Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

23 files changed, 823 insertions, 5 deletions

diff --git a/sci-libs/fftw/ChangeLog b/sci-libs/fftw/ChangeLog
new file mode 100644
index 000000000..5bac2521e
--- /dev/null
+++ b/sci-libs/fftw/ChangeLog
@@ -0,0 +1,18 @@
+# ChangeLog for sci-libs/fftw
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  07 Sep 2013; Christoph Junghans <ottxor@gentoo.org> fftw-3.3.3-r3.ebuild,
+  fftw-9999.ebuild:
+  final clean up
+
+  02 Sep 2013; Christoph Junghans <ottxor@gentoo.org> fftw-3.3.3-r3.ebuild,
+  fftw-9999.ebuild:
+  clean up
+
+*fftw-3.3.3-r3 (01 Sep 2013)
+*fftw-9999 (01 Sep 2013)
+
+  01 Sep 2013; Christoph Junghans <ottxor@gentoo.org> +fftw-3.3.3-r3.ebuild,
+  +fftw-9999.ebuild, +files/fftw-3.3.3-install-header.patch, +metadata.xml:
+  import from gx86
diff --git a/sci-libs/fftw/Manifest b/sci-libs/fftw/Manifest
new file mode 100644
index 000000000..2aab3f825
--- /dev/null
+++ b/sci-libs/fftw/Manifest
@@ -0,0 +1 @@
+DIST fftw-3.3.3.tar.gz 3920661 SHA256 85cdfc0a0ba10d8fa4f0f8e733aac1a5936c859832a9e3d5c0731fb5c54a97f3 SHA512 1d88b6376ba8c15cceafd3381de1d181a974b921b72b31dd89c297e5771e8d665aa3c121ef2504a70e7b0bb562b1e0612ac2a02121c412d27df06c4d687507c4 WHIRLPOOL b410cb4d854988f9a57f08344d9207ece4ebf218ec6fa605036235e472bef91f5037d852793fa6a7bc0f8a6a7081dc1e71b25b15ab1259e299bb95affca40d3b
diff --git a/sci-libs/fftw/fftw-3.3.3-r3.ebuild b/sci-libs/fftw/fftw-3.3.3-r3.ebuild
new file mode 100644
index 000000000..fb359955f
--- /dev/null
+++ b/sci-libs/fftw/fftw-3.3.3-r3.ebuild
@@ -0,0 +1,187 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/fftw/fftw-3.3.3-r2.ebuild,v 1.3 2013/06/27 14:30:29 aballier Exp $
+
+EAPI=5
+
+#AUTOTOOLS_AUTORECONF=1
+FORTRAN_NEEDED=fortran
+
+inherit autotools-multilib eutils flag-o-matic fortran-2 multibuild toolchain-funcs versionator
+
+DESCRIPTION="Fast C library for the Discrete Fourier Transform"
+HOMEPAGE="http://www.fftw.org/"
+
+if [[ ${PV} = *9999 ]]; then
+	inherit git-2
+	EGIT_REPO_URI="https://github.com/FFTW/fftw3.git"
+	KEYWORDS=""
+	AUTOTOOLS_AUTORECONF=1
+else
+	SRC_URI="http://www.fftw.org/${P}.tar.gz"
+	KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos"
+fi
+
+LICENSE="GPL-2"
+SLOT="3.0"
+IUSE="altivec avx doc fma fortran mpi neon openmp quad sse sse2 static-libs test threads zbus"
+
+RDEPEND="
+	mpi? ( virtual/mpi )
+	abi_x86_32? ( !<=app-emulation/emul-linux-x86-soundlibs-20130224-r2
+					!app-emulation/emul-linux-x86-soundlibs[-abi_x86_32(-)] )"
+DEPEND="${RDEPEND}
+	test? ( dev-lang/perl )"
+
+#can go once mpi is multlib
+MULTILIB_WRAPPED_HEADERS=(
+	/usr/include/fftw3-mpi.h
+	/usr/include/fftw3l-mpi.f03
+	/usr/include/fftw3-mpi.f03
+	/usr/include/fftw3q.f03
+)
+
+pkg_setup() {
+	# XXX: this looks like it should be used with BUILD_TYPE!=binary
+
+	if use openmp; then
+		if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
+			ewarn "OpenMP is not available in your current selected gcc"
+			die "need openmp capable gcc"
+		fi
+		FORTRAN_NEED_OPENMP=1
+	fi
+
+	fortran-2_pkg_setup
+
+	MULTIBUILD_VARIANTS=( single double longdouble )
