Version bump

Package-Manager: portage-2.2.01.21688-prefix/cvs/Linux x86_64
Manifest-Sign-Key: 0x13CB1360

4 files changed, 213 insertions, 36 deletions

diff --git a/sci-libs/shogun/ChangeLog b/sci-libs/shogun/ChangeLog
index 70fc401cdb6b..f2f081c901f1 100644
--- a/sci-libs/shogun/ChangeLog
+++ b/sci-libs/shogun/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/shogun
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/ChangeLog,v 1.5 2013/02/21 21:24:38 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/ChangeLog,v 1.6 2013/03/03 07:14:13 bicatali Exp $
+
+*shogun-2.0.0 (03 Mar 2013)
+
+  03 Mar 2013; Sébastien Fabbro <bicatali@gentoo.org> +shogun-2.0.0.ebuild,
+  metadata.xml:
+  Version bump
 
   21 Feb 2013; Justin Lecher <jlec@gentoo.org> shogun-1.1.0.ebuild,
   metadata.xml:
diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
index 1f20adfa9ebb..2ad0c2de8dcc 100644
--- a/sci-libs/shogun/Manifest
+++ b/sci-libs/shogun/Manifest
@@ -1,19 +1,22 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
+Hash: SHA256
 
 AUX shogun-1.1.0-as-needed.patch 2137 SHA256 de8bb8e6f42873b0fbc3c4f816869684b93d0ecceb6ea6db7c77e9e86bf79617 SHA512 c755d1f557eecd433ff8b2394ebb5d9687a5482ea081f2c9dd174492f5ab24f5bc4d50665491f40dbc01f8db1c6f5eec63c2e869f3f1ee3395e6587b227ef57a WHIRLPOOL 22421d20f345e3a8141d76fd6e0beebee32c9e1a0006f95331a3aaa2ef1736ddc18e5b0e3996ce42d0e9a540c8a91356832c7f84d6889edcb438769117a1f758
 AUX shogun-1.1.0-respect-ldflags.patch 332 SHA256 596e37d9bac7904808cf5cd58221f97f3ce3e583aed58697b4a4f995c9dd0eff SHA512 496a5dfd0da302fd333651e6e363bd01ecc6dcc6ec06f2589f8dc3d42999936817f41144f9814717d311e47611a31b2cb57bee7d46df30ea20c8afe909f5f376 WHIRLPOOL c7d3701e573be10157432352263df70905c4f720d7767361487742bcb925c25cb39d4252f165db4368d0599079756907192b28f7237be1f13a3564cc910ac7cf
 AUX shogun-1.1.0-test-readline.patch 352 SHA256 a8e0ecc78bf702bdfb8193fc94abd7745e8bfcee0fe1e6b4ba5efeac4c6df0cc SHA512 6963b8e66361b02b894d48e5b8b2dbc15b4569947ba5be7db56c4aeff142f2c949583cfbbc713cc5900815072e80999dd804f8a342011247b34c7ac30db0fd86 WHIRLPOOL f22f31a231a56f4d805539388ae96e4742f7bf99a0a49887daefad14bb1d13454e800050528df48b5bed0e5db51dd9d867812e148ec4e5533fd8b19758541bdf
 AUX shogun-1.1.0-test-snappy.patch 506 SHA256 ef0489b05cd1dd494c4a9b5070277dbd7733b920cfcf045e87d6abcbd871f01f SHA512 04b4f29ec7d23377fb31474c9ef9c7d243b8ed9ef8e81c6340462763a4dc6ac6361c4e067d680089192ccd5bf5d50ffc2fca6087d74e17341c9b4ae858851096 WHIRLPOOL 302365d7ecd2ed235536a886a3ff1d2834bf51885e4acd4dd0d2a581e8776c7cdcee8632a8470c6b2df969df7fe0cba1d5574c7c870323a866825a0235eb0b76
 DIST shogun-1.1.0.tar.bz2 3485714 SHA256 9f69638f0bc18995358c38cd6eed6437e6b90c1fceab7c6e64c9739b7e6cc40b SHA512 853168e3d68ad02ef543391b78c51682d004af46acddfa09a76b41e373e27199fc9be0598892207e116a82f24437e3f1c0dc97c3e28ca32879594fbe112bd157 WHIRLPOOL dd044ff2cc9fd9376b80f1efd9bbcf901b11765a2f85eb2325ddd640ea547e513df8c9da548634e49758ef124147666f86b6b4082e118c6d35ef2d5010527cf9
+DIST shogun-2.0.0.tar.bz2 4106437 SHA256 b18e30515b9f4432d02602d0dd66dbc57c70a46f71636275071afaee94e245ee SHA512 e7c8d515afbcb3198aade32d2962e8d94b669b9c79ddbcd7425f04bbb0379803f7353c50ba8897356842cddb401d303fefaf8a7f9dd6a2e751e176deba1e46f1 WHIRLPOOL aa9ef89f28acc012ee2894c4ff6858f7bf01585d02160d5b2df33159c7c87593ea352833765a7a78cc0ed16fd10713d285eb711606f0e3771ec685778f703570
