gentoo resync : 30.06.2018

11 files changed, 58 insertions, 17 deletions

diff --git a/sci-chemistry/mdanalysis/mdanalysis-0.7.7.ebuild b/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0.ebuild
index adb280c4b634..65fd1f237e74 100644
--- a/sci-chemistry/mdanalysis/mdanalysis-0.7.7.ebuild
+++ b/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0.ebuild
@@ -1,18 +1,15 @@
 # Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=6
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python{2_7,3_5,3_6} )
 
 inherit distutils-r1
 
-MY_PN="MDAnalysis"
-MY_P="${MY_PN}-${PV}"
-
 DESCRIPTION="A python library to analyze and manipulate molecular dynamics trajectories"
 HOMEPAGE="https://www.mdanalysis.org"
-SRC_URI="https://mdanalysis.googlecode.com/files/${MY_P}.tar.gz"
+SRC_URI="mirror://pypi/M/${PN}/${P}.tar.gz"
 
 SLOT="0"
 LICENSE="GPL-2"
@@ -24,11 +21,12 @@ RDEPEND="
 	sci-libs/scipy[${PYTHON_USEDEP}]
 	sci-biology/biopython[${PYTHON_USEDEP}]
 	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/scientificpython[${PYTHON_USEDEP}]
 	dev-python/GridDataFormats[${PYTHON_USEDEP}]
 	dev-python/netcdf4-python[${PYTHON_USEDEP}]
+	dev-python/mmtf-python[${PYTHON_USEDEP}]
+	dev-python/gsd[${PYTHON_USEDEP}]
+	dev-python/mock[${PYTHON_USEDEP}]
+	dev-python/duecredit[${PYTHON_USEDEP}]
 "
 DEPEND="${RDEPEND}
 	test? ( dev-python/nose[${PYTHON_USEDEP}] )"
-
-S="${WORKDIR}"/${MY_P}
diff --git a/sci-chemistry/MDAnalysis/Manifest b/sci-chemistry/MDAnalysis/Manifest
new file mode 100644
index 000000000000..ff49fd7ac3e4
--- /dev/null
+++ b/sci-chemistry/MDAnalysis/Manifest
@@ -0,0 +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
diff --git a/sci-chemistry/mdanalysis/metadata.xml b/sci-chemistry/MDAnalysis/metadata.xml
index 8425c0d53cb0..8425c0d53cb0 100644
--- a/sci-chemistry/mdanalysis/metadata.xml
+++ b/sci-chemistry/MDAnalysis/metadata.xml
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 1d5d40d45a0c..44dfbce86655 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index b2a5926f20f7..bafc06193a0b 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -14,8 +14,8 @@ EBUILD gromacs-2016.2.ebuild 7971 BLAKE2B 90510b56d31e59f2f7f76e7772b55e4acdb825
 EBUILD gromacs-2016.5.ebuild 7987 BLAKE2B 02bfdcce78718a1e16ad0cdf63e521d656eaa886ddf2ef7016f22abc398b95e240ecb4705a894609f188afbf4ec17c96ee9441ee7510cfaeb02c0ceced4e1b17 SHA512 5d762c0f9212ec0b91fba7565c15787201b1fcd923111b7055d6362b813d92b850f67becff023c57d3846c2f01a7df29e2b5e52d1bd643f797305c59449b1f46
 EBUILD gromacs-2016.9999.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb0f5c40cdf1a75e81b59bd2d603b4235f6e4942e40211b748b7cf8239c90f8d613b20bdc44fca48d23f9c45ae14 SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f
 EBUILD gromacs-2018.1.ebuild 7899 BLAKE2B f70665f54e2103275dbf7466d15c15ce41593264bb768b542a49eebd76b1764871ac9b82e9eacee5db1a413cac8863a6e87d751cdb2196ff5a431a096c7f6f3f SHA512 3cb7bab30e822420e308b15af997f01ab3ce3072ddefc752d5f0d314040f699febcd804d983cf9af160d1388b38a62e81c9ee6fc7a6647a5d7e199262b3afec9