+	if use quad; then
+		if [[ $(tc-getCC) == *gcc ]] && ! version_is_at_least 4.6 $(gcc-version); then
+			ewarn "quad precision only available for gcc >= 4.6"
+			die "need quad precision capable gcc"
+		fi
+		MULTIBUILD_VARIANTS+=( quad )
+	fi
+}
+
+src_prepare() {
+	# fix info file for category directory
+	[[ ${PV} = *9999 ]] || sed -i \
+		-e 's/Texinfo documentation system/Libraries/' \
+		doc/fftw3."info" || die "failed to fix info file"
+
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	local x
+
+	# filter -Os according to docs
+	replace-flags -Os -O2
+
+	my_configure() {
+		#a bit hacky improve after #483758 is solved
+		local x=${BUILD_DIR%-${ABI}}
+		x=${x##*-}
+		# there is no abi_x86_32 port of virtual/mpi right now
+		local enable_mpi=$(use_enable mpi)
+		multilib_is_native_abi || enable_mpi="--disable-mpi"
+
+		#jlec reported USE=quad on abi_x86_32 has too less registers
+		#stub Makefiles
+		if use amd64 && ! multilib_is_native_abi && [[ $x = quad ]]; then
+			mkdir -p "${BUILD_DIR}/tests" || die
+			echo "all: ;" > "${BUILD_DIR}/Makefile" || die
+			echo "install: ;" >> "${BUILD_DIR}/Makefile" || die
+			echo "smallcheck: ;" > "${BUILD_DIR}/tests/Makefile" || die
+			return 0
+		fi
+
+		myeconfargs=(
+			$(use_enable fma)
+			$(use_enable fortran)
+			$(use_enable zbus mips-zbus-timer)
+			$(use_enable threads)
+			$(use_enable openmp)
+		)
+		if [[ $x == single ]]; then
+			#altivec, sse, single-paired only work for single
+			myeconfargs+=(
+				--enable-single
+				$(use_enable altivec)
+				$(use_enable avx)
+				$(use_enable sse)
+				${enable_mpi}
+				$(use_enable neon)
+			)
+		elif [[ $x == double ]]; then
+			myeconfargs+=(
+				$(use_enable avx)
+				$(use_enable sse2)
+				${enable_mpi}
+			)
+		elif [[ $x == longdouble ]]; then
+			myeconfargs+=(
+				--enable-long-double
+				${enable_mpi}
+				)
+		elif [[ $x == quad ]]; then
+			#quad does not support mpi
+			myeconfargs+=( --enable-quad-precision )
+		else
+			die "${x} precision not implemented in this ebuild"
+		fi
+
+		autotools-utils_src_configure
+	}
+
+	multibuild_foreach_variant multilib_parallel_foreach_abi my_configure
+}
+
+src_compile() {
+	multibuild_foreach_variant autotools-multilib_src_compile
+}
+
+src_test () {
+	# We want this to be a reasonably quick test, but that is still hard...
+	ewarn "This test series will take 30 minutes on a modern 2.5Ghz machine"
+	# Do not increase the number of threads, it will not help your performance
+	#local testbase="perl check.pl --nthreads=1 --estimate"
+	#		${testbase} -${p}d || die "Failure: $n"
+	multibuild_foreach_variant autotools-multilib_src_compile -C tests smallcheck
+}
+
+src_install () {
+	local u x
+	DOCS=( AUTHORS ChangeLog NEWS README TODO COPYRIGHT CONVENTIONS )
+	HTML_DOCS=( doc/html/ )
+
+	#copied from autotools-multilib_secure_install
+	my_abi_src_install() {
+		autotools-utils_src_install
+		#https://github.com/FFTW/fftw3/pull/6
+		# f03 are installed unconditionally, not a big problem as the quad
+		# header is the only one to be wrapped.
