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

8 files changed, 219 insertions, 0 deletions

diff --git a/sci-chemistry/reduce/Manifest b/sci-chemistry/reduce/Manifest
new file mode 100644
index 000000000000..06e2812c62a9
--- /dev/null
+++ b/sci-chemistry/reduce/Manifest
@@ -0,0 +1,3 @@
+DIST reduce.3.13.080428.src.tgz 4387407 SHA256 6290dad33e395c5a40fe3634db86fb6035ea88ce19c3f25b80fb6378507ac066
+DIST reduce.3.14.080821.src.tgz 5199731 SHA256 0c32f3e9f818b976e0996f088639a194cde63f227eff32c35e14526ec05c930a SHA512 9c8d72983b376b1f741afeb08630ad69b6888f526aac0ad72c658e96a6c2d6f17df60dfbf03a35a217be254bbb858f99bd2088aba8877e504a45270371dbad44 WHIRLPOOL aac80449eeceae8afbc5ec8d4ea53152c4f0bff7080fc36d7d74d8e0aaad8e6cb3e5750d67dcab6c7669f58a5f09910a3253db6371828257d03832f1ccbc3418
+DIST reduce.3.16.111118.src.zip 20342632 SHA256 a9f45dd31eb7022e056cdab1efbbed17fd8be7453396313904c95c839d41dbb3 SHA512 f7b4d8d91f1f57e9e96c91139fa919c570aebd07f3a440faf3df54bf5deb3a05ad998996a24b5fe9aff6280e00329c9914e338cbfe802c047c055f52ce8312a9 WHIRLPOOL 5d5e3c988e39986888eb23907e87ad180a2a441cf236c53406fc43f1cddd25e9e9051ae41d287f35bcf17f3882d720f9cee4c925cbae32139de5848c1fbcccdd
diff --git a/sci-chemistry/reduce/files/3.13.080428-CFLAGS.patch b/sci-chemistry/reduce/files/3.13.080428-CFLAGS.patch
new file mode 100644
index 000000000000..7daa5336f689
--- /dev/null
+++ b/sci-chemistry/reduce/files/3.13.080428-CFLAGS.patch
@@ -0,0 +1,22 @@
+diff --git a/reduce_src/Makefile b/reduce_src/Makefile
+index 598e367..067ace4 100644
+--- a/reduce_src/Makefile
++++ b/reduce_src/Makefile
+@@ -12,7 +12,7 @@ PROG_FLGS   = -DAROMATICS_ACCEPT_HBONDS \
+ #              -DDEBUGMOVABLENODE -DDEBUGDOTCOUNTS
+ #              -DMINPREDEFINED -DMAXPREDEFINED\
+ 
+-CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC)\
++CXXFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC)\
+          -I$(PDBHOME) -I$(TOOLHOME) 
+ #         -Wall
+ 
+@@ -26,7 +26,7 @@ OBJLIST = GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o A
+ CXX		= g++
+ 
+ .cpp.o:
+-	$(CXX) -c $*.cpp $(CFLAGS)
++	$(CXX) -c $*.cpp $(CXXFLAGS)
+ 
+ OPT             = -O3
+ DEBUG           = $(CXXDEBUGFLAGS)
diff --git a/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch
new file mode 100644
index 000000000000..bcee1a9fe8f3
--- /dev/null
+++ b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch
@@ -0,0 +1,11 @@
+--- reduce_src/Makefile	2009-08-09 10:11:29.000000000 +0200
++++ reduce_src/Makefile.new	2009-08-09 10:13:31.000000000 +0200
+@@ -34,7 +34,7 @@
+ all:    reduce
+ 
+ reduce: $(OBJLIST)
+-	$(CXX) -o $@ $(OBJLIST) $(LFLAGS)
++	$(CXX) $(LDFLAGS) -o $@ $(OBJLIST) $(LFLAGS)
+ 
+ clean:
+ 	@rm -rf *.o *.ckp ii_files
diff --git a/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch b/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch
new file mode 100644
index 000000000000..8294c8ca385d
--- /dev/null
+++ b/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch
@@ -0,0 +1,22 @@
+diff --git a/reduce_src/Makefile b/reduce_src/Makefile
+index 598e367..067ace4 100644
+--- a/reduce_src/Makefile
++++ b/reduce_src/Makefile
+@@ -12,7 +12,7 @@ PROG_FLGS   = -DAROMATICS_ACCEPT_HBONDS \
+ #              -DDEBUGMOVABLENODE -DDEBUGDOTCOUNTS
+ #              -DMINPREDEFINED -DMAXPREDEFINED\
+ 
+-CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC) $(DICT_LOCOLD)\
++CXXFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC) $(DICT_LOCOLD)\
+          -I$(PDBHOME) -I$(TOOLHOME) 
+ #         -Wall
+ 
+@@ -26,7 +26,7 @@ OBJLIST = GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o A
+ CXX		= g++
+ 
+ .cpp.o:
+-	$(CXX) -c $*.cpp $(CFLAGS)
++	$(CXX) -c $*.cpp $(CXXFLAGS)
