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-rw-r--r--sci-chemistry/Manifest.gzbin18060 -> 18060 bytes
-rw-r--r--sci-chemistry/avogadro/Manifest12
-rw-r--r--sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild56
-rw-r--r--sci-chemistry/avogadro/avogadro-1.1.0.ebuild62
-rw-r--r--sci-chemistry/avogadro/avogadro-1.1.1.ebuild3
-rw-r--r--sci-chemistry/avogadro/avogadro-1.2.0_p20170207.ebuild90
-rw-r--r--sci-chemistry/avogadro/files/1.0.1-gl2ps.patch39
-rw-r--r--sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch29
-rw-r--r--sci-chemistry/avogadro/files/avogadro-1.1.1-gcc-version.patch23
-rw-r--r--sci-chemistry/avogadro/files/avogadro-1.2.0-numpy.patch13
-rw-r--r--sci-chemistry/molequeue/Manifest3
-rw-r--r--sci-chemistry/molequeue/files/molequeue-0.8.0-cmake.patch106
-rw-r--r--sci-chemistry/molequeue/molequeue-0.8.0.ebuild26
13 files changed, 257 insertions, 205 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 956a59b48530..5c77a1d62ab3 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
Binary files differ
diff --git a/sci-chemistry/avogadro/Manifest b/sci-chemistry/avogadro/Manifest
index 7c09d780df85..e1221628478b 100644
--- a/sci-chemistry/avogadro/Manifest
+++ b/sci-chemistry/avogadro/Manifest
@@ -1,16 +1,14 @@
-AUX 1.0.1-gl2ps.patch 1511 BLAKE2B 4c4e4f52c2275530a286201a5db492fcd63aeb2174225de3f78fab1ad65033496557695340edd29a4b2abb6f9b45169f295b35b90a0fe5aa969636213484c0a0 SHA512 b4a8d0138bffa7c018e2125e16a47cefefba01f19ce3d460488f36e44f55b212cea9c9875429e7c0c596388366adea045b50ace579b6352d2b7e0b073420c67f
-AUX avogadro-1.1.0-textrel.patch 1535 BLAKE2B 0843b52977e53679f6e3490a6e6a389e9fd32bebd167cc3b68ffaf831f88249cfa1a2006ab8d4d611e40ac28ccc051a42f79ffd40be54d1569e35402fb7cc31d SHA512 5872a773668cb38b27ab0dbaf14d947eff4cb3d4ae99410c8968cafe576a9df5d3b0937d028b9ffd076c212c5f9b8e213cda74a63afff6caa713346ee338be77
AUX avogadro-1.1.0-xlibs.patch 680 BLAKE2B 381597d8b1444f412ecefdf1de2860f557172b195b400e869ee1404b1614b494015c1815a0cafbdf1b19483aa23d0793f09c68df6e6a3a53e9de19524b431528 SHA512 df2727e4aea1549daada56778d7710656f3f6ff9fa31c441c06e82241c8e5b0733c39d575c98f2d1b57b9be0a52d445412ecd6cca7a1f319c6982035e789f21d
AUX avogadro-1.1.1-boost-join-moc.patch 2051 BLAKE2B 8711c60f2ad0d63d6b4cb39c8461a70f5ced9d9045e5b9b18cea5577721f15e7c9314c8d86d844f47fca5b769837167268903d91328219c5eda16c72f3007967 SHA512 d4e4ef54d94cccb0f34c4960d302772f9da47e27cb79e1ee0a4e928ef248ac629fd59f1564bedf7c82a2a7ca8b25456878c22569dbcda26478a6c06e5815a084
AUX avogadro-1.1.1-eigen3.patch 2230 BLAKE2B c22f039d1c91a8fbe06d8e7f272900111bde03635b1120accc73ca47a241c36fffe68ed9766bba088eb3137de1ccd6acb1c70a26f0970cac5a9ab6096b87eeda SHA512 df6a53cacebee613739d230fc0c7dc21cb67d553950af82cf83d04750f1d9fa98a3bb052c15fffebacf41d2e53dcd3503bffff2aa8dfbfcb47e2d1ebccd77614
+AUX avogadro-1.1.1-gcc-version.patch 997 BLAKE2B d04059442cf31f4224c6be12b695b379f580717131b590b43e919e7b4789ccb643f93ec3f89d7a4572ca94a08442ea17b01e430162f7187078fe5688af78fd25 SHA512 1a1d204a7f8a050446d5691fce0b7c46e0a6e619a042e769771f8a3a3596f9ae176c33b070d212c07dc977b20db82e19a9ee1e64963e5cae68c43a9d379818b4
AUX avogadro-1.1.1-mkspecs-dir.patch 580 BLAKE2B ca9da1dcbf5560fbedd84f12023d921f9cb11f8475aea5094454195eeb37eb21a1a92cbef268b166e26f7477a086a74337b0c262eab729c8012d1067987bee6d SHA512 6c5b67d9f9e1e9fa3c11ae235f467525129fa9d81f34211ed8b97c199690e12cd1457df3aac861615d94efb452af306df6b53218309ff87f6ca1f68edffbf6b2
