sci-biology/shrimp: Drop old; block collision with emboss, #450426; move to new python eclasses

Package-Manager: portage-2.2.0_alpha163/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

6 files changed, 46 insertions, 96 deletions

diff --git a/sci-biology/shrimp/ChangeLog b/sci-biology/shrimp/ChangeLog
index ead111a77c40..48b0c3bb3798 100644
--- a/sci-biology/shrimp/ChangeLog
+++ b/sci-biology/shrimp/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/shrimp
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.18 2013/02/05 18:26:59 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.19 2013/02/17 09:38:27 jlec Exp $
+
+  17 Feb 2013; Justin Lecher <jlec@gentoo.org> shrimp-2.0.1.ebuild,
+  -shrimp-2.1.0.ebuild, shrimp-2.2.3.ebuild, metadata.xml:
+  Drop old; block collision with emboss, #450426; move to new python eclasses
 
   05 Feb 2013; Ulrich Müller <ulm@gentoo.org> shrimp-2.0.1.ebuild,
   shrimp-2.1.0.ebuild, shrimp-2.2.3.ebuild:
diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest
index 742b0b10b29e..0dbbd38fc680 100644
--- a/sci-biology/shrimp/Manifest
+++ b/sci-biology/shrimp/Manifest
@@ -1,28 +1,16 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 DIST SHRiMP_2_0_1.src.tar.gz 158535 SHA256 62557cf256421aea17a2b221ef485410be177cfc777a6bb8a3de89718d186f63
-DIST SHRiMP_2_1_0.src.tar.gz 189121 SHA256 72a414fcbc528e98af70967942ecf32b377df0582c8076a0bf32c95fa8a8c39e SHA512 01a54dbcb645bfa55ec280d932cc947cab9b6f5266d273d8ea4103cb298e747da00aa04b56753f880d6de11663d9c4219b2402f84d5c15ebe4f1c5bb94e80a8a WHIRLPOOL d0f87dbad1a61c83527be166181eabd491fc3e5a2bd6e22aacd4b369146940e2d843b44ab6e6e9b7c092afe6c08b1cb7b060e3944e47f3d3c87acc634a2c7f36
 DIST SHRiMP_2_2_3.src.tar.gz 4596867 SHA256 a8bed999baeda2ae17ae5c128b2161b20b896228d754e6e446439c1040d6dd8c SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5 WHIRLPOOL 84325b9db3f2e10baa3db935d6e3e2ecae9fd0f47cf5666ea7493f7a975fcd31515f2c77dbe8fcf5cfa099ac2735973e791fa96f0fe8371c5279353bc3f9995a
-EBUILD shrimp-2.0.1.ebuild 1366 SHA256 a0aeef34c36e1f598fb8336a490674a14a04f6d848b6149fa46ce7fe9b6c7f8c SHA512 a6648387642b2f0dd2b58ee2bb908d813bf29b2abdf619ff97fb27a0a2c4f55bbf13fe47fe5d9530e03a95d62d29741c9b03e89cc41317162deb99c4dc7c9eb3 WHIRLPOOL 56994acc8663cb9938332d53de13dc73f251ccceb792895e4570c7277d3259662e22c25216ad8d0c643750a6dfd1094bb6c4456e23a64b3ce460ab82d3a45873
-EBUILD shrimp-2.1.0.ebuild 1357 SHA256 77ad50ef34d1156e0991f9a313befa2fcb3cdd7267c2ae591e471ecee495f062 SHA512 2902273f3640d44cd309d76d39159a0faac95bfc32a6fe1a7bdee50841d8eb8b0524b84072bb0c3aaa8aa6bc9895168d703272e2a9ae51a5815363caaee287fe WHIRLPOOL 44fb35228e9981f1b81e20416b70bc0d90f42e36d48ff6b4fb69dfda3d84dffb4dc5ead94ee909bc4fd96ca343eee12ef4367f0c07b823336702051511da0844
-EBUILD shrimp-2.2.3.ebuild 1657 SHA256 0a5a2916f6614b5da2b65b74899446fbb71a9206c3abc9e2095badf1b1ab4465 SHA512 180ab9b1a355cc966dad5b684230282e5ccbe965faf9b373eb1a30e00947691ad95c8fd8ea8a8403eeac5c8a6adfb93afddd4f8e524e52d23a60d0e160625758 WHIRLPOOL e7bf04141caff9bf320b4ce04ed4d4246db9b17606907b9f62e35133ffa53d48c4f04d4f8c5162f41ea3fea5461c9794892a6458aea398b7f246811d2c45fddf