+ 
+ OPT             = -O3
+ DEBUG           = $(CXXDEBUGFLAGS)
diff --git a/sci-chemistry/reduce/metadata.xml b/sci-chemistry/reduce/metadata.xml
new file mode 100644
index 000000000000..e42d0af60f42
--- /dev/null
+++ b/sci-chemistry/reduce/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-chemistry</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild b/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild
new file mode 100644
index 000000000000..f2af6fcda84a
--- /dev/null
+++ b/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=3
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}.${PV}.src"
+
+DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.tgz"
+
+LICENSE="richardson"
+SLOT="0"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	app-arch/unzip"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-LDFLAGS.patch \
+		"${FILESDIR}"/${PV}-CFLAGS.patch
+}
+
+src_compile() {
+	DICT_DIR="/usr/share/reduce"
+	DICT_FILE="reduce_het_dict.txt"
+
+	emake \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		OPT="${CXXFLAGS}" \
+		DICT_HOME="${EPREFIX}/${DICT_DIR}/${DICT_FILE}" \
+		|| die "make failed"
+}
+
+src_install() {
+	dobin "${S}"/reduce_src/reduce || die
+	insinto ${DICT_DIR}
+	doins "${S}"/${DICT_FILE} "${S}"/reduce_wwPDB_het_dict.txt || die
+	dodoc README.usingReduce.txt || die
+}
+
+pkg_postinst() {
+	elog "To use the PDBv3 dictionary instead of PDBv2, set the environment"
+	elog "variable REDUCE_HET_DICT to ${EPREFIX}/usr/share/reduce/reduce_wwPDB_het_dict.txt"
+}
diff --git a/sci-chemistry/reduce/reduce-3.14.080821.ebuild b/sci-chemistry/reduce/reduce-3.14.080821.ebuild
new file mode 100644
index 000000000000..824ee735ef0f
--- /dev/null
+++ b/sci-chemistry/reduce/reduce-3.14.080821.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}.${PV}.src"
+
+DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.tgz"
+
+LICENSE="richardson"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	app-arch/unzip"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/3.13.080428-LDFLAGS.patch \
+		"${FILESDIR}"/${PV}-CFLAGS.patch
+}
+
+src_compile() {
+	DICT_DIR="/usr/share/reduce"
+	DICT_FOLD="reduce_het_dict.txt"
+	DICT_FNEW="reduce_wwPDB_het_dict.txt"
+
+	emake clean
+	emake \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		OPT="${CXXFLAGS}" \
+		DICT_HOME="${EPREFIX}/${DICT_DIR}/${DICT_FNEW}" \
+		DICT_OLD="${EPREFIX}/${DICT_DIR}/${DICT_FOLD}"
+}
+
+src_install() {
+	dobin "${S}"/reduce_src/reduce
+	insinto ${DICT_DIR}
+	doins "${S}"/${DICT_FOLD} "${S}"/${DICT_FNEW}
+	dodoc README.usingReduce.txt
+}
diff --git a/sci-chemistry/reduce/reduce-3.16.111118.ebuild b/sci-chemistry/reduce/reduce-3.16.111118.ebuild
new file mode 100644
index 000000000000..6871341758b8
--- /dev/null
+++ b/sci-chemistry/reduce/reduce-3.16.111118.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}.${PV}.src"
+
+DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.zip"
+
+LICENSE="richardson"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	app-arch/unzip"
+
+S="${WORKDIR}/"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/3.13.080428-LDFLAGS.patch \
+		"${FILESDIR}"/3.14.080821-CFLAGS.patch
+}
+
+src_compile() {
+	DICT_DIR="/usr/share/reduce"
+	DICT_FOLD="reduce_het_dict.txt"
+	DICT_FNEW="reduce_wwPDB_het_dict.txt"
+
+	emake clean
+	emake \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		OPT="${CXXFLAGS}" \
+		DICT_HOME="${EPREFIX}/${DICT_DIR}/${DICT_FNEW}" \
+		DICT_OLD="${EPREFIX}/${DICT_DIR}/${DICT_FOLD}"
+}
+
+src_install() {
+	dobin "${S}"/reduce_src/reduce
+	insinto ${DICT_DIR}
+	doins "${S}"/${DICT_FOLD} "${S}"/${DICT_FNEW}
+	dodoc README.usingReduce.txt
+}