+		[[ ${BUILD_DIR} = *-quad* ]] || rm -f "${ED}/usr/include/fftw3q.f03"
+		if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then
+			multilib_prepare_wrappers
+			multilib_check_headers
+		fi
+	}
+	multibuild_foreach_variant multilib_foreach_abi my_abi_src_install
+	multilib_install_wrappers
+
+	if use doc; then
+		dodoc doc/*.pdf
+		insinto /usr/share/doc/${PF}/faq
+		doins -r doc/FAQ/fftw-faq.html/*
+	else
+		rm -r "${ED}"/usr/share/doc/${PF}/html
+	fi
+
+	for x in "${ED}"/usr/lib*/pkgconfig/*.pc; do
+		for u in $(usev mpi) $(usev threads) $(usex openmp omp ""); do
+			sed -e "s|-lfftw3[flq]\?|&_$u &|" "$x" > "${x%.pc}_$u.pc" || die
+		done
+	done
+}
diff --git a/sci-libs/fftw/fftw-9999.ebuild b/sci-libs/fftw/fftw-9999.ebuild
new file mode 100644
index 000000000..fb359955f
--- /dev/null
+++ b/sci-libs/fftw/fftw-9999.ebuild
@@ -0,0 +1,187 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/fftw/fftw-3.3.3-r2.ebuild,v 1.3 2013/06/27 14:30:29 aballier Exp $
+
+EAPI=5
+
+#AUTOTOOLS_AUTORECONF=1
+FORTRAN_NEEDED=fortran
+
+inherit autotools-multilib eutils flag-o-matic fortran-2 multibuild toolchain-funcs versionator
+
+DESCRIPTION="Fast C library for the Discrete Fourier Transform"
+HOMEPAGE="http://www.fftw.org/"
+
+if [[ ${PV} = *9999 ]]; then
+	inherit git-2
+	EGIT_REPO_URI="https://github.com/FFTW/fftw3.git"
+	KEYWORDS=""
+	AUTOTOOLS_AUTORECONF=1
+else
+	SRC_URI="http://www.fftw.org/${P}.tar.gz"
+	KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos"
+fi
+
+LICENSE="GPL-2"
+SLOT="3.0"
+IUSE="altivec avx doc fma fortran mpi neon openmp quad sse sse2 static-libs test threads zbus"
+
+RDEPEND="
+	mpi? ( virtual/mpi )
+	abi_x86_32? ( !<=app-emulation/emul-linux-x86-soundlibs-20130224-r2
+					!app-emulation/emul-linux-x86-soundlibs[-abi_x86_32(-)] )"
+DEPEND="${RDEPEND}
+	test? ( dev-lang/perl )"
+
+#can go once mpi is multlib
+MULTILIB_WRAPPED_HEADERS=(
+	/usr/include/fftw3-mpi.h
+	/usr/include/fftw3l-mpi.f03
+	/usr/include/fftw3-mpi.f03
+	/usr/include/fftw3q.f03
+)
+
+pkg_setup() {
+	# XXX: this looks like it should be used with BUILD_TYPE!=binary
+
+	if use openmp; then
+		if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
+			ewarn "OpenMP is not available in your current selected gcc"
+			die "need openmp capable gcc"
+		fi
+		FORTRAN_NEED_OPENMP=1
+	fi
+
+	fortran-2_pkg_setup
+
+	MULTIBUILD_VARIANTS=( single double longdouble )
+	if use quad; then
+		if [[ $(tc-getCC) == *gcc ]] && ! version_is_at_least 4.6 $(gcc-version); then
+			ewarn "quad precision only available for gcc >= 4.6"
+			die "need quad precision capable gcc"
+		fi
+		MULTIBUILD_VARIANTS+=( quad )
+	fi
+}
+
+src_prepare() {
+	# fix info file for category directory
+	[[ ${PV} = *9999 ]] || sed -i \
+		-e 's/Texinfo documentation system/Libraries/' \
+		doc/fftw3."info" || die "failed to fix info file"
+
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	local x
+
+	# filter -Os according to docs
+	replace-flags -Os -O2
+
+	my_configure() {
+		#a bit hacky improve after #483758 is solved
+		local x=${BUILD_DIR%-${ABI}}
+		x=${x##*-}
+		# there is no abi_x86_32 port of virtual/mpi right now
+		local enable_mpi=$(use_enable mpi)
+		multilib_is_native_abi || enable_mpi="--disable-mpi"
+
+		#jlec reported USE=quad on abi_x86_32 has too less registers
+		#stub Makefiles
+		if use amd64 && ! multilib_is_native_abi && [[ $x = quad ]]; then
+			mkdir -p "${BUILD_DIR}/tests" || die
+			echo "all: ;" > "${BUILD_DIR}/Makefile" || die
+			echo "install: ;" >> "${BUILD_DIR}/Makefile" || die
+			echo "smallcheck: ;" > "${BUILD_DIR}/tests/Makefile" || die
+			return 0
+		fi
+
+		myeconfargs=(
+			$(use_enable fma)
+			$(use_enable fortran)
+			$(use_enable zbus mips-zbus-timer)
+			$(use_enable threads)
+			$(use_enable openmp)
+		)
+		if [[ $x == single ]]; then
+			#altivec, sse, single-paired only work for single
+			myeconfargs+=(
+				--enable-single
+				$(use_enable altivec)
+				$(use_enable avx)
+				$(use_enable sse)
+				${enable_mpi}
+				$(use_enable neon)
+			)
+		elif [[ $x == double ]]; then
+			myeconfargs+=(
+				$(use_enable avx)
+				$(use_enable sse2)
+				${enable_mpi}
+			)
+		elif [[ $x == longdouble ]]; then
+			myeconfargs+=(
+				--enable-long-double
+				${enable_mpi}
+				)
+		elif [[ $x == quad ]]; then
+			#quad does not support mpi
+			myeconfargs+=( --enable-quad-precision )
+		else
+			die "${x} precision not implemented in this ebuild"
+		fi
+
+		autotools-utils_src_configure
+	}
+
+	multibuild_foreach_variant multilib_parallel_foreach_abi my_configure
+}
+
+src_compile() {
+	multibuild_foreach_variant autotools-multilib_src_compile
+}
+
+src_test () {
+	# We want this to be a reasonably quick test, but that is still hard...
