Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci

28 files changed, 271 insertions, 37 deletions

diff --git a/dev-cpp/eigen/ChangeLog b/dev-cpp/eigen/ChangeLog
index 9f17a2e4d..595a02db0 100644
--- a/dev-cpp/eigen/ChangeLog
+++ b/dev-cpp/eigen/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/dev-cpp/eigen/ChangeLog,v 1.44 2011/03/25 16:01:28 jlec Exp $
 
+*eigen-3.1.1-r1 (26 Jul 2012)
+
+  26 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org> +eigen-3.1.1-r1.ebuild,
+  -eigen-3.1.0-r1.ebuild, eigen-9999.ebuild:
+  dev-cpp/eigen: Version bump. Changed license to MPL-2
+
 *eigen-3.1.0-r1 (09 Jul 2012)
 *eigen-3.0.6-r1 (09 Jul 2012)
 
@@ -255,4 +261,3 @@
   15 May 2007; Marcus D. Hanwell <cryos@gentoo.org> +metadata.xml,
   +eigen-1.0.5.ebuild:
   Initial import.
-
diff --git a/dev-cpp/eigen/Manifest b/dev-cpp/eigen/Manifest
index 2931017f6..fbd4652fb 100644
--- a/dev-cpp/eigen/Manifest
+++ b/dev-cpp/eigen/Manifest
@@ -1,2 +1,2 @@
 DIST eigen-3.0.6.tar.bz2 961722 SHA256 32e1275a105339003ba34007dd07dc1c62077d75882f3eeddd40a7ec5a5bfd87 SHA512 97cf5126984848f31b3c45c44d7ee6b8d42eca459ff2cc5535413efc768254a1ab738d935c70f9a457a9eaee5faa3c1b08c1f17193b6fcecb5ae0f0b6b32d1fa WHIRLPOOL e17409a807228b63b866c282f767c9107e6c0b45ad84bb311a5ef70053dca3d48580c8839bb6b8fcf5c5bab1a0c102413a96c06007bfbd2218bf260c4a522586
-DIST eigen-3.1.0.tar.bz2 1023451 SHA256 3c64a6792a55d8ee672ce45d5a1d1de1ffc50daaf6e8a3677bf8580ad99f036c SHA512 dbe39e5a0314d658b7d34f5a4216d4b11a92a37dd35e1d54d68ee2ec653af3b6a6d1107bff87d705660c04749ab15deaaf31adcbb0ae4b69b82beb94cc71b345 WHIRLPOOL a57f21a033c6d38757733ee300db36b7bf9d24945bf4a0cc3aca8972a400fe1ae64d77334f9b009685fe870a1f389a9275b2b9dac5e273ffb45b49ba7baed9ba
+DIST eigen-3.1.1.tar.bz2 1049447 SHA256 531a97c3d96d151c72951e6f295b5e5f3f68f668fd04c9b1a0d84187547121ab SHA512 099310095c2b0a0e5e6af389414ab35c73828699d489813d527345307bc4cdc7f40eca24cb798fb2b29f3048938ae82219b0e3a410e64f32724bd0d27a134d50 WHIRLPOOL a02818d046dc80cbcd7cdf601ab97917d22e8ec80c88107098b47833571da6282c5ea12bb0575eac9d20ef5c73630edd68485de546bfd9632d93eb733f8f62e3
diff --git a/dev-cpp/eigen/eigen-3.1.0-r1.ebuild b/dev-cpp/eigen/eigen-3.1.1-r1.ebuild
index eafd77401..eafd77401 120000
--- a/dev-cpp/eigen/eigen-3.1.0-r1.ebuild
+++ b/dev-cpp/eigen/eigen-3.1.1-r1.ebuild
diff --git a/dev-cpp/eigen/eigen-9999.ebuild b/dev-cpp/eigen/eigen-9999.ebuild
index 610c6060c..973ffbfa0 100644
--- a/dev-cpp/eigen/eigen-9999.ebuild
+++ b/dev-cpp/eigen/eigen-9999.ebuild
@@ -19,7 +19,7 @@ inherit cmake-utils alternatives-2 fortran-2 multilib ${_SCM}
 DESCRIPTION="C++ template library for linear algebra"
 HOMEPAGE="http://eigen.tuxfamily.org/"
 
-LICENSE="|| ( LGPL-3 GPL-2 )"
+LICENSE="MPL-2.0"
 SLOT="3"
 IUSE="adolc doc fortran fftw gmp mkl sparse static-libs test"
 
