gentoo resync : 18.11.2019

7 files changed, 39 insertions, 16 deletions

diff --git a/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0.ebuild b/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0-r1.ebuild
index 65fd1f237e74..0e9af8987fab 100644
--- a/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0.ebuild
+++ b/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python{2_7,3_5,3_6} )
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
 
 inherit distutils-r1
 
@@ -28,5 +28,7 @@ RDEPEND="
 	dev-python/mock[${PYTHON_USEDEP}]
 	dev-python/duecredit[${PYTHON_USEDEP}]
 "
-DEPEND="${RDEPEND}
+BDEPEND="${RDEPEND}
 	test? ( dev-python/nose[${PYTHON_USEDEP}] )"
+
+RESTRICT="!test? ( test )"
diff --git a/sci-chemistry/MDAnalysis/Manifest b/sci-chemistry/MDAnalysis/Manifest
index ff49fd7ac3e4..5918592720ec 100644
--- a/sci-chemistry/MDAnalysis/Manifest
+++ b/sci-chemistry/MDAnalysis/Manifest
@@ -1,3 +1,3 @@
 DIST MDAnalysis-0.18.0.tar.gz 11085390 BLAKE2B 70b5530a0800370fbee2805d8c4cb495f2e339b29c13c0a2442e3310c1b941ccf459a19d0a490c47a28b77ffeeaca581100ef06b7196cb9fcdb1b71d5d0c871f SHA512 b235471c04ab2e117fe25e972d88a6245b1641f96d30eafd2f68949c8af8c1360eed49b1ec9960d8c386c0bbca8b3749cec322eb19f9975f15225983af0f5819
-EBUILD MDAnalysis-0.18.0.ebuild 903 BLAKE2B 6b35431dccd6c330cc590196b383dc51b8441056ee1ed6c3d7ecd7d2e7849f8e33e4b57a3636dc67cf6d26eec3be00107152206d0a5e33ccbac918d1fdf5d469 SHA512 6bacf24df020e77bdbf7fd873e7ed1141a99d6b1f43979ae7822d12f265f1b6d235f076bc03a1b818e7a85ca37a83ab21d53e620f6c324cd9a1e8de28c716b0a
-MISC metadata.xml 259 BLAKE2B dfc879984b6adce945d0e0a50f6ede2bca87147b9db99491359cdeccc2e74a20d56e14ae8903dbb80c94854f89bee539f14a4e3ce864204e277accf3f124a748 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706
+EBUILD MDAnalysis-0.18.0-r1.ebuild 935 BLAKE2B e20982f0b1532c30382a9f3a11fff7fe423dc1e06c8be7cacecc5f9cd6ad3f3249334729f4f1ee790bd97a6af8d5954a9ff80d1fddfcbdd3e7172187a45f2d71 SHA512 545868919c247f71b06264cf3b99d70a6f52d32978bf165c795c58bb544305fe2d50508f8434b52581a3b5cfe47a74dd713dc86fad7944ae984dd8e39db6144e
+MISC metadata.xml 496 BLAKE2B 1b6faf13663ab39bbb2c5b123f67cd7688c188459133d77411c857bd901f8133f9791d8c54e8fe7dc84e8150187b6562f297e706d36e167b3c20cf7df6e6a682 SHA512 674265a9bdb74cc5d4b059ce2b33cdba84bee097bb5940b3cc55cfdc6b74de5f28a4cfa34e9f0fd4db5d3c336a6f7b3be39235c2d9697d5adf9c7311e348d8a1
diff --git a/sci-chemistry/MDAnalysis/metadata.xml b/sci-chemistry/MDAnalysis/metadata.xml
index 8425c0d53cb0..6b7aa8ce58ab 100644
--- a/sci-chemistry/MDAnalysis/metadata.xml
+++ b/sci-chemistry/MDAnalysis/metadata.xml
@@ -1,8 +1,16 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <maintainer type="project">
-    <email>sci@gentoo.org</email>
-    <name>Gentoo Science Project</name>
-  </maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexxy@gentoo.org</email>
+		<name>Alexey Shvetsov</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">MDAnalysis</remote-id>
+		<remote-id type="github">MDAnalysis/MDAnalysis</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index c70eca4a8dc0..893a1088c3e2 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/molden/Manifest b/sci-chemistry/molden/Manifest
index e3496da35ceb..1c85a8486821 100644
--- a/sci-chemistry/molden/Manifest
+++ b/sci-chemistry/molden/Manifest
@@ -4,10 +4,11 @@ AUX molden-4.8-ldflags.patch 866 BLAKE2B ba4e859d0706e17e926b3f55ed03bac5d50dcb0
 AUX molden-4.8-overflow.patch 714 BLAKE2B fe94c6192632388f9e88f68abf2c9467e11fec068d13f510217870a897f4ac685fc5651a8a60db2f1b72d967275b34f84aeb9d598cad7d8323ace3d66ec44b36 SHA512 ecc4f4501166a4ed4a1c451901d3aed49e3ad7fd3833cb4419a62b1864e689399ca68562fbc82784813881a003a405d4eea5d0e351a9181cbb164beb702d3765
 AUX molden-5.0-ambfor.patch 523 BLAKE2B 1443a26ff5fbaab3092a6df6a5ab0d514547d59788030ea1c761b8867cf042ff53f6382b85c7aa5383a85504c99e625e9e9c13cd96e1c52a2e05347286be474a SHA512 f531d3bd50374bf658e710f2e4b649559503b378ab663f03cd9259b9105b6c25eab61318bb3d02814425ecb596802569aa3281741d611d4e1c8fc4da771fd481
