Version Bump, Prefixify, keyworeded for ~-linux

(Portage version: 2.2_rc67/git/Linux x86_64)
 (Signed Manifest commit)

6 files changed, 89 insertions, 279 deletions

diff --git a/sci-chemistry/modeller/ChangeLog b/sci-chemistry/modeller/ChangeLog
index 75662c3ae..17fea516e 100644
--- a/sci-chemistry/modeller/ChangeLog
+++ b/sci-chemistry/modeller/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-chemistry/modeller
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*modeller-9.8 (16 Jun 2010)
+
+  16 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/9v5-setup.patch,
+  -modeller-9.3.ebuild, -modeller-9.4.ebuild, -modeller-9.5.ebuild,
+  +modeller-9.8.ebuild:
+  Version Bump, Prefixify, keyworeded for ~-linux
+
   10 Apr 2008; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
   Fixing license thanks to Justin Schmitz.
 
diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest
index 59db8c6ac..48cceb463 100644
--- a/sci-chemistry/modeller/Manifest
+++ b/sci-chemistry/modeller/Manifest
@@ -1,6 +1,15 @@
-DIST modeller-9v3.tar.gz 49912561 RMD160 9472bc951faa8e4a28b0834c58aa0d7100492412 SHA1 5f7589536923a9504ad52430fabf8dfc49dde3b1 SHA256 b70052c1fae18f4cba598ce15d3cfd46c2c0df10d23e066a65aceea59063f3ae
-DIST modeller-9v4.tar.gz 49949423 RMD160 1dc1b97099708ce79055ec6496155c7e27a3efb1 SHA1 2d1432782714b54b01190e9ef4fc9bb454210a23 SHA256 c291ad617b3bd697e5bd5efede00d9869bb019d0a60d26344617fafa82b3d779
-EBUILD modeller-9.3.ebuild 3089 RMD160 e9b9d8dd7b60c93cadb848b666bd9c0611f6fa27 SHA1 cc6e2bd791b12b897a5f0357128761d0c1ba48b4 SHA256 5641da3c9c78507b3bc7b1acc5e9b763c2abb43f5d40a52264fa7d7573041958
-EBUILD modeller-9.4.ebuild 3089 RMD160 40e75f9d72b4f72aa79b35a9cd826fc55c0114fe SHA1 158dc73e82e933182f1d1b0c3fb068529d88c3b4 SHA256 7bdf27bb0b68ec365fd169d6c960d7e40639eae368d1b4df142ea9e6eb3fa209
-MISC ChangeLog 366 RMD160 c8e3df06513eba7af76d56f3f023881cbb7556f2 SHA1 40d13fa7a97a6fb959793c42be6afdb61e9dace8 SHA256 7aebd9473568ad2f12d41d4241479ed163cbed2eb116be1772f80eb08f5214d4
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 9v5-setup.patch 675 RMD160 5a2b138e6b8a379535d819ab811a948a9568d310 SHA1 409ff97417d22c6805f3981a65e5417d99513c11 SHA256 2f2306ab7a0d7c7da7f37b8f57d04f7180fa3fe281f69298ae0d1da4b80d71d0
+DIST modeller-9v8.tar.gz 51539572 RMD160 455a1506b04608a797317386524fa44b6af9a2d7 SHA1 41ae0c85df512a4646bdcc2ee537e041dfe4bf8b SHA256 3d5c629f97a2b89722fe5b7414ad97b0361799714db0323536df45f55b2777c7
+EBUILD modeller-9.8.ebuild 4000 RMD160 8920752ff0572a3dbed7f2db123eb3608852cf2a SHA1 f56c1063e96c4df765f5bc248eb50e6cfa8a1c14 SHA256 5fa53715129a7ad7a0c83490769d24235e6f08809dd46e4ef84f9ee654d0798e
+MISC ChangeLog 609 RMD160 628c5fad5921be1f0ce942a64682ae6817b3e95b SHA1 95f22c8ad73040cecbe8dc817c747fb328581a95 SHA256 8f0a25b735ee864c251540da5f27e477bb8a2f410160d39183dc5c935f5725e2