AUX avogadro-1.1.1-no-strip.patch 745 BLAKE2B d06400dc0737b7991fe5da6888159b41e7765c851c7ade14619a12571d40c40332363b34da1b0b4af521ee37d2575c28d8cb075bbcf7916b78596af21f395e89 SHA512 921b1333bf37135d5890222193ebdb5b351739d16bf1434c59509e8aab0135ea5cde6812b63d4159fafac29d4eb6297320d03513e474466a7fb857ed16301d6e
AUX avogadro-1.1.1-openbabel.patch 655 BLAKE2B a0bee7e87a75db2c0881036f977e5a8513ba1f6a66360f8e8cad26eaf269df16140721c4b33d3cf4abde35c0be7f13614e6466b6bc34edcc158cf340b42da20e SHA512 23f477c9deb4befb87a92eb1edaabdd8e52a25f24a36ec9dbf345b0686442cec229a16fbb118e3336cf28592d8af4fc51d0a3e5e9d7a7d7c11a65080c08a074d
AUX avogadro-1.1.1-pkgconfig_eigen.patch 387 BLAKE2B f842b6f0eacdf351688f2a8c83b248cee0602cf1e96bf180bc0be8181e3cb6c3bbbf8e67572088d763d69d0eadfb7936199d29b5e68076cd6ec89138d5051845 SHA512 4e1e838f7cd88ef3ef49c26565aecf16a3cfb5c735d67c2525e877aa64671ac787733b0eee7f02ef79c6ada05d7dd7fc3c4a470e6d4549fcd0fea7d49e780e99
-DIST avogadro-1.0.3.tar.bz2 4971989 BLAKE2B 1cebca8c36c265475e68adbcd3dd451088654095545d9546c1d786920d13d312c035b9d6f7f34ea655e7778d392feaf5dedf36fe93775b18f0d644f97229c47d SHA512 49e7b8ca43f0f52a65efc7bf9dc45670ae5a5de5d1aa6bf7b58b8368e816be30fe6529c45fa658d7337d4a69327bb0aa8799d8d4b4805860aace28011cc74210
-DIST avogadro-1.1.0.tar.bz2 10741835 BLAKE2B 1427eb5c060f4566b431ecbd3847526d6ea4cc22067fa78e2e55ae113550c818959d96f1441432872eb5e96bae13f23e17d0a6640c7b034c90140da3e92df073 SHA512 d621dd3ea9e9223d3a29c6b0c0eec89a935837d0c587fcaaa549f91274a76f78a8c60c2a68a67d2f3aa2e107826befb6658be601c46c5bc0760c95bf7284540a
+AUX avogadro-1.2.0-numpy.patch 448 BLAKE2B 2bbde3ba9e4b8fd5ead2afa3a9cecb458600cf454b50011034ce445ff569212052d04cce9142aab4207da8d84a6b9290d567c4d9262547dcd41c71f7071fa0e3 SHA512 20155043af3ef2f5a01d63dd80cfb3dc7402a2ea43bb3d47dd57e7850671fba62981310280d9361d37ac3359e9dda2daa80f6627836ac53a8dec0f0c2a009905
DIST avogadro-1.1.1.tar.bz2 11118046 BLAKE2B 358eda508c56247fb34e9cf4b4d790859cc156e000fa10f9e2f2700e9e295557dd5e615ca626227a918fa4f699c089bee23596d186f613f8934a73b8cfeeb358 SHA512 37e2fc9400f8727b7e69d84c13989aaba6fc88287e106a6ed137e4d0fd8ea181dc4ab49b08148d2077754f014748c8ed6f46881f31a1455029f876b599754827
-EBUILD avogadro-1.0.3-r2.ebuild 1298 BLAKE2B 6c6f753b79322c3185523184048a03520b2910555731b2f51e8ca890815abf742332ae721a7d98bf5d5a563c5715f6df3ae58fc27db348ae143a56f7fce83add SHA512 54b364267975e585b7fdc510688d92f3aa7e5cf477a0288f6ccfe7d468c496d785b1c9f3d37e7b0ce7df8729565614b63fa3544507c50359d5e67189a4ab6e45
-EBUILD avogadro-1.1.0.ebuild 1482 BLAKE2B 36daec6e20a5dd3f85e63f6dfc6146d685ee96f11ac9a63e09667a7d886d54bc70096eed95926cd3373bb71041e62cb4adbb173f4d94730261d2e16c6a0d9d2c SHA512 d3f0095e7b1644cb963ad4223a43fcc0201f5c14247b0e0b04c570f47ce2c33f52bb46373d347dedeee662cdfd4924dce27d809bdc9826e785e34e5f73f935d9
-EBUILD avogadro-1.1.1.ebuild 1976 BLAKE2B 7d9e7710407c0a88b1af84280325e09e738dcfcfa5d9eeacee35d2a68fdcee6a6756517687c0a947491be8dcbb26843e333d492621d9df6005aa3678db734c3f SHA512 c6a83d047ab126e32ce74adc07f6702da476c19c96483b30753a634a66521f712ca302c71f1ff7bc72e92da0874e419f5a7edaf1a926631baa0e05634bccd909
+DIST avogadro-1.2.0_p20170207.tar.gz 16805634 BLAKE2B 012ac0fa6e86bdff1ec117e81faf88ddda2e3264b36c3997ce60814f5a5900dc8722266a52bda70715279e640a3deb04a38bc2bfdfc4ae856182d94e25b7c705 SHA512 c5088ba1e1b48f3202766e38b1c3f2016c3facbf4ea544e24eedb0706328815e7500bcebdedfea2a330e665b97f76c7f86b669339c6f5a765533bfd3a88d7b51