@@ -53,6 +53,7 @@ src_configure() {
 	# TOFIX: is it worth fixing all the automagic given no library is built?
 	mycmakeargs=(
 		-DEIGEN_BUILD_BTL=OFF
+		-DEIGEN_TEST_NO_OPENGL=ON
 		$(cmake-utils_use test EIGEN_BUILD_TESTS)
 		$(cmake-utils_use !fortran EIGEN_TEST_NO_FORTRAN)
 	)
diff --git a/dev-java/flexdock/ChangeLog b/dev-java/flexdock/ChangeLog
index 49794812f..2ed21fcb7 100644
--- a/dev-java/flexdock/ChangeLog
+++ b/dev-java/flexdock/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*flexdock-1.2.0 (28 Jul 2012)
+
+  28 Jul 2012; Guillaume Horel <guillaume.horel@gmail.com>
+  +flexdock-1.2.0.ebuild, +files/flexdock-1.2.0-nodemo.patch:
+  version bump.
+  remove jgoodies-looks dependencies since we don't build demos
+
   23 May 2012; Sébastien Fabbro <bicatali@gentoo.org> flexdock-1.1.1.ebuild:
   add missing jgoodies-looks dependency
 
diff --git a/dev-java/flexdock/Manifest b/dev-java/flexdock/Manifest
index 40a273fcd..4d08759fc 100644
--- a/dev-java/flexdock/Manifest
+++ b/dev-java/flexdock/Manifest
@@ -1 +1,2 @@
 DIST flexdock-1.1.1-src.zip 6163036 SHA256 e0bed4b633dd09da20651d495eb87b985150938564dd124083483c98bda09cf3 SHA512 104398a573b2aade0ed6b848920f8a3903964feabd755c653d8e62ea986251d9c31a07e88308c9cffe7e696c99109a3dfca249f0ca0357e88a896fc5769170f4 WHIRLPOOL 3265875a173911f5635d76824c1c98bc5f0fef3761abc7f5efc3ddc3582f354562391982f6c6f0f286ac2677bafc94237ce09e63ae877da79cad7dfcd50855b9
+DIST flexdock-1.2.0-src.zip 6159196 SHA256 7506b49c902d7d48ef0c06a145327fa9e1166a522e0990e74b37a8936f62ebf5 SHA512 cafdc84037af81c5f2fccb3642cd6db7a2b16b10156c7536c566624ecba9dd42e50cd08dfc0ed49c83e88b07cede6d8c2afb6ed707451c39906dffcf274327d7 WHIRLPOOL 8d06b0840db904f75905927d3990613e18f71cb183a27d4ff2d9c01318cf6a5136b5e4e8cfaed775d9a595c83cabb5aeeaa9d2244b43ab345d7d116fdce98ae8
diff --git a/dev-java/flexdock/files/flexdock-1.2.0-nodemo.patch b/dev-java/flexdock/files/flexdock-1.2.0-nodemo.patch
new file mode 100644
index 000000000..415301d20
--- /dev/null
+++ b/dev-java/flexdock/files/flexdock-1.2.0-nodemo.patch
@@ -0,0 +1,12 @@
+diff -urN flexdock-orig/build.xml flexdock/build.xml
+--- flexdock-orig/build.xml	2011-12-09 11:11:26.000000000 -0500
++++ flexdock/build.xml	2011-12-20 18:47:57.277051174 -0500
+@@ -145,8 +145,6 @@
+          <src path="${java.src.drag}"/>
+          <src path="${java.src.perspective}"/>
+       </javac>
+-      <javac classpathref="javac.classpath.demo" srcdir="${java.src.demo}" destdir="${bin.dir.demo}" debug="true" source="1.5" target="1.5" includeAntRuntime="no"/>
+-      <javac classpathref="javac.classpath.test" srcdir="${java.src.test}" destdir="${bin.dir.test}" debug="true" source="1.5" target="1.5"  includeAntRuntime="no"/>
+    </target>
+ 
+ 
diff --git a/dev-java/flexdock/flexdock-1.2.0.ebuild b/dev-java/flexdock/flexdock-1.2.0.ebuild
new file mode 100644
index 000000000..f24cc2510
--- /dev/null
+++ b/dev-java/flexdock/flexdock-1.2.0.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="A Java docking framework for use in cross-platform Swing applications"
+HOMEPAGE="http://flexdock.dev.java.net/"
+SRC_URI="http://forge.scilab.org/index.php/p/flexdock/downloads/get/${P}-src.zip"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+
+IUSE=""
+
+RDEPEND=">=virtual/jre-1.4"
+DEPEND=">=virtual/jdk-1.4
+	app-arch/unzip
+	dev-java/skinlf"
+
+EANT_BUILD_TARGET="jar"
+EANT_DOC_TARGET="doc"
+
+src_unpack() {
+	mkdir "${WORKDIR}/${P}"
+	cd "${S}"
+	unpack ${A}
+}
+
+java_prepare() {
+	epatch "${FILESDIR}"/${P}-nodemo.patch
+
+	#some cleanups
+	find . -name '*.so' -exec rm -v {} \;|| die
+	find . -name '*.dll' -exec rm -v {} \;|| die
+
+	#remove built-in jars and use the system ones
+	cd lib || die
+	rm -rvf *.jar jmf|| die
+	java-pkg_jar-from skinlf
+}
+
+src_install() {
+	java-pkg_newjar "build/${P}.jar" "${PN}.jar"
+	use doc && java-pkg_dojavadoc build/docs/api
+	use source && java-pkg_dosrc src
+}
