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, 142 insertions, 0 deletions

diff --git a/sci-chemistry/moldy/Manifest b/sci-chemistry/moldy/Manifest
new file mode 100644
index 00000000000..9e0e3883fa2
--- /dev/null
+++ b/sci-chemistry/moldy/Manifest
@@ -0,0 +1 @@
+DIST moldy-2.16e.tar.gz 488410 RMD160 ef9c1c6cf1afa6e28e78a51a6a771d127aac2c83 SHA1 e7984f59170a11b5dab0beae89c5f4cf4da20ad1 SHA256 51abefc5e7de355022f48084382c30e72738cc1f21cd3d67fde7f047f1822ea8
diff --git a/sci-chemistry/moldy/files/2.16e-as-needed.patch b/sci-chemistry/moldy/files/2.16e-as-needed.patch
new file mode 100644
index 00000000000..67399e08560
--- /dev/null
+++ b/sci-chemistry/moldy/files/2.16e-as-needed.patch
@@ -0,0 +1,65 @@
+diff --git a/Makefile.in b/Makefile.in
+index 0b02f00..ec588a8 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -115,25 +115,25 @@ VMSBUILD=	compile_moldy.com link_moldy.com defcomm.com\
+ 
+ DOSBUILD=	Makefile.mak OFILES.RSP SHAKOBJS.RSP Makefile.w32
+ 
+-all:		moldy utilities Makefile
++all:		moldy utilities
+ 
+ moldy:		$(OFILES) $(EXTRA_OBJ) $(HFILES)
+-		$(CC) -o moldy $(LDFLAGS) $(OFILES) $(EXTRA_OBJ)  $(LIBS)
++		$(CC) $(LDFLAGS) -o moldy $(LDFLAGS) $(OFILES) $(EXTRA_OBJ)  $(LIBS)
+ 
+ moldyext:	moldyext.c $(LIBOBJS) $(HFILES)
+-		$(CC) $(CFLAGS) -o moldyext $(OPT) $(DEFS) $(LDFLAGS1) moldyext.c $(LIBOBJS) $(LDFLAGS) $(LIBS)
++		$(CC) $(LDFLAGS) $(CFLAGS) -o moldyext $(OPT) $(DEFS) $(LDFLAGS1) moldyext.c $(LIBOBJS) $(LIBS)
+ 
+ manalyze:	manalyze.c $(HFILES)
+-		$(CC) $(CFLAGS)  -o manalyze $(OPT) $(DEFS) $(LDFLAGS1) manalyze.c $(LDFLAGS) $(LIBS)
++		$(CC) $(LDFLAGS) $(CFLAGS)  -o manalyze $(OPT) $(DEFS) $(LDFLAGS1) manalyze.c $(LIBS)
+ 
+ dumpanal:	dumpanal.c xdr.o $(HFILES)
+-		$(CC) $(CFLAGS) -o dumpanal $(OPT) $(DEFS) $(LDFLAGS1) dumpanal.c xdr.o  $(LDFLAGS) $(LIBS)
++		$(CC) $(LDFLAGS) $(CFLAGS) -o dumpanal $(OPT) $(DEFS) $(LDFLAGS1) dumpanal.c xdr.o $(LIBS)
+ 
+ dumpext:	dumpext.c xdr.o utlsup.o matrix.o $(LIBOBJS) $(HFILES)
+-		$(CC) $(CFLAGS) -o dumpext $(OPT) $(DEFS) $(LDFLAGS1) dumpext.c xdr.o utlsup.o matrix.o $(LIBOBJS) $(LDFLAGS) $(LIBS)
++		$(CC) $(LDFLAGS) $(CFLAGS) -o dumpext $(OPT) $(DEFS) $(LDFLAGS1) dumpext.c xdr.o utlsup.o matrix.o $(LIBOBJS) $(LIBS)
+ 
+ dumpconv:	dumpconv.c xdr.o $(HFILES)
+-		$(CC) $(CFLAGS) -o dumpconv $(OPT) $(DEFS) $(LDFLAGS1) dumpconv.c xdr.o $(LDFLAGS) $(LIBS)
++		$(CC) $(LDFLAGS) $(CFLAGS) -o dumpconv $(OPT) $(DEFS) $(LDFLAGS1) dumpconv.c xdr.o $(LIBS)
+ 
+ #mdtraj:		mdtraj.o $(SHAKOBJS) $(LIBOBJS) 
+ #		$(CC) -o mdtraj $(LDFLAGS) mdtraj.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
+@@ -142,21 +142,21 @@ mdshak:		mdshak.o $(SHAKOBJS) $(LIBOBJS)
+ 		$(CC) -o mdshak $(LDFLAGS) mdshak.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
+ 
+ msd:		msd.o $(SHAKOBJS) $(LIBOBJS) 
+-		$(CC) -o msd $(LDFLAGS1) msd.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS)
++		$(CC) $(LDFLAGS) -o msd $(LDFLAGS1) msd.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
+ 
+ mdvaf:		mdvaf.o $(SHAKOBJS) $(LIBOBJS) 
+-		$(CC) -o mdvaf $(LDFLAGS1) mdvaf.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS)