+EBUILD avogadro-1.1.1.ebuild 2014 BLAKE2B fc1c386acd5ee23c6609fdfdf2bfa77571818c4b7f1aad7db978dc4274963e3c28b1840d6e66d05f67931fd8b17006772f4d97e3c30566f18ad9b9aee818a6a3 SHA512 08bb5a96d92ae5f81f266dd141f31ec2a3e7dd3b61b841c275ebc68750ec6b778ae26b4d7c7f76179c889f908ccde9ef89a78561912cce8a5a14309e7dc6a4f0
+EBUILD avogadro-1.2.0_p20170207.ebuild 2107 BLAKE2B 80c56bab7a8c08d9023c8cd187996f05df7f2316353884a139980d2b2794a34ac050922c9e9c58de67d481a01d3c694a9b104bc2d18cde37454bb8fba2d445e3 SHA512 4ef7346cab4937ba189de8439ee78a710d3e398519bbe077b38b2099d412e913baee830d134e770e060f947ce23ab8ffd9d2ddd7930400c1b281f90f36715327
MISC metadata.xml 703 BLAKE2B 64270fc03ee237b6778aa8b07bef13c3d283cf4b43c341c7e529a8a99cf465a548c8f6b64bba21d68c3f5f298104fd3a6e4e719a6a8f6c9749d71376b1248b0d SHA512 3602707feca1ecb4317f30fd06404b087fb7264929204dd488138c60e82a3d6a11537ba3e29d9f2c491f2be6e06ba874167509905f587ec147b83b773f341c67
diff --git a/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild b/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild
deleted file mode 100644
index ce624e4ae71f..000000000000
--- a/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils eutils python-single-r1
-
-DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL"
-HOMEPAGE="http://avogadro.openmolecules.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~x86"
-IUSE="+glsl python cpu_flags_x86_sse2"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
- >=sci-chemistry/openbabel-2.2.3
- >=dev-qt/qtgui-4.5.3:4
- >=dev-qt/qtopengl-4.5.3:4
- x11-libs/gl2ps
- glsl? ( >=media-libs/glew-1.5.0:0= )
- python? (
- >=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/sip[${PYTHON_USEDEP}]
- ${PYTHON_DEPS}
- )"
-DEPEND="${RDEPEND}
- dev-cpp/eigen:2"
-
-PATCHES=(
- "${FILESDIR}"/1.0.1-gl2ps.patch
-)
-
-pkg_setup() {
- use python && python-single-r1_pkg_setup
-}
-
-src_configure() {
- local mycmakeargs=(
- -DENABLE_THREADGL=OFF
- -DENABLE_RPATH=OFF
- -DENABLE_UPDATE_CHECKER=OFF
- -DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs"
- -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs
- $(cmake-utils_use_enable glsl)
- $(cmake-utils_use_with cpu_flags_x86_sse2 SSE2)
- $(cmake-utils_use_enable python)
- )
-
- cmake-utils_src_configure
-}
diff --git a/sci-chemistry/avogadro/avogadro-1.1.0.ebuild b/sci-chemistry/avogadro/avogadro-1.1.0.ebuild
deleted file mode 100644
index ff3a9036301b..000000000000
--- a/sci-chemistry/avogadro/avogadro-1.1.0.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils eutils python-single-r1
-
-DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL"
-HOMEPAGE="http://avogadro.openmolecules.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~x86"
-IUSE="+glsl python cpu_flags_x86_sse2 test"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
- >=sci-chemistry/openbabel-2.3.0
- >=dev-qt/qtgui-4.5.3:4
- >=dev-qt/qtopengl-4.5.3:4
- x11-libs/gl2ps
- glsl? ( >=media-libs/glew-1.5.0:0= )
- python? (
- >=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/sip[${PYTHON_USEDEP}]
- ${PYTHON_DEPS}
- )"
-DEPEND="${RDEPEND}
- dev-cpp/eigen:2"
-
-# https://sourceforge.net/p/avogadro/bugs/653/
-RESTRICT="test"
-
-PATCHES=(
- "${FILESDIR}"/${P}-textrel.patch
- "${FILESDIR}"/${P}-xlibs.patch
- "${FILESDIR}"/${PN}-1.1.1-openbabel.patch
-)
-
-pkg_setup() {
- use python && python-single-r1_pkg_setup
-}
-
-src_configure() {
- local mycmakeargs=(