-EBUILD gromacs-2018.2.ebuild 7899 BLAKE2B f70665f54e2103275dbf7466d15c15ce41593264bb768b542a49eebd76b1764871ac9b82e9eacee5db1a413cac8863a6e87d751cdb2196ff5a431a096c7f6f3f SHA512 3cb7bab30e822420e308b15af997f01ab3ce3072ddefc752d5f0d314040f699febcd804d983cf9af160d1388b38a62e81c9ee6fc7a6647a5d7e199262b3afec9
-EBUILD gromacs-2018.9999.ebuild 7899 BLAKE2B 8053de4c12e2201d37e8d0a077d33fc0b103b79d73379488c46bc638ba763b55ebf69ae53180ffd850e4b860fc03a1c3ec57049f1b257e04e0322ed482afcd51 SHA512 734710474160c6a55206b332e5370bd9e2d0092aed19c4c1ccab7f5d9567eac2a47d163a50aa607f8c7e8e2ccc6eadeb9b394e9f638ac85eafe5f74ced68fd02
+EBUILD gromacs-2018.2.ebuild 7859 BLAKE2B 43d1ce476e49201e337c214fa6fcd5fdd83d0f8f209057ee00edffbcbdbfd7cc08177f029702dc26eb111c725b3347e72623a1008857911b1866142395e0d066 SHA512 f080df3b8befb1b6de337f297b561dd76069d15e4053149d1e6e3d98938349ce6e6acab8a73286dd239798be79d0ee9f081b9631aeac5e671de582e68099f574
+EBUILD gromacs-2018.9999.ebuild 7859 BLAKE2B 43d1ce476e49201e337c214fa6fcd5fdd83d0f8f209057ee00edffbcbdbfd7cc08177f029702dc26eb111c725b3347e72623a1008857911b1866142395e0d066 SHA512 f080df3b8befb1b6de337f297b561dd76069d15e4053149d1e6e3d98938349ce6e6acab8a73286dd239798be79d0ee9f081b9631aeac5e671de582e68099f574
 EBUILD gromacs-4.6.9999.ebuild 8110 BLAKE2B dd8ac9cbc4abfcc75a3a188c59cdbe5111f363404ff5a787f64b05d4bd411deebb50f172f09963800ed87997788b2e678617805e65a523bed19aa6ef18fe2b96 SHA512 2206e257f0b29b6f3a90c5d7739079b9add3e04f2a3acbd58c814811b389b5d51b3594815a94529d1de43deb380504029c302d18fc16d63a81c92727254e863e
 EBUILD gromacs-5.0.4.ebuild 8429 BLAKE2B c06c423365fa79befd5a4f0b6314e77b96d983c84df776ce84fddc79d35ce735d856d1184e5913af0c8cd3a0c4e9087110af9bd4402e2bce1f014e64a8a585a7 SHA512 d1e91cc25c5f90bd0fbad15060cae9c8bf1235ca45a2b72521b3a4f5f091bdd7d32ec2e6ff2bb22cd3fe165092f11a24ea148ae8000b8517f0b8671f6c2af6f2
 EBUILD gromacs-5.0.9999.ebuild 8439 BLAKE2B 33d51254e62593a58c636bd902f43edc553ad11af306d1d022278b223eda15b0772097f26565df74a1118bd5b144e5b93aac09cdb995123ccbae2856889c31b2 SHA512 6756116cdeae9c21b094f74ea1b1d9f41617467dc736878cdcff27fed9f53b338830a608e23e87238d0756884799fbc5d62f02685774ea86c239ecc3e8804814
diff --git a/sci-chemistry/gromacs/gromacs-2018.2.ebuild b/sci-chemistry/gromacs/gromacs-2018.2.ebuild
index 11f2b2483a38..d4ea677a994c 100644
--- a/sci-chemistry/gromacs/gromacs-2018.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2018.2.ebuild
@@ -158,7 +158,6 @@ src_configure() {
 		-DGMX_HWLOC=$(usex hwloc)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 		-DBUILD_TESTING=$(usex test)
 		-DGMX_BUILD_UNITTESTS=$(usex test)
diff --git a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild
index 315835fdc606..d4ea677a994c 100644
--- a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2018.9999.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
@@ -158,7 +158,6 @@ src_configure() {
 		-DGMX_HWLOC=$(usex hwloc)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 		-DBUILD_TESTING=$(usex test)