diff --git a/dev-java/jgraphx/ChangeLog b/dev-java/jgraphx/ChangeLog
index 0ad818981..1e6b6660e 100644
--- a/dev-java/jgraphx/ChangeLog
+++ b/dev-java/jgraphx/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*jgraphx-1.8.0.6 (28 Jul 2012)
+
+  28 Jul 2012; Guillaume Horel <guillaume.horel@gmail.com>
+  +jgraphx-1.8.0.6.ebuild:
+  version bump
+
   12 May 2012; Alexey Shvetsov <alexxy@gentoo.org> jgraphx-1.2.0.7.ebuild,
   jgraphx-1.3.0.2.ebuild, jgraphx-1.4.1.0.ebuild, jgraphx-1.4.1.2.ebuild:
   [dev-java/jgraphx] Fix ebuild eapi parsing and other minor issues
diff --git a/dev-java/jgraphx/Manifest b/dev-java/jgraphx/Manifest
index 92545f5c6..126a5a322 100644
--- a/dev-java/jgraphx/Manifest
+++ b/dev-java/jgraphx/Manifest
@@ -1,4 +1,5 @@
-DIST jgraphx-1.2.0.7.zip 3034071 RMD160 665dd0344582d3363924ffd4faf21b7a78ffcf9b SHA1 7548b568f66683b46d19b9fb42083992afa34c87 SHA256 9dfc39de448d9ba28ab6b27fe3c8e920033779feb38dbe45cf96145c6d506b08
-DIST jgraphx-1.3.0.2.zip 3055762 RMD160 3d38cd07e5826bc445344f8c2e8cf632c2415367 SHA1 1b045cf66211c68dd102053208d6cb7b5781f294 SHA256 c58aa9e3b1f334f54633017f1f9b35204e19d18524c41df3a5e68c2aa50d2c2d
-DIST jgraphx-1.4.1.0.zip 4052749 RMD160 eebf308aaac3380c9619de6ff5853454a88e6513 SHA1 fe0f892c81f5346542f9a676f37fbbf7e3cdae49 SHA256 086cd3de7d2b381a61f5a7d5eea19e80d3f1f1aaff9642d2b9e582d86a312f59
-DIST jgraphx-1.4.1.2.zip 4148011 RMD160 23d0f962f4795e525d988ced4a25438c16389a2b SHA1 2f18ce5eae18a199d32011ccb7fbfb3c4dd8f9a8 SHA256 cb0216df6fe3e9351afae7f02585e6f5c50e28e764d9504dd8aa558a87d3fe95
+DIST jgraphx-1.2.0.7.zip 3034071 SHA256 9dfc39de448d9ba28ab6b27fe3c8e920033779feb38dbe45cf96145c6d506b08
+DIST jgraphx-1.3.0.2.zip 3055762 SHA256 c58aa9e3b1f334f54633017f1f9b35204e19d18524c41df3a5e68c2aa50d2c2d
+DIST jgraphx-1.4.1.0.zip 4052749 SHA256 086cd3de7d2b381a61f5a7d5eea19e80d3f1f1aaff9642d2b9e582d86a312f59
+DIST jgraphx-1.4.1.2.zip 4148011 SHA256 cb0216df6fe3e9351afae7f02585e6f5c50e28e764d9504dd8aa558a87d3fe95
+DIST jgraphx-1.8.0.6.zip 4216848 SHA256 237035982616769f0c15b805b4ce12616915498a5995fbdae814b97f434c860d SHA512 07985168625f094a8de9ab0e5c6050dd1a5d537b21eb6c73e468ad21db2758ac78a272dfedf22b94585eff4f77288ad99f8f1b70b18462754f0f3048ad06e40f WHIRLPOOL 403b784bdf934fc4a6aae643badb4380279bd15ea87520d6df0ed3d3ed58b020d3f0f979e9d2a2de338256bbdb5793e1e9d50634c60e83d104ceb88b96fcefba
diff --git a/dev-java/jgraphx/jgraphx-1.8.0.6.ebuild b/dev-java/jgraphx/jgraphx-1.8.0.6.ebuild
new file mode 100644
index 000000000..895650d27
--- /dev/null
+++ b/dev-java/jgraphx/jgraphx-1.8.0.6.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+JAVA_PKG_IUSE="doc source"
+inherit java-pkg-2 java-ant-2 versionator
+
+MY_PV=$(replace_all_version_separators '_')
+
+DESCRIPTION="Open-source graph component for Java"
+SRC_URI="http://www.jgraph.com/downloads/jgraphx/archive/${PN}-${MY_PV}.zip\
+		-> ${P}.zip"
+HOMEPAGE="http://www.jgraph.com"
+IUSE="doc examples source"
+DEPEND=">=virtual/jdk-1.5
+	app-arch/unzip"
+RDEPEND=">=virtual/jre-1.5"
+LICENSE="as-is"
+SLOT="1.8"
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+	# don't do javadoc always
+	sed -i \
+		-e 's/depends="doc"/depends="compile"/' \
+		build.xml || die "sed failed"
+	rm -rf doc/api lib/jgraphx.jar || die
+}
+
+EANT_BUILD_TARGET="build"
+EANT_DOC_TARGET="doc"
+
+src_install() {
+	java-pkg_dojar lib/${PN}.jar
+
+	use doc && java-pkg_dojavadoc docs/api
+	use source && java-pkg_dosrc src/org
+	use examples && java-pkg_doexamples examples
+}
diff --git a/dev-java/scirenderer/ChangeLog b/dev-java/scirenderer/ChangeLog
index 438092b75..886c3dbc4 100644
--- a/dev-java/scirenderer/ChangeLog
+++ b/dev-java/scirenderer/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*scirenderer-0.5.1 (28 Jul 2012)
+
+  28 Jul 2012; Guillaume Horel <guillaume.horel@gmail.com>
+  -scirenderer-0.5.0.ebuild, +scirenderer-0.5.1.ebuild:
+  version bump
+
 *scirenderer-0.5.0 (11 Jul 2012)
 