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.15 (GNU/Linux)
+
+iEYEARECAAYFAkwYt74ACgkQgAnW8HDreRbuLwCfdi24aTE3SS/IfO0v1Ahfbo6a
+d2wAoJ72tFnaZNjTET8DRghDyj4J6UFG
+=Z9JI
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/modeller/files/9v5-setup.patch b/sci-chemistry/modeller/files/9v5-setup.patch
new file mode 100644
index 000000000..5fe460580
--- /dev/null
+++ b/sci-chemistry/modeller/files/9v5-setup.patch
@@ -0,0 +1,12 @@
+diff -Nu -Nu -uarN modeller-9v3.orig/src/swig/setup.py modeller-9v3/src/swig/setup.py
+--- modeller-9v4.orig/src/swig/setup.py	2008-04-15 12:57:50.000000000 +0200
++++ modeller-9v4/src/swig/setup.py	2008-04-15 12:57:59.000000000 +0200
+@@ -19,7 +19,7 @@
+                 include_dirs=['../include', '../include/%s' % exetype] + \
+                              glib['include_dirs'],
+                 libraries=['modeller'] + glib['libraries'],
+-                library_dirs=['../../lib/%s' % exetype] + glib['library_dirs'])
++                library_dirs=['../../lib/%s' % exetype])
+ 
+ setup(name='Modeller',
+       description='Protein structure modeling by satisfaction of ' \
diff --git a/sci-chemistry/modeller/modeller-9.3.ebuild b/sci-chemistry/modeller/modeller-9.3.ebuild
deleted file mode 100644
index 668637b0d..000000000
--- a/sci-chemistry/modeller/modeller-9.3.ebuild
+++ /dev/null
@@ -1,117 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit eutils python
-
-MY_PV="${PV/./v}"
-LICENSE="modeller"
-KEYWORDS="~amd64 ~x86"
-DESCRIPTION="MODELLER is used for homology or comparative modeling of protein three-dimensional structures"
-SRC_URI="http://salilab.org/${PN}/${MY_PV}/${PN}-${MY_PV}.tar.gz"
-HOMEPAGE="http://salilab.org/modeller/"
-IUSE=""
-RESTRICT="mirror"
-SLOT="0"
-
-RDEPEND=">=dev-lang/python-2.4"
-DEPEND=""
-
-src_install(){
-	python_version
-
-	VER=9v3
-	case ${ARCH} in
-		x86)	EXECUTABLE_TYPE="i386-intel8";;
-		amd64)	EXECUTABLE_TYPE="x86_64-intel8";;
-		*)		ewarn "Your arch "${ARCH}" does not appear supported at this time."||\
-				die "Unsupported Arch";;
-	esac
-
-	sed -e "s:EXECUTABLE_TYPE${MY_PV}=xxx:EXECUTABLE_TYPE${MY_PV}=${EXECUTABLE_TYPE}:g" \
-		-e "s:MODINSTALL${MY_PV}=xxx:MODINSTALL${MY_PV}=\"${IN_PATH}\":g" \
-		bin/modscript > "${T}/mod${MY_PV}"
-	exeinto ${IN_PATH}/bin/
-	doexe "${T}/mod${MY_PV}"
-	dosym ${IN_PATH}/bin/mod${MY_PV} /opt/bin/mod${MY_PV}
-
-	sed -e "s;@TOPDIR\@;\"${IN_PATH}\";" \
-		-e "s;@EXETYPE\@;$EXECUTABLE_TYPE;" \
-		bin/modpy.sh.in > "${T}/modpy.sh"
-	doexe "${T}/modpy.sh"
-
-	insinto ${IN_PATH}
-	doins -r modlib
-
-	insinto ${IN_PATH}/bin
-	doins -r bin/{lib,*top}
-	exeinto ${IN_PATH}/bin
-	doexe bin/{modslave.py,mod${MY_PV}_${EXECUTABLE_TYPE}}
-
-	exeinto ${IN_PATH}/lib/${EXECUTABLE_TYPE}/
-	doexe lib/${EXECUTABLE_TYPE}/lib*
-	dosym libmodeller.so.3 ${IN_PATH}/lib/${EXECUTABLE_TYPE}/libmodeller.so
-	doexe src/swig/build/lib.linux-$(uname -m)-${PYVER}/_modeller.so
