gentoo resync 08.09.2018

7 files changed, 52 insertions, 90 deletions

diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild
deleted file mode 100644
index 4c953dd73e3c..000000000000
--- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-if [[ $PV = *9999* ]]; then
-	scm_eclass=git-2
-	EGIT_REPO_URI="https://github.com/orbeckst/${PN}.git"
-	EGIT_BRANCH="develop"
-	SRC_URI=""
-	KEYWORDS=""
-else
-	scm_eclass=vcs-snapshot
-	SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-inherit eutils distutils-r1 ${scm_eclass}
-
-DESCRIPTION="Python framework for Gromacs"
-HOMEPAGE="https://orbeckst.github.com/GromacsWrapper/"
-
-LICENSE="GPL-3 LGPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND="
-		>=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}]
-		>=dev-python/RecSQL-0.3[${PYTHON_USEDEP}]
-		>=sci-libs/scipy-0.9[${PYTHON_USEDEP}]
-		"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}/0001-Drop-chmod-hack.patch"
-)
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.2.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.2.ebuild
deleted file mode 100644
index dc2488dd3b95..000000000000
--- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.2.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-if [[ $PV = *9999* ]]; then
-	scm_eclass=git-2
-	EGIT_REPO_URI="https://github.com/orbeckst/${PN}.git"
-	EGIT_BRANCH="develop"
-	SRC_URI=""
-	KEYWORDS=""
-else
-	scm_eclass=vcs-snapshot
-	SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-inherit eutils distutils-r1 ${scm_eclass}
-
-DESCRIPTION="Python framework for Gromacs"
-HOMEPAGE="https://orbeckst.github.com/GromacsWrapper/"
-
-LICENSE="GPL-3 LGPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND="
-	>=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}]
-	>=dev-python/RecSQL-0.3[${PYTHON_USEDEP}]
-	>=sci-libs/scipy-0.9[${PYTHON_USEDEP}]
-	"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}/0001-Drop-chmod-hack.patch"
-)
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.5.1.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.7.0.ebuild
index 3e946ea31dd4..55ff025bcf66 100644
--- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.5.1.ebuild
+++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.7.0.ebuild
@@ -1,26 +1,26 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python{2_7,3_5,3_6} )
 
 if [[ $PV = *9999* ]]; then
-	scm_eclass=git-2
-	EGIT_REPO_URI="https://github.com/orbeckst/${PN}.git"
+	scm_eclass=git-r3
+	EGIT_REPO_URI="https://github.com/Becksteinlab/${PN}.git"
 	EGIT_BRANCH="develop"
 	SRC_URI=""
 	KEYWORDS=""
 else
 	scm_eclass=vcs-snapshot
-	SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz"
+	SRC_URI="https://github.com/Becksteinlab/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz"
 	KEYWORDS="~amd64 ~x86"
 fi
 
 inherit eutils distutils-r1 ${scm_eclass}
 
 DESCRIPTION="Python framework for Gromacs"
-HOMEPAGE="https://orbeckst.github.com/GromacsWrapper/"
+HOMEPAGE="https://gromacswrapper.readthedocs.io"
 
 LICENSE="GPL-3 LGPL-3"
 SLOT="0"
@@ -28,7 +28,6 @@ IUSE=""
 
