Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci

82 files changed, 499 insertions, 1089 deletions

diff --git a/dev-python/opal-client/ChangeLog b/dev-python/opal-client/ChangeLog
index ac3fec3a2..d9bb7eb3e 100644
--- a/dev-python/opal-client/ChangeLog
+++ b/dev-python/opal-client/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for dev-python/opal-client
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*opal-client-2.4.1 (15 Jun 2013)
+
+  15 Jun 2013; Justin Lecher <jlec@gentoo.org> -opal-client-2.2-r1.ebuild,
+  +opal-client-2.4.1.ebuild, metadata.xml:
+  Version BUmp; BUmp to EAPI5 and python-r1.eclass
+
 *opal-client-2.2-r1 (02 Dec 2010)
 
   02 Dec 2010; Justin Lecher <jlec@gentoo.org> -opal-client-2.2.ebuild,
diff --git a/dev-python/opal-client/Manifest b/dev-python/opal-client/Manifest
index 45e1445b1..adef77f5c 100644
--- a/dev-python/opal-client/Manifest
+++ b/dev-python/opal-client/Manifest
@@ -1 +1 @@
-DIST opal-py-2.2.tar.gz 1012870 SHA256 d11588ed29dac2812b4293204e0f0d75ba3b765f31af095e0e6333365afe0b47
+DIST opal-py-2.4.1.tar.gz 1089581 SHA256 78d82dbdab607a3acb40e0462a0418b856f3ef8c83cb302f55c4549d672e7085 SHA512 8b8563507d5905a2bc2d36552b52a9ce4da555910496242cfed207ea573da973ac78678fff158066db91154a6f38b5dc8701b8484781143ebd4134b440d01292 WHIRLPOOL 3ebd0992c2ff85974fc369820d42f44a866a1a5fcbbdca80839b14e66b27cb4f1cf2a70a9375078700b117316493934ef8e82965045f4d5602a6d669b6d38587
diff --git a/dev-python/opal-client/metadata.xml b/dev-python/opal-client/metadata.xml
index efb490d78..4bf6dbc6b 100644
--- a/dev-python/opal-client/metadata.xml
+++ b/dev-python/opal-client/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
+  <herd>sci</herd>
+  <maintainer>
+    <email>sci@gentoo.org</email>
+  </maintainer>
 </pkgmetadata>
diff --git a/dev-python/opal-client/opal-client-2.2-r1.ebuild b/dev-python/opal-client/opal-client-2.2-r1.ebuild
deleted file mode 100644
index 69f0ed7e4..000000000
--- a/dev-python/opal-client/opal-client-2.2-r1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="3.*"
-
-inherit python
-
-MY_PN="${PN/client/py}"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Python Opal Web Service Client"
-HOMEPAGE="http://nbcr.net/software/opal/"
-SRC_URI="mirror://sourceforge/opaltoolkit/${MY_P}.tar.gz"
-
-LICENSE="opal"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	>=dev-python/zsi-2.1_alpha1
-	!=sci-chemistry/apbs-1.1.0"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${MY_P}
-
-src_prepare() {
-	python_copy_sources
-}
-
-src_install() {
-		"${EPREFIX}"/usr/bin/wsdl2py  wsdl/opal.wsdl || die
-
-	installation() {
-		insinto $(python_get_sitedir)/AppService
-		doins AppService_*.py || die
-	}
-	python_execute_function -s installation
-
-	dodoc README CHANGELOG etc/* *Client.py || die
-	dohtml docs/* || die
-}
-
-pkg_postinst() {
-	python_mod_optimize AppService
-}
-
-pkg_postrm() {
-	python_mod_cleanup AppService
-}
diff --git a/dev-python/opal-client/opal-client-2.4.1.ebuild b/dev-python/opal-client/opal-client-2.4.1.ebuild
new file mode 100644
index 000000000..0eefd41b6
--- /dev/null
+++ b/dev-python/opal-client/opal-client-2.4.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit python-r1 versionator
+
+MY_PN="${PN/client/py}"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="Python Opal Web Service Client"
+HOMEPAGE="http://www.nbcr.net/data/docs/opal/documentation.html"
+SRC_URI="mirror://sourceforge/opaltoolkit/opal-python/$(get_version_component_range 1-2)/${MY_P}.tar.gz"
+
+LICENSE="opal"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+	>=dev-python/zsi-2.1_alpha1[${PYTHON_USEDEP}]
+	!=sci-chemistry/apbs-1.1.0"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${MY_P}
+
+src_install() {
+	"${EPREFIX}"/usr/bin/wsdl2py  wsdl/opal.wsdl || die
+
+	installation() {
+		python_moduleinto AppService
+		python_domodule AppService_*.py
+		python_optimize "${ED}"/$(python_get_sitedir)
+	}
+	python_parallel_foreach_impl installation
+
+	dodoc README CHANGELOG etc/* *Client.py
+	dohtml docs/*
+}
diff --git a/licenses/GRL b/licenses/GRL
new file mode 100644
index 000000000..8a897b7c9
--- /dev/null
+++ b/licenses/GRL
@@ -0,0 +1,15 @@
+This software has been created by Genome Research Limited (GRL). 
+GRL hereby grants permission to use, copy, modify and distribute 
+this software and its documentation for non-commercial purposes 
+without fee at the user's own risk on the basis set out below.
+GRL neither undertakes nor accepts any duty whether contractual or 
+otherwise in connection with the software, its use or the use of 
+any derivative, and makes no representations or warranties, express
+or implied, concerning the software, its suitability, fitness for
+a particular purpose or non-infringement.
+In no event shall the authors of the software or GRL be 
+responsible or liable for any loss or damage whatsoever arising in
+any way directly or indirectly out of the use of this software or 
+ its derivatives, even if advised of the possibility of such damage.
+Our software can be freely distributed under the conditions set 
+out above, and must contain this copyright notice.
\ No newline at end of file
diff --git a/licenses/Tablet b/licenses/Tablet
index 984a28b72..d81931aad 100644
--- a/licenses/Tablet
+++ b/licenses/Tablet
@@ -6,7 +6,7 @@
 
    The licence and copyright for Tablet is as follows:
 
-   Copyright © 2009-2010, Plant Bioinformatics Group, SCRI
+   Copyright © 2009-2013, Information & Computational Sciences, JHI.
    All rights reserved.
 
    Redistribution and use in binary form, without modification, is
@@ -15,9 +15,9 @@
    - Redistributions must reproduce the above copyright notice, this list
    of conditions and the following disclaimer in the documentation and/or
    other materials provided with the distribution.
-   - Neither the name of SCRI nor the names of its contributors may be
-   used to endorse or promote products derived from this software without
-   specific prior written permission.
+   - Neither the name of The James Hutton Institute nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
 
    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
    IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
diff --git a/sci-biology/YASRA/ChangeLog b/sci-biology/YASRA/ChangeLog
index 77b3b5e07..342684d59 100644
--- a/sci-biology/YASRA/ChangeLog
+++ b/sci-biology/YASRA/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> -YASRA-2.1.ebuild,
+  +YASRA-2.32.ebuild:
+  Version BUmp; add KEYWORDS
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> YASRA-2.1.ebuild, metadata.xml:
   Drop keywords as deps are unkeyworded
 
diff --git a/sci-biology/YASRA/Manifest b/sci-biology/YASRA/Manifest
index 4c218feef..f7399f074 100644
--- a/sci-biology/YASRA/Manifest
+++ b/sci-biology/YASRA/Manifest
@@ -1 +1 @@
-DIST YASRA-2.1.tar.gz 11949120 SHA256 d196cea91a69db3d2feb98d3a8dddbfe1c4c9b4689cdc706a58df44daba3d2d5 SHA512 1e5c648042b8c522c708eb80b90f5a7e965b4f0214a732ba19a46d826ea85bd7074946a2355e509df1ce1dfcec1700c7c6f3ad08c7052f754fed6241c078ec5b WHIRLPOOL 4419ce639b2afb95013b8896b059c037100dc58dc1664b2416ed05c68fd3fcce4eca01219dfa59874a26d566e1df393e975c8d6132811591a251f1acc3db00a4
+DIST YASRA-2.32.tar.gz 12404230 SHA256 03ce7d89949fdd44c97af51b65f57bb5f49f1ac1d5c2be225419513887ea1c61 SHA512 2bdf3f62567c5f2a12b58de9961c3fa55cf38b1000feb73170af6c0f0c035c79e8052009419d2d49423a4b9d52cb44196171bd7235108fdf3ada97c5e03c30c1 WHIRLPOOL 6fdda6a1abe64b5bb91fcb298fd867cff593c3bb0540cce5134cebd63a8254ef4ba24edc788830be963c001c8e915bb4f2546f37aadbbcf16d26aaf8a8fb6f40
diff --git a/sci-biology/YASRA/YASRA-2.1.ebuild b/sci-biology/YASRA/YASRA-2.32.ebuild
index c8288fc52..246d65d40 100644
--- a/sci-biology/YASRA/YASRA-2.1.ebuild
+++ b/sci-biology/YASRA/YASRA-2.32.ebuild
@@ -2,23 +2,16 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
 
 DESCRIPTION="Yet Another Short Read Assembler aligning to a reference using LASTZ"
 HOMEPAGE="http://www.bx.psu.edu/miller_lab/"
-SRC_URI="http://www.bx.psu.edu/miller_lab/dist/YASRA-"${PV}".tar.gz"
+SRC_URI="http://www.bx.psu.edu/miller_lab/dist/YASRA-${PV}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
 DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/lastz"
-
-S="${WORKDIR}"/YASRA
-
-src_install(){
-	emake install DESTDIR="$D"
-}
+RDEPEND="sci-biology/lastz"
diff --git a/sci-biology/caftools/ChangeLog b/sci-biology/caftools/ChangeLog
new file mode 100644
index 000000000..af2ad47b4
--- /dev/null
+++ b/sci-biology/caftools/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/caftools
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> -caftools-2.0.ebuild,
+  caftools-2.0.2.ebuild, metadata.xml:
+  Drop old; Bump to EAPI=5 and fix license
+
diff --git a/sci-biology/caftools/Manifest b/sci-biology/caftools/Manifest
index 61d49e197..dbbbb7f44 100644
--- a/sci-biology/caftools/Manifest
+++ b/sci-biology/caftools/Manifest
@@ -1,2 +1,2 @@
-DIST caftools-2.0.2.tar.gz 2645554 SHA256 7be5eafbd6817a7869f73c7540b5fdfe184b0be28624cc6ca9a01c52a140d4a2
-DIST caftools-2.0.tar.gz 2644892 SHA256 b41f323ceb3fd260d6c2ecff1f285548f40301065cea54687eb96717534eaad9
+DIST caftools-2.0.2.tar.gz 2645554 SHA256 7be5eafbd6817a7869f73c7540b5fdfe184b0be28624cc6ca9a01c52a140d4a2 SHA512 0c1a7f2127538ef932139cfee6bc6acb2411765d1006d508e65647ec74d1677a6ecd25b98cc37075bd8e5b0b1a245c11c1029cbbc51eefb46023bd121fdb2f1d WHIRLPOOL 84313e00f6f4c018bc65b6e173827a6e1ef8fd2dc5e5e63e186fb56bc9e5b66b2f25037a1536a8cb57af71603b31ed74ff505dbc43d4deb7d2eeae57ea729bfe
+DIST caftools-2.0.tar.gz 2644892 SHA256 b41f323ceb3fd260d6c2ecff1f285548f40301065cea54687eb96717534eaad9 SHA512 0b2b5d09d503b900b275efd61dfa1c5b01259e53c392d68626d9c5081add27ca87b324b5702ec18293415b788208c547eb31e461861f1244b759e28221244417 WHIRLPOOL 13c2e24ce803c09f1d596a4c05f146b869e5ebdeff9f648a0468853feb7d142927d3d78339ac2414482335e5f7ca8352ea9b196f8542f4b3ff5e36fef762398e
diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild
index c1932e1f4..3f8ece67d 100644
--- a/sci-biology/caftools/caftools-2.0.2.ebuild
+++ b/sci-biology/caftools/caftools-2.0.2.ebuild
@@ -1,45 +1,45 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
 
 inherit eutils
 
 DESCRIPTION="CAF is a text format for describing sequence assemblies"
 HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.2.tar.gz
-		ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.tar.gz"
-# another source with only the old version is at
-# ftp://ftp.sanger.ac.uk/pub4/resources/software/caf/caftools-2.0.tar.gz
-# newer version will probably appear at ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/
+SRC_URI="
+	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz
+	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${PN}-2.0.tar.gz"
 