   11 Jul 2012; Guillaume Horel <guillaume.horel@gmail.com>
diff --git a/dev-java/scirenderer/Manifest b/dev-java/scirenderer/Manifest
index 52b544148..ac0fbca9a 100644
--- a/dev-java/scirenderer/Manifest
+++ b/dev-java/scirenderer/Manifest
@@ -1 +1 @@
-DIST scirenderer-0.5.0.tar.gz 107089 SHA256 c6911a12ab6990f9f1468fa3072279f6890f93fbe8cb9dafed2fd36c9eb5d552 SHA512 01f45a0f85fa6fd3b3599321c84bae4dc34a7b48d141457d15b5408dcbe9da2b500461670be50203cc9bfa7b8331884102ee2aaf786168ffbd8dea1153fce3a9 WHIRLPOOL b8a5bd3ef8de89abff69ccb3000b37ddb058b24e33596d6b61cc3b6f55860e1d4c7c31d44a9c2f0a3743a5cc31c448e4e9e2ee911e5352f350824623565cefa1
+DIST scirenderer-0.5.1.tar.gz 108309 SHA256 6a8b426eab7e6be5d67ed1dd43f4688772d1cc054f06a5e2783d438918af6a4c SHA512 ba4fb55be7c0dd477875c1bb90e432b9fdf0a611e8a8e9eb82a5c2397716624824ffc2dc50c5632e1029255f3cca5df26066037baafa152a3d9b5c7c360f6265 WHIRLPOOL cceb2411520603f15039c56faee14ef853f9cd7e320eef3dae231f63e6ffd0ef27276a68ba06cd7ca24a61fd5b2fbc3d5038f36af3d02583b317ed2716d9092f
diff --git a/dev-java/scirenderer/scirenderer-0.5.0.ebuild b/dev-java/scirenderer/scirenderer-0.5.1.ebuild
index 3a710e21a..3a710e21a 100644
--- a/dev-java/scirenderer/scirenderer-0.5.0.ebuild
+++ b/dev-java/scirenderer/scirenderer-0.5.1.ebuild
diff --git a/eclass/alternatives-2.eclass b/eclass/alternatives-2.eclass
index 1180c2419..b303694f1 100644
--- a/eclass/alternatives-2.eclass
+++ b/eclass/alternatives-2.eclass
@@ -9,7 +9,7 @@
 