 DIST shogun-data-0.3.tar.bz2 126676026 SHA256 34272e3f5e6b6989a4941b925ab3a9cd1525d73180681884e948a673aff4ef89 SHA512 92c7e7dae1df5a7a79428a7f2116b1d9d825a37d4145edfdff1fb7b707853eab19ffe848c4ae2bc2338a93373e78c7cae4087df260411a9576b031e7a6f0de95 WHIRLPOOL 24987580c967b05e61ee5402fe30701cabe17d7ffb29b4966ff0abd0d03e197b928f018e617e254395c6939f93de3e397f5ce7df7c3d4ae7dfe4e782c345fe85
+DIST shogun-data-0.4.tar.bz2 127377123 SHA256 103ef944c7211f64957833cd6ace85e32629d73ef286273424e239fa454ecfcc SHA512 c178f6d5d8e4b6b6a94b74da5c133b01e83a1d4c7bf5d0fd66b4812b259934dbc998cfc1ef64f19b17b5099e8c389b8e359e69f1cc1bef6b82b940dc97cac46d WHIRLPOOL cef5d84f342523bad8b810fa3018669e9cd838c7c45bb37b8e7308dce448dc9b98f9aa6716aa724d64746539ef9c041a71cd2f3a1af71ed1077d276a192573d5
 EBUILD shogun-1.1.0.ebuild 4480 SHA256 f7231e45448652f2e983811e8d36b8a7566d03121b5a7ba005a444c3dfd73c5d SHA512 cf28663e5b959bbe687ac0dcf31075bcb7959df4e70a808dff7f7a1e8f013f7c769926a39afdfe0db21cd25b6a2b5cf4687edcc67359b3c140fe62db8b8feed9 WHIRLPOOL cc20a34f43dfe3ba7d8ab4872cdd52eb30c3b133f38a3f5ae6050a08f0a43b98e8fd07906bd21be418399acc24f49402473c661e48c4c92660b517de96510019
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+EBUILD shogun-2.0.0.ebuild 4701 SHA256 01f52a5addee634960a6154c49fa308cc04fd5b1ab5f635237437dd9f19d9b43 SHA512 84b95f71beeb4078d3bd46f1774bd00c4833fcee611f3eb69b06d7df77a6113ed05356bb92b9ef37a8c6359a33455941b0e8c86cdf4af122da2d47bf17c999a8 WHIRLPOOL 1fd8d763ea4d747f230e65c11185a95be30df78ccfe107a67bd40d408309434e3357cf7afc37a6e7cc44c495337437ba556f544028071f82f5d9382f186edf3a
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diff --git a/sci-libs/shogun/metadata.xml b/sci-libs/shogun/metadata.xml
index 5722adc1ff45..70e3e2616088 100644
--- a/sci-libs/shogun/metadata.xml
+++ b/sci-libs/shogun/metadata.xml
@@ -1,34 +1,37 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <herd>sci</herd>
-  <longdescription lang="en">
-   SHOGUN - is a new machine learning toolbox with focus on large
-   scale kernel methods and especially on Support Vector Machines
-   (SVM) with focus to bioinformatics. It provides a generic SVM
-   object interfacing to several different SVM implementations. Each
-   of the SVMs can be combined with a variety of the many kernels
-   implemented. It can deal with weighted linear combination of a
-   number of sub-kernels, each of which not necessarily working on the
-   same domain, where  an optimal sub-kernel weighting can be learned
-   using Multiple Kernel Learning.  Apart from SVM 2-class
-   classification and regression problems, a number of linear methods
-   like Linear Discriminant Analysis (LDA), Linear Programming Machine
-   (LPM), (Kernel) Perceptrons and also algorithms to train hidden
-   markov models are implemented. The input feature-objects can be
-   dense, sparse or strings and of type int/short/double/char and can
-   be converted into different feature types. Chains of preprocessors
-   (e.g. substracting the mean) can be attached to each feature object
-   allowing for on-the-fly pre-processing.