-LICENSE="as-is"
+LICENSE="GRL"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND="sci-libs/io_lib
-		>=dev-lang/perl-5.002"
+DEPEND="
+	sci-libs/io_lib
+	dev-lang/perl"
 RDEPEND="${DEPEND}"
 
 src_prepare(){
-	epatch "${FILESDIR}"/Makefile.in-"${PV}".patch || die
-	mv "${WORKDIR}"/caftools-2.0/man/*.1 "${WORKDIR}"/caftools-2.0/man/*.5 "${S}"/man || die
+	epatch "${FILESDIR}"/Makefile.in-"${PV}".patch
+	mv "${WORKDIR}"/caftools-2.0/man/*.{1,5} "${S}"/man/ || die
 }
 
 src_configure(){
-	econf || die
-	sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' Makefile || die
-	sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' src/Makefile || die
+	default
+	sed \
+		-e 's:prefix = /usr:prefix = $(DESTDIR)/usr:' \
+		-i Makefile src/Makefile || die
 }
 
 # TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME
 # The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files,
 # not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help.
 src_install(){
-	emake install DESTDIR="${D}" || die
+	default
 	doman man/*.[1-5] || die
-	einfo "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/"
-	einfo "for some reason caf_find_misassemblies is gone from 2.0.2 version"
+	elog "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/"
+	elog "for some reason caf_find_misassemblies is gone from 2.0.2 version"
 }
diff --git a/sci-biology/caftools/caftools-2.0.ebuild b/sci-biology/caftools/caftools-2.0.ebuild
deleted file mode 100644
index 482bddf92..000000000
--- a/sci-biology/caftools/caftools-2.0.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils
-
-DESCRIPTION="CAF is a text format for describing sequence assemblies"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.tar.gz"
-# another source with only the old version is at
-# ftp://ftp.sanger.ac.uk/pub4/resources/software/caf/caftools-2.0.tar.gz
-# newer version will probably appear at ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/
-
-LICENSE="as-is"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="sci-libs/io_lib
-		>=dev-lang/perl-5.002"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	epatch "${FILESDIR}"/Makefile.in.patch || die
-}
-
-src_configure(){
-	econf || die
-	sed -i 's#prefix = /usr#prefix = $(DESTDIR)/usr#' Makefile || die
-	sed -i 's#prefix = /usr#\#prefix = $(DESTDIR)/usr#' src/Makefile || die
-}
-
-src_install(){
-	emake install DESTDIR="${D}" || die
-	einfo "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/"
-}
diff --git a/sci-biology/caftools/metadata.xml b/sci-biology/caftools/metadata.xml
index 4f255d9b2..e57f444c5 100644
--- a/sci-biology/caftools/metadata.xml
+++ b/sci-biology/caftools/metadata.xml
@@ -1,10 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<longdescription>CAF is a text format for describing sequence assemblies. It is acedb-compliant and is an extension of the ace-file format used earlier, but with support for base quality measures and a more extensive description of the Sequence data.</longdescription>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <longdescription>
+  CAF is a text format for describing sequence assemblies. It is acedb-compliant
+  and is an extension of the ace-file format used earlier, but with support for 
+  base quality measures and a more extensive description of the Sequence data.
+  </longdescription>
 </pkgmetadata>
diff --git a/sci-biology/cutadapt/ChangeLog b/sci-biology/cutadapt/ChangeLog
index 7a23b4e2a..ad14cdd33 100644
--- a/sci-biology/cutadapt/ChangeLog
+++ b/sci-biology/cutadapt/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/cutadapt
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> -cutadapt-1.0.ebuild,
+  +cutadapt-1.2.1.ebuild, metadata.xml:
+  Version BUmp; BUmp to EAPI5 and distutils-r1.eclass
+
 *cutadapt-1.0 (02 Mar 2012)
 
   02 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/cutadapt/Manifest b/sci-biology/cutadapt/Manifest
index 4bbdb1cc0..d1f5dc4ae 100644
--- a/sci-biology/cutadapt/Manifest
+++ b/sci-biology/cutadapt/Manifest
@@ -1 +1 @@
-DIST cutadapt-1.0.tar.gz 66166 SHA256 8b2a608eb6f73d9cbc3ee04eb4726d4067d6b128d23eba585ceed1aa532e4416 SHA512 dea81ab4ffd640ce43fd2184bb01223d6f23428bbb26ddaf8659046dbf1e635b8ec3e4d66fd0d5ffd26c4b43df3a1e981ea08345d0639c98e5ea887faa3f4adb WHIRLPOOL 7926863a727176ab13c381cd732207a55dc5f0220edabf83353ec16d4fbbb0dcf08558085bc7aec9b438a265010a85d020c9c92d81395cac8f0d63d370776eba
+DIST cutadapt-1.2.1.tar.gz 104440 SHA256 1baf91c7351ee3464cd01a7f767fe474675ab1b1f7bb110ffe3722e8126ed5cf SHA512 5cd48f342ed75d18780ec63c73f2c42d239253d8dded3161c39f7a26e915f195055c8c4097305246a1418f8b4d3c8853adc1074cbe2a9c1a1b0af644e36771b6 WHIRLPOOL b5c6ceb65be0fcfe418b31cb4c2f8b427d017f71eed182585dc4353079df21ba2ae16354bb6cfcc17bfb39d155ae87fc97fed55b3d0f6ebc68197d98c395c31e
diff --git a/sci-biology/cutadapt/cutadapt-1.0.ebuild b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
index add090cc6..40ece0c59 100644
--- a/sci-biology/cutadapt/cutadapt-1.0.ebuild
+++ b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=2
-PYTHON_DEPEND="2:2.6"
-SUPPORT_PYTHON_ABIS="1"
+EAPI=5
 
-inherit distutils
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1
 
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/"
@@ -16,6 +16,3 @@ LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/cutadapt/metadata.xml
+++ b/sci-biology/cutadapt/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog
index 3205cfc85..87308e6e1 100644
--- a/sci-biology/tablet-bin/ChangeLog
+++ b/sci-biology/tablet-bin/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-biology/tablet-bin
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> tablet-bin-1.13.05.17.ebuild:
+  Version BUmp; BUmp to EAPI5 and python-r1.eclass; drop addpredict
+
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> -tablet-bin-1.11.05.03.ebuild,
+  -tablet-bin-1.11.11.01.ebuild, +tablet-bin-1.13.05.17.ebuild, metadata.xml:
+  Version BUmp; BUmp to EAPI5 and python-r1.eclass
+
   07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   tablet-bin-1.11.11.01.ebuild:
   adjust PATH to point to the installation place
diff --git a/sci-biology/tablet-bin/Manifest b/sci-biology/tablet-bin/Manifest
index ae6afbe26..18833160e 100644
--- a/sci-biology/tablet-bin/Manifest
+++ b/sci-biology/tablet-bin/Manifest
@@ -1,3 +1,2 @@
 DIST coveragestats.py 4800 SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc SHA512 d5688832c13dc9c2e2e015df0b5c50113f72e2eeae076d479c43b65a4b028f8dcfa5f0fb833b4341d76d3956ea27707c55a51389b73a2efed6abd2b96ccdc3cd WHIRLPOOL 0b1eb20189b343d6014097748c053f35f8ad162400312cfbde16bac7fee52f24ac8b0055e991c823dcb64d7a20df3fbb88d8cd6119f838d4e9a5f26e82604664
-DIST tablet_linux_x86_1_11_05_03.sh 24035425 SHA256 3c7de5f0e5d37019485612723dfd3b17fd34e24df8986eb535fcb0335f8b2e99
-DIST tablet_linux_x86_1_11_11_01.sh 23481558 SHA256 9dbbd9ecf1c20e39b978a4be88707593c37073407af951cbf7a9b3d16e6daf23 SHA512 95da451959304aafe36c70895cd9f0a89c1749a403e47a4f32b7605e6cbdb5b2f69b03b4177fd6db45cbdba76e2f054742179000d29b0574a1f4541f335aeaa2 WHIRLPOOL cae67ca8338aa23781f91cd235ecc1bd082b04ada80a158d827acf33c04d8bd63e89883790dd3945938e1405c2b6a0903d4e10ffe40c3fe7e0e042390ba1cabe
+DIST tablet-bin-1.13.05.17.sh 35467547 SHA256 6da2cbb8d15433cdf022c93f466d355515a9c1c8f89dcdab4c2e9543bee415e4 SHA512 532900242ef3b3a46a6e6379c29b627c9f337198cf230273eb1da4c269b6f09a49bc7c5ea28a1ee4caa4f7d7a76ba0e0f18330a538428e49b8f1d36c3bfecb78 WHIRLPOOL 299f23da5f6192a7802f86e61e2c5655711d0d672e28cdd257fdd179d76e15e1b951fa42ec2b28e4568063197b14e1884d61992b7ff2e864fa86c3dad2141c14
diff --git a/sci-biology/tablet-bin/metadata.xml b/sci-biology/tablet-bin/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/tablet-bin/metadata.xml
+++ b/sci-biology/tablet-bin/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-biology/tablet-bin/tablet-bin-1.11.11.01.ebuild b/sci-biology/tablet-bin/tablet-bin-1.11.11.01.ebuild
deleted file mode 100644
index 3e6d6e64f..000000000
--- a/sci-biology/tablet-bin/tablet-bin-1.11.11.01.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit java-pkg-2 python
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-SRC_URI="http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_1_11_11_01.sh
-		http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
-
-# Upstream says regarding source code unavailability:
-# Tablet uses a modified version of the BSD License which has been edited to
-# remove references to distribution and use in source forms. This means that
-# we are happy for you to distribute and use Tablet however you please, but we
-# do not (yet) want to make the source code publicly available.
-
-# The licence file itself is in the installer, and ends up on disk after
-# installation at /opt/Tablet/docs/tablet.html
-# The original BSD licence was modified to remove references to distribution
-# and use in source forms, because we cannot make the source code available
-# for Tablet.
-
-LICENSE="Tablet"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-		virtual/jre
-		dev-lang/python"
-
-MYPV="$(replace_all_version_separators '_')"
-
-pkg_setup() {
-	einfo "Fixing java access violations ..."
-	# bug 387227
-	addpredict /proc/self/coredump_filter
-}
-
-src_install() {
-	# In theory it seems this binary package could be installed through ant
-	# instead of the install4j package which is not easy to be forced
-	# non-interactive. The below approach via install4j is not ideal but works.
-	sed "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile > "${DISTDIR}"/response.varfile || die "sed failed"
-
-	# the intallation script somehow does not pickup
-	# -varfile="${DISTDIR}"/response.varfile from the commandline and therefore
-	# we place the file rather directly into the place where it should reside.
-	# In the file you can read details how the variables were mangled. For
-	# example, the trick with sys.symlinkDir in the response.varfile is to
-	# disable the installation process to symlink from /usr/local/bin/table to
-	# /opt/Tablet/tablet. That was logged in that file with the following line:
-	#
-	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
-	#
-	# The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile
-	mkdir -p "${D}"/opt/Tablet/.install4j || die "Cannot pre-create	"${D}"/opt/Tablet/.install4j/"
-	cat "${DISTDIR}"/response.varfile >	"${D}"/opt/Tablet/.install4j/response.varfile || die "Cannot write	"${D}"/opt/Tablet/.install4j/response.varfile"
-
-	# make sure we force java to point a to $HOME which is inside our sanbox
-	# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
-	# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
-	sed "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" -i "${DISTDIR}"/tablet_linux_x86_"${MYPV}".sh || die "failed to set userHome value"
-	sh "${DISTDIR}"/tablet_linux_x86_"${MYPV}".sh -q -overwrite -varfile="${DISTDIR}"/response.varfile --destination="${D}"/opt/Tablet -dir "${D}"/opt/Tablet || die "Failed to run the self-extracting exe file"
-	dobin "${DISTDIR}"/coveragestats.py
-
-	echo "PATH=/opt/Tablet" > 99Tablet
-	doenvd 99Tablet || die
-}
diff --git a/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild b/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild
index 32cc463ee..762e888aa 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild
@@ -1,15 +1,18 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
 
-inherit java-pkg-2 python
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit java-pkg-2 python-r1
 
 DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
 HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-SRC_URI="http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_1_11_05_03.sh
-		http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
+SRC_URI="
+	http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh
+	http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
 