-MISC ChangeLog 2639 SHA256 f39a17a4718e4005f19a780038cee7997cb89faa6ceb27f5cdc332d2f57b2fe8 SHA512 4c92bbc46e195c2a85f7f9cdeaa912508449ad5a1b082b0913c03ea02ad5077c8bdc89311027241f4840862118b5d70217fe8a250d36337b94765d7168d65f5e WHIRLPOOL 86d7e3c7c4f90a013d577970d1e540bfd713b9602e99b276c0836a840653df62e5f34151f32de80b616325f6d25ab83e04c26191bd1e1601484c158f68909adc
-MISC metadata.xml 259 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 SHA512 c3aea4d69d75075af0108a03b7e109cfed6a1fe324f8ccbda3d4e5ca8a5070f1b24ddeb46b64787e10fd22252d867abcee1f31316d602f7e32fe3c990ae60d74 WHIRLPOOL e50da2f26fd4c908446d22da3edb595d60e61d72def374be46440358802a211fc34045b7ad970c4f94b57f7b17ff24cfe64dc94254fea20e047f1fbbbcae0c64
+EBUILD shrimp-2.0.1.ebuild 1390 SHA256 1300b850c9856da0ec493c88e0701cba5269ed6966ec97f8cdd448e2b9c4320d SHA512 b52b2b0ea20fcd691d9f0b390232044ca571e724be2a910bbfaa75cd7e68adab1bcab6864b14fc7b4c4beec577d140afcbc2c5a287d2c2911a39428ce18c6bfe WHIRLPOOL 7c7cbb027c1c89506d30119f94b0ad92282d288a628d32990740c4a11e9f0cc92ce6be341f389b443fceac5734abeabd0aa6fd2a1351e9d856c38c6c4c761f09
+EBUILD shrimp-2.2.3.ebuild 1768 SHA256 8bac0e7a8375934a98f3a4e3c212195cc3d909df0c337efc6a001fb35725dc05 SHA512 e034db95843fc402c9e5e459af692ed23528e5ed2df704f57b839f0d0c650c771c16a030420ca5e6fa491e25549cee9d28995e1ea145fddf9f6f46f884a48e6d WHIRLPOOL 053621cc1c24ec5e338e880ed236cf2dc90d7ac441f0948795d6056f9c71588771cb732153e12ccd9e5f91a583d8cea0a91b1208a2c744b698f342e58667bf43
+MISC ChangeLog 2846 SHA256 139da5b535551a919b82e0854717eb2af48c45b9f2b20445b9d4160a0da78cce SHA512 9dbb4c9162385ab1e13040e79e5fb4a02f779821cfc30cb1144ed2634884a673ce359d6a43da1bd1597b2ae2ff7ffdec17abcc338a91304d79e9bd455a25eef2 WHIRLPOOL 2d46927900a051335120ebcb6bdcb363f3aedab17b3d44cc7c75a087658ac31e16e1bbd2cb0494f57293315ae8cc9255b36db0d5126b021b93d985cc60980362
+MISC metadata.xml 266 SHA256 98c7d1da8a728a1f1d796a79d51f25e4164e24048ec1aacbbf0ae2ffb171ff35 SHA512 879cdcca092d4c82b8c63672c91e08e7b01e81419d2c7c7b766de96ba2a32dd1e21c18968ed7172eec8604f52c92b19a31773f428bce9461d9b8190384680194 WHIRLPOOL 0f46288ab7090ad3da5b31816792427e4ad1a950e39a503bb406ebe8789cffedd9c85b46bfbf040fffb8aad443f512c28716a0a6436d0c06309155277060cdcd
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diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml
index 3302123e5718..fc7c76942a10 100644
--- a/sci-biology/shrimp/metadata.xml
+++ b/sci-biology/shrimp/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <herd>sci-biology</herd>
 </pkgmetadata>
diff --git a/sci-biology/shrimp/shrimp-2.0.1.ebuild b/sci-biology/shrimp/shrimp-2.0.1.ebuild
index 7aea341d3447..697a1bb5c821 100644
--- a/sci-biology/shrimp/shrimp-2.0.1.ebuild
+++ b/sci-biology/shrimp/shrimp-2.0.1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.8 2013/02/05 18:26:59 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.0.1.ebuild,v 1.9 2013/02/17 09:38:27 jlec Exp $
 
