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

7 files changed, 170 insertions, 0 deletions

diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest
new file mode 100644
index 000000000000..1628482e5af4
--- /dev/null
+++ b/sci-chemistry/tinker/Manifest
@@ -0,0 +1 @@
+DIST tinker-7.1.2.tar.gz 28468683 SHA256 fdee18915cff9044fd083bb2271083c221db6d05de2cb98fc111b136e23e6899 SHA512 4524259754b0f11d7e2e8997ebd85eae7d28f8dbb1edb2d9818aa0a96640de0049aa4937236694f1a11743dee187d612f775b233a73cc96c2708d620457a7dc2 WHIRLPOOL f3e29eaf67d25ae6d4f3c4e3546798e66bd626929fddd45b9d1ff9f2143cd57dcc5079226f3ceaa142f4c6a168c4a150a51be1336a5ca13384338795ef3a6d46
diff --git a/sci-chemistry/tinker/files/5.1.09-Makefile.patch b/sci-chemistry/tinker/files/5.1.09-Makefile.patch
new file mode 100644
index 000000000000..68a095add706
--- /dev/null
+++ b/sci-chemistry/tinker/files/5.1.09-Makefile.patch
@@ -0,0 +1,13 @@
+diff --git a/make/Makefile b/make/Makefile
+index 221ab45..7634474 100644
+--- a/make/Makefile
++++ b/make/Makefile
+@@ -607,7 +607,7 @@ clean:
+ listing:
+ 	cat *.i *.f > tinker.txt
+ 
+-rename:
++rename: ${EXEFILES}
+ 	mv  alchemy.x    $(BINDIR)/alchemy
+ 	mv  analyze.x    $(BINDIR)/analyze
+ 	mv  anneal.x     $(BINDIR)/anneal
diff --git a/sci-chemistry/tinker/files/6-openmp.patch b/sci-chemistry/tinker/files/6-openmp.patch
new file mode 100644
index 000000000000..3666fbd0bfc4
--- /dev/null
+++ b/sci-chemistry/tinker/files/6-openmp.patch
@@ -0,0 +1,15 @@
+diff --git a/source/initial.f b/source/initial.f
+index 835f228..4099c74 100644
+--- a/source/initial.f
++++ b/source/initial.f
+@@ -73,8 +73,8 @@ c
+ c
+ c     Intel compiler extensions to OpenMP standard
+ c
+-!$    call kmp_set_stacksize (2**30)
+-!$    call kmp_set_blocktime (0)
++!    call kmp_set_stacksize (2**30)
++!    call kmp_set_blocktime (0)
+ c
+ c     values of machine precision constants
+ c
diff --git a/sci-chemistry/tinker/files/7.1.2-openmp.patch b/sci-chemistry/tinker/files/7.1.2-openmp.patch
new file mode 100644
index 000000000000..f3e8e2932b4a
--- /dev/null
+++ b/sci-chemistry/tinker/files/7.1.2-openmp.patch
@@ -0,0 +1,15 @@
+diff --git a/source/initial.f b/source/initial.f
+index 835f228..4099c74 100644
+--- a/source/initial.f
++++ b/source/initial.f
+@@ -73,8 +73,8 @@ c
+ c
+ c     Intel compiler extensions to OpenMP standard
+ c
+-!$    call kmp_set_stacksize_s (2**28)
+-!$    call kmp_set_blocktime (0)
++!    call kmp_set_stacksize_s (2**28)
++!    call kmp_set_blocktime (0)
+ c
+ c     values of machine precision constants
+ c
diff --git a/sci-chemistry/tinker/files/tinker-7.1.2-build.patch b/sci-chemistry/tinker/files/tinker-7.1.2-build.patch
new file mode 100644
index 000000000000..d6ef484b19a4
--- /dev/null
+++ b/sci-chemistry/tinker/files/tinker-7.1.2-build.patch
@@ -0,0 +1,17 @@
+ make/Makefile | 3 +--
+ 1 file changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/make/Makefile b/make/Makefile