 # Upstream says regarding source code unavailability:
 # Tablet uses a modified version of the BSD License which has been edited to
@@ -28,16 +31,26 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND=""
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}"
 RDEPEND="${DEPEND}
-		virtual/jre
-		dev-lang/python"
+		virtual/jre"
+
+S="${WORKDIR}"
+
+src_unpack() {
+	local file
+	for file in ${A}; do
+		cp "${DISTDIR}"/${file} "${WORKDIR}" || die
+	done
+}
 
 src_install() {
 	# In theory it seems this binary package could be installed through ant
 	# instead of the install4j package which is not easy to be forced
 	# non-interactive. The below approach via install4j is not ideal but works.
-	sed "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile > "${DISTDIR}"/response.varfile || die "sed failed"
+	sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed"
 
 	# the intallation script somehow does not pickup
 	# -varfile="${DISTDIR}"/response.varfile from the commandline and therefore
@@ -47,16 +60,30 @@ src_install() {
 	# disable the installation process to symlink from /usr/local/bin/table to
 	# /opt/Tablet/tablet. That was logged in that file with the following line:
 	#
-	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
+	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
+	#	Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
 	#
 	# The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile
-	mkdir -p "${D}"/opt/Tablet/.install4j || die "Cannot pre-create	"${D}"/opt/Tablet/.install4j/"
-	cat "${DISTDIR}"/response.varfile >	"${D}"/opt/Tablet/.install4j/response.varfile || die "Cannot write	"${D}"/opt/Tablet/.install4j/response.varfile"
+	dodir /opt/Tablet/.install4j
+	cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die
 
 	# make sure we force java to point a to $HOME which is inside our sanbox
 	# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
 	# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
-	sed "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${D}"/../temp -Dinstall4j.jvmDir#" -i "${DISTDIR}"/tablet_linux_x86_1_11_05_03.sh || die "failed to set userHome value"
-	sh "${DISTDIR}"/tablet_linux_x86_1_11_05_03.sh -q -overwrite -varfile="${DISTDIR}"/response.varfile --destination="${D}"/opt/Tablet -dir "${D}"/opt/Tablet || die "Failed to run the self-extracting exe file"
-	dobin "${DISTDIR}"/coveragestats.py
+	sed \
+		-e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \
+		-i "${WORKDIR}"/${P}.sh || die
+	sh \
+		"${WORKDIR}"/${P}.sh \
+		-q -overwrite \
+		-varfile="${DISTDIR}"/response.varfile \
+		--destination="${ED}"/opt/Tablet \
+		-dir "${ED}"/opt/Tablet || die
+
+	rm -rf "${ED}"/opt/Tablet/jre || die
+
+	python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+
+	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+	doenvd 99Tablet || die
 }
diff --git a/sci-chemistry/chemBuild/ChangeLog b/sci-chemistry/chemBuild/ChangeLog
index a592f6b45..7aa6b2ef5 100644
--- a/sci-chemistry/chemBuild/ChangeLog
+++ b/sci-chemistry/chemBuild/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-chemistry/chemBuild
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> chemBuild-1.0.2.ebuild,
+  files/chemBuild, metadata.xml:
+  Bump EAPI and python eclass
+
   21 Sep 2012; Justin Lecher <jlec@gentoo.org> chemBuild-1.0.2.ebuild:
   Needs webkit support in pyside
 
diff --git a/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild b/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild
index dece95eb2..3f4733f8b 100644
--- a/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild
+++ b/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
 
-PYTHON_DEPEND="2"
+PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit python toolchain-funcs
+inherit python-single-r1 toolchain-funcs
 
 DESCRIPTION="Graphical tool to construct chemical compound definitions for NMR"
 HOMEPAGE="http://www.ccpn.ac.uk/software/chembuild"
@@ -17,7 +17,9 @@ LICENSE="|| ( CCPN LGPL-2.1 )"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
-RDEPEND="dev-python/pyside[webkit]"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="dev-python/pyside[webkit,${PYTHON_USEDEP}]"
 DEPEND=""
 
 S="${WORKDIR}"/ccpnmr/ccpnmr3.0/
@@ -28,11 +30,6 @@ S="${WORKDIR}"/ccpnmr/ccpnmr3.0/
 #unbundle inchi
 #parallel build
 
-pkg_setup() {
-	python_set_active_version 2
-	python_pkg_setup
-}
-
 src_install() {
 	local in_path=$(python_get_sitedir)/${PN}
 	local _file
@@ -44,25 +41,17 @@ src_install() {
 	-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
 	-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
 	-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
-	-e "s|gentoopython|$(PYTHON -a)|g" \
+	-e "s|gentoopython|${PYTHON}|g" \
 	-e "s|gentoousr|${EPREFIX}/usr|g" \
 	-e "s|//|/|g" \
 		"${FILESDIR}"/${PN} > "${ED}"/usr/bin/${PN} || die
 	fperms 755 /usr/bin/${PN}
 
-	insinto ${in_path}
-
 	rm -rf cNg license || die
 
 	ebegin "Installing main files"
-		doins -r *
+	python_moduleinto ${PN}
+	python_domodule *
+	python_optimize
 	eend
 }
-
-pkg_postinst() {
-	python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/chemBuild/files/chemBuild b/sci-chemistry/chemBuild/files/chemBuild
index c6d3d31ac..308804158 100644
--- a/sci-chemistry/chemBuild/files/chemBuild
+++ b/sci-chemistry/chemBuild/files/chemBuild
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 export CCPNMR_TOP_DIR=gentoo_sitedir
-export PYTHONPATH=.:${CCPNMR_TOP_DIR}/chemBuild/python
+export PYTHONPATH=${CCPNMR_TOP_DIR}/chemBuild/python
 export LD_LIBRARY_PATH=gentoolibdir
 export TCL_LIBRARY=gentootcl
 export TK_LIBRARY=gentootk
diff --git a/sci-chemistry/chemBuild/metadata.xml b/sci-chemistry/chemBuild/metadata.xml
index d369d068f..897aa2e6b 100644
--- a/sci-chemistry/chemBuild/metadata.xml
+++ b/sci-chemistry/chemBuild/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci</herd>
+  <herd>sci</herd>
 </pkgmetadata>
diff --git a/sci-chemistry/cnsface/ChangeLog b/sci-chemistry/cnsface/ChangeLog
index 8b8ef62da..91fb75e01 100644
--- a/sci-chemistry/cnsface/ChangeLog
+++ b/sci-chemistry/cnsface/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-chemistry/cnsface
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> cnsface-0.0.12.ebuild,
+  metadata.xml:
+  Bump to EAPI5 and distutils-r1.eclass
+
 *cnsface-0.0.12 (01 Dec 2010)
 
   01 Dec 2010; Justin Lecher <jlec@gentoo.org> +files/0.0.12-binary.patch,
diff --git a/sci-chemistry/cnsface/Manifest b/sci-chemistry/cnsface/Manifest
index b1bdb72df..a9914275b 100644
--- a/sci-chemistry/cnsface/Manifest
+++ b/sci-chemistry/cnsface/Manifest
@@ -1 +1 @@
-DIST cnsface-0.0.12-altoona.tar.gz 1442309 SHA256 add1a1f17fc103a5bb3a75003d8c0e64626b35c6ebbb8e2aa87fed1a0c05b655
+DIST cnsface-0.0.12-altoona.tar.gz 1442309 SHA256 add1a1f17fc103a5bb3a75003d8c0e64626b35c6ebbb8e2aa87fed1a0c05b655 SHA512 73bfaf75e89da0066d3ddab1e005b487b837719d5fe4235f8ebad31e84ab715fe829b094769982784c65641cb8c4febc827b2abe7737cf2c251bf4ae293e37c7 WHIRLPOOL f91dfaa22e619f3ab88c0f42d0cbed7df0dfc3d50707097808dc676ec47c067104bb1fcc8ef365a72b7c8d0853ede8b4b52d047ee5dc95ccd48779c1afc9f4a3
diff --git a/sci-chemistry/cnsface/cnsface-0.0.12.ebuild b/sci-chemistry/cnsface/cnsface-0.0.12.ebuild
index 6c2903879..55e42f653 100644
--- a/sci-chemistry/cnsface/cnsface-0.0.12.ebuild
+++ b/sci-chemistry/cnsface/cnsface-0.0.12.ebuild
@@ -1,18 +1,16 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="3"
+EAPI=5
 
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="3.*"
+PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit distutils eutils
+inherit distutils-r1
 
 DESCRIPTION="GUI for the Crystallography and NMR System"
 HOMEPAGE="http://cnsface.sourceforge.net"
-SRC_URI="mirror://sourceforge/${P}-altoona.tar.gz"
+SRC_URI="mirror://sourceforge/project/cnsface/cnsface/Altoona/${P}-altoona.tar.gz"
 
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
@@ -20,13 +18,10 @@ LICENSE="GPL-2"
 IUSE=""
 
 RDEPEND="
-	dev-python/wxpython:2.8
+	dev-python/wxpython:2.8[${PYTHON_USEDEP}]
 	sci-chemistry/cns"
 DEPEND="${RDEPEND}"
 
 S="${WORKDIR}"/${P}-altoona
 
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-binary.patch
-	distutils_src_prepare
-}
+PATCHES=( "${FILESDIR}"/${PV}-binary.patch )
diff --git a/sci-chemistry/cnsface/metadata.xml b/sci-chemistry/cnsface/metadata.xml
index 0fbe927f0..d410f1573 100644
--- a/sci-chemistry/cnsface/metadata.xml
+++ b/sci-chemistry/cnsface/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>sci@gentoo.org</email>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-chemistry/modeller/ChangeLog b/sci-chemistry/modeller/ChangeLog
index 17fea516e..198256b1f 100644
--- a/sci-chemistry/modeller/ChangeLog
+++ b/sci-chemistry/modeller/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-chemistry/modeller
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> -modeller-9.8.ebuild,
+  +modeller-9.12.ebuild, metadata.xml:
+  Version BUmp; BUmp to EAPI5 and distutils-r1.eclass
+
 *modeller-9.8 (16 Jun 2010)
 
   16 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/9v5-setup.patch,
diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest
index f3078a1c8..a5b04d5c2 100644
--- a/sci-chemistry/modeller/Manifest
+++ b/sci-chemistry/modeller/Manifest
@@ -1 +1 @@
-DIST modeller-9v8.tar.gz 51539572 SHA256 3d5c629f97a2b89722fe5b7414ad97b0361799714db0323536df45f55b2777c7
+DIST modeller-9.12.tar.gz 29273842 SHA256 65051f7f1682cf7dcf77f0bc4d68f1ee5b64789f750e9aa6900e1cc92dc4e1f9 SHA512 5c0acaf453771347a9de3a0c7240f7ce376244803748edb28923dbaefda779041211ef4b26af5a2774bdf6bc63d7c7d7e62e1354e1550a6742c9575076864352 WHIRLPOOL a363efdd2bba8db8268774745f32b1e8e6a9d88e6a6154ce00c7be65861fc834ef1a804fa9f0575d2af2ff1211728aacf8408d28319df68b14f3a3598d55c307
diff --git a/sci-chemistry/modeller/metadata.xml b/sci-chemistry/modeller/metadata.xml
index 9ac9ffdb3..51fdedab1 100644
--- a/sci-chemistry/modeller/metadata.xml
+++ b/sci-chemistry/modeller/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
+  <herd>sci-chemistry</herd>
 </pkgmetadata>
diff --git a/sci-chemistry/modeller/modeller-9.8.ebuild b/sci-chemistry/modeller/modeller-9.12.ebuild
index b0c24c18c..0cabf476a 100644
--- a/sci-chemistry/modeller/modeller-9.8.ebuild
+++ b/sci-chemistry/modeller/modeller-9.12.ebuild
@@ -1,19 +1,17 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="3"
+EAPI=5
 
-PYTHON_DEPEND="2:2.6"
+PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} )
+PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit distutils eutils versionator
-
-MY_PV="$(replace_all_version_separators v)"
-MY_P="${PN}-${MY_PV}"
+inherit distutils-r1 eutils versionator
 
 DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures"
-SRC_URI="http://salilab.org/${PN}/${MY_PV}/${PN}-${MY_PV}.tar.gz"
 HOMEPAGE="http://salilab.org/modeller/"
+SRC_URI="http://salilab.org/${PN}/${PV}/${P}.tar.gz"
 