- -DENABLE_THREADGL=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)
- $(cmake-utils_use_enable python)
- )
-
- cmake-utils_src_configure
-}
diff --git a/sci-chemistry/avogadro/avogadro-1.1.1.ebuild b/sci-chemistry/avogadro/avogadro-1.1.1.ebuild
index 5e9225721e1d..63150ada5fa9 100644
--- a/sci-chemistry/avogadro/avogadro-1.1.1.ebuild
+++ b/sci-chemistry/avogadro/avogadro-1.1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -45,6 +45,7 @@ PATCHES=(
"${FILESDIR}"/${P}-pkgconfig_eigen.patch
"${FILESDIR}"/${P}-openbabel.patch
"${FILESDIR}"/${P}-boost-join-moc.patch
+ "${FILESDIR}"/${P}-gcc-version.patch
)
pkg_setup() {
diff --git a/sci-chemistry/avogadro/avogadro-1.2.0_p20170207.ebuild b/sci-chemistry/avogadro/avogadro-1.2.0_p20170207.ebuild
new file mode 100644
index 000000000000..28d5724b0e50
--- /dev/null
+++ b/sci-chemistry/avogadro/avogadro-1.2.0_p20170207.ebuild
@@ -0,0 +1,90 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+COMMIT=258105b4d8957e0245a341cdf1dc12c72234c833
+PYTHON_COMPAT=( python2_7 )
+inherit cmake-utils flag-o-matic python-single-r1 vcs-snapshot xdg-utils
+
+DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL"
+HOMEPAGE="http://avogadro.openmolecules.net/"
+SRC_URI="https://github.com/cryos/${PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~x86"
+IUSE="cpu_flags_x86_sse2 +glsl python test"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+RDEPEND="
+ dev-qt/qtcore:4
+ dev-qt/qtgui:4
+ dev-qt/qtopengl:4
+ media-libs/glew:=
+ sci-chemistry/openbabel:=
+ virtual/glu
+ x11-libs/gl2ps
+ glsl? ( >=media-libs/glew-1.5.0:0= )
+ python? (
+ ${PYTHON_DEPS}
+ dev-libs/boost:=[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/sip[${PYTHON_USEDEP}]
+ )
+"
+DEPEND="${RDEPEND}
+ dev-cpp/eigen:3
+ virtual/pkgconfig
+"
+
+# https://sourceforge.net/p/avogadro/bugs/653/
+RESTRICT="test"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-1.1.1-mkspecs-dir.patch
+ "${FILESDIR}"/${PN}-1.1.1-no-strip.patch
+ "${FILESDIR}"/${PN}-1.1.1-pkgconfig_eigen.patch
+ "${FILESDIR}"/${PN}-1.1.1-openbabel.patch
+ "${FILESDIR}"/${PN}-1.1.1-boost-join-moc.patch
+ "${FILESDIR}"/${PN}-1.2.0-numpy.patch
+)
+
+pkg_setup() {
+ use python && python-single-r1_pkg_setup
+}
+
+src_prepare() {
+ sed -e "s:_BSD_SOURCE:_DEFAULT_SOURCE:g" \
+ -i CMakeLists.txt || die
+
+ sed -e "/Version/s/1\.2/1\.0/" \
+ -i avogadro/src/avogadro.desktop || die
+
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DENABLE_THREADEDGL=OFF
+ -DENABLE_RPATH=OFF
+ -DENABLE_UPDATE_CHECKER=OFF
+ -DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs"
+ -DWITH_SSE2=$(usex cpu_flags_x86_sse2)
+ -DENABLE_GLSL=$(usex glsl)
+ -DENABLE_PYTHON=$(usex python)
+ -DENABLE_TESTS=$(usex test)
+ )
+
+ QT_MKSPECS_RELATIVE=share/qt4/mkspecs cmake-utils_src_configure
+}
+
+pkg_postinst() {
+ xdg_mimeinfo_database_update
+ xdg_desktop_database_update
+}
+
+pkg_postrm() {
+ xdg_mimeinfo_database_update
+ xdg_desktop_database_update
+}
diff --git a/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch b/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch
deleted file mode 100644
index d8a0c0f758e1..000000000000
--- a/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-diff --git a/avogadro/src/CMakeLists.txt b/avogadro/src/CMakeLists.txt
-index 75b6dfb..d87ac2c 100644
---- a/avogadro/src/CMakeLists.txt
-+++ b/avogadro/src/CMakeLists.txt
-@@ -45,7 +45,7 @@ endif(ENABLE_UPDATE_CHECKER)