 ALTERNATIVES_DIR="/etc/env.d/alternatives"
 
-DEPEND=">=app-admin/eselect-1.3-r1"
+DEPEND=">=app-admin/eselect-1.3.1-r1"
 RDEPEND="${DEPEND}
 	!app-admin/eselect-blas
 	!app-admin/eselect-cblas
diff --git a/profiles/package.mask b/profiles/package.mask
index 4e5d129e5..1de782603 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -33,6 +33,8 @@
 # Guillaume Horel <guillaume.horel@gmail.com> (11 July 2012)
 # masked for upcoming scilab-5.4.0
 =dev-java/jrosetta-1.0.4
+=dev-java/flexdock-1.2.0
+>=dev-java/jgraphx-1.8
 
 # Nicolas Bock <nicolasbock@gmail.com> (05 July 2012)
 # live ebuild
diff --git a/sci-astronomy/zpeg/ChangeLog b/sci-astronomy/zpeg/ChangeLog
new file mode 100644
index 000000000..72e4b6d54
--- /dev/null
+++ b/sci-astronomy/zpeg/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-astronomy/zpeg
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*zpeg-5.23 (26 Jul 2012)
+
+  26 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org> +metadata.xml,
+  +zpeg-5.23.ebuild:
+  sci-astronomy/zpeg: Initial import
diff --git a/sci-astronomy/zpeg/Manifest b/sci-astronomy/zpeg/Manifest
new file mode 100644
index 000000000..25296ee59
--- /dev/null
+++ b/sci-astronomy/zpeg/Manifest
@@ -0,0 +1 @@
+DIST zpeg_5.23.tar.gz 37541120 SHA256 de2b6dd120a4bf89e3b49c924923334b8d25e9209539a7de5264f501698b4fc2 SHA512 4bc05bb504531317de7dbb76b9f949ee346b401d3ab90e5a4a08d1b268f98aa1f2ca2895003a48a136e0f9316e976daa5ee2198e31353eaf7462ad40a302cadc WHIRLPOOL eb228ae069ddc3fa71da8e0858ff09cf6518ba5e506e54c68b097402ac053b6e4242b0781720287c37b8ea6b43b457dc015115617044b19ca3e2cf71da2f980c
diff --git a/sci-astronomy/zpeg/metadata.xml b/sci-astronomy/zpeg/metadata.xml
new file mode 100644
index 000000000..46307f890
--- /dev/null
+++ b/sci-astronomy/zpeg/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-astronomy</herd>
+<longdescription lang="en">
+  Z-PEG is a software anybody can use to compute photometric
+  redshifts. In short, Z-PEG performs a chi square minimization of the
+  distance between observed photometric bands and synthetic photometry
+  from galaxies simulated by the evolutionary code PEGASE.
+</longdescription>
+<use>
+<flag name='gdl'>Install GDL/IDL plotting routines</flag>
+</use>
+</pkgmetadata>
diff --git a/sci-astronomy/zpeg/zpeg-5.23.ebuild b/sci-astronomy/zpeg/zpeg-5.23.ebuild
new file mode 100644
index 000000000..51792f95b
--- /dev/null
+++ b/sci-astronomy/zpeg/zpeg-5.23.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit fortran-2
+
+MYP=${PN}_${PV}
+
+DESCRIPTION="Galaxy photometric redshifts from evolutionary synthesis"
+HOMEPAGE="http://imacdlb.iap.fr:8080/cgi-bin/zpeg/zpeg.pl"
+SRC_URI="ftp://ftp.iap.fr/pub/from_users/leborgne/${PN}/${MYP}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="gdl"