 LICENSE="modeller"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
@@ -25,82 +23,77 @@ RESTRICT="mirror"
 DEPEND=">=dev-lang/swig-1.3"
 RDEPEND=""
 
-S="${WORKDIR}/${MY_P}"
-
 INPATH="${EPREFIX}"/opt/modeller${ver}
 
-QA_TEXTRELS="${INPATH#/}/*"
-QA_EXECSTACK="${INPATH#/}/*"
-QA_PRESTRIPPED="${INPATH#/}/bin/.* ${INPATH#/}/lib/*/.*"
-QA_DT_HASH="
-	${INPATH#/}/bin/.*
-	${INPATH#/}/lib/*/.*"
+QA_PREBUILT="/opt/*"
 
-pkg_setup() {
-	python_set_active_version 2
+DISTUTILS_NO_PARALLEL_BUILD=true
 
+pkg_setup() {
 	case ${ARCH} in
-		x86)	EXECTYPE="i386-intel8";;
-		amd64)	EXECTYPE="x86_64-intel8";;
-		*)		ewarn "Your arch "${ARCH}" does not appear supported at this time."||\
-				die "Unsupported Arch";;
+		x86)
+			EXECTYPE="i386-intel8";;
+		amd64)
+			EXECTYPE="x86_64-intel8";;
+		*)
+			die "Your arch "${ARCH}" does not appear supported at this time.";;
 	esac
 }
 
-src_prepare(){
+python_prepare_all(){
 	sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
 }
 
-src_compile(){
+python_compile(){
+	cd src/swig
+	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die
+	distutils-r1_python_compile
+}
+
+python_install() {
 	cd src/swig
-	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i
-	distutils_src_compile
+	distutils-r1_python_install
 }
 
-src_install(){
+python_install_all(){
+	cd "${S}"
 	sed \
-		-e "s:EXECUTABLE_TYPE${MY_PV}=xxx:EXECUTABLE_TYPE${MY_PV}=${EXECTYPE}:g" \
-		-e "s:MODINSTALL${MY_PV}=xxx:MODINSTALL${MY_PV}=\"${INPATH}\":g" \
-		bin/modscript > "${T}/mod${MY_PV}"
+		-e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \
+		-e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \
+		-i bin/modscript || die
 
 	sed -e "s;@TOPDIR\@;\"${INPATH}\";" \
 		-e "s;@EXETYPE\@;${EXECTYPE};" \
 		bin/modpy.sh.in > "${T}/modpy.sh"
 
 	insinto ${INPATH}
-	doins -r modlib || die
+	doins -r modlib
+	python_foreach_impl python_domodule modlib/modeller
 
 	insinto ${INPATH}/bin
-	doins -r bin/{lib,*top} || die
+	doins -r bin/{lib,*top}
+
 	exeinto ${INPATH}/bin
-	doexe bin/{modslave.py,mod${MY_PV}_${EXECTYPE}} || die
-	doexe "${T}/mod${MY_PV}" || die
-	doexe "${T}/modpy.sh" || die
-	dosym ${INPATH}/bin/mod${MY_PV} /opt/bin/mod${MY_PV} || die
-	dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh || die
+	doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh
+
+	python_foreach_impl python_doscript bin/modslave.py
+	dosym ${INPATH}/bin/modscript /opt/bin/mod${PV}
+	dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh
 
 	exeinto ${INPATH}/lib/${EXECTYPE}/
-	doexe lib/${EXECTYPE}/lib* || die
-	dosym libmodeller.so.5 ${INPATH}/lib/${EXECTYPE}/libmodeller.so || die
-	doexe src/swig/build/lib.linux-$(uname -m)-$(python_get_version)/_modeller.so || die
+	doexe lib/${EXECTYPE}/lib*
+	dosym libmodeller.so.5 ${INPATH}/lib/${EXECTYPE}/libmodeller.so
+
+	use doc && HTML_DOCS=( doc/. )
+	distutils-r1_python_install_all
 
-	dodoc README INSTALLATION || die
-	if use doc; then
-		dohtml doc/* || die
-	fi
 	if use examples; then
 		insinto /usr/share/${PN}/
-		doins -r examples || die
+		doins -r examples
 	fi
-
-	dosym ${INPATH}/lib/${EXECTYPE}/_modeller.so \
-		  $(python_get_sitedir)/_modeller.so || die
-	dosym _modeller.so $(python_get_sitedir)/modeller.so || die
 }
 
 pkg_postinst() {
-	python_mod_optimize "${INPATH}/"
-
 	if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then
 		echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py
 	fi
@@ -117,7 +110,6 @@ pkg_postinst() {
 }
 
 pkg_postrm() {
-	python_mod_cleanup "${INPATH}/"
 	ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py"
 	ewarn "that you need to remove to completely get rid of modeller."
 }
diff --git a/sci-chemistry/nmrpipe/ChangeLog b/sci-chemistry/nmrpipe/ChangeLog
index d966a7b72..3c50b507a 100644
--- a/sci-chemistry/nmrpipe/ChangeLog
+++ b/sci-chemistry/nmrpipe/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org>
+  nmrpipe-7.9.2013.021.23.09-r2.ebuild:
+  Bump to EAPI=5 and fix license
+
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org>
+  nmrpipe-7.9.2013.021.23.09-r2.ebuild:
+  Bump to EAPI=5 and fix license
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org>
   nmrpipe-7.9.2013.021.23.09-r2.ebuild:
   Fix quoting
diff --git a/sci-chemistry/nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild b/sci-chemistry/nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild
index 2abd96b21..daf50ce8f 100644
--- a/sci-chemistry/nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild
+++ b/sci-chemistry/nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild
@@ -4,7 +4,7 @@
 
 # Versioning is output of nmrPipe -help
 
-EAPI=4
+EAPI=5
 
 inherit eutils virtualx
 
@@ -25,7 +25,7 @@ SRC_URI="
 	"
 
 SLOT="0"
-LICENSE="as-is"
+LICENSE="all-rights-reserved"
 # Right now, precompiled executables are only available for Linux on the
 # x86 architecture. The maintainer chose to keep the sources closed, but
 # says he will gladly provide precompiled executables for other platforms
diff --git a/sci-chemistry/nmrview/ChangeLog b/sci-chemistry/nmrview/ChangeLog
index c84d1a869..63f2974b1 100644
--- a/sci-chemistry/nmrview/ChangeLog
+++ b/sci-chemistry/nmrview/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-chemistry/nmrview
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> nmrview-5.2.2-r3.ebuild,
+  metadata.xml:
+  Bump to EAPI=5 and fix license
+
   01 Jun 2012; Justin Lecher <jlec@gentoo.org> nmrview-5.2.2-r3.ebuild,
   metadata.xml:
   Move to EAPI=4, specify QA_PREBUILT
diff --git a/sci-chemistry/nmrview/metadata.xml b/sci-chemistry/nmrview/metadata.xml
index 95180e10e..b3618ba38 100644
--- a/sci-chemistry/nmrview/metadata.xml
+++ b/sci-chemistry/nmrview/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<maintainer>
-		<email>jlec@gentoo.org</email>
-		<name>Justin Lecher</name>
-	</maintainer>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+    <name>Justin Lecher</name>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild b/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild
index e302f9714..ad5da95f1 100644
--- a/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild
+++ b/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
 
 DESCRIPTION="Visualisation and analysis of processed NMR data"
 HOMEPAGE="http://www.onemoonscientific.com/nmrview/"
@@ -11,7 +11,7 @@ SRC_URI="
 	${PN}${PV//./_}_01_linux.gz"
 
 SLOT="0"
-LICENSE="as-is"
+LICENSE="all-rights-reserved"
 IUSE=""
 KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
 
@@ -38,19 +38,14 @@ pkg_nofetch() {
 	echo
 }
 
-src_compile() {
-	echo
-	einfo "Nothing to compile."
-	echo
-}
-
 src_install() {
 	insinto ${INSTDIR}
 
 	sed \
 		-e "s:/opt:${EPREFIX}/opt:g" \
 		"${FILESDIR}"/${PN}.sh-r1 \
-		> "${T}"/${PN}
+		> "${T}"/${PN} || die
+
 	dobin "${T}"/${PN}
 	exeinto ${INSTDIR}
 	doexe ${PN}${PV//./_}_01_linux
diff --git a/sci-chemistry/nwchem/ChangeLog b/sci-chemistry/nwchem/ChangeLog
index a93271c16..01bbf7962 100644
--- a/sci-chemistry/nwchem/ChangeLog
+++ b/sci-chemistry/nwchem/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> -nwchem-6.1.1.ebuild,
+  nwchem-6.3.ebuild:
+  Drop old; drop virtual/fortran as the eclass depends on it
+
   04 Jun 2013; Justin Lecher <jlec@gentoo.org> nwchem-6.3.ebuild:
   Fix for correct usage of new python eclasses
 
diff --git a/sci-chemistry/nwchem/Manifest b/sci-chemistry/nwchem/Manifest
index 56aeb6eca..d717621f9 100644
--- a/sci-chemistry/nwchem/Manifest
+++ b/sci-chemistry/nwchem/Manifest
@@ -1,2 +1 @@
-DIST Nwchem-6.1.1-src.2012-06-27.tar.gz 77838112 SHA256 153a975e18fa88afbacfa2c7d4384e31bc25c43bd5c99c2f4074006a8e035dab SHA512 b2cc796f6fd0e37385a9b8c0a5dbc3c219849938b52809a616cb5c3fa5a3a54a7c61be215cf8975d1287d09ecfae1bedd41e69e445e61adb5a7aac505802170d WHIRLPOOL d6107522fadca8597d0fdff758169a2c25adb8da0ccfbad9a9f408708d0060922fef443f9c92ccd97b3772c70ba9fe90a1ec7c059de536e6a294719080c9bfaf
 DIST Nwchem-6.3-src.2013-05-17.tar.gz 112227871 SHA256 c8049adb14f198d3ee40e38ed6e00dd4d59ef7cf992c4d45f392172df217f378 SHA512 05cb37aae41746c56ab715a47830bdf336cfe469b5f1b492be369c620d300039529ea30ed75f885fc06a5d3a45a64297341555ea71ef5b56efcca14798dcf8d3 WHIRLPOOL 40d46a7bf7b99455219325a03fe72b426f60c058110aa3c17308b57be962210100b58bac6e2e99cfc60b4d7cf87f7e8c5fd712d3c815b260790ff58d59380f36
diff --git a/sci-chemistry/nwchem/nwchem-6.1.1.ebuild b/sci-chemistry/nwchem/nwchem-6.1.1.ebuild
deleted file mode 100644
index a0196083d..000000000
--- a/sci-chemistry/nwchem/nwchem-6.1.1.ebuild
+++ /dev/null
@@ -1,126 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-inherit eutils fortran-2 multilib python toolchain-funcs
-
-DATE="2012-06-27"
-
-DESCRIPTION="NWChem: Delivering High-Performance Computational Chemistry to Science"
-HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
-SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV}-src.${DATE}.tar.gz"
-
-LICENSE="ECL-2.0"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="mpi examples nwchem-tests python"
-
-RDEPEND="sys-fs/sysfsutils"
-DEPEND="${RDEPEND}
-	virtual/fortran
-	mpi? ( virtual/mpi[fortran] )"
-
-S="${WORKDIR}/${P}-src"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	use python && python_set_active_version 2 &&  python_pkg_setup
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/nwchem-${PV}-makefile.patch \
-		"${FILESDIR}"/nwchem-${PV}-nwchemrc.patch \
-		"${FILESDIR}"/nwchem-${PV}-adjust-dir-length.patch
-	use python && "${FILESDIR}"/nwchem-${PV}-python_makefile.patch
-
-	sed \
-		-e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
-		-i src/basis/MakeFile src/basis/GNUmakefile || die
-	sed \
-		-e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
-		-i src/nwpw/libraryps/GNUmakefile || die
-	sed \
-		-e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \
-		-i src/GNUmakefile src/MakeFile || die
-
-	if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then
-		sed \
-			-e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \
-			-e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \
-			-i src/config/makefile.h || die
-	fi
-}
-
-src_compile() {
-	export USE_SUBGROUPS=yes
-	if use mpi ; then
-		export MSG_COMMS=MPI
-		export USE_MPI=yes
-		export MPI_LOC=/usr
-		export MPI_INCLUDE=$MPI_LOC/include
-		export MPI_LIB=$MPI_LOC/$(get_libdir)
-		export LIBMPI="$(mpif90 -showme:link)"
-	fi
-	if [ "$ARCH" = "amd64" ]; then
-		export NWCHEM_TARGET=LINUX64
-	elif [ "$ARCH" = "ia64" ]; then
-		export NWCHEM_TARGET=LINUX64
-	elif [ "$ARCH" = "x86" ]; then
-		export NWCHEM_TARGET=LINUX
-	elif [ "$ARCH" = "ppc" ]; then
-		export NWCHEM_TARGET=LINUX
-	else
-		die "Unknown architecture"
-	fi
-	if use python ; then
-		if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then
-			export USE_PYTHON64=yes
-		fi
-		export PYTHONHOME=/usr
-		export PYTHONVERSION=$(eselect python show|awk -Fpython '{ print $2 }')
-		export PYTHONPATH="./:${S}/contrib/python/"
-		export NWCHEM_MODULES="all python"
-	else
-		export NWCHEM_MODULES="all"
-	fi
-
-	cd src
-	emake \
-		DIAG=PAR \
-		FC=$(tc-getFC) \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		NWCHEM_TOP="${S}" \
-		NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem"
-}
-
-src_install() {
-	dobin bin/${NWCHEM_TARGET}/nwchem
-
-	insinto /usr/share/NWChem/basis/
-	doins -r src/basis/libraries src/data
-	insinto /usr/share/NWChem/nwpw
-	doins -r src/nwpw/libraryps
-
-	insinto /etc
-	doins nwchemrc
-
-	use examples && \
-		insinto /usr/share/NWChem/ && \
-		doins -r examples
-
-	use nwchem-tests \
-		insinto /usr/share/NWChem \
-		doins -r QA/tests
-}
-
-pkg_postinst() {
-	echo
-	elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc"
-	elog "or copy it in order to tell NWChem the right position of the"
-	elog "basis library and other necessary data."
-	echo
-}
diff --git a/sci-chemistry/nwchem/nwchem-6.3.ebuild b/sci-chemistry/nwchem/nwchem-6.3.ebuild
index 69748f28a..4395d150d 100644
--- a/sci-chemistry/nwchem/nwchem-6.3.ebuild
+++ b/sci-chemistry/nwchem/nwchem-6.3.ebuild
@@ -5,11 +5,12 @@
 EAPI=5
 