+index 61d5037..9be384a 100644
+--- a/make/Makefile
++++ b/make/Makefile
+@@ -719,8 +719,7 @@ EXEFILES = alchemy.x \
+ %.x: %.o libtinker.a
+ 	${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@
+ 
+-all:
+-	${EXEFILES}
++all: ${EXEFILES}
+ 
+ install:
+ 	rename
diff --git a/sci-chemistry/tinker/metadata.xml b/sci-chemistry/tinker/metadata.xml
new file mode 100644
index 000000000000..e42d0af60f42
--- /dev/null
+++ b/sci-chemistry/tinker/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/tinker/tinker-7.1.2.ebuild b/sci-chemistry/tinker/tinker-7.1.2.ebuild
new file mode 100644
index 000000000000..e81b4a6b6a1d
--- /dev/null
+++ b/sci-chemistry/tinker/tinker-7.1.2.ebuild
@@ -0,0 +1,104 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs
+
+DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM"
+HOMEPAGE="http://dasher.wustl.edu/tinker/"
+SRC_URI="http://dasher.wustl.edu/${PN}/downloads/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="Tinker"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+DEPEND="
+	>=virtual/jdk-1.6"
+RDEPEND="
+	>=sci-libs/fftw-3.2.2-r1[fortran,threads]
+	dev-libs/maloc
+	!dev-util/diffuse
+	>=virtual/jre-1.6"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${PN}/source
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	java-pkg-opt-2_pkg_setup
+	tc-has-openmp || die "Please use an openmp capable compiler like gcc[openmp]"
+}
+
+src_prepare() {
+	sed 's:strip:true:g' -i ../make/Makefile
+	[[ $(tc-getFC) =~ "ifort" ]] || epatch "${FILESDIR}"/${PV}-openmp.patch
+	cd .. && epatch "${FILESDIR}"/${P}-build.patch
+}
+
+src_compile() {
+	local javalib=
+	for i in $(java-config -g LDPATH | sed 's|:| |g'); do
+		[[ -f ${i}/libjvm.so ]] && javalib=${i}
+	done
+
+	# use dummy routines in pmpb.f instead of apbs calls
+	rm pmpb.c || die
+
+	if [[ $(tc-getFC) =~ "gfortran" ]]; then
+		append-flags -fopenmp
+		_omplib="-lgomp"
+	else
+		append-flags -openmp
+		_omplib="-liomp5"
+	fi
+
+	_fftwlib="$($(tc-getPKG_CONFIG) --libs fftw3 fftw3_threads)"
+
+	emake \
+		-f ../make/Makefile \
+		F77="$(tc-getFC)" \
+		CC="$(tc-getCC) -c" \
+		F77FLAGS=-c \
+		OPTFLAGS="${FFLAGS}" \
+		LINKFLAGS="${LDFLAGS} -Wl,-rpath ${javalib}" \
+		INCLUDEDIR="$(java-pkg_get-jni-cflags) -I${EPREFIX}/usr/include" \
+		LIBS="-lmaloc -L${javalib} -ljvm ${_omplib} ${_fftwlib}" \
+		all
+
+	mkdir "${S}"/../bin || die
+
+	emake \
+		-f ../make/Makefile \
+		BINDIR="${S}"/../bin \
+		rename
+}
+
+src_test() {
+	cd "${WORKDIR}"/${PN}/test/
+	for test in *.run; do
+		einfo "Testing ${test} ..."
+		bash ${test} || die
+	done
+}
+
+src_install() {
+	dobin "${WORKDIR}"/${PN}/perl/mdavg "${WORKDIR}"/${PN}/bin/*
+
+	insinto /usr/share/${PN}/
+	doins -r "${WORKDIR}"/${PN}/params
+
+	dodoc \
+		"${WORKDIR}"/${PN}/doc/{*.txt,*.pdf,0README}
+
+	if use examples; then
+		insinto /usr/share/${P}
+		doins -r "${WORKDIR}"/${PN}/example
+
+		doins -r "${WORKDIR}"/${PN}/test
+	fi
+
+}