reinit the tree, so we can have metadata

4 files changed, 149 insertions, 0 deletions

diff --git a/sci-chemistry/moldy/Manifest b/sci-chemistry/moldy/Manifest
new file mode 100644
index 000000000000..1966e387b8d1
--- /dev/null
+++ b/sci-chemistry/moldy/Manifest
@@ -0,0 +1,6 @@
+AUX 2.16e-as-needed.patch 3226 SHA256 304343516efed00901c996a8948705047a7fa46a4b5c26243ded0bf73118e98b SHA512 b32461bb052c908106f0f8d74be4eba52daa41ba592a7ba6083edc2a54c4a14003cf33560572e57f2b370ad5ea1f703e388855e8e7fa67ccec40e3015a8f5803 WHIRLPOOL bdef755c8d8dd0e6ccfaa20537b211a44886e8c6db1c704bec0c5457662e320c9a3127c1f5dbc9a7ca4cd1350f27e13787f8c734a41b2e9fc1f6d5df6c52052e
+DIST moldy-2.16e.tar.gz 488410 SHA256 51abefc5e7de355022f48084382c30e72738cc1f21cd3d67fde7f047f1822ea8 SHA512 b672f4e5c8843277d1b66eedf5f7ad87be0b4c014e0d6bfda4ef941cd9bfeec68d94a361e28531cc3794ee2e4a6937f15c462c69f9adcfcfe5254c3c677fe877 WHIRLPOOL 390237d87580d2f6e438dfcc01e5f47353f72392090c576785f0143482fced508c4a7cff737c9134ecda0b467565260fdb97dcc45b2b64909641da6f8d031448
+EBUILD moldy-2.16e-r2.ebuild 1811 SHA256 d352c930e7585a67ebbe0862ba477477d018981a97a8041137481341fa6e1628 SHA512 6f6280a30cef11539d27b6efa5326f3ca5b365e179dbc3f3e2b5b237b92e66786f4969ebd7ff1d67b3e3f53f2c52a3bc46ccb5ba45078db17e7d325c4640fff0 WHIRLPOOL afdf9d73d931de6d3e034fd18869ed9c1566e6bf6d6ccb8c34f4335db69704c3cf2056013eefcb0044630aa1636a0e750ed8659228e97cf2af70b42e61a3ce98
+MISC ChangeLog 2462 SHA256 cba96a830b9a475ac248ca7f51c62de46372967f328749eecbe77fff1df0eded SHA512 4e584b34d985666849087406f4ea049a4dba0cdadeb0c82ebc5f2e5545fbe40191eceef923b8a2699e7831e938cdbb20936fe11d54cd3434b7853a2c2b83a8ec WHIRLPOOL eb2786390b446556792de8f948a5bb69ef37e1b44c6314c31fd8de776c37af822fdb505be39cf6bf6fc85004bfb911b8e42cbb635b6af2e70ab2f7b43c5616a2
+MISC ChangeLog-2015 4173 SHA256 c32e66feea954789bdef0e3903bb406af1fc1661ee258d020a9138a63be2fbb6 SHA512 3bdb6d9e787956d2ef14f3cb8296637f08750e8fa28ade69b478c0320e7ee5e206960dc9147a1bf9d42f52b5796569eb948409b492af1ff3d23e310f9fe5785d WHIRLPOOL 639c1d1745433d4a08cb729b92ddb30e0f42c2e70927c8362564ce6812f889ee0e5b798a40f90d0ae76540648c1d324c40cbb7a6a6e4e6b701320ff6288751eb
+MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d
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 000000000000..67399e08560e
--- /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) $(UTILS2)
+ 
diff --git a/sci-chemistry/moldy/metadata.xml b/sci-chemistry/moldy/metadata.xml
new file mode 100644
index 000000000000..da36ecbfcd6a
--- /dev/null
+++ b/sci-chemistry/moldy/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild
new file mode 100644
index 000000000000..8ba71f621898
--- /dev/null
+++ b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Molecular dynamics simulations platform"
+HOMEPAGE="http://www.ccp5.ac.uk/moldy/moldy.html"
+SRC_URI="ftp://ftp.earth.ox.ac.uk/pub/keith/${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
+}