 PYTHON_COMPAT=( python{2_6,2_7} )
+
 inherit eutils fortran-2 multilib python-single-r1 toolchain-funcs
 
 DATE="2013-05-17"
 
-DESCRIPTION="NWChem: Delivering High-Performance Computational Chemistry to Science"
+DESCRIPTION="Delivering High-Performance Computational Chemistry to Science"
 HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
 SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV}-src.${DATE}.tar.gz"
 
@@ -20,13 +21,14 @@ IUSE="mpi doc examples nwchem-tests python"
 
 REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
 
-RDEPEND="sys-fs/sysfsutils
+RDEPEND="
+	sys-fs/sysfsutils
 	python? ( ${PYTHON_DEPS} )"
 DEPEND="${RDEPEND}
-	virtual/fortran
 	app-shells/tcsh
 	mpi? ( virtual/mpi[fortran] )
-	doc? ( dev-texlive/texlive-latex
+	doc? (
+		dev-texlive/texlive-latex
 		dev-tex/latex2html )"
 
 S="${WORKDIR}/${P}-src.${DATE}"
diff --git a/sci-chemistry/phaser/ChangeLog b/sci-chemistry/phaser/ChangeLog
deleted file mode 100644
index bc908bd4b..000000000
--- a/sci-chemistry/phaser/ChangeLog
+++ /dev/null
@@ -1,21 +0,0 @@
-# ChangeLog for sci-chemistry/phaser
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  25 Oct 2011; Justin Lecher <jlec@gentoo.org> metadata.xml:
-  Removed no-herd from herd tag in metadata.xml
-
-  10 Jul 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de>
-  phaser-2.1.4.ebuild, phaser-2.1.4-r1.ebuild:
-  Silence repoman.
-
-*phaser-2.1.4-r1 (29 May 2009)
-*phaser-2.1.4 (29 May 2009)
-
-  29 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +files/2.1.4-sadf.patch, +phaser-2.1.4.ebuild, +phaser-2.1.4-r1.ebuild,
-  +metadata.xml:
-  version 2.1.4 written by me 
-  2.1.4-r1 seperatly written by Johan Hattne Thanks!
-  builds phaser staticaly against bundled cctbx.
-
diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest
deleted file mode 100644
index eb8b8c568..000000000
--- a/sci-chemistry/phaser/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST phaser-2.1.4-cctbx-src.tar.gz 22388206 SHA256 594829cc82cb3c57e223ded99faf1fe86b192f2b48a935f93d2a4b89b9018970
diff --git a/sci-chemistry/phaser/files/2.1.4-sadf.patch b/sci-chemistry/phaser/files/2.1.4-sadf.patch
deleted file mode 100644
index ee1abe375..000000000
--- a/sci-chemistry/phaser/files/2.1.4-sadf.patch
+++ /dev/null
@@ -1,64 +0,0 @@
---- ccp4-6.1.1/src/phaser/source/phaser/src/RefineSADf.cc	2009-02-05 19:03:10.000000000 +0100
-+++ ccp4-6.1.1/src/phaser/source/phaser/src/RefineSADf.cc.new	2008-07-14 15:25:47.000000000 +0200
-@@ -161,7 +161,8 @@
-     if (atoms_extra[a].REJECTED) PHASER_ASSERT(atoms[a].occupancy == 0);
-   }
- 
--  cctbx::xray::fast_gradients<dFloatType> fast_gradients(
-+  typedef cctbx::xray::fast_gradients<dFloatType> fast_gradients_t;
-+  fast_gradients_t fast_gradients(
-       cctbxUC,
-       atoms.const_ref(),
-       scattering_type_registry,
-@@ -206,9 +205,9 @@
-     sc.flags.set_tan_u_iso(false);
-   }
- 
--  af::const_ref<dCmplxType, cctbx::maptbx::c_grid_padded_p1<3> > gradmap_const_ref(
--    gradmap_fft_ref.begin(),
--    cctbx::maptbx::c_grid_padded_p1<3>(cfft.n(), cfft.n()));
-+  typedef fast_gradients_t::accessor_type fgat;
-+  af::const_ref<dCmplxType, fgat>
-+    gradmap_const_ref(gradmap_fft_ref.begin(), fgat(cfft.n(), cfft.n()));
-   bool sampled_density_must_be_positive(true);
-   fast_gradients.sampling(
-       atoms.const_ref(),
---- ccp4-6.1.1/src/phaser/source/phaser/io/Errors.cc      2007-11-14 15:46:41.000000000 +0100
-+++ ccp4-6.1.1/src/phaser/source/phaser/io/Errors.cc.new      2007-11-14 15:46:41.000000000 +0100
-@@ -1,6 +1,7 @@
- //(c) 2000-2007 Cambridge University Technical Services Ltd
- //All rights reserved
- #include <phaser/io/Errors.h>
-+#include <cstdio>
- 
- namespace phaser {
- 
-@@ -20,7 +21,7 @@
-     sfile.erase(sfile.begin(),sfile.begin()+i+1);
-     std::string::size_type j = sfile.rfind("\\"); //microsoft file separator
-     sfile.erase(sfile.begin(),sfile.begin()+j+1);
--    sprintf(buf, "%ld", line);
-+    std::sprintf(buf, "%ld", line);
-     msg_ =   std::string("Program") + s + " error in source file "
-               + sfile + " (line " + buf + ")\n";
-     if (msg.size()) msg_ += "*** "+ msg + " ***";
---- ccp4-6.1.1/src/phaser/source/phaser/SConscript        2008-06-19 11:57:30.000000000 +0200
-+++ ccp4-6.1.1/src/phaser/source/phaser/SConscript.new        2008-06-19 11:57:30.000000000 +0200
-@@ -12,13 +12,15 @@
- 
- cxxflags = env_etc.cxxflags_base
- print "Compiling distributed version of phaser"
-+ccp4io_lib = getattr(env_etc, "ccp4io_lib", "cmtz")
-+  # XXX backward compatibility 2008-09-10
- env_etc.phaser_common_libs = [
-   "phaserrun",
-   "phasersrc",
-   "phaserio",
-   "phaserkey",
-   "phaserlib",
--  "cmtz",
-+  ccp4io_lib,
-   "cctbx",
- ]
- env_etc.phaser_common_includes = [
-
diff --git a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch
deleted file mode 100644
index ecc98490c..000000000
--- a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-6.1.1/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py.orig	2009-05-27 16:55:30.712547511 -0500
-+++ ccp4-6.1.1/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py	2009-05-27 16:55:44.446546721 -0500
-@@ -802,8 +802,6 @@
-     else:
-       action = self.write_bin_sh_dispatcher
-       ext = ""
--      try: os.chmod(source_file, 0755)
--      except OSError: pass
-     target_file_ext = target_file + ext
-     remove_or_rename(target_file_ext)
-     try: action(source_file, target_file_ext)
diff --git a/sci-chemistry/phaser/metadata.xml b/sci-chemistry/phaser/metadata.xml
deleted file mode 100644
index deb55d19f..000000000
--- a/sci-chemistry/phaser/metadata.xml
+++ /dev/null
@@ -1,30 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<!-- 
-$Header: $
-
-This is the example metadata file.
-The root element of this file is <pkgmetadata>. Within this element a 
-number of subelements are allowed: herd, maintainer, and 
-longdescription. herd is a required subelement.
-
-For a full description look at:
-http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=2&chap=4
-
-
-Before committing, please remove the comments from this file. They are 
-not relevant for general metadata.xml files.
--->
-<pkgmetadata>
-	<maintainer>
-		<email>jlec@gentoo.org</email>
-		<!--  <description>coding for fun</description> -->
-	</maintainer>
-	<!-- <longdescription>Long description of the package</longdescription> -->
-	<!--
-<use>
-  <flag name='flag'>Description of how USE='flag' affects this package.</flag>
-  <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this package.</flag>
-</use>
--->
-</pkgmetadata>
diff --git a/sci-chemistry/phaser/phaser-2.1.4-r1.ebuild b/sci-chemistry/phaser/phaser-2.1.4-r1.ebuild
deleted file mode 100644
index 2f8cafac4..000000000
--- a/sci-chemistry/phaser/phaser-2.1.4-r1.ebuild
+++ /dev/null
@@ -1,138 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit base flag-o-matic python
-
-DESCRIPTION="A program for phasing macromolecular crystal structures"
-HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser"
-SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/${PN}-${PV}-cctbx-src.tar.gz"
-
-LICENSE="|| ( phaser phaser-com ccp4 )"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="openmp"
-RDEPEND=""
-DEPEND="${RDEPEND}
-		  app-shells/tcsh"
-
-S="${WORKDIR}"/ccp4-6.1.1
-
-PATCHES=(
-	"${FILESDIR}"/phaser-2.1.4-chmod.patch
-	)
-
-src_prepare() {
-	base_src_prepare
-
-	use openmp && append-flags -fopenmp
-
-	for i in ${CXXFLAGS}; do
-		OPTS="${OPTS} \"${i}\","
-	done
-
-	OPTS=${OPTS%,}
-
-	sed -i \
-		-e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \
-		"${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die
-
-	for i in ${LDFLAGS}; do
-		OPTSLD="${OPTSLD} \"${i}\","
-	done
-
-	sed -i \
-		-e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\"\]:g" \
-		"${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die
-
-}
-
-src_compile() {
-	local compiler
-	local mtype
-	local mversion
-	local nproc
-
-	# Valid compilers are win32_cl, sunos_CC, unix_gcc, unix_ecc,
-	# unix_icc, unix_icpc, tru64_cxx, hp_ux11_aCC, irix_CC,
-	# darwin_c++, darwin_gcc.  The build systems seems to prepend
-	# unix_ all by itself.  Can this be derived from $(tc-getCC)?
-	compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-
-	# Breaks cross compilation.
-	mtype=$(src/${PN}/bin/machine_type)
-	mversion=$(src/${PN}/bin/machine_version)
-	nproc=`echo "-j1 ${MAKEOPTS}" \
-		| sed -e "s/.*\(-j\s*\|--jobs=\)\([0-9]\+\).*/\2/"`
-
-	einfo "Creating build directory $nproc "
-	mkdir build
-	cd    build
-	ln -sf "${S}/lib/cctbx/cctbx_sources/scons"  scons
-	ln -sf "${S}/lib/cctbx/cctbx_sources/libtbx" libtbx
-
-	# It is difficult to rely on sci-libs/cctbx for the cctbx
-	# dependency, because upstream releases new versions quite
-	# frequently.  Perhaps better to link statically to the bundled
-	# cctbx.
-	einfo "Configuring phaser components"
-	python_version
-	${python} "libtbx/configure.py" \
-		--build=release \
-		--compiler=${compiler} \
-		--repository="${S}"/src/${PN}/source \
-		--repository="${S}"/lib/cctbx/cctbx_sources \
-		--static_libraries \
-		ccp4io="${S}" \
-		mmtbx \
-		phaser || die "configure.py failed"
-
-	einfo "Setting up build environment"
-	source setpaths.sh
-
-	einfo "Compiling phaser components"
-	libtbx.scons -j ${nproc} || die "libtbx.scons failed"
-
-	# Hardcoded /usr/bin does not look nice.  Should these files,
-	# perhaps, be installed somewhere?
-#	einfo "Creating env.csh"
-#	cat >> "${T}"/env.csh <<- EOF
-#	#! /bin/csh
-#
-#	setenv PHASER             /usr/bin
-#	setenv PHASER_ENVIRONMENT 1
-#	setenv PHASER_MTYPE       ${mtype}
-#	setenv PHASER_MVERSION    ${mversion}
-#	setenv PHASER_VERSION     ${PV}
-#	EOF
-
-#	einfo "Creating env.sh"
-	cat >> "${T}"/53${PN} <<- EOF
-
-	PHASER="/usr/bin"
-	PHASER_ENVIRONMENT="1"
-	PHASER_MTYPE="${mtype}"
-	PHASER_MVERSION="${mversion}"
-	PHASER_VERSION="${PV}"
-	EOF
-
-	doenvd "${T}"/53${PN}
-}
-
-# Why do some tests say that CNS and SHELX is not available?  Same for
-# cctbx ebuild tests.
-src_test() {
-	cd "${S}//build" && \
-	source setpaths.sh && \
-	csh ./run_tests.csh || die "run_test.csh failed"
-}
-
-# This is a bit thin.  Maybe install other files from the distribution
-# as well?
-src_install() {
-	dobin build/exe/phaser || die
-}
diff --git a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild
deleted file mode 100644
index 73f18f4ee..000000000
--- a/sci-chemistry/phaser/phaser-2.1.4.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit eutils python toolchain-funcs
-
-DESCRIPTION="Phasing macromolecular crystal structures with maximum likelihood methods"
-SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/${P}-cctbx-src.tar.gz"
-HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser/"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~x86 ~amd64"
-IUSE="openmp"
-
-DEPEND="dev-util/scons"
-RDEPEND="sci-libs/cctbx"
-
-S="${WORKDIR}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	rm -rf lib/*
-	cp -rf $CCP4/lib/cctbx/cctbx_sources/libtbx "${WORKDIR}"
-
-	mkdir -p "${WORKDIR}"/scons/src/
-	ln -sf /usr/$(get_libdir)/scons-1.2.0 "${WORKDIR}"/scons/src/engine || die
-
-	epatch "${FILESDIR}"/${PV}-sadf.patch
-}
-
-src_compile(){
-	python_version
-
-	local MYCONF
-	local MAKEOPTS_EXP
-	local OPTS
-	local OPTSLD
-
-	MYCONF="${S}/libtbx/configure.py"
-
-	MYCONF="${MYCONF} --repository ${S}/ccp4-6.1.1/src/${PN}/source --repository /usr/$(get_libdir)/cctbx/cctbx_sources/ \
-	--build=release ccp4io=${CCP4}/$(get_libdir)/cctbx/cctbx_sources/ccp4io/"
-
-	MAKEOPTS_EXP=${MAKEOPTS/j/j }
-	MAKEOPTS_EXP=${MAKEOPTS_EXP%-l[0-9]*}
-
-	# Get CXXFLAGS in format suitable for substitition into SConscript
-	for i in ${CXXFLAGS}; do
-	OPTS="${OPTS} \"${i}\","
-	done
-
-	# Strip off the last comma
-	OPTS=${OPTS%,}
-
-	# Fix CXXFLAGS
-	sed -i \
-	-e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \
-	"${S}"/libtbx/SConscript
-
-	# Get LDFLAGS in format suitable for substitition into SConscript
-	for i in ${LDFLAGS}; do
-	OPTSLD="${OPTSLD} \"${i}\","
-	done
-
-	# Fix LDFLAGS which should be as-needed ready
-	sed -i \
-	-e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\":g" \
-	"${S}"/libtbx/SConscript
-
-	# Get compiler in the right way
-	COMPILER=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-	MYCONF="${MYCONF} --compiler=${COMPILER}"
-
-	# Additional USE flag usage
-	check_use openmp
-	MYCONF="${MYCONF} --enable-openmp-if-possible=${USE_openmp}"
-	use threads && USEthreads="--enable-boost-threads" && \
-	ewarn "If using boost threads openmp support is disabled"
-
-	MYCONF="${MYCONF} ${USE_threads} --scan-boost"
-
-	MYCONF="${MYCONF} phaser"
-	einfo "configuring with ${python} ${MYCONF}"
-
-	${python} ${MYCONF} \
-	|| die "configure failed"
-
-	source setpaths_all.sh
-
-	einfo "compiling with libtbx.scons ${MAKEOPTS_EXP}"
-	libtbx.scons ${MAKEOPTS_EXP} .|| die "make failed"
-}
-
-src_install() {
-	rm lib/libboost*
-	dolib.so lib/*.so || die
-	dolib.a lib/*.a || die
-	dobin exe/phaser || die
-}
-
-check_use() {
-
-	for var in $@; do
-	if use ${var}; then
-	printf -v "USE_$var" True
-	else
-	printf -v "USE_$var" False
-
-	fi
-	shift
-	done
-}
diff --git a/sci-chemistry/polygon/ChangeLog b/sci-chemistry/polygon/ChangeLog
index 354b0fef7..4a9ca0394 100644
--- a/sci-chemistry/polygon/ChangeLog
+++ b/sci-chemistry/polygon/ChangeLog
@@ -1,7 +1,12 @@
 # ChangeLog for sci-chemistry/polygon
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> +polygon-0612.ebuild,
+  -polygon-0710.ebuild, +files/0612-db.patch, -files/0710-db.patch,
+  metadata.xml:
+  Version BUmp; fixed license
+
 *polygon-0710 (23 Oct 2009)
 