+
+RDEPEND="gdl? ( dev-lang/gdl )"
+DEPEND="virtual/fortran"
+
+S="${WORKDIR}/${MYP}"
+
+FORTRAN_STANDARD="90"
+
+src_prepare() {
+	# save configure for tests
+	cp configure{,.orig}
+	# install data in FHS
+	sed -i \
+		-e "s:ZPEG_ROOT=.*:ZPEG_ROOT=${EPREFIX}/usr/share/${PN}:" \
+		configure || die
+}
+
+src_compile() {
+	# not worth debugging parallell build failures which is due to
+	# fortran modules missing dependencies)
+	emake -j1 -C src
+}
+
+src_test() {
+	# test only works with hardcoded path, so reconfigure and recompile
+	mv bin/zpeg{,.orig}
+	mv configure{.orig,}
+	emake -C src clean && econf && emake -j1 -C src
+	cd test
+	../bin/zpeg -V ZPEG1_cata.cat -o hdf.zpeg -p hdf.par -t hdf.par.tmp || die
+	mv bin/zpeg{.orig,}
+}
+
+src_install() {
+	dobin bin/zpeg
+	insinto /usr/share/${PN}
+	doins -r data VERSION
+	dodoc HISTORY
+	echo > 99zpeg "ZPEG_ROOT=${EROOT}/usr/share/${PN}"
+	doenvd 99zpeg
+	if use gdl; then
+		insinto /usr/share/gnudatalanguage/${PN}
+		doins idl/*.pro
+	fi
+}
diff --git a/sci-libs/atlas/ChangeLog b/sci-libs/atlas/ChangeLog
index edd02dbd7..22ed8b7a1 100644
--- a/sci-libs/atlas/ChangeLog
+++ b/sci-libs/atlas/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  27 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org>
+  +files/atlas-3.10.0-x32-support.patch, -files/atlas-3.10-x32-support.patch,
+  atlas-3.10.0.ebuild, metadata.xml:
+  sci-libs/atlas: added a generic flag for more generic architectures, and
+  possibility for user to pass configure options via standard EXTRA_ECONF flags
+
   16 Jul 2012; Olivier Huber <oli.huber@gmail.com>
   +files/atlas-3.10-x32-support.patch, -files/3.9.76-x32.patch,
   atlas-3.10.0.ebuild:
diff --git a/sci-libs/atlas/atlas-3.10.0.ebuild b/sci-libs/atlas/atlas-3.10.0.ebuild
index ea605c39e..e4f80bcd7 100644
--- a/sci-libs/atlas/atlas-3.10.0.ebuild
+++ b/sci-libs/atlas/atlas-3.10.0.ebuild
@@ -14,8 +14,8 @@ SRC_URI="mirror://sourceforge/math-atlas/${PN}${PV}.tar.bz2
 
 LICENSE="BSD"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="fortran doc lapack static-libs threads"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="fortran doc generic lapack static-libs threads"
 
 RDEPEND="fortran? ( virtual/fortran )"
 DEPEND="${RDEPEND}
@@ -34,7 +34,7 @@ pkg_setup() {
 				ewarn "Run cpufreq-set -r -g performance as root"
 				die "${PN} needs all cpu set to performance"
 			fi
-			cpu=$(( cpu + 1 ))
+			cpu=$((cpu + 1))
 		done
 	else
 		ewarn "Please make sure to disable CPU throttling completely"
@@ -47,7 +47,7 @@ pkg_setup() {
 }
 
 src_prepare() {
-	epatch "${FILESDIR}"/atlas-3.10-x32-support.patch
+	epatch "${FILESDIR}"/${P}-x32-support.patch
 }
 
