sci-chemistry/rosetta: Version Bump

Package-Manager: portage-2.2.0_alpha166

14 files changed, 204 insertions, 85 deletions

diff --git a/sci-chemistry/rosetta/ChangeLog b/sci-chemistry/rosetta/ChangeLog
index 62d568387..e13d7f385 100644
--- a/sci-chemistry/rosetta/ChangeLog
+++ b/sci-chemistry/rosetta/ChangeLog
@@ -1,7 +1,20 @@
 # ChangeLog for sci-chemistry/rosetta
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*rosetta-3.4 (19 Mar 2013)
+
+  19 Mar 2013; Justin Lecher <jlec@gentoo.org> -files/3.0-boinc.patch,
+  -rosetta-3.0-r1.ebuild, +rosetta-3.4.ebuild, +files/rosetta-3.4-boinc.patch,
+  -files/3.0-fix-scons-warnings.patch, +files/rosetta-3.4-boost.patch,
+  +files/rosetta-3.4-gcc4.7.patch, -files/3.0-fix-valgrind.patch,
+  +files/rosetta-3.4-fix-scons-warnings.patch,
+  +files/rosetta-3.4-platform.patch, -files/3.0-platform.patch,
+  +files/rosetta-3.4-fix-valgrind.patch, +files/rosetta-3.4-unbundle.patch,
+  -files/3.0-user-settings.patch, +files/rosetta-3.4-user-settings.patch,
+  -files/3.0-zlib.patch, +files/rosetta-3.4-zlib.patch, metadata.xml:
+  Version Bump
+
   19 Sep 2010; Justin Lecher <jlec@gentoo.org> rosetta-3.0.ebuild,
   rosetta-3.0-r1.ebuild:
   virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl
diff --git a/sci-chemistry/rosetta/Manifest b/sci-chemistry/rosetta/Manifest
index d1cd64006..9cc6fbf0a 100644
--- a/sci-chemistry/rosetta/Manifest
+++ b/sci-chemistry/rosetta/Manifest
@@ -1 +1 @@
-DIST rosetta3_source.tgz 98443598 RMD160 09c7bdaef58ef761bfdc8143c38f81f814be41a4 SHA1 3477856807a6fb4898c8c2aa7852b3b6e4fe90ee SHA256 1870727caea342c3b55af7c353b991758fe1cf4a395a65b48543708e52dc75c5
+DIST rosetta3.4_source.tgz 89734375 SHA256 5ad2d06f7e4e08ef7e87c91bfe7c6d5687601f609892203c75b1abe465954e19 SHA512 d887e3660a8baecc91609463e5d64a86a48c76c72394b211cc388bf6eb49d5696a531eb1cfe19342c3bf9d399b49f1b0fb0a9682a0e166ab6594acc050a5f31e WHIRLPOOL f28706d46335da74934a4339c24c71b084fc8b2a2a2177f16a959ee2b9ea23710598b41c136ba4e18699ae7ddacb327f02a58620782554777651d50281e97fd2
diff --git a/sci-chemistry/rosetta/files/3.0-user-settings.patch b/sci-chemistry/rosetta/files/3.0-user-settings.patch
deleted file mode 100644
index bb1201bd2..000000000
--- a/sci-chemistry/rosetta/files/3.0-user-settings.patch
+++ /dev/null
@@ -1,26 +0,0 @@
---- tools/build/user.settings		2009-04-07 18:51:37.000000000 +0200
-+++ tools/build/user.settings.new	2009-04-07 18:51:37.000000000 +0200
-@@ -21,16 +21,22 @@
- settings = {
-     "user" : {
-         "prepends" : {
-+            "program_path"  : os.environ["PATH"].split(":"),
-+            "include_path"  : [ "/usr/include" ],
-+            "library_path"  : [ "/usr/GENTOO_LIBDIR" ],
-         },
-         "appends" : {
-             # Uncomment the line below and the "import os" line above
-             # to let SCons find ICC (assuming it's on your PATH already)
--            "program_path"  : os.environ["PATH"].split(":"),
- 
-             # Uncomment the line below to begin building the "devel" project too.
-             #"projects": { "src" : [ "devel", ], },
-         },
-         "overrides" : {
-+            "flags" : {
-+                  "compile" : [ GENTOO_CXXFLAGS ],
-+                  "link"    : [ GENTOO_LDFLAGS ],
-+            },
-         },
-         "removes" : {
-         },
diff --git a/sci-chemistry/rosetta/files/3.0-boinc.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch
index 1f6da965c..1f6da965c 100644
--- a/sci-chemistry/rosetta/files/3.0-boinc.patch
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch
new file mode 100644
index 000000000..7c1e1ffc2
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch
@@ -0,0 +1,16 @@
+ tools/build/basic.settings | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/tools/build/basic.settings b/tools/build/basic.settings
+index ecf3237..356cd61 100644
+--- a/tools/build/basic.settings
++++ b/tools/build/basic.settings
+@@ -610,7 +610,7 @@ settings = {
+     "gcc, boost_thread" : {
+         "appends" : {
+             "defines" : [ "MULTI_THREADED" ],
+-            "libraries"     : [ "pthread", "boost_thread" ],
++            "libraries"     : [ "pthread", "boost_thread", "boost_system" ],
+ 	    "library_path"  : [ "/usr/local/lib", "/opt/boost/lib" ],
+             "flags"         : {
+                 "compile"   : [ "pthread" ],
diff --git a/sci-chemistry/rosetta/files/3.0-fix-scons-warnings.patch b/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch
index 321d0a784..321d0a784 100644
--- a/sci-chemistry/rosetta/files/3.0-fix-scons-warnings.patch
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch
diff --git a/sci-chemistry/rosetta/files/3.0-fix-valgrind.patch b/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch
index bc98773c1..bc98773c1 100644
--- a/sci-chemistry/rosetta/files/3.0-fix-valgrind.patch
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch
new file mode 100644
index 000000000..d0893c183
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch
@@ -0,0 +1,32 @@
+ tools/build/options.settings | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/tools/build/options.settings b/tools/build/options.settings
+index 30fb65e..f79ef5b 100644
+--- a/tools/build/options.settings
++++ b/tools/build/options.settings
+@@ -9,7 +9,7 @@
+ options = {
+ 
+     "cxx" : {
+-        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ],
++        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "*" ],