   23 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/polygon/Manifest b/sci-chemistry/polygon/Manifest
index 693c1c379..0c1b4065b 100644
--- a/sci-chemistry/polygon/Manifest
+++ b/sci-chemistry/polygon/Manifest
@@ -1,2 +1,2 @@
-DIST pdb_2009-04-29_ord.zip 4371434 SHA256 cd949ded9c7c656e4cc9d5f9c28584b648fec3bd2df2e80811ea8eb7baf81f69
-DIST polygon0710.tcl 128282 SHA256 db1b985805c750550328d0092bbf826c30df68e38453f2866329fd96cbfe45d8
+DIST pdb_2009-04-29_ord.zip 4371434 SHA256 cd949ded9c7c656e4cc9d5f9c28584b648fec3bd2df2e80811ea8eb7baf81f69 SHA512 3d1621c96f7e65197a5a7b7e655648ec957717bc38622b64f900142bac98d9b6450c8c9d128055dc9d673ae031c0a7b379a7d28ae97b22a070337b9563169287 WHIRLPOOL 258848856c4375fc00bda3382bed18a30de159348a246aa82f94569249ea24ee851109064a4800f2e17fc7d755d48d3c3f60d1608b418a198dd367a900de45fb
+DIST polygon0612.tcl 124276 SHA256 d5b2c55faa37097db04a98c70cee5a49480f0b9e6e4e93345b67eee72c2c6aac SHA512 20d5e2011d28fe38c39f92be3d2221186f43048f173eb8b3971238836b5a09ae55cb44c0aad9e9efb3206e3c8a6e0017b749ce3911455e63dd8fcdba5c7c9dfe WHIRLPOOL cbde37636166a60ea1eeabf53da5398bb10e0e2ed7742beb87738773ffd45015f3ffe1df97745a98d52b7e00a5a1700279fa73ecf20ba456d8a8c2429c3db012
diff --git a/sci-chemistry/polygon/files/0710-db.patch b/sci-chemistry/polygon/files/0612-db.patch
index faab35e4a..a12225f29 100644
--- a/sci-chemistry/polygon/files/0710-db.patch
+++ b/sci-chemistry/polygon/files/0612-db.patch
@@ -1,11 +1,11 @@
---- polygon0710.tcl	2009-10-15 16:11:36.000000000 +0200
-+++ polygon0710.tcl.new	2009-10-23 17:59:32.723500534 +0200
+--- polygon0612.tcl	2009-10-15 16:11:36.000000000 +0200
++++ polygon0612.tcl.new	2009-10-23 17:59:32.723500534 +0200
 @@ -22,7 +22,7 @@
- #

- #database name

- #

--set currentFile1 pdb_2009-04-29_ord.txt

-+set currentFile1 /usr/share/polygon/pdb_2009-04-29_ord.txt

- 

- # numcol - number of columns in the database

-   set numcol 63

+ #
+ #database name
+ #
+-set currentFile1 pdb_2009-04-29_ord.txt
++set currentFile1 /usr/share/polygon/pdb_2009-04-29_ord.txt
+ 
+ # numcol - number of columns in the database
+   set numcol 63
diff --git a/sci-chemistry/polygon/metadata.xml b/sci-chemistry/polygon/metadata.xml
index 0fbe927f0..d410f1573 100644
--- a/sci-chemistry/polygon/metadata.xml
+++ b/sci-chemistry/polygon/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>sci@gentoo.org</email>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-chemistry/polygon/polygon-0710.ebuild b/sci-chemistry/polygon/polygon-0612.ebuild
index ba2415f16..ac2335746 100644
--- a/sci-chemistry/polygon/polygon-0710.ebuild
+++ b/sci-chemistry/polygon/polygon-0612.ebuild
@@ -1,7 +1,9 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
+EAPI=5
+
 inherit eutils
 
 DB="pdb_2009-04-29_ord"
@@ -15,23 +17,27 @@ SRC_URI="
 "
 
 SLOT="0"
+LICENSE="all-rights-reserved"
 KEYWORDS="~amd64 ~x86"
-LICENSE="as-is"
 IUSE=""
 
 RDEPEND="dev-lang/tcl"
 DEPEND="app-arch/unzip"
 
+S="${WORKDIR}"
+
 src_unpack() {
 	unpack ${DB}.zip
-	cp "${DISTDIR}"/${MY_P}.tcl "${WORKDIR}"
-	cd "${WORKDIR}"
+	cp "${DISTDIR}"/${MY_P}.tcl "${S}" || die
+}
+
+src_prepare() {
 	epatch "${FILESDIR}"/${PV}-db.patch
 }
 
 src_install() {
 	edos2unix ${MY_P}.tcl
-	newbin ${MY_P}.tcl ${PN} || die
+	newbin ${MY_P}.tcl ${PN}
 	insinto /usr/share/${PN}
-	doins ${DB}.txt || die
+	doins ${DB}.txt
 }
diff --git a/sci-chemistry/pymol-apbs-plugin/ChangeLog b/sci-chemistry/pymol-apbs-plugin/ChangeLog
index deaec995f..9bfa57450 100644
--- a/sci-chemistry/pymol-apbs-plugin/ChangeLog
+++ b/sci-chemistry/pymol-apbs-plugin/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-chemistry/pymol-apbs-plugin
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> pymol-apbs-plugin-9999.ebuild:
+  Drop KEYWORDS from live ebuild
+
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> pymol-apbs-plugin-9999.ebuild,
+  metadata.xml:
+  Bump to EAPI=5 and bump to python-r1.eclass
+
   29 Jun 2010; Justin Lecher <jlec@gentoo.org>
   pymol-apbs-plugin-9999.ebuild:
   Python ABI fixes
diff --git a/sci-chemistry/pymol-apbs-plugin/metadata.xml b/sci-chemistry/pymol-apbs-plugin/metadata.xml
index 0fbe927f0..d410f1573 100644
--- a/sci-chemistry/pymol-apbs-plugin/metadata.xml
+++ b/sci-chemistry/pymol-apbs-plugin/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>sci@gentoo.org</email>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-9999.ebuild b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-9999.ebuild
index 48a055c8a..70bbba7ec 100644
--- a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-9999.ebuild
+++ b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-9999.ebuild
@@ -1,56 +1,41 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="3"
+EAPI=5
 