 		-DGMX_BUILD_UNITTESTS=$(usex test)
diff --git a/sci-chemistry/mdanalysis/Manifest b/sci-chemistry/mdanalysis/Manifest
deleted file mode 100644
index 45f2902026d6..000000000000
--- a/sci-chemistry/mdanalysis/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST MDAnalysis-0.7.7.tar.gz 3262287 BLAKE2B e1161e44f40de99b425e5f9667c9d207ecc7ec5fd93b1d29bfaad52a0dc532f09ed754dc9c5898a273363a770c9ecec863286fcc40dc0296dbc5e2e20a91a1a4 SHA512 c26085c767ec213d5aa27709029e5a3b9df786c10e23e3841ffc9644e2fd66c8add0358f013c51a95fa3452c5c900b44901db736830504b669916ea45a924712
-EBUILD mdanalysis-0.7.7.ebuild 876 BLAKE2B 741e83613c33453578ed9eb82d72a85171397a0d927eb30e1e5744386fa7a5ffa5c871c622197e5e30885a720dc69fd45a0509cdcd2f2a6920a995f9625f37e0 SHA512 db775932e5ae655b2742c8312a3279056f662b37edc24ede67d0dc031babe9bf10e301c3b0915825f3e4b58fd0120a26cb9f90192b28a575b456f9754fadee56
-MISC metadata.xml 259 BLAKE2B dfc879984b6adce945d0e0a50f6ede2bca87147b9db99491359cdeccc2e74a20d56e14ae8903dbb80c94854f89bee539f14a4e3ce864204e277accf3f124a748 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706
diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest
new file mode 100644
index 000000000000..d4b7e143cac0
--- /dev/null
+++ b/sci-chemistry/mdtraj/Manifest
@@ -0,0 +1,3 @@
+DIST mdtraj-1.9.1.tar.gz 1985711 BLAKE2B 625b7c1da998bd46732604dcc93c76f970f3c79f10e81aa9f4b3051ee45101efea8afd803d539ba1831dac3e7ed208d7c3773f74189a3887063cbff2b4d79df6 SHA512 015d9d1e258a7a207ac3b7e7a81b87c308e8684ee0a173ae9b722a90910e95e7f2ee18158c163212fae39d093b0cf397293d6e713538acb1fd20a7b70f2adc76
+EBUILD mdtraj-1.9.1.ebuild 889 BLAKE2B fd2423ca08f4666101c409c52be19c717d222c19da08424c2923e91bb9ad6961c64b3fb97a6b71e1d5a9a9cd568f0325510943c388c35c59049f4597ce0cca02 SHA512 61c0a2351c18155aec9bf5fcd6a3f7b2e319c096f493866f94789b11bfbef4a6bbfe849a111acad74503bb30d327c10e15b34338f752763f77e3033b2e287680
+MISC metadata.xml 259 BLAKE2B dfc879984b6adce945d0e0a50f6ede2bca87147b9db99491359cdeccc2e74a20d56e14ae8903dbb80c94854f89bee539f14a4e3ce864204e277accf3f124a748 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
new file mode 100644
index 000000000000..2ac95db2c57d
--- /dev/null
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_5,3_6} )
+
+inherit distutils-r1
+
+DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
+HOMEPAGE="http://mdtraj.org"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/pytables[${PYTHON_USEDEP}]
+	dev-python/networkx[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}
+	test? ( dev-python/nose[${PYTHON_USEDEP}] )"
+
+python_prepare() {
+	sed -e "s:re.match('build.*(mdtraj.*)', output_dir).group(1):'.':g" \
+		-i basesetup.py || die
+	distutils-r1_python_prepare_all
+}
diff --git a/sci-chemistry/mdtraj/metadata.xml b/sci-chemistry/mdtraj/metadata.xml
new file mode 100644
index 000000000000..8425c0d53cb0
--- /dev/null
+++ b/sci-chemistry/mdtraj/metadata.xml
@@ -0,0 +1,8 @@
+<?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>
+</pkgmetadata>