- FILE(GLOB projectDelegates_SRCS "projectdelegates/*.cpp")
- set(avogadro_SRCS ${avogadro_SRCS} ${projectDelegates_SRCS})
- # Add GL2PS to the executable
--set(avogadro_SRCS ${avogadro_SRCS} "../gl2ps/gl2ps.c")
-+#set(avogadro_SRCS ${avogadro_SRCS} "../gl2ps/gl2ps.c")
-
- if( WIN32 )
- set(avogadro_SRCS ${avogadro_SRCS} windows/avogadro.rc)
-diff --git a/avogadro/src/mainwindow.cpp b/avogadro/src/mainwindow.cpp
-index 66785fd..2933953 100644
---- a/avogadro/src/mainwindow.cpp
-+++ b/avogadro/src/mainwindow.cpp
-@@ -51,7 +51,7 @@
- //#endif
-
- // Include the GL2PS header
--#include "../gl2ps/gl2ps.h"
-+#include <gl2ps.h>
-
- #include <avogadro/pluginmanager.h>
-
-diff --git a/libavogadro/src/CMakeLists.txt b/libavogadro/src/CMakeLists.txt
-index cce8ece..cc084fb 100644
---- a/libavogadro/src/CMakeLists.txt
-+++ b/libavogadro/src/CMakeLists.txt
-@@ -152,7 +152,7 @@ endforeach(headerFile ${libavogadro_HDRS})
- add_library(avogadro SHARED ${libavogadro_SRCS} ${libavogadro_QM} ${pythontool_RC_SRCS})
- set_target_properties(avogadro
- PROPERTIES VERSION ${Avogadro_VERSION_FULL} SOVERSION 1 )
--target_link_libraries(avogadro ${AVO_LINK_LIBRARIES})
-+target_link_libraries(avogadro ${AVO_LINK_LIBRARIES} gl2ps)
-
- install(TARGETS avogadro DESTINATION ${LIB_INSTALL_DIR})
- install(FILES ${libavogadro_HDRS}
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch b/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch
deleted file mode 100644
index 6d4536ef7c9b..000000000000
--- a/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch
+++ /dev/null
@@ -1,29 +0,0 @@
- libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt | 2 +-
- libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt
-index fb88316..2ddcfdf 100644
---- a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt
-+++ b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt
-@@ -20,6 +20,6 @@ add_library(spglib STATIC ${spglib_SRCS})
- set_target_properties(spglib PROPERTIES COMPILE_FLAGS "-w")
-
- # Set -fPIC on x86_64
--if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
-+if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64|ppc|ppc64)$")
- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC" )
- endif()
-diff --git a/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt b/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt
-index 0cd0c3e..9e89daf 100644
---- a/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt
-+++ b/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt
-@@ -19,7 +19,7 @@ add_library(tubegen STATIC ${tubegen_SRCS})
- set_target_properties(tubegen PROPERTIES COMPILE_FLAGS "-w")
-
- # Set -fPIC on x86_64
--if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
-+if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64|ppc|ppc64)$")
- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC" )
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC" )
- endif()
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-gcc-version.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-gcc-version.patch
new file mode 100644
index 000000000000..48840204a8a0
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-gcc-version.patch
@@ -0,0 +1,23 @@
+From a8bf7bcd7881147c3bcec97d247a2fa4160019d9 Mon Sep 17 00:00:00 2001
+From: Heiko Becker <heirecka@exherbo.org>
+Date: Tue, 5 Jul 2016 00:10:26 +0200
+Subject: [PATCH] Fix detection of gcc6's version number
+
+...and be safe for further new versions.