 DEPEND="
 	>=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}]
-	>=dev-python/RecSQL-0.3[${PYTHON_USEDEP}]
 	>=sci-libs/scipy-0.9[${PYTHON_USEDEP}]
-	"
+	dev-python/six[${PYTHON_USEDEP}]"
 RDEPEND="${DEPEND}"
diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest
index 5ce00a7c0188..ae9d72746d05 100644
--- a/sci-chemistry/GromacsWrapper/Manifest
+++ b/sci-chemistry/GromacsWrapper/Manifest
@@ -1,8 +1,4 @@
 AUX 0001-Drop-chmod-hack.patch 863 BLAKE2B 974af7be159438f5afdaab56ec92be293396bb3dedd64a759af53634905ff24b46acdac29bdf1046ddda25fac8850f9e66691e8bf03464e2de0975922b9e7090 SHA512 d37a73ca6ecd54c149699177cd10af9782a7ee48c77911a027705728f76a1631f71b37d0263285373877c2e5db8b00dcaafd3e1d6a8dd7d62b1253a905fc5d58
-DIST GromacsWrapper-0.3.1.tar.gz 1575486 BLAKE2B 3ffb89f1e2facc281c58b48e1acf50fe14d2f0e095ac59a1fc9a571118926fa3d054bfc3ee1debdc46f7ec09fcd60944de460933048d6cc9f10d0411bc246c1a SHA512 655dae431bf575963af58a5f75abe6703fe1ecdddba5839b671d9237ddee0e33ab19b528e89bcba4db9063fe30622d44e8f47c7b6452b4d1eed8c7400873a012
-DIST GromacsWrapper-0.3.2.tar.gz 1592147 BLAKE2B 5b04deab9ab8f19f4fee9c7f0d1a614e64996635a5c8923e2271f26dc3ff7a03886a0306199e894b48267adc8dfc2dd853aeb37860007b27edd2d0c2424a7b35 SHA512 a9e0abb5e7ad0c6831e23b6a8c09c6e4cc74b33d66cd17df8e00b876dc275dda11c3d3723565d8d58c45bdf6b2b00323bf85e24e2d5324a8d8b597cc3e5d78a4
-DIST GromacsWrapper-0.5.1.tar.gz 1247839 BLAKE2B acab6411167c68fe8e1761418ab6f96918fa0eda91a2de15ccebacaf47e7352455576b2666982c25f5a6af4f10a443b4f20a6887998b68f12b13e1cfb4b8e838 SHA512 43b6b47e24cbb118492495370b165eb4b0e7672ba4e1c868d3039a0ad0b9828058f30ab7344118c7b0e7dd166ac325ea2b3483bd28b8f65dd972a101a5b9facd
-EBUILD GromacsWrapper-0.3.1.ebuild 848 BLAKE2B cfc7cfc4153f12a8bce73ab447b465b0659de54fabc9d1ceb61300d562e93386dbef8200b00e32f05501fc4f09a0cd4f18019641e198dd4ba619bc4c280cefd4 SHA512 0bf92353d341f72ab5dee745cae125329032fb9109524d9a388853b8a6c8ff425da8d7a806f98a9d5a5ce6d29646c5755d39e4ab18815429b58b987eb06e5ce0
-EBUILD GromacsWrapper-0.3.2.ebuild 844 BLAKE2B f1ebc15f0b1cbbeec8f963b651d9c25e51056d307f5b2548bc50e26e13914181e6f3a2187c53865b6325bf65c07e1cc4c401d76a1187f11f8d61739b47629573 SHA512 84d8ca613fd783ea77f916ae44390bed18d36a445ef06abfdfc7c9f413eb05a00a6b4c35706d78eef0cae209343e6c7246270dfd2d3d682f028b56ef00fbd057
-EBUILD GromacsWrapper-0.5.1.ebuild 789 BLAKE2B 5cc2a80e07eb20bcd463239f3990f31a115ba241f4a572114fb7aace02d5d43b2c42835761fb12d8b6b912ba882afb690124e73c14c9ccd4ce19c6f117003c15 SHA512 47a145cee1780f80a90a289d29d795141ff1a7d98a443b3fedf44bd173358e1a86b04ec2c72118faa9f715484973c15877e1bc92696ab65f84ecf1dd3f3f98ca
+DIST GromacsWrapper-0.7.0.tar.gz 1177718 BLAKE2B 88515b14ce85ecdf0323c3e4a68ac702cfc14569508be015fafc8192174af792507f6d10935aed2f969417ad34d5a1216688e9dce2f6dc6fc47529b87572d229 SHA512 74f6c5b84556b79ced128e48bf111cc40306b8854c8fcf53cab8f2fcf2dce56367e075c116f50aa1aa0947c83af0641bc78045e7d5035f2a8813f9709edce097
+EBUILD GromacsWrapper-0.7.0.ebuild 791 BLAKE2B 37fc7272107e139932930627ecaacebc074addcb0cf6208835d9034b18d6ba9012fa94ce27662f3f71d7baa7c2b44fc2f7a7b99553378bfa17f641087b76ec33 SHA512 d98ee09bc0326207469eb832bfdf3fc61fc83b526ade01994c17bd4cd37313f42913f6bf62665e3834eaf12231e176887192bfb6d709edbb7b547152464a65d2