+         "icc"     : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK
+         "msvc"    : [ "7.0", "7.1", "8.0", "8.1", "*" ],
+         "xlc"     : [ "7.0", "8.0", "9.0", "XL", "*" ],
+ src/protocols/jd2/SingleFileBuffer.cc | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc
+index aa78d91..61ca823 100644
+--- a/src/protocols/jd2/SingleFileBuffer.cc
++++ b/src/protocols/jd2/SingleFileBuffer.cc
+@@ -28,6 +28,8 @@
+ #include <ctime>      // for clock()
+ #endif
+ 
++#include <unistd.h>
++
+ namespace protocols {
+ namespace jd2 {
+ using namespace core;
diff --git a/sci-chemistry/rosetta/files/3.0-platform.patch b/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch
index 82f0ba63f..82f0ba63f 100644
--- a/sci-chemistry/rosetta/files/3.0-platform.patch
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch b/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch
new file mode 100644
index 000000000..ba810b162
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch
@@ -0,0 +1,47 @@
+ src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh   | 3 +--
+ .../pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh    | 3 +--
+ src/utility/io/zipstream.hpp                                           | 3 +--
+ 3 files changed, 3 insertions(+), 6 deletions(-)
+
+diff --git a/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh b/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
+index 0aa44a6..299e0c5 100644
+--- a/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
++++ b/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
+@@ -402,8 +402,7 @@
+ #include <boost/function.hpp>
+ #include <boost/pool/detail/mutex.hpp>
+ #include <boost/pool/poolfwd.hpp>
+-#include <zlib/zlib.h>
+-#include <zlib/zutil.h>
++#include <zlib.h>
+ 
+ namespace core {
+ namespace pack {
+diff --git a/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh b/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
+index 2396126..700e78d 100644
+--- a/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
++++ b/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
+@@ -405,8 +405,7 @@
+ #include <boost/function.hpp>
+ #include <boost/pool/detail/mutex.hpp>
+ #include <boost/pool/poolfwd.hpp>
+-#include <zlib/zlib.h>
+-#include <zlib/zutil.h>
++#include <zlib.h>
+ 
+ namespace core {
+ namespace pack {
+diff --git a/src/utility/io/zipstream.hpp b/src/utility/io/zipstream.hpp
+index adaf88c..c7d36d0 100644
+--- a/src/utility/io/zipstream.hpp
++++ b/src/utility/io/zipstream.hpp
+@@ -43,8 +43,7 @@
+ 
+ 
+ // Zlib headers
+-#include <zlib/zlib.h>
+-#include <zlib/zutil.h>
++#include <zlib.h>
+ 
+ 
+ 
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch b/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch
new file mode 100644
index 000000000..d7297cfc0
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch
@@ -0,0 +1,29 @@
+ tools/build/user.settings | 8 +++++++-
+ 1 file changed, 7 insertions(+), 1 deletion(-)
+
+diff --git a/tools/build/user.settings b/tools/build/user.settings
+index 27a001f..9696e3e 100644
+--- a/tools/build/user.settings
++++ b/tools/build/user.settings
+@@ -22,7 +22,7 @@
+ # and select between them from the options.  For now there is only the
+ # single "user" settings.
+ 
+-#import os
++import os
+ settings = {
+     "user" : {
+         "prepends" : {
+@@ -38,6 +38,12 @@ settings = {
+             #"program_path"  : os.environ["PATH"].split(":"),
+         },
+         "overrides" : {
++            "flags" : {
++                  "compile" : [ GENTOO_CXXFLAGS ],
++                  "link"    : [ GENTOO_LDFLAGS ],
++            },
++            "cc"     : os.environ["CC"],
++            "cxx"     : os.environ["CXX"],
+         },
+         "removes" : {
+         },
diff --git a/sci-chemistry/rosetta/files/3.0-zlib.patch b/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch
index 18060add4..18060add4 100644
--- a/sci-chemistry/rosetta/files/3.0-zlib.patch
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch
diff --git a/sci-chemistry/rosetta/metadata.xml b/sci-chemistry/rosetta/metadata.xml
index 6db87655b..3468184a1 100644
--- a/sci-chemistry/rosetta/metadata.xml
+++ b/sci-chemistry/rosetta/metadata.xml
@@ -1,17 +1,17 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
-<use>
-	<flag name='boinc'>compile rosetta as a rosetta@home client</flag>
-	<flag name='boost'>compile rosetta with boost supported code</flag>
-</use>
-<upstream>
-	<bugs-to>general-support@mail.rosettacommons.org</bugs-to>
-</upstream>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>sci@gentoo.org</email>
+  </maintainer>
+  <use>
+    <flag name="boinc">compile rosetta as a rosetta@home client</flag>
+    <flag name="boost">compile rosetta with boost supported code</flag>
+    <flag name="float">Build with floats rather than doubles</flag>
+    <flag name="custom-flags">Use your own flags</flag>
+  </use>
+  <upstream>
+    <bugs-to>general-support@mail.rosettacommons.org</bugs-to>
+  </upstream>
 </pkgmetadata>
-
-
diff --git a/sci-chemistry/rosetta/rosetta-3.0-r1.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
index da1d22620..e38bbcfb6 100644
--- a/sci-chemistry/rosetta/rosetta-3.0-r1.ebuild
+++ b/sci-chemistry/rosetta/rosetta-3.4.ebuild
@@ -1,14 +1,15 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
 # boinc support is BROKEN !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-EAPI="2"
+EAPI=5
 