+---
+ CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1cbeb8f10..8d2958739 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -69,7 +69,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
+ # Now check if we can use visibility to selectively export symbols
+ # Get the GCC version - from KDE4 cmake files
+ exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info)
+- string (REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
++ string (REGEX MATCH "[3-9]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
+ # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
+ # patch level, handle this here:
+ if (NOT _gcc_version)
diff --git a/sci-chemistry/avogadro/files/avogadro-1.2.0-numpy.patch b/sci-chemistry/avogadro/files/avogadro-1.2.0-numpy.patch
new file mode 100644
index 000000000000..4869fa4ea79d
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.2.0-numpy.patch
@@ -0,0 +1,13 @@
+diff --git a/cmake/modules/FindNumpy.cmake b/cmake/modules/FindNumpy.cmake
+index b348418..49ba206 100644
+--- a/cmake/modules/FindNumpy.cmake
++++ b/cmake/modules/FindNumpy.cmake
+@@ -10,7 +10,7 @@
+ #endif (NUMPY_INCLUDE_DIR)
+
+ EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} -c
+- "import numpy; print numpy.get_include()"
++ "import numpy; print (numpy.get_include())"
+ OUTPUT_VARIABLE NUMPY_INCLUDE_DIR
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+
diff --git a/sci-chemistry/molequeue/Manifest b/sci-chemistry/molequeue/Manifest
index 93372b06da13..65a52494b05b 100644
--- a/sci-chemistry/molequeue/Manifest
+++ b/sci-chemistry/molequeue/Manifest
@@ -1,3 +1,4 @@
+AUX molequeue-0.8.0-cmake.patch 4285 BLAKE2B 916f0c248f487b6d7c11dd34e20364b5dfb494d2e27e657bc5a13f9d6c3f71ae2ab6818bace7df04c0a1388f6f85c42e3e0ab96fc5d3d892c0a95612532baf28 SHA512 9031fd3e5efe0a9332db4b1f46d82486fc804cef55c9fab35030bc562d1a40f5f16a02a5eb8c31bf4c50c7a0abcf22c11da5bdd4e2a45a37a8b6f4ff994d3ad6
DIST molequeue-0.8.0.tar.gz 643072 BLAKE2B c9ba0a93e4dac3027de1aeb5ae6c62fc3e4229786973d6c3b56af4b70476b0ed54a563837d489912a40c76b9ce0013e13633a327eb314c34305ba17d7f0b4cf7 SHA512 b9539d2ad2c67188ad254f186c1d67c122a15a32047801c632a1613a4f9c887f38baf2da1bb80cb123391948c2a44604fb1082e475ca6de1e683fbe51266ac84
-EBUILD molequeue-0.8.0.ebuild 1555 BLAKE2B 9ecafc79e0a82bf653b8b6b7d8f28103a2d14c795624b641e4046f29a777c577cd2f850d9c8397ab6bace5e6d1c9c01cec2287760df08c64dc38ea77efba91ab SHA512 ba103e6c00b1957389c5b092fce810bb4ed3b2e32b432f93643fd093118f9106829f2091bee9f80cded61b88cf81a92baf5d9902894072df12e319f78e316e55
+EBUILD molequeue-0.8.0.ebuild 1613 BLAKE2B 21ddbe84fb9ad674cc796330ee2a26f5fdcfc7f6187869d2775e5679bbb2bf2dc147d80c79617867f9b1424bf07eb797315fb5cab3cb59359c39171315cf353c SHA512 6971db16063f3c1dfad7a780adae7aaf438c2957f46698a1739a65ac3d658ccac501f687db18eddc1305a4e6a220cac206d781f5783cdcb0d38b4e952c550ed7
MISC metadata.xml 1257 BLAKE2B 181f9234f11d0cb14fd6b93b42ef153c089d4df8dcb7cf72bc710dbee11bf4bb573f37ea703d02dbe17fa1f39c0aaf591c6d28ad1429abced5108b9ce39f2030 SHA512 10e3dd48ec1e54bc0d47d4c2f0aca427875cc0ceb59a93ab41ab2734607aa6474e80f3ae622e45fa319753591f16439118dd0b301068cb3e16fd79ff11a4f058
diff --git a/sci-chemistry/molequeue/files/molequeue-0.8.0-cmake.patch b/sci-chemistry/molequeue/files/molequeue-0.8.0-cmake.patch
new file mode 100644
index 000000000000..3fd8a9db76be
--- /dev/null
+++ b/sci-chemistry/molequeue/files/molequeue-0.8.0-cmake.patch
@@ -0,0 +1,106 @@
+From 45cbc9f167d1158bc73e87618cc08ede2e3f2911 Mon Sep 17 00:00:00 2001
+From: "Marcus D. Hanwell" <marcus.hanwell@kitware.com>
+Date: Thu, 1 Jun 2017 13:17:20 -0400
+Subject: [PATCH] Removed GenerateExportHeader, bumped CMake min
+
+Removed the GenerateExportHeader copy we had, use CMake's, and bump the
+minimum to ensure it has the features we expect.