 src_configure() {
@@ -69,7 +69,11 @@ src_configure() {
 		# OpenMP shown to decreased performance over POSIX threads
 		# (at least in 3.9.x, see atlas-dev mailing list)
 		if use threads; then
-			myconf+=( "-t -1" "-Si omp 0" )
+			if use generic; then # 2 threads is most generic
+				myconf+=( "-t 2" "-Si omp 0" )
+			else
+				myconf+=( "-t -1" "-Si omp 0" )
+			fi
 		else
 			myconf+=( "-t  0" "-Si omp 0" )
 		fi
@@ -107,6 +111,11 @@ src_configure() {
 		else
 			myconf+=( "-Si latune 0" "--nof77" )
 		fi
+		# generic stuff found by make make xprint_enums in atlas build dir
+		# basically assuming sse2+sse1 and 2 threads max
+		use generic && use x86   && myconf+=( "-V 384 -A 13")
+		use generic && use amd64 && myconf+=( "-V 384 -A 24")
+
 		local confdir="${S}_${1}"; shift
 		myconf+=( $@ )
 		mkdir "${confdir}" && cd "${confdir}"
@@ -115,8 +124,8 @@ src_configure() {
 		"${S}"/configure ${myconf[@]} || die "configure in ${confdir} failed"
 	}
 
-	atlas_configure shared "-Fa alg -fPIC"
-	use static-libs && atlas_configure static
+	atlas_configure shared "-Fa alg -fPIC" ${EXTRA_ECONF}
+	use static-libs && atlas_configure static ${EXTRA_ECONF}
 }
 
 src_compile() {
@@ -267,5 +276,5 @@ src_install() {
 	dodoc INDEX.txt AtlasCredits.txt ChangeLog
 	use doc && dodoc atlas*pdf cblas.pdf cblasqref.pdf
 	use doc && use fortran && dodoc f77blas*pdf
-	use doc && use fortran && use lapack && dodoc lapack*pdf
+	use doc && use fortran && use lapack && dodoc *lapack*pdf
 }
diff --git a/sci-libs/atlas/files/atlas-3.10-x32-support.patch b/sci-libs/atlas/files/atlas-3.10.0-x32-support.patch
index 82e698069..82e698069 100644
--- a/sci-libs/atlas/files/atlas-3.10-x32-support.patch
+++ b/sci-libs/atlas/files/atlas-3.10.0-x32-support.patch
diff --git a/sci-libs/atlas/metadata.xml b/sci-libs/atlas/metadata.xml
index 94634e439..4aeff0d55 100644
--- a/sci-libs/atlas/metadata.xml
+++ b/sci-libs/atlas/metadata.xml
@@ -10,4 +10,8 @@
    a subset of the linear algebra routine LAPACK library or the full
    LAPACK using the reference LAPACK from Netlib.
 </longdescription>
+<use>
+<flag name='generic'>Build atlas assuming a fairly generic
+architecture (sse2 for x86, core2 for amd64)</flag>
+</use>
 </pkgmetadata>
diff --git a/sci-mathematics/scilab/ChangeLog b/sci-mathematics/scilab/ChangeLog
index a47ca9861..9dedb9416 100644
--- a/sci-mathematics/scilab/ChangeLog
+++ b/sci-mathematics/scilab/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  28 Jul 2012; Guillaume Horel <guillaume.horel@gmail.com>
+  scilab-5.3.999.ebuild, -files/scilab-5.3.999-blas-libs.patch,
+  files/scilab-5.3.999-java-heap.patch:
+  live ebuild update
+
 *scilab-5.3.999 (11 Jul 2012)
 
   11 Jul 2012; Guillaume Horel <guillaume.horel@gmail.com>
diff --git a/sci-mathematics/scilab/files/scilab-5.3.999-blas-libs.patch b/sci-mathematics/scilab/files/scilab-5.3.999-blas-libs.patch
deleted file mode 100644
index b2921f708..000000000
--- a/sci-mathematics/scilab/files/scilab-5.3.999-blas-libs.patch
+++ /dev/null
@@ -1,12 +0,0 @@
- upstream http://bugzilla.scilab.org/show_bug.cgi?id=9824
-
---- scilab-5.3.2-orig/m4/libsmath.m4	2011-09-19 14:08:11.167292730 -0400
-+++ scilab-5.3.2/m4/libsmath.m4	2011-09-19 14:08:26.477292283 -0400
-@@ -37,7 +37,6 @@
- AC_PREREQ(2.50)
- AC_REQUIRE([AC_F77_LIBRARY_LDFLAGS])
- acx_blas_ok=no
--BLAS_LIBS=
- acx_blas_save_LIBS="$LIBS"
- 
- AC_ARG_WITH(blas-library,
diff --git a/sci-mathematics/scilab/files/scilab-5.3.999-java-heap.patch b/sci-mathematics/scilab/files/scilab-5.3.999-java-heap.patch
index e493a3bd1..5e4baae7e 100644
--- a/sci-mathematics/scilab/files/scilab-5.3.999-java-heap.patch
+++ b/sci-mathematics/scilab/files/scilab-5.3.999-java-heap.patch
@@ -1,5 +1,5 @@
---- scilab-5.3.3.orig//etc/jvm_options.xml	2011-05-25 23:20:12.145833420 -0400
-+++ scilab-5.3.3/etc/jvm_options.xml	2011-05-25 23:20:58.760833451 -0400
+--- scilab-orig/etc/jvm_options.xml	2011-05-25 23:20:12.145833420 -0400
++++ scilab/etc/jvm_options.xml	2011-05-25 23:20:58.760833451 -0400
 @@ -22,7 +22,7 @@
    <!-- ENABLE Just In Time java compiler -->
    <option value="-Djava.compiler=JIT"/>
diff --git a/sci-mathematics/scilab/scilab-5.3.999.ebuild b/sci-mathematics/scilab/scilab-5.3.999.ebuild
index 83f751844..6e74de41d 100644
--- a/sci-mathematics/scilab/scilab-5.3.999.ebuild
+++ b/sci-mathematics/scilab/scilab-5.3.999.ebuild
@@ -7,7 +7,7 @@ EAPI=4
 JAVA_PKG_OPT_USE="gui"
 VIRTUALX_REQUIRED="manual"
 