-inherit eutils multilib versionator
+inherit eutils multilib prefix scons-utils toolchain-funcs versionator
 
-MY_P="${PN}$(get_major_version)_source"
+#MY_P="${PN}$(get_major_version)_source"
+MY_P="${PN}${PV}_source"
 
 DESCRIPTION="Prediction and design of protein structures, folding mechanisms, and protein-protein interactions"
 HOMEPAGE="http://www.rosettacommons.org/"
@@ -16,43 +17,53 @@ SRC_URI="${MY_P}.tgz"
 
 LICENSE="|| ( rosetta-academic rosetta-commercial )"
 SLOT="0"
-KEYWORDS=""
-IUSE="boinc boost debug doc mpi X"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="boinc +boost custom-flags debug doc float mpi +openmp X"
+
+REQUIRED_USE="?? ( mpi boinc )"
+
 RESTRICT="fetch"
 
-RDEPEND="mpi? ( virtual/mpi )
+RDEPEND="
+	dev-db/cppdb
+	mpi? ( virtual/mpi )
 	boinc? ( sci-misc/boinc[X?] )
 	boost? ( dev-libs/boost )
 	sci-libs/rosetta-db"
 DEPEND="${RDEPEND}
-	>=dev-util/scons-0.96.1
+	dev-util/scons
 	doc? ( app-doc/doxygen )
 	X? ( media-libs/freeglut )"
 
 MYCONF=""
 
-S="${WORKDIR}/${MY_P}"
+S="${WORKDIR}/${PN}_source"
 
 pkg_nofetch() {
 	einfo "Go to ${HOMEPAGE} and get ${A}"
 	einfo "which must be placed in ${DISTDIR}"
 }
 
-pkg_setup() {
-	use mpi && use boinc && \
-	die "you can either use mpi or boinc support"
-}
-
 src_prepare() {
 	local myCXXFLAGS
 	local myLDFLAGS
 