+---
+ CMakeLists.txt | 2 +-
+ cmake/GenerateExportHeader.cmake | 375 ---------------------------------------
+ cmake/exportheader.cmake.in | 35 ----
+ 3 files changed, 1 insertion(+), 411 deletions(-)
+ delete mode 100644 cmake/GenerateExportHeader.cmake
+ delete mode 100644 cmake/exportheader.cmake.in
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index df93bc8..a107c8f 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-cmake_minimum_required(VERSION 2.8.8 FATAL_ERROR)
++cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
+
+ project(MoleQueue)
+
+From aae92632d10fe98728c3e73bfd891e502e8712fd Mon Sep 17 00:00:00 2001
+From: "Marcus D. Hanwell" <marcus.hanwell@kitware.com>
+Date: Thu, 16 Nov 2017 15:10:25 -0500
+Subject: [PATCH] Remove deprecated calls for export flags
+
+Move them to the project default variables in the top level.
+---
+ CMakeLists.txt | 8 ++++++++
+ molequeue/client/CMakeLists.txt | 1 -
+ molequeue/servercore/CMakeLists.txt | 1 -
+ molequeue/zeromq/CMakeLists.txt | 1 -
+ thirdparty/qt5json/CMakeLists.txt | 1 -
+ 5 files changed, 8 insertions(+), 4 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index a107c8f..e68d81f 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -4,6 +4,14 @@ project(MoleQueue)
+
+ set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
+
++# Request C++11 standard, using new CMake variables.
++set(CMAKE_CXX_STANDARD 11)
++set(CMAKE_CXX_STANDARD_REQUIRED True)
++set(CMAKE_CXX_EXTENSIONS False)
++# Set symbol visibility defaults for all targets.
++set(CMAKE_CXX_VISIBILITY_PRESET "hidden")
++set(CMAKE_VISIBILITY_INLINES_HIDDEN True)
++
+ include(BuildType)
+ include(BuildLocation)
+ include(CompilerFlags)
+diff --git a/molequeue/client/CMakeLists.txt b/molequeue/client/CMakeLists.txt
+index 674f91a..8cb131a 100644
+--- a/molequeue/client/CMakeLists.txt
++++ b/molequeue/client/CMakeLists.txt
+@@ -20,7 +20,6 @@ set_target_properties(MoleQueueClient PROPERTIES AUTOMOC TRUE)
+ include(GenerateExportHeader)
+ generate_export_header(MoleQueueClient EXPORT_FILE_NAME molequeueclientexport.h)
+ list(APPEND headers "${CMAKE_CURRENT_BINARY_DIR}/molequeueclientexport.h")
+-add_compiler_export_flags(molequeue_export_flags)
+ set_property(TARGET MoleQueueClient APPEND
+ PROPERTY COMPILE_FLAGS ${molequeue_export_flags})
+
+diff --git a/molequeue/servercore/CMakeLists.txt b/molequeue/servercore/CMakeLists.txt
+index 8d4f7ee..aab0bec 100644
+--- a/molequeue/servercore/CMakeLists.txt
++++ b/molequeue/servercore/CMakeLists.txt
+@@ -30,7 +30,6 @@ set(hdrs
+ generate_export_header(MoleQueueServerCore
+ EXPORT_FILE_NAME molequeueservercoreexport.h)
+ include_directories(${CMAKE_CURRENT_BINARY_DIR})
+-add_compiler_export_flags(molequeue_export_flags)
+ set_property(TARGET MoleQueueServerCore APPEND
+ PROPERTY COMPILE_FLAGS ${molequeue_export_flags})
+
+diff --git a/molequeue/zeromq/CMakeLists.txt b/molequeue/zeromq/CMakeLists.txt