-inherit eutils autotools check-reqs eutils fdo-mime flag-o-matic \
+inherit eutils autotools check-reqs eutils fdo-mime flag-o-matic git-2\
 	java-pkg-opt-2 fortran-2 flag-o-matic toolchain-funcs virtualx
 
 # Comments:
@@ -26,7 +26,8 @@ inherit eutils autotools check-reqs eutils fdo-mime flag-o-matic \
 DESCRIPTION="Scientific software package for numerical computations"
 LICENSE="CeCILL-2"
 HOMEPAGE="http://www.scilab.org/"
-SRC_URI="http://guillaume.horel.free.fr/${P}.tar.gz"
+#SRC_URI="http://guillaume.horel.free.fr/${P}.tar.gz"
+EGIT_REPO_URI="git://git.scilab.org/scilab"
 
 SLOT="0"
 IUSE="bash-completion debug doc fftw +gui +matio nls openmp
@@ -68,7 +69,7 @@ CDEPEND="dev-libs/libpcre
 		>=dev-java/jrosetta-1.0.4:0
 		dev-java/scirenderer:0
 		dev-java/skinlf:0
-		dev-java/xmlgraphics-commons:1.3
+		dev-java/xmlgraphics-commons:1.5
 		virtual/opengl
 		doc? ( dev-java/saxon:6.5 )
 		xcos? ( dev-java/jgraphx:1.8 ) )
@@ -93,7 +94,8 @@ DEPEND="${CDEPEND}
 		dev-java/junit
 		gui? ( ${VIRTUALX_DEPEND} ) )"
 
-S="${WORKDIR}/${PN}"
+EGIT_SOURCEDIR="${WORKDIR}/${PN}"
+S="${WORKDIR}/${PN}/${PN}"
 DOCS=( "ACKNOWLEDGEMENTS" "README_Unix" "Readme_Visual.txt" )
 
 pkg_pretend() {
@@ -124,7 +126,6 @@ pkg_setup() {
 src_prepare() {
 	epatch \
 		"${FILESDIR}"/${P}-fortran-link.patch \
-		"${FILESDIR}"/${P}-blas-libs.patch \
 		"${FILESDIR}"/${P}-followlinks.patch \
 		"${FILESDIR}"/${P}-gluegen.patch
 
@@ -157,7 +158,7 @@ src_prepare() {
 	java-pkg_jar-from jgraphx-1.8,jlatexmath,hdf-java,flexdock,skinlf
 	java-pkg_jar-from jgoodies-looks-2.0,jrosetta,scirenderer
 	java-pkg_jar-from avalon-framework-4.2,saxon-6.5,jeuclid-core
-	java-pkg_jar-from xmlgraphics-commons-1.3,commons-io-1,jlatexmath-fop
+	java-pkg_jar-from xmlgraphics-commons-1.5,commons-io-1,jlatexmath-fop
 	java-pkg_jar-from jogl-2 jogl.all.jar jogl2.jar
 	java-pkg_jar-from gluegen-2 gluegen-rt.jar gluegen2-rt.jar
 	java-pkg_jar-from batik-1.7 batik-all.jar