+	ewarn "This test series will take 30 minutes on a modern 2.5Ghz machine"
+	# Do not increase the number of threads, it will not help your performance
+	#local testbase="perl check.pl --nthreads=1 --estimate"
+	#		${testbase} -${p}d || die "Failure: $n"
+	multibuild_foreach_variant autotools-multilib_src_compile -C tests smallcheck
+}
+
+src_install () {
+	local u x
+	DOCS=( AUTHORS ChangeLog NEWS README TODO COPYRIGHT CONVENTIONS )
+	HTML_DOCS=( doc/html/ )
+
+	#copied from autotools-multilib_secure_install
+	my_abi_src_install() {
+		autotools-utils_src_install
+		#https://github.com/FFTW/fftw3/pull/6
+		# f03 are installed unconditionally, not a big problem as the quad
+		# header is the only one to be wrapped.
+		[[ ${BUILD_DIR} = *-quad* ]] || rm -f "${ED}/usr/include/fftw3q.f03"
+		if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then
+			multilib_prepare_wrappers
+			multilib_check_headers
+		fi
+	}
+	multibuild_foreach_variant multilib_foreach_abi my_abi_src_install
+	multilib_install_wrappers
+
+	if use doc; then
+		dodoc doc/*.pdf
+		insinto /usr/share/doc/${PF}/faq
+		doins -r doc/FAQ/fftw-faq.html/*
+	else
+		rm -r "${ED}"/usr/share/doc/${PF}/html
+	fi
+
+	for x in "${ED}"/usr/lib*/pkgconfig/*.pc; do
+		for u in $(usev mpi) $(usev threads) $(usex openmp omp ""); do
+			sed -e "s|-lfftw3[flq]\?|&_$u &|" "$x" > "${x%.pc}_$u.pc" || die
+		done
+	done
+}
diff --git a/sci-libs/fftw/files/fftw-3.3.3-install-header.patch b/sci-libs/fftw/files/fftw-3.3.3-install-header.patch
new file mode 100644
index 000000000..4456c189e
--- /dev/null
+++ b/sci-libs/fftw/files/fftw-3.3.3-install-header.patch
@@ -0,0 +1,35 @@
+From f450afa1cc0bb962abecfc1ffdbef8e1f7b748e4 Mon Sep 17 00:00:00 2001
+From: Christoph Junghans <ottxor@gentoo.org>
+Date: Sat, 31 Aug 2013 21:21:28 -0600
+Subject: [PATCH] Only install f03 header of the active precision
+
+---
+ api/Makefile.am | 11 ++++++++++-
+ 1 file changed, 10 insertions(+), 1 deletion(-)
+
+diff --git a/api/Makefile.am b/api/Makefile.am
+index e4eaad7..bb6c042 100644
+--- a/api/Makefile.am
++++ b/api/Makefile.am
+@@ -4,8 +4,17 @@ AM_CFLAGS = $(STACK_ALIGN_CFLAGS)
+ 
+ EXTRA_DIST = f03api.sh genf03.pl fftw3.f03.in
+ 
+-include_HEADERS = fftw3.h fftw3.f fftw3l.f03 fftw3q.f03
++include_HEADERS = fftw3.h fftw3.f
++noinst_HEADERS = fftw3l.f03 fftw3q.f03
++if LDOUBLE
++include_HEADERS += fftw3l.f03
++else
++if QUAD
++include_HEADERS += fftw3q.f03
++else
+ nodist_include_HEADERS = fftw3.f03
++endif
++endif
+ noinst_LTLIBRARIES = libapi.la
+ 
+ # pkgincludedir = $(includedir)/fftw3@PREC_SUFFIX@
+-- 
+1.8.1.5
+
diff --git a/sci-libs/fftw/metadata.xml b/sci-libs/fftw/metadata.xml
new file mode 100644
index 000000000..50e74c164
--- /dev/null
+++ b/sci-libs/fftw/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci</herd>
+  <longdescription lang="en">
+  The Fastest Fourier Transform in the West is a C subroutine library
+  for computing the Discrete Fourier Transform (DFT) in one or more
+  dimensions, of both real and complex data, and of arbitrary input
+  size. It is becoming the FFT library of choice for most
+  applications. Benchmarks, performed on a variety of platforms, show
+  that FFTW's performance is typically superior to that of other
+  publicly available FFT software.
