sci-chemistry/pdb-tools: Drop old, #478590; mv generic helper modules to PN subdir, #480026

(Portage version: 2.2.0_alpha196/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

4 files changed, 17 insertions, 163 deletions

diff --git a/sci-chemistry/pdb-tools/ChangeLog b/sci-chemistry/pdb-tools/ChangeLog
index 7add3d4224e8..4dff4a33eced 100644
--- a/sci-chemistry/pdb-tools/ChangeLog
+++ b/sci-chemistry/pdb-tools/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/pdb-tools
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-tools/ChangeLog,v 1.16 2013/08/07 11:55:07 mgorny Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-tools/ChangeLog,v 1.17 2013/08/11 12:14:34 jlec Exp $
+
+*pdb-tools-0.2.1-r2 (11 Aug 2013)
+
+  11 Aug 2013; Justin Lecher <jlec@gentoo.org> -pdb-tools-0.1.4-r3.ebuild,
+  -pdb-tools-0.1.4-r4.ebuild, -pdb-tools-0.2.1.ebuild,
+  +pdb-tools-0.2.1-r2.ebuild:
+  Drop old, #478590; mv generic helper modules to PN subdir, #480026
 
   07 Aug 2013; Michał Górny <mgorny@gentoo.org> pdb-tools-0.1.4-r4.ebuild,
   pdb-tools-0.2.1-r1.ebuild, pdb-tools-0.2.1.ebuild:
diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.1.4-r3.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.1.4-r3.ebuild
deleted file mode 100644
index 43176a6a74aa..000000000000
--- a/sci-chemistry/pdb-tools/pdb-tools-0.1.4-r3.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-tools/pdb-tools-0.1.4-r3.ebuild,v 1.2 2012/10/19 10:11:54 jlec Exp $
-
-EAPI=3
-
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="3.*"
-
-inherit fortran-2 python toolchain-funcs
-
-DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files"
-HOMEPAGE="http://code.google.com/p/pdb-tools/"
-SRC_URI="http://${PN}.googlecode.com/files/${PN}_${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="sci-chemistry/dssp"
-DEPEND=""
-
-S="${WORKDIR}"/${PN}_${PV}
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python_pkg_setup
-}
-
-src_prepare() {
-	sed "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" -i pdb_sasa.py || die
-	sed "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" -i pdb_satk.py || die
-}
-
-src_compile() {
-	mkdir bin
-	cd satk
-	for i in *.f; do
-		einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}"
-		$(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die
-		$(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die
-		sed "s:${i/.f}.out:${i/.f}:g" -i ../pdb_satk.py || die
-	done
-}
-
-src_install() {
-	insinto /usr/share/${PN}
-	doins -r pdb_data/peptides || die
-	rm -rf pdb_data/peptides || die
-
-	installation() {
-		insinto $(python_get_sitedir)
-		doins -r helper pdb_data || die
-
-		insinto $(python_get_sitedir)/${PN}
-		doins *.py || die
-
-		for i in pdb_*.py; do
-			cat > ${i/.py} <<- EOF
-			#!${EPREFIX}/bin/bash
-			$(PYTHON) -O "${EPREFIX}$(python_get_sitedir)/${PN}/${i}" \$@
-			EOF
-			dobin ${i/.py}
-		done
-	}
-
-	python_execute_function installation
-
-	dobin bin/* || die
-	dodoc README || die
-}
-
-pkg_postinst() {
-	python_mod_optimize ${PN} helper pdb_data
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN} helper pdb_data
-}
diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.1.4-r4.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.1.4-r4.ebuild
deleted file mode 100644
index b29c0f8c4f75..000000000000
--- a/sci-chemistry/pdb-tools/pdb-tools-0.1.4-r4.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-tools/pdb-tools-0.1.4-r4.ebuild,v 1.4 2013/08/07 11:55:07 mgorny Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} pypy1_9 )
-
-inherit fortran-2 python-single-r1 toolchain-funcs
-
-DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files"
-HOMEPAGE="http://code.google.com/p/pdb-tools/"
-SRC_URI="http://${PN}.googlecode.com/files/${PN}_${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	sci-chemistry/dssp"
-DEPEND="${PYTHON_DEPS}"
-
-S="${WORKDIR}"/${PN}_${PV}
-
-pkg_setup() {
-	python-single-r1_pkg_setup
-	fortran-2_pkg_setup
-}
-
-src_prepare() {
-	sed \
-		-e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \
-		-i pdb_sasa.py || die
-	sed \
-		-e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \
-		-i pdb_satk.py || die
-}
-
-src_compile() {
-	mkdir bin
-	cd satk
-	for i in *.f; do
-		einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}"
-		$(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die
-		$(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die
-		sed \
-			-e "s:${i/.f}.out:${i/.f}:g" \
-			-i ../pdb_satk.py || die
-	done
-}
-
-src_install() {
-	local script
-	insinto /usr/share/${PN}
-	doins -r pdb_data/peptides
-	rm -rf pdb_data/peptides || die
-
-	python_domodule helper pdb_data
-
-	python_moduleinto ${PN/-/_}
-	python_domodule *.py
-
-	for i in pdb_*.py; do
-		cat > ${i/.py} <<- EOF
-		#!${EPREFIX}/bin/bash
-		${PYTHON} -O "${EPREFIX}$(python_get_sitedir)/${PN/-/_}/${i}" \$@
-		EOF
-		dobin ${i/.py}
-	done
-
-	dobin bin/*
-	dodoc README
-}
diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild
index 6c2c50f61105..dedc56285714 100644
--- a/sci-chemistry/pdb-tools/pdb-tools-0.2.1.ebuild
+++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-tools/pdb-tools-0.2.1.ebuild,v 1.3 2013/08/07 11:55:07 mgorny Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild,v 1.1 2013/08/11 12:14:34 jlec Exp $
 
 EAPI=5
 
-PYTHON_COMPAT=( python{2_6,2_7} pypy1_9 )
+PYTHON_COMPAT=( python{2_6,2_7} pypy{1_8,1_9} )
 
 inherit fortran-2 python-single-r1 toolchain-funcs
 
@@ -41,6 +41,10 @@ src_prepare() {
 	sed \
 		-e 's:> %:>%:g' \
 		-i pdb_seq.py || die
+
+	sed \
+		-e "/import/s:helper:${PN/-/_}.helper:g" \
+		-i *.py || die
 }
 
 src_compile() {
@@ -62,15 +66,15 @@ src_install() {
 	doins -r pdb_data/peptides
 	rm -rf pdb_data/peptides || die
 
-	python_domodule helper pdb_data
+	python_domodule pdb_data
 
 	python_moduleinto ${PN/-/_}
-	python_domodule *.py
+	python_domodule helper *.py
 
 	for i in pdb_*.py; do
 		cat > ${i/.py} <<- EOF
 		#!${EPREFIX}/bin/bash
-		${PYTHON} -O "${EPREFIX}$(python_get_sitedir)/${PN/-/_}/${i}" \$@
+		${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@
 		EOF
 		dobin ${i/.py}
 	done