-
-	dodoc README INSTALLATION
-	if use doc; then
-		dohtml doc/*
-	fi
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples
-	fi
-
-	dosym ${IN_PATH}/lib/${EXECUTABLE_TYPE}/_modeller.so \
-		  /usr/$(get_libdir)/python${PYVER}/site-packages/_modeller.so
-}
-
-pkg_postinst() {
-	python_mod_optimize "${ROOT%/}/${IN_PATH}/"
-	
-	if [[ ! -e "${IN_PATH}/modlib/modeller/config.py" ]]; then
-		echo install_dir = '"'"${IN_PATH}/"'"'> ${IN_PATH}/modlib/modeller/config.py
-	fi
-
-	if grep -q license ${IN_PATH}/modlib/modeller/config.py; then
-		einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py"
-	else
-		ewarn "Obtain a license Key from"
-		ewarn "http://salilab.org/modeller/registration.html"
-		ewarn "And run this before using modeller:"
-		ewarn "emerge --config =${CATEGORY}/${PF}"
-		ewarn "That way you can [re]enter your license key."
-	fi
-}
-
-pkg_postrm() {
-	python_mod_cleanup "${ROOT%/}/${IN_PATH}/"
-	ewarn "This package leaves a license Key file in ${IN_PATH}/modlib/modeller/config.py"
-	ewarn "that you need to remove to completely get rid of modeller."
-}
-
-pkg_config() {
-	ewarn "Your license key is NOT checked for validity here."
-	ewarn "  Make sure you type it in correctly."
-	eerror "If you CTRL+C out of this, modeller will not run!"
-	while true
-	do
-		einfo "Please enter your license key:"
-		read license_key1
-		einfo "Please re-enter your license key:"
-		read license_key2
-		if [[ "$license_key1" == "" ]]
-		then
-			echo "You entered a blank license key.  Try again."
-		else
-			if [[ "$license_key1" == "$license_key2" ]]
-			then
-				echo license = '"'$license_key1'"' >> "${IN_PATH}/modlib/modeller/config.py"
-				einfo "Thank you!"
-				break
-			else
-				eerror "Your license key entries do not match.  Try again."
-			fi
-		fi
-	done
-}
diff --git a/sci-chemistry/modeller/modeller-9.4.ebuild b/sci-chemistry/modeller/modeller-9.4.ebuild
deleted file mode 100644
index 19e87cf40..000000000
--- a/sci-chemistry/modeller/modeller-9.4.ebuild
+++ /dev/null
@@ -1,117 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit eutils python
-
-MY_PV="${PV/./v}"
-LICENSE="modeller"
-KEYWORDS="~amd64 ~x86"
-DESCRIPTION="MODELLER is used for homology or comparative modeling of protein three-dimensional structures"
-SRC_URI="http://salilab.org/${PN}/${MY_PV}/${PN}-${MY_PV}.tar.gz"
-HOMEPAGE="http://salilab.org/modeller/"
-IUSE=""
-RESTRICT="mirror"
-SLOT="0"
-
-RDEPEND=">=dev-lang/python-2.4"
-DEPEND=""
-
-src_install(){
-	python_version
-
-	VER=9v4
-	case ${ARCH} in
-		x86)	EXECUTABLE_TYPE="i386-intel8";;
-		amd64)	EXECUTABLE_TYPE="x86_64-intel8";;
-		*)		ewarn "Your arch "${ARCH}" does not appear supported at this time."||\
-				die "Unsupported Arch";;
-	esac
-
-	sed -e "s:EXECUTABLE_TYPE${MY_PV}=xxx:EXECUTABLE_TYPE${MY_PV}=${EXECUTABLE_TYPE}:g" \