+</longdescription>
+  <use>
+    <flag name="avx">Adds support for Advanced Vector Extensions</flag>
+    <flag name="fma">Use the Fused Multiply Add instruction set (fma3/fma4 either one)</flag>
+    <flag name="quad">Build quadruple precision lib</flag>
+    <flag name="zbus">Adds support for ZBus cycle-counter of mips</flag>
+  </use>
+  <upstream>
+    <remote-id type="freecode">fftw</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-libs/itk/ChangeLog b/sci-libs/itk/ChangeLog
new file mode 100644
index 000000000..618618847
--- /dev/null
+++ b/sci-libs/itk/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-libs/itk
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*itk-4.4.2 (12 Sep 2013)
+
+  12 Sep 2013; Sébastien Fabbro <bicatali@gentoo.org> +itk-4.4.2.ebuild,
+  -files/itk-4.4-v3compat_I2VI_const-fix.patch, -itk-4.4.0.ebuild, metadata.xml:
+  sci-libs/itk: Version bump. Cleaned-up ebuild and metadata.xml
diff --git a/sci-libs/itk/Manifest b/sci-libs/itk/Manifest
new file mode 100644
index 000000000..2a83eb01b
--- /dev/null
+++ b/sci-libs/itk/Manifest
@@ -0,0 +1 @@
+DIST InsightToolkit-4.4.2.tar.gz 231905134 SHA256 071a7929c295b80bc8a6ab80d50c06cdfb0e6aafd936103c6d0a4a086cf8bec3 SHA512 c65beca4dd60aa769871bb3089cbb421729a2dcbd8bd3ec42c378ed60828e4327f1faf062f77bcca34306315a1daee6bc29d858dab9aea1c08f4843405fd21e3 WHIRLPOOL 4036bce61d0900ef2f1484ca06e9b513f6154c2233122e41fe694c648dd6eef53510749bf75368f9851a4dbd45777ca7033ad43f28c86259d5efae9e0d4200bd
diff --git a/sci-libs/itk/itk-4.4.2.ebuild b/sci-libs/itk/itk-4.4.2.ebuild
new file mode 100644
index 000000000..542216b7e
--- /dev/null
+++ b/sci-libs/itk/itk-4.4.2.ebuild
@@ -0,0 +1,116 @@
+# Copyright 2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_5,2_6,2_7} )
+
+inherit eutils toolchain-funcs cmake-utils python-single-r1
+
+MYP=InsightToolkit-${PV}
+
+DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
+HOMEPAGE="http://www.itk.org"
+SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.gz"
+
+RESTRICT="primaryuri"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="debug examples fftw itkv3compat python review sse2 test"
+
+RDEPEND="
+	sci-libs/hdf5[cxx]
+	virtual/jpeg
+	media-libs/libpng
+	media-libs/tiff:0
+	sys-libs/zlib
+	fftw? ( sci-libs/fftw:3.0 )
+"
+DEPEND="${RDEPEND}
+	python? ( ${PYTHON_DEPS}
+			  >=dev-lang/swig-2.0
+			  >=dev-cpp/gccxml-0.9.0_pre20120309 )
+"
+
+S="${WORKDIR}/${MYP}"
+
+pkg_pretend() {
+	if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
+		elog "To tune ITK to make the best use ouf working memory you can set"
+		elog "    ITK_COMPUTER_MEMORY_SIZE=XX"
+		elog "in make.conf, default is 1 (unit is GB)"
+	fi
+	if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
+		elog "For Python language bindings, you can define the dimensions"
+		elog "you want to create bindings for by setting"
+		elog "    ITK_WRAP_DIMS=X;Y;Z..."