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
+PYTHON_COMPAT=( python2_7 )
 
-inherit python subversion
+inherit python-single-r1 subversion
 
 MY_PV="${PV##*_p}"
 
 DESCRIPTION="APBS plugin for pymol"
 HOMEPAGE="http://sourceforge.net/projects/pymolapbsplugin/"
+SRC_URI=""
 ESVN_REPO_URI="https://pymolapbsplugin.svn.sourceforge.net/svnroot/pymolapbsplugin/trunk/"
 
 SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
 LICENSE="pymol"
+KEYWORDS=""
 IUSE=""
 
-RDEPEND="
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
 	sci-chemistry/apbs
 	sci-chemistry/pdb2pqr
-	!<sci-chemistry/pymol-1.2.2-r1"
+	>sci-chemistry/pymol-1.5"
 DEPEND="${RDEPEND}"
-RESTRICT_PYTHON_ABIS="3.*"
-
-src_unpack() {
-	subversion_src_unpack
-	python_copy_sources
-}
 
 src_install() {
-	installation() {
-		sed \
-			-e "s:^APBS_BINARY_LOCATION.*:APBS_BINARY_LOCATION = \"${EPREFIX}/usr/bin/apbs\":g" \
-			-e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/src/\":g" \
-			-e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/\":g" \
-			-e "s:^TEMPORARY_FILE_DIR.*:TEMPORARY_FILE_DIR = \"./\":g" \
-			-i src/apbsplugin.py
-
-		insinto $(python_get_sitedir)/pmg_tk/startup/
-		newins src/apbsplugin.py apbs_tools.py || die
-	}
-	python_execute_function -s installation
-}
-
-pkg_postinst() {
-	python_mod_optimize pmg_tk/startup/apbs_tools.py
-}
-
-pkg_postrm() {
-	python_mod_cleanup pmg_tk/startup/apbs_tools.py
+	sed \
+		-e "s:^APBS_BINARY_LOCATION.*:APBS_BINARY_LOCATION = \"${EPREFIX}/usr/bin/apbs\":g" \
+		-e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/src/\":g" \
+		-e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/\":g" \
+		-e "s:^TEMPORARY_FILE_DIR.*:TEMPORARY_FILE_DIR = \"./\":g" \
+		-i src/apbsplugin.py > apbs_tools.py || die
+	python_moduleinto pmg_tk/startup/
+	python_domodule apbs_tools.py
+	python_optimize
 }
diff --git a/sci-chemistry/pymol-plugins-ezviz/ChangeLog b/sci-chemistry/pymol-plugins-ezviz/ChangeLog
index 1ccd39164..86dd9cb13 100644
--- a/sci-chemistry/pymol-plugins-ezviz/ChangeLog
+++ b/sci-chemistry/pymol-plugins-ezviz/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/www/viewcvs.gentoo.org/raw_cvs/gentoo-x86/sci-chemistry/pymol-plugins-ezviz/ChangeLog,v 1.2 2010/04/08 18:47:57 jlec dead $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org>
+  pymol-plugins-ezviz-1.0.2005.ebuild:
+  Bump to EAPI=5 and bump to python-r1.eclass
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Fix missing DOCTYPE
 
diff --git a/sci-chemistry/pymol-plugins-ezviz/Manifest b/sci-chemistry/pymol-plugins-ezviz/Manifest
index d7b39ced4..900a20e11 100644
--- a/sci-chemistry/pymol-plugins-ezviz/Manifest
+++ b/sci-chemistry/pymol-plugins-ezviz/Manifest
@@ -1 +1 @@
-DIST pymol-plugins-ezviz-1.0.2005.zip 137431 SHA256 742c18d338ccc0567203c122a5f7ce0f903bf3247f7620337828d9dd5ae4f008
+DIST pymol-plugins-ezviz-1.0.2005.zip 137431 SHA256 742c18d338ccc0567203c122a5f7ce0f903bf3247f7620337828d9dd5ae4f008 SHA512 d0281e16dac76e519c725945bdaa5da233f8975411b9d39258a03206c39349014a05e52b6f8cd08b0c667e9d6a177eba2545861ee853ba43810f9ed0d4beb7a1 WHIRLPOOL 87deac54993ca87e4c61512f54d2c5063e9d641064780d999603d934c11755ad36bd211210c04f6a8e2bf302476b54ef8b3cad6efe1f7c0fa74378b549699366
diff --git a/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005.ebuild b/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005.ebuild
index 8e84a9af2..5f044c6e3 100644
--- a/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005.ebuild
+++ b/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005.ebuild
@@ -1,63 +1,51 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/www/viewcvs.gentoo.org/raw_cvs/gentoo-x86/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005.ebuild,v 1.2 2010/04/08 18:47:57 jlec dead $
 
-EAPI="3"
+EAPI=5
 
-SUPPORT_PYTHON_ABIS="1"
+PYTHON_COMPAT=( python2_7 )
 
-inherit eutils python
+inherit eutils python-r1
 
-DESCRIPTION="assistance tool for the difficult to understand user interface of PyMOL"
+DESCRIPTION="Assistance tool for the difficult to understand user interface of PyMOL"
 HOMEPAGE="http://www.rit.edu/cos/ezviz/index.html"
-SRC_URI="
-	mirror://gentoo/${P}.zip
-	mirror://gentoo/${P}.zip"
+SRC_URI="http://www.rit.edu/cos/ezviz/EZ_Viz.zip -> ${P}.zip"
 
 SLOT="0"
+LICENSE="all-rights-reserved"
 KEYWORDS="~amd64 ~x86"
-LICENSE="as-is"
 IUSE="doc"
 
-RDEPEND="sci-chemistry/pymol"
-DEPEND="
-	app-arch/unzip
-	${RDEPEND}"
-
-RESTRICT_PYTHON_ABIS="3.*"
+RDEPEND="sci-chemistry/pymol[${PYTHON_USEDEP}]"
+DEPEND="app-arch/unzip"
 
 S="${WORKDIR}/EZ_Viz Folder"
 
 src_prepare() {
 	edos2unix ez-viz.py
+	epatch "${FILESDIR}"/gentoo.patch
+	for gif in *.GIF; do
+		mv ${gif} ${gif/.GIF/.gif} || die
+	done
 	python_copy_sources
 	preperation() {
-		epatch "${FILESDIR}"/gentoo.patch
+		cd "${BUILD_DIR}" || die
 		sed \
 			-e "s:GENTOOPYMOL:${EPREFIX}/$(python_get_sitedir):g" \
 			-i ez-viz.py || die
 	}
-	python_execute_function -s preperation
+	python_foreach_impl preperation
 }
 
 src_install() {
 	installation() {
-		insinto $(python_get_sitedir)/pmg_tk/startup/
-		doins *.py || die
-		insinto $(python_get_sitedir)/pmg_tk/startup/ez-viz/
-		doins *.gif || die
-		for gif in *.GIF; do
-			newins ${gif} ${gif/.GIF/.gif} || die
-		done
+		python_moduleinto pmg_tk/startup/
+		python_domodule *.py
+		python_moduleinto pmg_tk/startup/ez-viz/
+		python_domodule *.gif
 	}
-	python_execute_function -s installation
-	dodoc readme.txt || die
-}
-
-pkg_postinst() {
-	python_mod_optimize pmg_tk/startup
-}
-
-pkg_postrm() {
-	python_mod_cleanup pmg_tk/startup
+	python_foreach_impl installation
+	python_parallel_foreach_impl python_optimize
+	dodoc readme.txt
 }
diff --git a/sci-chemistry/pymol-plugins-psico/ChangeLog b/sci-chemistry/pymol-plugins-psico/ChangeLog
index 8c346ed68..e73fd24a3 100644
--- a/sci-chemistry/pymol-plugins-psico/ChangeLog
+++ b/sci-chemistry/pymol-plugins-psico/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> pymol-plugins-psico-9999.ebuild:
+  Bump to EAPI=5 and distutils-r1.eclass
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> pymol-plugins-psico-9999.ebuild,
   metadata.xml:
   Rename sci-chemistry/mmtk to sci-libs/mmtk
diff --git a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild
index d074fc52f..fd8f89921 100644
--- a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild
+++ b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild
@@ -2,14 +2,11 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
 
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="3.*"
-PYTHON_MODNAME="psico"
+PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit distutils git-2
+inherit distutils-r1 git-2
 
 DESCRIPTION="Pymol ScrIpt COllection"
 HOMEPAGE="https://github.com/speleo3/pymol-psico/"
@@ -22,9 +19,9 @@ LICENSE="BSD-2"
 IUSE="minimal"
 
 RDEPEND="
-	dev-python/numpy
-	sci-biology/biopython
-	sci-libs/mmtk
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-biology/biopython[${PYTHON_USEDEP}]
+	sci-libs/mmtk[${PYTHON_USEDEP}]
 	!minimal? (
 		media-libs/qhull
 		media-video/mplayer
diff --git a/sci-chemistry/pyquante/ChangeLog b/sci-chemistry/pyquante/ChangeLog
index ff079af0e..fee67569c 100644
--- a/sci-chemistry/pyquante/ChangeLog
+++ b/sci-chemistry/pyquante/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-chemistry/pyquante
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> pyquante-1.6.3-r1.ebuild,
+  metadata.xml:
+  Bump to EAPI=5 and distutils-r1.eclass
+
 *pyquante-1.6.3-r1 (29 Jun 2010)
 
   29 Jun 2010; Justin Lecher <jlec@gentoo.org> -pyquante-1.6.3.ebuild,
diff --git a/sci-chemistry/pyquante/Manifest b/sci-chemistry/pyquante/Manifest
index 02e7d8362..ddde6e594 100644
--- a/sci-chemistry/pyquante/Manifest
+++ b/sci-chemistry/pyquante/Manifest
@@ -1 +1 @@
-DIST PyQuante-1.6.3.tar.gz 329029 SHA256 9bba2d6eefebbb3f2296c69e8b8c9714d8ac1689abaf4ce9468441d19c1e9d20
+DIST PyQuante-1.6.3.tar.gz 329029 SHA256 9bba2d6eefebbb3f2296c69e8b8c9714d8ac1689abaf4ce9468441d19c1e9d20 SHA512 7442fd1a25bf10db81f86d6811a3e57c38a3c5a6ac26764663e25028b45a1a3ae5da896a5219e467265d7128829386e2295fccf470018c45dc70b8a20d592fbf WHIRLPOOL 53e854f2bb02d4cffa2d16f9acb5ee9db4f3abb23d590a4b4dcd759bcde51337146518341aa7d8d2c2caf2b3cc1d3e3a4932cd39d82768811acd2c4577247764
diff --git a/sci-chemistry/pyquante/metadata.xml b/sci-chemistry/pyquante/metadata.xml
index 9ac9ffdb3..51fdedab1 100644
--- a/sci-chemistry/pyquante/metadata.xml
+++ b/sci-chemistry/pyquante/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
+  <herd>sci-chemistry</herd>
 </pkgmetadata>
diff --git a/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild b/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild
index 93f085554..88f7f96d2 100644
--- a/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild
+++ b/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="3"
+EAPI=5
 
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
+PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit distutils
+inherit distutils-r1
 
 MY_PN="PyQuante"
 MY_P="${MY_PN}-${PV}"
@@ -16,8 +15,8 @@ DESCRIPTION="Quantum chemistry package written in Python"
 HOMEPAGE="http://pyquante.sourceforge.net/"
 SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
 
-LICENSE="GPL-2"
 SLOT="0"
+LICENSE="GPL-2"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
diff --git a/sci-chemistry/shiftx/ChangeLog b/sci-chemistry/shiftx/ChangeLog
index 3284d504c..e588d4f23 100644
--- a/sci-chemistry/shiftx/ChangeLog
+++ b/sci-chemistry/shiftx/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-chemistry/shiftx
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx-1.1.ebuild, metadata.xml:
+  Bump to EAPI=5 and fix license
+
 *shiftx-1.1 (14 Jun 2009)
 