++		$(CC) $(LDFLAGS) -o mdvaf $(LDFLAGS1) mdvaf.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
+ mdavpos:	mdavpos.o $(SHAKOBJS) $(LIBOBJS) 
+-		$(CC) -o mdavpos $(LDFLAGS1) mdavpos.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS)  $(LIBS)
++		$(CC) $(LDFLAGS) -o mdavpos $(LDFLAGS1) mdavpos.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
+ 
+ mdbond:	mdbond.o $(SHAKOBJS) $(LIBOBJS) 
+-		$(CC) -o mdbond $(LDFLAGS1) mdbond.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS)  $(LIBS)
++		$(CC) $(LDFLAGS) -o mdbond $(LDFLAGS1) mdbond.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
+ 
+ bdist:	bdist.c $(HFILES)
+-		$(CC) $(CFLAGS)  -o bdist $(OPT) $(DEFS) $(LDFLAGS1) bdist.c $(LIBOBJS) $(LDFLAGS) $(LIBS)
++		$(CC) $(CFLAGS) $(LDFLAGS) -o bdist $(OPT) $(DEFS) $(LDFLAGS1) bdist.c $(LIBOBJS) $(LIBS)
+ 
+ ransub:	ransub.o $(SHAKOBJS) $(LIBOBJS) 
+-		$(CC) -o ransub $(LDFLAGS1) ransub.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS)  $(LIBS)
++		$(CC) $(LDFLAGS) -o ransub $(LDFLAGS1) ransub.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
+ 
+ utilities:	$(UTILS) $(UTILS2)
+ 
diff --git a/sci-chemistry/moldy/metadata.xml b/sci-chemistry/moldy/metadata.xml
new file mode 100644
index 00000000000..e42d0af60f4
--- /dev/null
+++ b/sci-chemistry/moldy/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/moldy/moldy-2.16e-r2.ebuild b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild
new file mode 100644
index 00000000000..27db651f82a
--- /dev/null
+++ b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Molecular dynamics simulations platform"
+HOMEPAGE="http://www.ccp5.ac.uk/moldy/moldy.html"
+SRC_URI="ftp://ftp.earth.ox.ac.uk/pub/keith/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc examples"
+
+DEPEND="doc? ( virtual/latex-base )"
+RDEPEND=""
+
+S="${WORKDIR}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-as-needed.patch
+	sed \
+		-e 's:-O2::g' \
+		-e 's:-ffast-math::g' \
+		-i configure || die
+}
+
+src_configure() {
+	#Individuals may want to edit the OPT* variables below.
+	#From the READ.ME:
+	#You may need to  "hand-tune" compiler or optimization options,
+	#which may be specified by setting the OPT and OPT2 environment
+	#variables.  OPT2 is used to compile only the most performance-critical
+	#modules and usually will select a very high level of optimization.
+	#It should be safe to select an optimization which means "treat all
+	#function arguments as restricted pointers which are not aliased to
+	#any other object".  OPT is used for less preformance-critical modules
+	#and may be set to a lower level of optimization than OPT2.
+
+	OPT="${CFLAGS}" \
+	OPT2="${CFLAGS} ${CFLAGS_OPT}" \
+	CC=$(tc-getCC) \
+	econf
+}
+
+src_compile() {
+	emake
+	# To prevent sandbox violations by metafont
+	if use doc; then
+		VARTEXFONTS="${T}"/fonts emake moldy.pdf
+	fi
+}
+
+src_install() {
+	dodir /usr/bin
+	emake prefix="${ED}"/usr install
+	dodoc BENCHMARK READ.ME RELNOTES
+
+	if use examples; then
+		rm Makefile.in configure.in config.h.in
+		insinto /usr/share/${PN}/examples/
+		doins *.in *.out control.* || die
+	fi
+	if use doc; then
+		insinto /usr/share/doc/${PF}/pdf
+		newins moldy.pdf moldy-manual.pdf
+	fi
+}