 AUX molden-5.0-overflow.patch 341 BLAKE2B c7285c87c0741ecf6bce3bad89883ed6e7720cb72a479c9bea7ad8a1dabcc1ae8894f6811e2d537555a00cb9138a7b579dee631221efb3a721b77b446abcb82d SHA512 342b7531179b8a3c3aedff085022d972bd795d2c56ebf4b49fce5ff60e6cc9ea48ed18258af53042ad72aae400f694aec9692bc0b1abfa960bc100ee02f57981
+AUX molden-5.5-gcc8.patch 328 BLAKE2B e098e680a5b75ff09fbaecf44609055584b0f1c49edc0ea16b81dbff68b06883dc6317340b3dc6b26836958d1f561b3aed383964f7c65126079f74b3023f96dd SHA512 cc1a8c08b9081ff138aedda11887295f0eb31b97174ce45bffae8e563318388035948775f03d39823280103ea522a20939b6294e3d3721e599e6790e4a5695e2
 DIST molden4.8.tar.gz 2969701 BLAKE2B 943bfd7bd8dde2da8e171f4a0f5e570ec1a064ef92e6ae4f6cbc48289e42c4660e021965670c132328e575d2ca388fccf7f8ae77d4f7342b55fe5522f2f63c6e SHA512 11f2406e54a077d044369b5eee4a8a1c1b10f052188d33d4162af0151a1e76a1d5274d8788bbc3610905ff271b0bd2100990b77540a0290ad608bd5c29b839e3
 DIST molden5.0.tar.gz 3063244 BLAKE2B 857f3276e45d05f92f291b0189cdcb7aeacd9ede0eeaf1ebe6b6942d397bbdd83812b4a5c8163be75a5a3c7bd0b29c9304d29ae596e04ba9bfbb30960e899326 SHA512 bf45849bf4efb67bc552767c28a6df6e5106a7d8ac2d73db2c7218412fb6cd2f2785c2be83a8589a5664ba9c0ca052cef5eb155c665ee1f3d6c7fe208f806a6b
 DIST molden5.5.tar.gz 4934764 BLAKE2B 6ce71f928ed9aacf8fe9830c4c36a675f81d63e97d08e96519ff74d172540ae0a9af25ca966d6c02cdcbbc43633a0ef80be9d31ef98a80d59a8e1a13374c2f51 SHA512 45269d2c7a52b3b2bf4fdb5f4ca3912637b3414ff9dfcd0d4f23815b3dcf7a53ffee717420d4fbf286b71c972539e756a440f5e37b7b7325ab312c25fc6c47b0
 EBUILD molden-4.8-r2.ebuild 1726 BLAKE2B ed9494e53f93b3de114e1032c88658628efe0e30af1b8670a32b090f7b6bd720c9a0795a4a4e5ba1fc7d6f50439b8f6b85e671854e1ae79e18d952356dce0483 SHA512 ca0772ada2086f91150f8a0ab2a86c9a9a6169a89e2c8c0f6b4ab4d368906f5d5d2807cd228e1f42292c6562d980a0e206f568433b396d23c7846beb65dd6f5a
 EBUILD molden-5.0.ebuild 1733 BLAKE2B 2d5e3657c53ae6f7ca67996d63ec98776d1de5330ae050b8d8191289d6800298bdccc1361b57df4573f2e99d2688edc09234a72b2c29431e482406c37bcf213e SHA512 0584ad6f157bab063a79b8e095dedec04e6a2f1d05d5483027dc8c7b0b8455956140ae69f9d6749b47ce69db30d62d391e9f7a7e00dba696d73687861d6bd604
-EBUILD molden-5.5.ebuild 1540 BLAKE2B 472584a4e2e5a03ab369442e5fccfae80833151ec125b895aa369d5d2770d2da64425409a39e3d79b3e8831ee4d86bf710662847968ef0ba7cfbd300da6731ac SHA512 01705f51b1b6992dbbb8e2fcab6cb43f40a3cbf6da1023a0ea12ef626d1995327ee0afd39bd70e0520a8fad015a1a76d5d1e9f3886ef5195fa6b9713d6bcf334
+EBUILD molden-5.5.ebuild 1639 BLAKE2B 7f3b42046e10a433442cc664c6552c9f74ca5bc142da2bc5fe813cc7deb78d4cb1e9231c0554b0ec3d500f72c6104595c053555f66c28e982394fc973bda8455 SHA512 185d8c4004d0023b3663f13b793fb99a6f17573c1dfdc87602b97f0735cb4a52f4c9f7f833f01ccbf837f311ded87f61418c16d918955a67c9c962d149f3d054
 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/molden/files/molden-5.5-gcc8.patch b/sci-chemistry/molden/files/molden-5.5-gcc8.patch
new file mode 100644
index 000000000000..b76cb6302679
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-5.5-gcc8.patch
@@ -0,0 +1,9 @@
+--- a/rdchx.f	2016-01-25 17:56:49.000000000 +0600
++++ b/rdchx.f	2018-08-24 16:51:14.000000000 +0700
+@@ -6004,5 +6004,5 @@
+       implicit double precision (a-h,p-z),integer (i-n),logical (o)
+       parameter (mxcon=10)
+-      dimension iconn(mxcon+1,*),icnn(mxcon+1)
++      dimension iconn(mxcon+1,*),icnn(*)
+ 
+       ibnds = 0
diff --git a/sci-chemistry/molden/molden-5.5.ebuild b/sci-chemistry/molden/molden-5.5.ebuild
index 9bc1635e9353..425238389f6e 100644
--- a/sci-chemistry/molden/molden-5.5.ebuild
+++ b/sci-chemistry/molden/molden-5.5.ebuild
@@ -1,9 +1,8 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
-
-inherit eutils fortran-2 flag-o-matic toolchain-funcs
+inherit desktop fortran-2 flag-o-matic toolchain-funcs
 