   14 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/shiftx/Manifest b/sci-chemistry/shiftx/Manifest
index 01ee9e803..87119a6e4 100644
--- a/sci-chemistry/shiftx/Manifest
+++ b/sci-chemistry/shiftx/Manifest
@@ -1 +1 @@
-DIST shiftx.tar.gz 318768 SHA256 2a4b00adfc39d39d2f28c09f78e3c9c7ab8b28e96c4e5efcdffeedfac00ab1ef
+DIST shiftx-1.1.tar.gz 504915 SHA256 a08bc301b119154675eb05d9c5c69b7f582e8c2fa0cc81c5040a6ac013ac1965 SHA512 2396ef31a9ce0c059b0c5cb0be60d7ab0489775e03439dcf3c62b8559a13b0e8ad37c8ef02e6422dd6b93acfe579c1abc86f520473836240d48840c7f38aed1f WHIRLPOOL 048873c70f8ae670e097039b4a29ec9eb27ea89879065b2155140914bc77b999e42af471aa15598691d12e0c11b58100a4d15fd29ccf4b562a885a8ea81afe7c
diff --git a/sci-chemistry/shiftx/metadata.xml b/sci-chemistry/shiftx/metadata.xml
index 0fbe927f0..d410f1573 100644
--- a/sci-chemistry/shiftx/metadata.xml
+++ b/sci-chemistry/shiftx/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>sci@gentoo.org</email>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-chemistry/shiftx/shiftx-1.1.ebuild b/sci-chemistry/shiftx/shiftx-1.1.ebuild
index 336c77cca..5f26ed3f9 100644
--- a/sci-chemistry/shiftx/shiftx-1.1.ebuild
+++ b/sci-chemistry/shiftx/shiftx-1.1.ebuild
@@ -1,33 +1,31 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
+EAPI=5
+
 inherit base toolchain-funcs
 
-DESCRIPTION="With this form you can predict 1H, 13C and 15N chemical shifts for your favorite protein"
-HOMEPAGE="http://redpoll.pharmacy.ualberta.ca/shiftx/"
-SRC_URI="http://redpoll.pharmacy.ualberta.ca/download/${PN}/${PN}.tar.gz"
+DESCRIPTION="Prediction of 1H, 13C and 15N chemical shifts for proteins"
+HOMEPAGE="http://shiftx.wishartlab.com/"
+SRC_URI="http://shiftx.wishartlab.com/download/${PN}.tar.gz -> ${P}.tar.gz"
 
-LICENSE="as-is"
+LICENSE="all-rights-reserved"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 S="${WORKDIR}"/${PN}
 
-PATCHES=(
-	"${FILESDIR}"/${PV}-Makefile.patch
-)
+PATCHES=( "${FILESDIR}"/${PV}-Makefile.patch )
 
 DOCS="README FEATURES *.pdb *.out"
 
 src_compile() {
-	emake \
-		CC="$(tc-getCC)" || \
-		die "compilation failed"
+	emake CC="$(tc-getCC)"
 }
 
 src_install() {
-	dobin ${PN} || die "installationof ${PN} failed"
-	dodoc ${DOCS} || die
+	dobin ${PN}
+	dodoc ${DOCS}
 }
diff --git a/sci-chemistry/smmp/ChangeLog b/sci-chemistry/smmp/ChangeLog
index cddd7bfbb..375ec723b 100644
--- a/sci-chemistry/smmp/ChangeLog
+++ b/sci-chemistry/smmp/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-chemistry/smmp
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> smmp-3.0.5.ebuild, metadata.xml:
+  Bump to EAPI=5 and python-r1.eclass
+
   24 Jun 2011; Justin Lecher <jlec@gentoo.org> smmp-3.0.5.ebuild:
   Streamlined fortran-2 eclass usage
 
diff --git a/sci-chemistry/smmp/Manifest b/sci-chemistry/smmp/Manifest
index 879b9f85b..1b54b5bcf 100644
--- a/sci-chemistry/smmp/Manifest
+++ b/sci-chemistry/smmp/Manifest
@@ -1 +1 @@
-DIST SMMP-3.0.5.tar.bz2 233378 SHA256 70d6b719d2c2ef1d34fd9897ad1c89a37c4d7531d80c904eee39dc8855aca31c
+DIST SMMP-3.0.5.tar.bz2 233378 SHA256 70d6b719d2c2ef1d34fd9897ad1c89a37c4d7531d80c904eee39dc8855aca31c SHA512 7a6701f267fc09ee966ec34854ca12443725dc01e3bdf6283eaac7fc82764030abbc10bd0c6eefef2652bb64a70d5a09dc338448ce9d0c31021219358d40920d WHIRLPOOL 1c2b390b85ad5a9cc4f00df6838f92b8dd29403648ca1a07bf8d71b409cc396fb3671201f271a65f4fecc70a99d25ed0be95c9f26ab15d6ce431c220c9e1d991
diff --git a/sci-chemistry/smmp/metadata.xml b/sci-chemistry/smmp/metadata.xml
index 0fbe927f0..d410f1573 100644
--- a/sci-chemistry/smmp/metadata.xml
+++ b/sci-chemistry/smmp/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>sci@gentoo.org</email>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-chemistry/smmp/smmp-3.0.5.ebuild b/sci-chemistry/smmp/smmp-3.0.5.ebuild
index 8f49f3d29..95dda9950 100644
--- a/sci-chemistry/smmp/smmp-3.0.5.ebuild
+++ b/sci-chemistry/smmp/smmp-3.0.5.ebuild
@@ -1,14 +1,12 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=2
+EAPI=5
 
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="3.*"
+PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit eutils fortran-2 python toolchain-funcs
+inherit eutils fortran-2 python-r1 toolchain-funcs
 
 MY_PN="SMMP"
 MY_P="${MY_PN}-${PV}"
@@ -18,13 +16,11 @@ HOMEPAGE="http://smmp.berlios.de/"
 SRC_URI="mirror://berlios/${PN}/${MY_P}.tar.bz2"
 
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
 LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86"
 IUSE="doc mpi test"
 
-RDEPEND="
-	virtual/fortran
-	mpi? ( virtual/mpi )"
+RDEPEND="mpi? ( virtual/mpi )"
 DEPEND="${RDEPEND}
 	doc? ( app-doc/doxygen )"
 
@@ -42,31 +38,22 @@ src_compile() {
 		target="${PN}"
 	fi
 
-	tc-export FC
-
-	emake ${target} || die
+	emake ${target}
 }
 
 src_test() {
-	emake examples || die
+	emake examples
 	cd EXAMPLES
 	bash smmp.cmd || die
 }
 
 src_install() {
-	dobin ${PN} || die
+	dobin ${PN}
 	installation() {
-		insinto $(python_get_sitedir)/${PN}
-		doins *.py || die
+		python_moduleinto ${PN}
+		python_domodule *.py
+		python_optimize
 	}
-	python_execute_function installation
-	dodoc README || die
-}
-
-pkg_postinst() {
-	python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN}
+	python_foreach_impl installation
+	dodoc README
 }
diff --git a/sci-chemistry/specView/ChangeLog b/sci-chemistry/specView/ChangeLog
index 09193d635..b6fe2af69 100644
--- a/sci-chemistry/specView/ChangeLog
+++ b/sci-chemistry/specView/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> specView-1.0.2.ebuild:
+  Bump to EAPI=5 and python-single-r1.eclass
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> specView-1.0.2.ebuild,
   metadata.xml:
   Fix quoting
diff --git a/sci-chemistry/specView/specView-1.0.2.ebuild b/sci-chemistry/specView/specView-1.0.2.ebuild
index 89666a69d..a0a5bac38 100644
--- a/sci-chemistry/specView/specView-1.0.2.ebuild
+++ b/sci-chemistry/specView/specView-1.0.2.ebuild
@@ -2,11 +2,11 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
 
-PYTHON_DEPEND="2"
+PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit python toolchain-funcs
+inherit multilib python-single-r1 toolchain-funcs
 
 DESCRIPTION="Fast way to visualise NMR spectrum and peak data"
 HOMEPAGE="http://www.ccpn.ac.uk/software/specview"
@@ -18,8 +18,8 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
 RDEPEND="
-	dev-python/pyopengl
-	dev-python/pyside[webkit]"
+	dev-python/pyopengl[${PYTHON_USEDEP}]
+	dev-python/pyside[webkit,${PYTHON_USEDEP}]"
 DEPEND="${RDEPEND}"
 
 S="${WORKDIR}"/ccpnmr/ccpnmr3.0/
@@ -30,11 +30,6 @@ S="${WORKDIR}"/ccpnmr/ccpnmr3.0/
 #unbundle inchi
 #parallel build
 
-pkg_setup() {
-	python_set_active_version 2
-	python_pkg_setup
-}
-
 src_prepare() {
 	sed \
 		-e "s|/usr|"${EPREFIX}"/usr|g" \
@@ -43,7 +38,7 @@ src_prepare() {
 		-e "/^OPT_FLAG/s:=.*$:= ${CFLAGS}:g" \
 		-e "/^LINK_FLAGS/s:$: ${LDFLAGS}:g" \
 		-e "/^PYTHON_DIR/s:=.*:= "${EPREFIX}"/usr:g" \
-		-e "/^PYTHON_LIB/s:=.*:= $(python_get_library -l):g" \
+		-e "/^PYTHON_LIB/s:=.*:= $(python_get_LIBS):g" \
 		-e "/^PYTHON_INCLUDE_FLAGS/s:=.*:= -I"${EPREFIX}"$(python_get_includedir) -I"${EPREFIX}"$(python_get_sitedir)/numpy/core/include/numpy:g" \
 		-e "/^PYTHON_LIB_FLAGS/s:=.*:= -L"${EPREFIX}"/usr/$(get_libdir):g" \
 		-e "/^SHARED_FLAGS/s:=.*:= -shared:g" \
@@ -72,37 +67,22 @@ src_install() {
 	find . -name "*.pyc" -type f -delete
 	dodir /usr/bin
 	sed \
-	-e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
-	-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
-	-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
-	-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
-	-e "s|gentoopython|$(PYTHON -a)|g" \
-	-e "s|gentoousr|${EPREFIX}/usr|g" \
-	-e "s|//|/|g" \
+		-e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
+		-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+		-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+		-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+		-e "s|gentoopython|${PYTHON}|g" \
+		-e "s|gentoousr|${EPREFIX}/usr|g" \
+		-e "s|//|/|g" \
 		"${FILESDIR}"/${PN} > "${ED}"/usr/bin/${PN} || die
 	fperms 755 /usr/bin/${PN}
 
-	insinto ${in_path}
-
 	dodir ${in_path}/cNg
 	rm -rf cNg || die
 
 	ebegin "Installing main files"
-		doins -r *
-	eend
-
-	ebegin "Adjusting permissions"
-
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
+	python_moduleinto ${PN}
+	python_domodule *
 	eend
-}
-
-pkg_postinst() {
-	python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN}
+	python_optimize
 }
diff --git a/sci-chemistry/ssp/ChangeLog b/sci-chemistry/ssp/ChangeLog
index 87325180c..dd0fd1e1a 100644
--- a/sci-chemistry/ssp/ChangeLog
+++ b/sci-chemistry/ssp/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-chemistry/ssp
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> ssp-09.11.ebuild, metadata.xml:
+  Bump to EAPI=5 and fix license
+
   30 Aug 2012; Justin Lecher <jlec@gentoo.org> ssp-09.11.ebuild:
   Fix offset of reference CS DB
 
diff --git a/sci-chemistry/ssp/metadata.xml b/sci-chemistry/ssp/metadata.xml
index 210ad0db0..5ef07a39e 100644
--- a/sci-chemistry/ssp/metadata.xml
+++ b/sci-chemistry/ssp/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci</herd>
-	<maintainer>
-		<email>jlec@gentoo.org</email>
-	</maintainer>
+  <herd>sci</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-chemistry/ssp/ssp-09.11.ebuild b/sci-chemistry/ssp/ssp-09.11.ebuild
index 59061425e..5d88b107e 100644
--- a/sci-chemistry/ssp/ssp-09.11.ebuild
+++ b/sci-chemistry/ssp/ssp-09.11.ebuild
@@ -1,15 +1,15 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
 
 DESCRIPTION="Secondary structure propensities"
 HOMEPAGE="http://abragam.med.utoronto.ca/software.html"
 SRC_URI="http://pound.med.utoronto.ca/${PN}-Nov09.tar.gz"
 
 SLOT="0"
-LICENSE="as-is"
+LICENSE="all-rights-reserved"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""