+<herd>sci</herd>
+<longdescription lang="en">
+  SHOGUN - is a new machine learning toolbox with focus on large
+  scale kernel methods and especially on Support Vector Machines
+  (SVM) with focus to bioinformatics. It provides a generic SVM
+  object interfacing to several different SVM implementations. Each
+  of the SVMs can be combined with a variety of the many kernels
+  implemented. It can deal with weighted linear combination of a
+  number of sub-kernels, each of which not necessarily working on the
+  same domain, where  an optimal sub-kernel weighting can be learned
+  using Multiple Kernel Learning.  Apart from SVM 2-class
+  classification and regression problems, a number of linear methods
+  like Linear Discriminant Analysis (LDA), Linear Programming Machine
+  (LPM), (Kernel) Perceptrons and also algorithms to train hidden
+  markov models are implemented. The input feature-objects can be
+  dense, sparse or strings and of type int/short/double/char and can
+  be converted into different feature types. Chains of preprocessors
+  (e.g. substracting the mean) can be attached to each feature object
+  allowing for on-the-fly pre-processing.
 </longdescription>
-  <use>
-    <flag name="arpack">Enable support for <pkg>sci-libs/arpack</pkg></flag>
-    <flag name="glpk">Enable support for <pkg>sci-mathematics/glpk</pkg></flag>
-    <flag name="json">Enable support for parsing JSON format</flag>
-    <flag name="lpsolve">Enable support for Linear Programming Solver</flag>
-    <flag name="R">Enable support for <pkg>dev-lang/R</pkg></flag>
-    <flag name="octave">Enable support for <pkg>sci-mathematics/octave</pkg></flag>
-    <flag name="snappy">Enable support for snappy compression</flag>
-    <flag name="superlu">Enable support for <pkg>sci-libs/superlu</pkg></flag>
-  </use>
+<use>
+  <flag name="arpack">Enable support for <pkg>sci-libs/arpack</pkg></flag>
+  <flag name="eigen">Enable support for matrix package <pkg>dev-cpp/eigen</pkg></flag>
+  <flag name="glpk">Enable support for <pkg>sci-mathematics/glpk</pkg></flag>
+  <flag name="json">Enable support for parsing JSON format</flag>
+  <flag name="lpsolve">Enable support for Linear Programming Solver</flag>
+  <flag name="nlopt">Enable support non linear optimization from
+  <pkg>sci-libs/nlopt</pkg></flag>
+  <flag name="R">Enable support for <pkg>dev-lang/R</pkg></flag>
+  <flag name="octave">Enable support for <pkg>sci-mathematics/octave</pkg></flag>
+  <flag name="snappy">Enable support for snappy compression</flag>
+  <flag name="superlu">Enable support for <pkg>sci-libs/superlu</pkg></flag>
+</use>
 </pkgmetadata>
diff --git a/sci-libs/shogun/shogun-2.0.0.ebuild b/sci-libs/shogun/shogun-2.0.0.ebuild
new file mode 100644
index 000000000000..390797c5afb2
--- /dev/null
+++ b/sci-libs/shogun/shogun-2.0.0.ebuild
@@ -0,0 +1,165 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/shogun-2.0.0.ebuild,v 1.1 2013/03/03 07:14:13 bicatali Exp $
+
+EAPI=5
+
+inherit eutils multilib versionator toolchain-funcs java-pkg-opt-2 flag-o-matic
+
+MYPV=$(get_version_component_range 1-2)
+MYPD=${PN}-data-0.4
+
+DESCRIPTION="Large Scale Machine Learning Toolbox"
+HOMEPAGE="http://shogun-toolbox.org/"
+SRC_URI="ftp://shogun-toolbox.org/shogun/releases/${MYPV}/sources/${P}.tar.bz2
+	test? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )
+	examples? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )"
+
+LICENSE="GPL-3 free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="arpack bzip2 doc eigen examples glpk gzip hdf5 json lapack lpsolve mono lua lzma
+	lzo nlopt java R ruby octave python readline smp snappy static-libs superlu test xml"
+
+RDEPEND="
+	sci-libs/gsl
+	sys-libs/zlib
+	arpack? ( sci-libs/arpack )
+	bzip2? ( app-arch/bzip2 )
+	eigen? ( >=dev-cpp/eigen-3 )
+	glpk? ( sci-mathematics/glpk )
+	gzip? ( app-arch/gzip )
+	hdf5? ( sci-libs/hdf5 )
+	java? ( >=virtual/jdk-1.5 )
+	json? ( dev-libs/json-c )
+	lapack? ( virtual/cblas virtual/lapack )
+	lpsolve? ( sci-mathematics/lpsolve )
+	lua? ( dev-lang/lua )
+	lzo? ( dev-libs/lzo )
+	mono? ( dev-lang/mono )
+	nlopt? ( sci-libs/nlopt )
+	octave? ( sci-mathematics/octave[hdf5=] )
+	python? ( dev-python/numpy )
+	R? ( dev-lang/R )
+	readline? ( sys-libs/readline )
+	ruby? ( >=dev-ruby/narray-0.6.0.1-r2 )
+	snappy? ( app-arch/snappy )
+	superlu? ( sci-libs/superlu )
+	xml? ( dev-libs/libxml2 )"
+
+DEPEND="${RDEPEND}
+	virtual/pkgconfig
+	doc? ( app-doc/doxygen[dot] )
+	java? ( >=dev-lang/swig-2.0.4 dev-java/ant )
+	octave? ( >=dev-lang/swig-2.0.4 )
+	python? ( >=dev-lang/swig-2.0.4 test? ( sci-libs/scipy ) )
+	ruby? ( >=dev-lang/swig-2.0.4 )"
+
+S="${WORKDIR}/${P}/src"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PN}-1.1.0-respect-ldflags.patch \
+		"${FILESDIR}"/${PN}-1.1.0-test-readline.patch \
+		"${FILESDIR}"/${PN}-1.1.0-as-needed.patch
+
+	# dist-packages is only for debian
+	# remove exagarated optimizations (-O9 does not exist...)