+		elog "in make.conf, default is 2;3 for 2D and 3D data"
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DWRAP_ITK_JAVA=OFF
+		-DWRAP_ITK_TCL=OFF
+		-DITK_USE_SYSTEM_HDF5=ON
+		-DITK_USE_SYSTEM_JPEG=ON
+		-DITK_USE_SYSTEM_PNG=ON
+		-DITK_USE_SYSTEM_TIFF=ON
+		-DITK_USE_SYSTEM_ZLIB=ON
+		-DITK_USE_SYSTEM_GCCXML=ON
+		-DITK_USE_SYSTEM_SWIG=ON
+		-DITK_BUILD_ALL_MODULES=ON
+		-DBUILD_SHARED_LIBS=ON
+		-DBUILD_EXAMPLES=OFF
+		-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
+		$(cmake-utils_use_build test TESTING)
+		$(cmake-utils_use review ITK_USE_REVIEW)
+		$(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY)
+		$(cmake-utils_use sse2 VNL_CONFIG_ENABLE_SSE2)
+	)
+	if use fftw; then
+		mycmakeargs+=(
+			-DUSE_FFTWD=ON
+			-DUSE_FFTWF=ON
+			-DUSE_SYSTEM_FFTW=ON
+			-DITK_WRAP_double=ON
+			-DITK_WRAP_vector_double=ON
+			-DITK_WRAP_covariant_vector_double=ON
+			-DITK_WRAP_complex_double=ON
+		)
+	fi
+	if use python; then
+		mycmakeargs+=(
+			-DITK_WRAP_PYTHON=ON
+			-DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
+		)
+	else
+		mycmakeargs+=(
+			-DITK_WRAP_PYTHON=OFF
+		)
+	fi
+	cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+
+	if use examples; then
+		insinto /usr/share/doc/${PF}/examples
+		docompress -x /usr/share/doc/${PF}/examples
+		doins -r "${S}"/Examples/*
+	fi
+
+	echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN}
+	local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit"
+	if use python; then
+		echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> ${T}/40${PN}
+		ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
+	fi
+	echo "LDPATH=${ldpath}" >> ${T}/40${PN}
+
+	doenvd "${T}"/40${PN}
+}
diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml
new file mode 100644
index 000000000..e941d4802
--- /dev/null
+++ b/sci-libs/itk/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+<maintainer>
+  <email>maintainer-wanted@gentoo.org</email>
+</maintainer>
+<longdescription lang="en">
+  Insight Segmentation and Registration Toolkit (ITK) is a library
+  that provides developers with an extensive suite of tools for image
+  analysis.
+</longdescription>
+<use>
+  <flag name="itkv3compat">Enable compatibility with ITK version 3</flag>
+  <flag name="review">Enable compilation of methods under review</flag>
+</use>
+</pkgmetadata>
+
diff --git a/sci-libs/modglue/ChangeLog b/sci-libs/modglue/ChangeLog
index 732b78492..eb811e97d 100644
--- a/sci-libs/modglue/ChangeLog
+++ b/sci-libs/modglue/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Sep 2013; François Bissey <francois.bissey@canterbury.ac.nz>
+  modglue-1.16.ebuild:
+  Fix PATCHES definition, it shouldn't include 'epatch'
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> modglue-1.16.ebuild,
   metadata.xml:
   Move to EPAI=5 and virtual/pkgconfig; clean usage of autotools-utils.eclass
@@ -39,4 +43,3 @@
 
   03 Apr 2009; Francois Bissey <f.r.bissey@massey.ac.nz> ChangeLog:
   Initial import for the science overlay
-
diff --git a/sci-libs/modglue/Manifest b/sci-libs/modglue/Manifest
index 05141a4d3..9c45f3be3 100644
--- a/sci-libs/modglue/Manifest
+++ b/sci-libs/modglue/Manifest
@@ -1 +1 @@
-DIST modglue-1.16.tar.gz 89987 SHA256 1da62910d7171cb5547c0757c366e5338f889c0155c33375e891df75e2ee429e
+DIST modglue-1.16.tar.gz 89987 SHA256 1da62910d7171cb5547c0757c366e5338f889c0155c33375e891df75e2ee429e SHA512 2ac93f771f99b33f6339ceb55ba95c034c37d84b3d8ee6a56a8c75e7b6129cf3a218adb5539df37da2c5f645983eb7c141c9716ad5c94699e2f44396609d7f2a WHIRLPOOL 39f399b30c3762fa6522444051f81bb8d484448681735e8e1c0d304f0f8ebc5e281853257dffc506ab3f864025cab373b608720e0645ed8397ec7fc2fe8625af
diff --git a/sci-libs/modglue/modglue-1.16.ebuild b/sci-libs/modglue/modglue-1.16.ebuild
index afabe76c7..ab4602cd4 100644
--- a/sci-libs/modglue/modglue-1.16.ebuild
+++ b/sci-libs/modglue/modglue-1.16.ebuild
@@ -25,12 +25,12 @@ AUTOTOOLS_IN_SOURCE_BUILD=1
 