-	epatch "${FILESDIR}"/${PV}-platform.patch
-	epatch "${FILESDIR}"/${PV}-fix-scons-warnings.patch
-	epatch "${FILESDIR}"/${PV}-user-settings.patch
-	epatch "${FILESDIR}"/${PV}-fix-valgrind.patch
-	epatch "${FILESDIR}"/${PV}-boinc.patch
-	rm bin/* -fv
+	use custom-flags || \
+		export CXXFLAGS="-O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -pipe"
+
+	epatch \
+		"${FILESDIR}"/${P}-platform.patch \
+		"${FILESDIR}"/${P}-user-settings.patch \
+		"${FILESDIR}"/${P}-fix-valgrind.patch \
+		"${FILESDIR}"/${P}-boinc.patch \
+		"${FILESDIR}"/${P}-boost.patch \
+		"${FILESDIR}"/${P}-gcc4.7.patch
+
+	eprefixify tools/build/*
+
+	rm bin/* external/{dbio,scons-local,lib} -rfv || die
+
+	find external/boost_1_46_1 -name "*.hpp" -delete || die
 
 	for i in ${CXXFLAGS}; do
 		myCXXFLAGS="${myCXXFLAGS} \"${i/-/}\","
@@ -62,14 +73,19 @@ src_prepare() {
 		myLDFLAGS="${myLDFLAGS} \"${i/-/}\","
 	done
 
-	sed -e "s:GENTOO_CXXFLAGS:${myCXXFLAGS}:g" \
+	sed \
+		-e "s:GENTOO_CXXFLAGS:${myCXXFLAGS}:g" \
 		-e "s:GENTOO_LDFLAGS:${myCXXFLAGS} ${myLDFLAGS}:g" \
 		-e "s:GENTOO_LIBDIR:$(get_libdir):g" \
-		-i tools/build/user.settings
+		-i tools/build/user.settings || die
 
-	use mpi && \
-	sed -e 's:mpiCC:mpicxx:g' \
-		-i tools/build/basic.settings
+	if use mpi; then
+		sed \
+			-e 's:mpiCC:mpicxx:g' \
+			-i tools/build/basic.settings || die
+	fi
+
+	tc-export CC CXX
 }
 
 src_configure() {
@@ -77,8 +93,11 @@ src_configure() {
 	local mymode=""
 	local mycxx=""
 
-	use boinc  && EXTRAS="boinc"
+	use boinc && EXTRAS="boinc"
 	use boost && EXTRAS=$(my_list_append "${EXTRAS}" "boost")
+	use boost && EXTRAS=$(my_list_append "${EXTRAS}" "boost_thread")
+	use float && EXTRAS=$(my_list_append "${EXTRAS}" "rosetta_float")
+	use openmp && EXTRAS=$(my_list_append "${EXTRAS}" "omp")
 	use X && EXTRAS=$(my_list_append "${EXTRAS}" "graphics")
 	use mpi && EXTRAS=$(my_list_append "${EXTRAS}" "mpi")
 
@@ -93,15 +112,12 @@ src_configure() {
 		mymode="release"
 	fi
 
-	MAKEOPTS=$(my_filter_option "${MAKEOPTS}" "--load-average[=0-9.]*")
-	MAKEOPTS=$(my_filter_option "${MAKEOPTS}" "-l[0-9.]*")
-
-	MYCONF="${MAKEOPTS} mode=${mymode} ${myextras} ${mycxx}"
+	MYCONF="mode=${mymode} ${myextras} ${mycxx}"
 }
 
 src_compile() {
 	einfo "running 'scons bin cat=src ${MYCONF}' ..."
-	scons bin cat=src ${MYCONF} || die "scons bin cat=src ${MYCONF} failed"
+	escons bin cat=src ${MYCONF}
 
 	if use doc; then
 		einfo "running 'scons ${MYCONF} cat=doc' ..."
@@ -110,25 +126,17 @@ src_compile() {
 }
 
 src_install() {
-	local BIT
-
-	use amd64 && BIT="64"
-	use x86 && BIT="32"
+	dolib.so build/src/release/linux/*/*/*/*/*/${EXTRAS//,/-}/*.so*
 
-	dolib.so build/src/release/linux/2.6/${BIT}/x86/${COMPILER}/${EXTRAS//,/-}/*.so || \
-	die "failed to install libs"
-
-	if use doc; then
-	   dohtml build/doc/rosetta++/docs/* || die "could not install docs"
-	fi
+	use doc && dohtml build/doc/rosetta++/docs/*
 
-	cd bin
+	cd bin || die
 	for BIN in *; do
 		newbin ${BIN} ${BIN%%.*} || die "could not install rosetta program files"
 	done
 
-	mv "${D}"/usr/bin/cluster{,-${PN}}
-	mv "${D}"/usr/bin/benchmark{,-${PN}}
+	mv "${ED}"/usr/bin/cluster{,-${PN}} || die
+	mv "${ED}"/usr/bin/benchmark{,-${PN}} || die
 }
 
 my_filter_option() {