+	# use gentoo lapack framework
+	sed -i \
+		-e 's/dist-packages/site-packages/g' \
+		-e '/^COMP_OPTS=/d' \
+		-e "s:-llapack -lcblas:$($(tc-getPKG_CONFIG) --libs cblas lapack):g" \
+		configure || die
+
+	# disable ldconfig which violates sandbox
+	# install in gentoo java standard paths
+	sed -i \
+		-e '/ldconfig/d' \
+		-e '/share\/java/d' \
+		-e '/jni/d' \
+		-e 's/OCTAVE_LOADPATH/OCTAVE_PATH/g' \
+		Makefile.template || die
+}
+
+src_configure() {
+	# define interfaces to shogun library to build
+	local x iface
+	for x in java lua octave python ruby ; do
+		use ${x} && iface="${iface}${x}_modular,"
+	done
+	use mono &&	iface="${iface}csharp_modular,"
+	use R && iface="${iface}r_modular,"
+	if use static-libs; then
+		iface="${iface}cmdline_static,"
+		use octave && iface="${iface}octave_static,"
+		use python && iface="${iface}python_static,"
+		use R && iface="${iface}r_static,"
+		use octave && use python && use R && iface="${iface}elwms_static,"
+	fi
+	iface="${iface%,}"
+
+	# gentoo bug #302621
+	use hdf5 && has_version sci-libs/hdf5[mpi] && export CXX=mpicxx CC=mpicc
+	use smp && append-ldflags -pthread
+	./configure \
+		--disable-cpudetection \
+		--destdir="${D}" \
+		--prefix="${EPREFIX}/usr" \
+		--mandir="${EPREFIX}/usr/share/man" \
+		--libdir="${EPREFIX}/usr/$(get_libdir)" \
+		--cc="$(tc-getCC)" \
+		--cxx="$(tc-getCXX)" \
+		--target="${CTARGET}" \
+		--interfaces=${iface} \
+		$(use_enable arpack) \
+		$(use_enable bzip2) \
+		$(use_enable doc doxygen) \
+		$(use_enable eigen eigen3) \
+		$(use_enable glpk) \
+		$(use_enable gzip) \
+		$(use_enable hdf5) \
+		$(use_enable json) \
+		$(use_enable lapack) \
+		$(use_enable lpsolve) \
+		$(use_enable lzma) \
+		$(use_enable lzo) \
+		$(use_enable nlopt) \
+		$(use_enable readline) \
+		$(use_enable smp hmm-parallel) \
+		$(use_enable snappy) \
+		$(use_enable static-libs static) \
+		$(use_enable superlu) \
+		$(use_enable xml) || die
+}
+
+src_compile() {
+	emake
+	use doc && emake -C ../doc
+}
+
+src_test() {
+	use lapack || return
+	ln -s ../../${MYPD}/* ../data/
+	emake DESTDIR="${D}" install
+	# disable because very long
+	# emake tests
+	emake -C shogun check-examples
+}
+
+src_install() {
+	default
+	use static-libs || rm "${ED}"/usr/$(get_libdir)/*.a
+	if use java; then
+		java-pkg_dojar interfaces/java_modular/shogun.jar
+		java-pkg_doso interfaces/java_modular/libmodshogun.so
+	fi
+
+	use doc && dohtml -r ../doc/html/*
+	if use examples; then
+		insinto /usr/share/doc/${PF}
+		emake -C ../examples clean && doins -r ../examples
+		insinto /usr/share/doc/${PF}/data
+		doins -r "${WORKDIR}"/${MYPD}/*
+	fi
+}