proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

4 files changed, 176 insertions, 0 deletions

diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest
new file mode 100644
index 000000000000..bf2e4bfa7dce
--- /dev/null
+++ b/sci-chemistry/pdb-tools/Manifest
@@ -0,0 +1 @@
+DIST pdbTools_0.2.1.tar.gz 103835 SHA256 317a5246e806a2b3d0425d080d679646fc77388e3e855412527603f945fa37ae SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724 WHIRLPOOL 36d8cf71ba9f9b28e3ad59828539f4e94bbb8bc4514f050ddcbec63857b154ecdc7c32c2945c0d15f4d718c4fe5ab3adcb2e62a4368bfd819b80e9641a9dfd88
diff --git a/sci-chemistry/pdb-tools/metadata.xml b/sci-chemistry/pdb-tools/metadata.xml
new file mode 100644
index 000000000000..13e9a3c93979
--- /dev/null
+++ b/sci-chemistry/pdb-tools/metadata.xml
@@ -0,0 +1,11 @@
+<?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>
+  </maintainer>
+  <upstream>
+    <remote-id type="google-code">pdb-tools</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild
new file mode 100644
index 000000000000..ad4ab1dec397
--- /dev/null
+++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 pypy )
+
+inherit fortran-2 python-single-r1 toolchain-funcs
+
+MY_PN="pdbTools"
+
+DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files"
+HOMEPAGE="http://code.google.com/p/pdb-tools/"
+SRC_URI="http://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${MY_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 = \"${EPREFIX}/usr/bin\":g" \
+		-i pdb_satk.py || die
+	sed \
+		-e 's:> %:>%:g' \
+		-i pdb_seq.py || die
+}
+
+src_compile() {
+	mkdir bin
+	cd satk
+	for i in *.f; do
+		einfo "$(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
+		${PYTHON} -O "$(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-r2.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild
new file mode 100644
index 000000000000..e56798f3c95b
--- /dev/null
+++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild
@@ -0,0 +1,84 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit fortran-2 python-single-r1 toolchain-funcs
+
+MY_PN="pdbTools"
+
+DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files"
+HOMEPAGE="http://code.google.com/p/pdb-tools/"
+SRC_URI="http://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${MY_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 = \"${EPREFIX}/usr/bin\":g" \
+		-i pdb_satk.py || die
+	sed \
+		-e 's:> %:>%:g' \
+		-i pdb_seq.py || die
+
+	sed \
+		-e "/import/s:helper:${PN/-/_}.helper:g" \
+		-i *.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 pdb_data
+
+	python_moduleinto ${PN/-/_}
+	python_domodule helper *.py
+
+	for i in pdb_*.py; do
+		cat > ${i/.py} <<- EOF
+		#!${EPREFIX}/bin/bash
+		${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@
+		EOF
+		dobin ${i/.py}
+	done
+
+	dobin bin/*
+	dodoc README
+}