-		-e "s:MODINSTALL${MY_PV}=xxx:MODINSTALL${MY_PV}=\"${IN_PATH}\":g" \
-		bin/modscript > "${T}/mod${MY_PV}"
-	exeinto ${IN_PATH}/bin/
-	doexe "${T}/mod${MY_PV}"
-	dosym ${IN_PATH}/bin/mod${MY_PV} /opt/bin/mod${MY_PV}
-
-	sed -e "s;@TOPDIR\@;\"${IN_PATH}\";" \
-		-e "s;@EXETYPE\@;$EXECUTABLE_TYPE;" \
-		bin/modpy.sh.in > "${T}/modpy.sh"
-	doexe "${T}/modpy.sh"
-
-	insinto ${IN_PATH}
-	doins -r modlib
-
-	insinto ${IN_PATH}/bin
-	doins -r bin/{lib,*top}
-	exeinto ${IN_PATH}/bin
-	doexe bin/{modslave.py,mod${MY_PV}_${EXECUTABLE_TYPE}}
-
-	exeinto ${IN_PATH}/lib/${EXECUTABLE_TYPE}/
-	doexe lib/${EXECUTABLE_TYPE}/lib*
-	dosym libmodeller.so.3 ${IN_PATH}/lib/${EXECUTABLE_TYPE}/libmodeller.so
-	doexe src/swig/build/lib.linux-$(uname -m)-${PYVER}/_modeller.so
-
-	dodoc README INSTALLATION
-	if use doc; then
-		dohtml doc/*
-	fi
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples
-	fi
-
-	dosym ${IN_PATH}/lib/${EXECUTABLE_TYPE}/_modeller.so \
-		  /usr/$(get_libdir)/python${PYVER}/site-packages/_modeller.so
-}
-
-pkg_postinst() {
-	python_mod_optimize "${ROOT%/}/${IN_PATH}/"
-	
-	if [[ ! -e "${IN_PATH}/modlib/modeller/config.py" ]]; then
-		echo install_dir = '"'"${IN_PATH}/"'"'> ${IN_PATH}/modlib/modeller/config.py
-	fi
-
-	if grep -q license ${IN_PATH}/modlib/modeller/config.py; then
-		einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py"
-	else
-		ewarn "Obtain a license Key from"
-		ewarn "http://salilab.org/modeller/registration.html"
-		ewarn "And run this before using modeller:"
-		ewarn "emerge --config =${CATEGORY}/${PF}"
-		ewarn "That way you can [re]enter your license key."
-	fi
-}
-
-pkg_postrm() {
-	python_mod_cleanup "${ROOT%/}/${IN_PATH}/"
-	ewarn "This package leaves a license Key file in ${IN_PATH}/modlib/modeller/config.py"
-	ewarn "that you need to remove to completely get rid of modeller."
-}
-
-pkg_config() {
-	ewarn "Your license key is NOT checked for validity here."
-	ewarn "  Make sure you type it in correctly."
-	eerror "If you CTRL+C out of this, modeller will not run!"
-	while true
-	do
-		einfo "Please enter your license key:"
-		read license_key1
-		einfo "Please re-enter your license key:"
-		read license_key2
-		if [[ "$license_key1" == "" ]]
-		then
-			echo "You entered a blank license key.  Try again."
-		else
-			if [[ "$license_key1" == "$license_key2" ]]
-			then
-				echo license = '"'$license_key1'"' >> "${IN_PATH}/modlib/modeller/config.py"
-				einfo "Thank you!"
-				break
-			else
-				eerror "Your license key entries do not match.  Try again."
-			fi
-		fi
-	done
-}
diff --git a/sci-chemistry/modeller/modeller-9.5.ebuild b/sci-chemistry/modeller/modeller-9.8.ebuild
index 7621cd470..b0c24c18c 100644
--- a/sci-chemistry/modeller/modeller-9.5.ebuild
+++ b/sci-chemistry/modeller/modeller-9.8.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -8,65 +8,80 @@ PYTHON_DEPEND="2:2.6"
 
