1856fea89ae5eba75db74b1012d
+DIST avogadro-1.1.1.tar.bz2 11118046 SHA256 fe6f7bdea17a27a20be25b70d975145999aae9d90ef320217af2bc4d6e7a0a14 SHA512 37e2fc9400f8727b7e69d84c13989aaba6fc88287e106a6ed137e4d0fd8ea181dc4ab49b08148d2077754f014748c8ed6f46881f31a1455029f876b599754827 WHIRLPOOL 6bea2c25675ba29729785b561cbaed33929aeb4638180454b1aed8913160cd6d0315bb09e6ee4033a8d27ce84fd7a4573851fd02c76b64b6aa86e615a19b8c38
diff --git a/sci-chemistry/avogadro/avogadro-1.1.0.ebuild b/sci-chemistry/avogadro/avogadro-1.1.0.ebuild
index 0de1b83085b6..4f7720d37e98 100644
--- a/sci-chemistry/avogadro/avogadro-1.1.0.ebuild
+++ b/sci-chemistry/avogadro/avogadro-1.1.0.ebuild
@@ -37,6 +37,7 @@ RESTRICT="test"
 PATCHES=(
 	"${FILESDIR}"/${P}-textrel.patch
 	"${FILESDIR}"/${P}-xlibs.patch
+	"${FILESDIR}"/${PN}-1.1.1-openbabel.patch
 )
 
 pkg_setup() {
diff --git a/sci-chemistry/avogadro/avogadro-1.1.1.ebuild b/sci-chemistry/avogadro/avogadro-1.1.1.ebuild
new file mode 100644
index 000000000000..090d99ccd477
--- /dev/null
+++ b/sci-chemistry/avogadro/avogadro-1.1.1.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils eutils flag-o-matic python-single-r1
+
+DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL"
+HOMEPAGE="http://avogadro.openmolecules.net/"
+SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~x86"
+IUSE="+glsl python cpu_flags_x86_sse2 test"
+
+RDEPEND="
+	>=sci-chemistry/openbabel-2.3.0
+	>=dev-qt/qtgui-4.8.5:4
+	>=dev-qt/qtopengl-4.8.5:4
+	x11-libs/gl2ps
+	glsl? ( >=media-libs/glew-1.5.0 )
+	python? (
+		>=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}]
+		dev-python/numpy[${PYTHON_USEDEP}]
+		dev-python/sip[${PYTHON_USEDEP}]
+	)"
+DEPEND="${RDEPEND}
+	dev-cpp/eigen:2"
+
+# https://sourceforge.net/p/avogadro/bugs/653/
+RESTRICT="test"
+
+PATCHES=(
+	#"${FILESDIR}"/${PN}-1.1.0-textrel.patch
+	"${FILESDIR}"/${PN}-1.1.0-xlibs.patch
+	"${FILESDIR}"/${P}-eigen3.patch
+	"${FILESDIR}"/${P}-mkspecs-dir.patch
+	"${FILESDIR}"/${P}-no-strip.patch
+	"${FILESDIR}"/${P}-pkgconfig_eigen.patch
+	"${FILESDIR}"/${P}-openbabel.patch
+)
+
+pkg_setup() {
+	use python && python-single-r1_pkg_setup
+}
+
+src_prepare() {
+	sed \
+		-e 's:_BSD_SOURCE:_DEFAULT_SOURCE:g' \
+		-i CMakeLists.txt || die
+	# warning: "Eigen2 support is deprecated in Eigen 3.2.x and it will be removed in Eigen 3.3."
+	append-cppflags -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DENABLE_THREADEDGL=OFF
+		-DENABLE_RPATH=OFF
+		-DENABLE_UPDATE_CHECKER=OFF
+		-DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs"
+		-DQT_MKSPECS_RELATIVE=share/qt4/mkspecs
+		$(cmake-utils_use_enable glsl)
+		$(cmake-utils_use_enable test TESTS)
+		$(cmake-utils_use_with cpu_flags_x86_sse2 SSE2)
+		$(cmake-utils_use_enable python)
+	)
+
+	cmake-utils_src_configure
+}
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch
new file mode 100644
index 000000000000..dc07d6974e12
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch
@@ -0,0 +1,51 @@
+--- avogadro-1.1.1/CMakeLists.txt.omv~	2014-01-30 13:58:22.999443609 +0100
++++ avogadro-1.1.1/CMakeLists.txt	2014-01-30 13:59:31.086106925 +0100
+@@ -230,13 +230,15 @@ 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
++find_package(Eigen3 REQUIRED) # 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
++   find_package(Eigen2) # Some version is required
+ else()
+ # Use Stage10 Eigen3 support
+    set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE)
++   add_definitions (-DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API)
++   set (EIGEN2_INCLUDE_DIR ${EIGEN3_INCLUDE_DIR})
+ endif()
+ 
+ find_package(ZLIB REQUIRED)
+--- avogadro-1.1.1/libavogadro/src/extensions/qtaim/CMakeLists.txt.omv~	2014-01-30 14:12:33.859401753 +0100
++++ avogadro-1.1.1/libavogadro/src/extensions/qtaim/CMakeLists.txt	2014-01-30 14:15:07.652727522 +0100
+@@ -4,6 +4,8 @@ set(LINK_LIBS avogadro)
+ set(PLUGIN_LABEL extensions)
+ set(PLUGIN_TARGET extensions)
+ 
++add_definitions(-DEIGEN2_SUPPORT_STAGE20_RESOLVE_API_CONFLICTS -std=gnu++11)
++
+ set(qtaimextension_SRCS
+     qtaimextension.cpp
+ #    qtaimdialog.cpp