 MISC metadata.xml 478 BLAKE2B 43348f9431c7456df96e838aeea11d6e3ce3c4c38c796d0746cd249f167e9a55fbd57c3e8d7b731facd530492e14ff165c54fc4c97facddba948dd02a2c4bd2e SHA512 2214eed914af825f9ab83c1de633c00cf2d3f39ad9f88dde4b21264856e3f7ba960fcacf512d0308f6d351857c76a8ad5aa494988c3c03bfd172a233a7f3207a
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 3ae4d9f58c39..64f12e2e4707 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/ParmEd/Manifest b/sci-chemistry/ParmEd/Manifest
index b778b1dfe512..63e7763ea1fa 100644
--- a/sci-chemistry/ParmEd/Manifest
+++ b/sci-chemistry/ParmEd/Manifest
@@ -1,3 +1,5 @@
 DIST ParmEd-2.7.3.tar.gz 34494858 BLAKE2B 8e3ac8776f30ac73b06fd2241e5d73ba54517805ffcef7cb2f71281248df4f8afdaa05c2186ff50ba0df45df313ebdecd69a4482c8339d41baf804c37069affe SHA512 a3444f915e188bcc924f28b6b4235246e2c063ae98881c48f6e13ebc685d085d6a1bcb61b29509a343cbe58369bc6233acc20ee620c6f1d42da2033772a12e07
+DIST ParmEd-3.0.3.tar.gz 35159355 BLAKE2B 76b4655905276fe498f38c6a3bd483e89e95d3a339fbcd9ceb90d16f68d417b62e0aacaf18143d0b57167ee7acdc726c44324c844462af4d2385872210daef2a SHA512 60b8ee100a301fbddec8323a3dba550c96ffa09624f41e457d4b3941a4e4a15e903c3da6de24a5183731406f19f9e6436a2111d654bc902c0f06ac8b643acf09
 EBUILD ParmEd-2.7.3.ebuild 834 BLAKE2B 6e4210b0f874f70b384373cfe13f56998850f9fad7eeafb4854054f847286e6b72da412328616245ba8df48cfb50d61c7c78c2f548e278ab3b1414859cd178c5 SHA512 af1046b0ea4ad34a6ec3871da13fb42b1290654d26278c77dc4a2d27bde941f4782acc0da7bf6c3b9fcb0599596938e1bce60572a7768bdef2cf516f888c6df3
+EBUILD ParmEd-3.0.3.ebuild 835 BLAKE2B 5ea026dffca8d6c7fca6514f8b0b0904d932125e980a9629b994cddcab47fb8d84886bebbef9748315c741bad2850db1e836d455343a8b643b50c5a98776cc0e SHA512 960747822dd07c0e24391f7bb3447e7518772af852ee7406f2fa80603a789293051ba2f0230504fdabf8c1a9afa3c88db262aa8749af92d05647d86b0832511a
 MISC metadata.xml 468 BLAKE2B 2e3781c6ebea297fb8480c2d54be22da0e8d6906607513e3b78fe89a926cf691048fb90576cadde7321d964e8269950437f48bb54270c9a1bd487bfe3ce30b84 SHA512 47e3516aabe02112a52e851ac9294a0096001373d546462f9185754356c72dd37a0a8efa3b40311e43e27e2953ea5879c1141488649f3faef0aa43a692205499
diff --git a/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild b/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild
new file mode 100644
index 000000000000..6ea7bdee606e
--- /dev/null
+++ b/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+
+if [[ $PV = *9999* ]]; then
+	scm_eclass=git-r3
+	EGIT_REPO_URI="https://github.com/${PN}/${PN}.git"
+	SRC_URI=""
+	KEYWORDS=""
+else
+	scm_eclass=vcs-snapshot
+	SRC_URI="https://github.com/${PN}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+inherit eutils distutils-r1 ${scm_eclass}
+
+DESCRIPTION="Parameter/topology editor and molecular simulator"
+HOMEPAGE="https://parmed.github.io/ParmEd/html/index.html"
+
+LICENSE="LGPL-2"
+SLOT="0"
+IUSE=""
+
+DEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+"
+
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	sed \
+		-e "/delfile/d" \
+		-e "/deldir/d" \
+		-i setup.py || die
+	distutils-r1_src_prepare
+}