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

(Portage version: 2.2.0_alpha163/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

5 files changed, 38 insertions, 76 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/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}