 inherit distutils eutils versionator
 
-MY_PV="${replace_all_version_separators v}"
+MY_PV="$(replace_all_version_separators v)"
+MY_P="${PN}-${MY_PV}"
 
 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/"
 
 LICENSE="modeller"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc examples"
 SLOT="0"
 
 RESTRICT="mirror"
 
 DEPEND=">=dev-lang/swig-1.3"
-DEPEND=""
+RDEPEND=""
 
-S="${WORKDIR}"/${MY_PN}-${MY_PV}
+S="${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/*/.*"
 
-src_install(){
-	local ver
-	local in_path
-	local exec_type
-
-	ver=$(replace_all_version_separators v)
-	in_path="${EPREFIX}"/opt/modeller${ver}
+pkg_setup() {
+	python_set_active_version 2
 
 	case ${ARCH} in
-		x86)	exec_type="i386-intel8";;
-		amd64)	exec_type="x86_64-intel8";;
+		x86)	EXECTYPE="i386-intel8";;
+		amd64)	EXECTYPE="x86_64-intel8";;
 		*)		ewarn "Your arch "${ARCH}" does not appear supported at this time."||\
 				die "Unsupported Arch";;
 	esac
+}
+
+src_prepare(){
+	sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
+}
+
+src_compile(){
+	cd src/swig
+	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i
+	distutils_src_compile
+}
 
+src_install(){
 	sed \
-		-e "s:EXECUTABLE_TYPE${MY_PV}=xxx:EXECUTABLE_TYPE${MY_PV}=${exec_type}:g" \
-		-e "s:MODINSTALL${MY_PV}=xxx:MODINSTALL${MY_PV}=\"${in_path}\":g" \
+		-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}"
-	exeinto ${in_path}/bin/
-	doexe "${T}/mod${MY_PV}" || die
-	dosym ${in_path}/bin/mod${MY_PV} /opt/bin/mod${MY_PV} || die
 
-	sed -e "s;@TOPDIR\@;\"${in_path}\";" \
-		-e "s;@EXETYPE\@;${exec_type};" \
+	sed -e "s;@TOPDIR\@;\"${INPATH}\";" \
+		-e "s;@EXETYPE\@;${EXECTYPE};" \
 		bin/modpy.sh.in > "${T}/modpy.sh"
-	doexe "${T}/modpy.sh" || die
 
-	insinto ${in_path}
+	insinto ${INPATH}
 	doins -r modlib || die
 
-	insinto ${in_path}/bin
+	insinto ${INPATH}/bin
 	doins -r bin/{lib,*top} || die
-	exeinto ${in_path}/bin
-	doexe bin/{modslave.py,mod${MY_PV}_${exec_type}} || die
+	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
 
-	exeinto ${in_path}/lib/${exec_type}/
-	doexe lib/${exec_type}/lib* || die
-	dosym libmodeller.so.3 ${in_path}/lib/${exec_type}/libmodeller.so || die
+	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
 
 	dodoc README INSTALLATION || die
@@ -78,18 +93,19 @@ src_install(){
 		doins -r examples || die
 	fi
 
-	dosym ${in_path}/lib/${exec_type}/_modeller.so \
-		  $(python_get_sitedir)/_modeller.so
+	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 "${in_path}/"
+	python_mod_optimize "${INPATH}/"
 
-	if [[ ! -e "${in_path}/modlib/modeller/config.py" ]]; then
-		echo install_dir = '"'"${in_path}/"'"'> ${in_path}/modlib/modeller/config.py
+	if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then
+		echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py
 	fi
 
-	if grep -q license ${in_path}/modlib/modeller/config.py; then
+	if grep -q license ${INPATH}/modlib/modeller/config.py; then
 		einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py"
 	else
 		ewarn "Obtain a license Key from"
@@ -101,8 +117,8 @@ pkg_postinst() {
 }
 
 pkg_postrm() {
-	python_mod_cleanup "${in_path}/"
-	ewarn "This package leaves a license Key file in ${in_path}/modlib/modeller/config.py"
+	python_mod_cleanup "${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."
 }
 
@@ -122,7 +138,7 @@ pkg_config() {
 		else
 			if [[ "$license_key1" == "$license_key2" ]]
 			then
-				echo license = '"'$license_key1'"' >> "${in_path}/modlib/modeller/config.py"
+				echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py"
 				einfo "Thank you!"
 				break
 			else