 MY_P="${PN}${PV}"
 
@@ -13,7 +12,7 @@ SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molgraph/${PN}/${MY_P}.tar.gz"
 
 LICENSE="MOLDEN"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="amd64 x86"
 IUSE="opengl"
 
 RDEPEND="
@@ -21,7 +20,8 @@ RDEPEND="
 		virtual/glu
 	opengl? (
 		media-libs/freeglut
-		virtual/opengl )"
+		virtual/opengl )
+"
 DEPEND="${RDEPEND}
 	x11-misc/gccmakedep
 	app-editors/vim"
@@ -34,6 +34,7 @@ PATCHES=(
 	"${FILESDIR}"/${PN}-5.0-overflow.patch
 	"${FILESDIR}"/${PN}-4.8-ldflags.patch
 	"${FILESDIR}"/${PN}-4.7-implicit-dec.patch
+	"${FILESDIR}"/${PN}-5.5-gcc8.patch
 )
 
 src_prepare() {
@@ -67,6 +68,8 @@ src_compile() {
 
 src_install() {
 	dobin ${PN} g${PN} $(usex opengl ${PN}ogl "")
+	doicon gmolden.png
+	make_desktop_entry gmolden MOLDEN gmolden.png
 
 	dodoc HISTORY README REGISTER
 	cd doc || die