 PATCHES=(
 	# Respect LDFLAGS
-	epatch "${FILESDIR}"/${P}-ldflags.patch
+	"${FILESDIR}"/${P}-ldflags.patch
 	# fix parallel make. test are made at the same time as the library??
-	epatch "${FILESDIR}"/${P}-parallelmake.patch
+	"${FILESDIR}"/${P}-parallelmake.patch
 	# take care of the lib/lib64 problem. Without this modglue installs
 	# stuff in /usr/usr/lib64 on 64bits systems.
-	epatch "${FILESDIR}"/${P}-lib64.patch
+	"${FILESDIR}"/${P}-lib64.patch
 )
 
 src_install() {
diff --git a/sci-libs/nibabel/metadata.xml b/sci-libs/nibabel/metadata.xml
new file mode 100644
index 000000000..7ffd788e6
--- /dev/null
+++ b/sci-libs/nibabel/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+	<email>h.chr@mail.ru</email>
+	<name>Horea Christian</name>
+</maintainer>
+<longdescription lang="en">
+	The package provides read and write access to some common medical and
+	neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI,
+	NIfTI1, MINC, MGH and ECAT as well as PAR/REC. It can read and write Freesurfer
+	geometry, and read Freesurfer morphometry and annotation files. There is some
+	very limited support for DICOM. NiBabel is the successor of PyNIfTI.
+</longdescription>
+<use>
+	<flag name="dicom">Adds limited read support for the DICOM imaging format.</flag>
+</use>
+</pkgmetadata>
diff --git a/sci-libs/nibabel/nibabel-9999.ebuild b/sci-libs/nibabel/nibabel-9999.ebuild
new file mode 100644
index 000000000..0070d0bfd
--- /dev/null
+++ b/sci-libs/nibabel/nibabel-9999.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="5"
+
+PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} )
+
+inherit distutils-r1 git-2
+
+DESCRIPTION="Access a cacophony of neuro-imaging file formats"
+HOMEPAGE="http://nipy.org/nibabel/"
+EGIT_REPO_URI="https://github.com/nipy/nibabel.git"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE="dicom doc test"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	dev-python/nose[${PYTHON_USEDEP}]
+	dicom? (
+		sci-libs/pydicom[${PYTHON_USEDEP}]
+		virtual/python-imaging[${PYTHON_USEDEP}]
+		)
+	"
+
+DEPEND="
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	test? ( ${RDEPEND} )
+	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
+	"
+
+python_test() {
+	distutils-r1_install_for_testing
+	cd "${BUILD_DIR}" || die
+	echo "backend: Agg" > matplotlibrc
+	MPLCONFIGDIR=. nosetests || die
+}
diff --git a/sci-libs/nipy/Manifest b/sci-libs/nipy/Manifest
new file mode 100644
index 000000000..e2730eee9
--- /dev/null
+++ b/sci-libs/nipy/Manifest
@@ -0,0 +1 @@
+DIST nipy-0.3.0.tar.gz 2143887 SHA256 74fef65c832795a35e1757d8bd852177fae190517a964afcb0812cfc1107d155 SHA512 3eaab4628bfa1706c99d516242387e1a27330bbf03b5b79da80d9a5e697b4e779f8f059e6f7bcc4253c5ad7af1bf6c600bcc5bd87db95d2e38f445d1f4416106 WHIRLPOOL 8a27c42abd8c7ae5ce66b8cfb0686b79e3208950107fcc5090d88fa2c23bf15d4ce4ae5b598f6f51c6e70122c40a343b9b7b2950ef09aefaeb22e24efd854af0
diff --git a/sci-libs/nipy/metadata.xml b/sci-libs/nipy/metadata.xml
new file mode 100644
index 000000000..ac599a834
--- /dev/null
+++ b/sci-libs/nipy/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+	<email>h.chr@mail.ru</email>
+	<name>Horea Christian</name>
+</maintainer>
+<longdescription lang="en">
+	NIPY is a python project for analysis of structural and functional neuroimaging data.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/nipy/nipy-0.3.0.ebuild b/sci-libs/nipy/nipy-0.3.0.ebuild
new file mode 100644
index 000000000..4d68e2a82
--- /dev/null
+++ b/sci-libs/nipy/nipy-0.3.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="5"
+
+PYTHON_COMPAT=( python{2_6,2_7,3_2} )
+DISTUTILS_NO_PARALLEL_BUILD=true
+
+inherit distutils-r1 eutils multilib flag-o-matic
+
+
+DESCRIPTION="Neuroimaging tools for Python"
+HOMEPAGE="http://nipy.org/"
+SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]"
+RDEPEND="${DEPEND}
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	dev-python/sympy[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]"
+
+python_prepare_all() {
+	distutils-r1_python_prepare_all
+	# bug #397605
+	[[ ${CHOST} == *-darwin* ]] \
+		&& append-ldflags -bundle "-undefined dynamic_lookup" \
+		|| append-ldflags -shared