+--- avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt.omv~	2014-01-30 13:59:05.889441500 +0100
++++ avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt	2014-01-30 13:59:08.832774688 +0100
+@@ -1,5 +1,5 @@
+ find_package(Qt4 4.6 REQUIRED)
+-find_package(Eigen2 REQUIRED)
++find_package(Eigen3 REQUIRED)
+ 
+ include_directories(${QT_INCLUDE_DIR} ${EIGEN2_INCLUDE_DIR})
+ 
+--- avogadro-1.1.1/cmake/modules/AvogadroUse.cmake.orig	2014-10-13 20:13:59.909828034 +0100
++++ avogadro-1.1.1/cmake/modules/AvogadroUse.cmake	2014-10-13 20:15:09.492822908 +0100
+@@ -12,7 +12,7 @@
+ 
+ # Add the Avogadro modules directory to the CMake module path
+ set(CMAKE_MODULE_PATH ${Avogadro_PLUGIN_DIR}/cmake ${CMAKE_MODULE_PATH})
+-find_package(Eigen2 REQUIRED)
++find_package(Eigen3 REQUIRED)
+ include_directories(${EIGEN2_INCLUDE_DIR})
+ if(Avogadro_ENABLE_GLSL)
+   find_package(GLEW)
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch
new file mode 100644
index 000000000000..45c616422efe
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch
@@ -0,0 +1,12 @@
+diff -up avogadro-1.1.1/CMakeLists.txt.mkspecs-dir avogadro-1.1.1/CMakeLists.txt
+--- avogadro-1.1.1/CMakeLists.txt.mkspecs-dir	2014-01-24 23:43:01.618510517 -0600
++++ avogadro-1.1.1/CMakeLists.txt	2014-01-24 23:44:03.236844746 -0600
+@@ -547,7 +547,7 @@ if(QT_MKSPECS_DIR AND INSTALL_QMAKE_PRF)
+ #    )
+     install(FILES
+       "${CMAKE_CURRENT_BINARY_DIR}/avogadro.prf"
+-      DESTINATION "${CMAKE_INSTALL_PREFIX}/${QT_MKSPECS_RELATIVE}/features"
++      DESTINATION "${QT_MKSPECS_DIR}/features"
+     )
+ #  endif ("${QT_MKSPECS_DIR}" MATCHES ^$"${CMAKE_INSTALL_PREFIX}/")
+ else()
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch
new file mode 100644
index 000000000000..490dd58907df
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch
@@ -0,0 +1,12 @@
+diff -up avogadro-1.1.1/CMakeLists.txt.no-strip avogadro-1.1.1/CMakeLists.txt
+--- avogadro-1.1.1/CMakeLists.txt.no-strip	2014-01-24 23:14:44.473840038 -0600
++++ avogadro-1.1.1/CMakeLists.txt	2014-01-24 23:15:46.869166459 -0600
+@@ -114,7 +114,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
+   endif()
+   # Set up additional build flags for particular build types. These will be added to CMAKE_CXX_FLAGS,
+   # they will not replace them.
+-  set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
++  set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT")
+   set(CMAKE_CXX_FLAGS_RELWITHDEBINFO
+     "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} ${CMAKE_CXX_FLAGS_WARN}")
+   set(CMAKE_CXX_FLAGS_DEBUG   "-g3 -fno-inline ${CMAKE_CXX_FLAGS_WARN}")
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch
new file mode 100644
index 000000000000..4bdc6b2e780e
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch
@@ -0,0 +1,16 @@
+ libavogadro/src/python/CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/libavogadro/src/python/CMakeLists.txt b/libavogadro/src/python/CMakeLists.txt
+index efb518a..1a3d91a 100644
+--- a/libavogadro/src/python/CMakeLists.txt
++++ b/libavogadro/src/python/CMakeLists.txt
+@@ -21,7 +21,7 @@ if (WIN32)
+   target_link_libraries(python-module avogadro ${PYTHON_LIBRARIES})
+ else()
+   target_link_libraries(python-module stdc++ avogadro
+-    ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${Boost_LIBRARIES})
++    ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${Boost_LIBRARIES} ${OPENBABEL2_LIBRARIES})
+ endif()
+ 
+ # Let's try to use this instead:
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch
new file mode 100644
index 000000000000..93dbe2ff4ecc
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch
@@ -0,0 +1,8 @@
+diff -up avogadro-1.1.1/avogadro.pc.in.eigen avogadro-1.1.1/avogadro.pc.in
+--- avogadro-1.1.1/avogadro.pc.in.eigen	2013-12-06 09:50:04.000000000 -0600
++++ avogadro-1.1.1/avogadro.pc.in	2014-01-25 00:37:45.732007852 -0600
+@@ -9,3 +9,4 @@ Description: Avogadro libraries
+ Version: @Avogadro_VERSION_FULL@
+ Libs: -L${libdir} -lavogadro
+ Cflags: -I${pkgincludedir}
++Requires.private: eigen3