 EAPI=4
 
@@ -18,7 +18,9 @@ KEYWORDS="amd64 x86"
 IUSE="custom-cflags"
 
 # file collision on /usr/bin/utils #453044
-DEPEND="!sci-mathematics/cado-nfs"
+DEPEND="
+	!sci-biology/emboss
+	!sci-mathematics/cado-nfs"
 RDEPEND="${DEPEND}"
 
 S=${WORKDIR}/SHRiMP_${MY_PV}
diff --git a/sci-biology/shrimp/shrimp-2.1.0.ebuild b/sci-biology/shrimp/shrimp-2.1.0.ebuild
deleted file mode 100644
index 757b7620c05f..000000000000
--- a/sci-biology/shrimp/shrimp-2.1.0.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.1.0.ebuild,v 1.4 2013/02/05 18:26:59 ulm Exp $
-
-EAPI=4
-
-inherit flag-o-matic toolchain-funcs
-
-MY_PV=${PV//./_}
-
-DESCRIPTION="SHort Read Mapping Package"
-HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
-SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
-
-LICENSE="shrimp"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="custom-cflags"
-
-# file collision on /usr/bin/utils #453044
-DEPEND="!sci-mathematics/cado-nfs"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}/SHRiMP_${MY_PV}
-
-pkg_setup() {
-	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
-		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
-		die "C compiler lacks OPENMP support"
-	fi
-}
-
-src_prepare() {
-	sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die
-	# respect LDFLAGS wrt 331823
-	sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
-		-e 's/-static//' Makefile || die
-}
-
-src_compile() {
-	append-flags -fopenmp
-	use custom-cflags || append-flags -O3 # per instructions in BUILDING
-	tc-export CXX
-	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin bin/*
-	insinto /usr/libexec/${PN}
-	doins -r utils/*
-	dodoc HISTORY README TODO SPLITTING_AND_MERGING
-}
diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild
index 83873f6b0b4e..60b5ec023245 100644
--- a/sci-biology/shrimp/shrimp-2.2.3.ebuild
+++ b/sci-biology/shrimp/shrimp-2.2.3.ebuild
@@ -1,12 +1,12 @@
 # Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.2.3.ebuild,v 1.3 2013/02/05 18:26:59 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.2.3.ebuild,v 1.4 2013/02/17 09:38:27 jlec Exp $
 
-EAPI=4
+EAPI=5
 
-PYTHON_DEPEND=2
+PYTHON_COMPAT=( python{2_5,2_6,2_7} )
 
-inherit flag-o-matic python toolchain-funcs
+inherit flag-o-matic python-single-r1 toolchain-funcs
 
 MY_PV=${PV//./_}
 
@@ -30,37 +30,45 @@ pkg_setup() {
 		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
 		die "C compiler lacks OPENMP support"
 	fi
-	python_set_active_version 2
-	python_pkg_setup
+	python-single-r1_pkg_setup
 }
 
 src_prepare() {
-	sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die
+	sed \
+		-e '1 a #include <stdint.h>' \
+		-i common/dag_glue.cpp || die
 	# respect LDFLAGS wrt 331823
-	sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
-		-e 's/-static//' Makefile || die
-	python_convert_shebangs -r -- 2 utils
-}
+	sed \
+		-e "s/LDFLAGS/LIBS/" \
+		-e "s/\$(LD)/& \$(LDFLAGS)/" \
+		-e 's/-static//' \
+		-i Makefile || die
 
-src_compile() {
 	append-flags -fopenmp
 	if ! use custom-cflags; then
 		append-flags -O3
-		replace-flags -O2 -O3
+		replace-flags -O* -O3
 	fi
 	tc-export CXX
+
+	cd utils || die
+	sed -e '/^#!/d' -i *py || die
+	sed -e '1i#!/usr/bin/python' -i *py || die
+}
+
+src_compile() {
 	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
 }
 
 src_install() {
 	local i
+	newdoc bin/README README.bin && rm bin/README
 	dobin bin/* utils/split-contigs utils/temp-sink
 	dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES
 
 	pushd utils > /dev/null
-	for i in *py; do
-		newbin ${i} ${i%.py}
-	done
+
+	python_doscript *py
 
 	rm *.py *.o *.c split-contigs temp-sink || die
 	insinto /usr/share/${PN}