+index bc1e893..188f437 100644
+--- a/molequeue/zeromq/CMakeLists.txt
++++ b/molequeue/zeromq/CMakeLists.txt
+@@ -20,7 +20,6 @@ target_link_libraries(MoleQueueZeroMq MoleQueueServerCore ${ZeroMQ_LIBRARIES})
+ generate_export_header(MoleQueueZeroMq
+ EXPORT_FILE_NAME molequeuezeromqexport.h)
+ include_directories(${CMAKE_CURRENT_BINARY_DIR})
+-add_compiler_export_flags(molequeue_export_flags)
+ set_property(TARGET MoleQueueZeroMq APPEND
+ PROPERTY COMPILE_FLAGS ${molequeue_export_flags})
+
+diff --git a/thirdparty/qt5json/CMakeLists.txt b/thirdparty/qt5json/CMakeLists.txt
+index 6d00685..52f5df2 100644
+--- a/thirdparty/qt5json/CMakeLists.txt
++++ b/thirdparty/qt5json/CMakeLists.txt
+@@ -54,7 +54,6 @@ include(GenerateExportHeader)
+ generate_export_header(${QT5_JSON_LIBRARY_NAME}
+ EXPORT_FILE_NAME qt5jsonexport.h
+ EXPORT_MACRO_NAME QT5JSON_EXPORT)
+-add_compiler_export_flags(qt5json_export_flags)
+
+ set_property(TARGET ${QT5_JSON_LIBRARY_NAME} APPEND
+ PROPERTY COMPILE_FLAGS ${qt5json_export_flags})
diff --git a/sci-chemistry/molequeue/molequeue-0.8.0.ebuild b/sci-chemistry/molequeue/molequeue-0.8.0.ebuild
index 3b5733ea45d2..2c20c0bfeeac 100644
--- a/sci-chemistry/molequeue/molequeue-0.8.0.ebuild
+++ b/sci-chemistry/molequeue/molequeue-0.8.0.ebuild
@@ -1,14 +1,14 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
PYTHON_COMPAT=( python2_7 )
-inherit cmake-utils multilib python-single-r1 versionator virtualx
+inherit cmake-utils python-single-r1 versionator virtualx
DESCRIPTION="Abstract, manage and coordinate execution of tasks"
-HOMEPAGE="http://www.openchemistry.org/OpenChemistry/project/molequeue.html"
+HOMEPAGE="https://www.openchemistry.org/projects/molequeue/"
SRC_URI="https://github.com/OpenChemistry/molequeue/archive/${PV}.tar.gz -> ${P}.tar.gz"
SLOT="0"
@@ -22,27 +22,33 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}
RDEPEND="${PYTHON_DEPS}
dev-qt/qtcore:5
+ dev-qt/qtgui:5
dev-qt/qtnetwork:5
dev-qt/qtwidgets:5
zeromq? ( net-libs/cppzmq:0= )"
DEPEND="${RDEPEND}
doc? ( app-doc/doxygen )"
+PATCHES=( "${FILESDIR}"/${P}-cmake.patch )
+
src_prepare() {
cmake-utils_src_prepare
+
+ rm cmake/{GenerateExportHeader.cmake,exportheader.cmake.in} || die
+
# delete bundled Qt5Json library
rm -r thirdparty || die
}
src_configure() {
local mycmakeargs=(
- $(cmake-utils_use_enable test TESTING)
- $(cmake-utils_use_use zeromq ZERO_MQ)
- $(cmake-utils_use_build doc DOCUMENTATION)
- $(cmake-utils_use client MoleQueue_BUILD_CLIENT)
- $(cmake-utils_use server MoleQueue_BUILD_APPLICATION)
+ -DBUILD_DOCUMENTATION=$(usex doc)
+ -DMoleQueue_BUILD_CLIENT=$(usex client)
+ -DoleQueue_BUILD_APPLICATION=$(usex server)
+ -DENABLE_TESTING=$(usex test)
+ -DUSE_ZERO_MQ=$(usex zeromq)
-DINSTALL_LIBRARY_DIR=$(get_libdir)
- )
+ )
use zeromq && \
mycmakeargs+=( -DZeroMQ_ROOT_DIR=\"${EPREFIX}/usr\" )
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-08 18:26:27 +0000