+
+	# nipy uses the horrible numpy.distutils automagic
+}
diff --git a/sci-libs/nipy/nipy-9999.ebuild b/sci-libs/nipy/nipy-9999.ebuild
new file mode 100644
index 000000000..6d752cbde
--- /dev/null
+++ b/sci-libs/nipy/nipy-9999.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_image/scikits_image-0.8.2.ebuild,v 1.3 2013/06/18 04:33:25 patrick Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7,3_2} )
+DISTUTILS_NO_PARALLEL_BUILD=true
+
+inherit distutils-r1 multilib git-2 flag-o-matic
+
+DESCRIPTION="Neuroimaging tools for Python"
+HOMEPAGE="http://nipy.org/"
+EGIT_REPO_URI="https://github.com/nipy/nipy"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE=""
+KEYWORDS=""
+
+DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]"
+RDEPEND="${DEPEND}
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	dev-python/sympy[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]"
+
+python_prepare_all() {
+	distutils-r1_python_prepare_all
+	# bug #397605
+	[[ ${CHOST} == *-darwin* ]] \
+		&& append-ldflags -bundle "-undefined dynamic_lookup" \
+		|| append-ldflags -shared
+
+	# nipy uses the horrible numpy.distutils automagic
+}
diff --git a/sci-libs/nipype/metadata.xml b/sci-libs/nipype/metadata.xml
new file mode 100644
index 000000000..d41e11fc9
--- /dev/null
+++ b/sci-libs/nipype/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+	<email>h.chr@mail.ru</email>
+	<name>Horea Christian</name>
+</maintainer>
+<longdescription lang="en">
+	Nipype, an open-source, community-developed initiative under the
+	umbrella of NiPy, is a Python project that provides a uniform interface
+	to existing neuroimaging software and facilitates interaction between
+	these packages within a single workflow. Nipype provides an environment
+	that encourages interactive exploration of algorithms from different
+	packages (e.g., SPM, FSL, FreeSurfer, Camino, MRtrix, MNE, AFNI, Slicer),
+	eases the design of workflows within and between packages, and reduces
+	the learning curve necessary to use different packages. Nipype is
+	creating a collaborative platform for neuroimaging software development
+	in a high-level language and addressing limitations of existing pipeline systems.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/nipype/nipype-9999.ebuild b/sci-libs/nipype/nipype-9999.ebuild
new file mode 100644
index 000000000..7afb3b5f0
--- /dev/null
+++ b/sci-libs/nipype/nipype-9999.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_image/scikits_image-0.8.2.ebuild,v 1.3 2013/06/18 04:33:25 patrick Exp $
+
+EAPI=5
+
+# pyamg missing py3 support
+# PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} )
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1 git-2
+
+DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
+HOMEPAGE="http://nipy.sourceforge.net/nipype/"
+EGIT_REPO_URI="https://github.com/nipy/nipype"
+
+LICENSE="BSD"
+SLOT="0"
+
+DEPEND="
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]"
+RDEPEND="
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	dev-python/traits[${PYTHON_USEDEP}]
+	dev-python/networkx[${PYTHON_USEDEP}]"
+
+python_test() {
+	nosetests -v || die
+}
+
+
diff --git a/sci-libs/pydicom/Manifest b/sci-libs/pydicom/Manifest
new file mode 100644
index 000000000..c6ce98860
--- /dev/null
+++ b/sci-libs/pydicom/Manifest
@@ -0,0 +1 @@
+DIST pydicom-0.9.8.zip 466418 SHA256 d73852cd6f2a0f95c5bd096806ca517f3c152f117638528dcbf7527793853141 SHA512 baba1963069caebd5f124e545356f07993733b4bd2e11d06e22b57b796bb48ad21734a72c0b4ced8e5607b40047ccc929886e449c956047cb293e5fb27038cbe WHIRLPOOL fba24f994ea76ab13bfa6432ba69afd61ca250c1f05573782d660b7c1b0db9aadfa15d6bce5a4a26b38f8cbdce7db16b1d00857f8f1bc4e54190217a8bedaa97
diff --git a/sci-libs/pydicom/pydicom-0.9.8.ebuild b/sci-libs/pydicom/pydicom-0.9.8.ebuild
new file mode 100644
index 000000000..1a31eb262
--- /dev/null
+++ b/sci-libs/pydicom/pydicom-0.9.8.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="A pure python package for parsing DICOM files"
+HOMEPAGE="https://code.google.com/p/pydicom/"
+SRC_URI="https://pydicom.googlecode.com/files/${P}.zip"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND=""
+DEPEND=""