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authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2015-01-15 10:55:55 +0100
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2015-01-15 10:55:55 +0100
commit5f86af85e0004ac47a3fed36ca1c8c92bd77160a (patch)
treef3d5cf5033c2e8956e28071114133fe3a14d2b11
parent version bump, masking a crappy package until at least the Makefile's propaga... (diff)
parentMerge remote-tracking branch 'github/master' (diff)
downloadsci-5f86af85e0004ac47a3fed36ca1c8c92bd77160a.tar.gz
sci-5f86af85e0004ac47a3fed36ca1c8c92bd77160a.tar.bz2
sci-5f86af85e0004ac47a3fed36ca1c8c92bd77160a.zip
Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-rw-r--r--dev-python/astropy-helpers/ChangeLog5
l---------[-rw-r--r--]dev-python/astropy-helpers/astropy-helpers-0.4.1.ebuild29
-rw-r--r--dev-python/astropy-helpers/metadata.xml4
-rw-r--r--dev-python/astropy/ChangeLog5
-rw-r--r--licenses/Mendeley-terms220
-rw-r--r--sci-libs/arrayfire/arrayfire-9999.ebuild2
-rw-r--r--sci-libs/dealii/ChangeLog8
-rw-r--r--sci-libs/dealii/Manifest2
l---------sci-libs/dealii/dealii-8.2.0.ebuild2
-rw-r--r--sci-libs/dealii/dealii-8.2.1.ebuild127
-rw-r--r--sci-libs/dealii/dealii-9999.ebuild7
-rw-r--r--sci-libs/libspatialindex/Manifest2
-rw-r--r--sci-libs/libspatialindex/files/libspatialindex-1.8.1-QA.patch15
-rw-r--r--sci-libs/libspatialindex/libspatialindex-1.6.1.ebuild19
-rw-r--r--sci-libs/libspatialindex/libspatialindex-1.8.5.ebuild37
-rw-r--r--sci-libs/libspatialindex/metadata.xml6
-rw-r--r--sci-misc/kaldi/ChangeLog10
-rw-r--r--sci-misc/kaldi/files/Makefile.patch19
-rw-r--r--sci-misc/kaldi/files/configure.patch71
-rw-r--r--sci-misc/kaldi/files/default_rules.mk.patch20
-rw-r--r--sci-misc/kaldi/kaldi-0_p20150101.ebuild59
-rw-r--r--sci-misc/kaldi/metadata.xml12
-rw-r--r--sci-misc/mendeleydesktop/ChangeLog14
-rw-r--r--sci-misc/mendeleydesktop/Manifest2
-rw-r--r--sci-misc/mendeleydesktop/mendeleydesktop-1.13.1.ebuild114
-rw-r--r--sci-misc/mendeleydesktop/metadata.xml9
26 files changed, 759 insertions, 61 deletions
diff --git a/dev-python/astropy-helpers/ChangeLog b/dev-python/astropy-helpers/ChangeLog
index c9fe2fc79..2c9ea827b 100644
--- a/dev-python/astropy-helpers/ChangeLog
+++ b/dev-python/astropy-helpers/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for dev-python/astropy-helpers
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 14 Jan 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ Symlink
+
*astropy-helpers-0.4.1 (08 Aug 2014)
*astropy-helpers-9999 (08 Aug 2014)
diff --git a/dev-python/astropy-helpers/astropy-helpers-0.4.1.ebuild b/dev-python/astropy-helpers/astropy-helpers-0.4.1.ebuild
index f23588953..79b8b4c43 100644..120000
--- a/dev-python/astropy-helpers/astropy-helpers-0.4.1.ebuild
+++ b/dev-python/astropy-helpers/astropy-helpers-0.4.1.ebuild
@@ -1,28 +1 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} )
-inherit distutils-r1
-
-if [ ${PV} == "9999" ] ; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/astropy/${PN}.git"
-else
- SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
- KEYWORDS="~amd64"
-fi
-
-DESCRIPTION="Helpers for Astropy and Affiliated packages"
-HOMEPAGE="https://github.com/astropy/astropy-helpers"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE=""
-
-python_prepare_all() {
- sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
- distutils-r1_python_prepare_all
-}
+astropy-helpers-9999.ebuild \ No newline at end of file
diff --git a/dev-python/astropy-helpers/metadata.xml b/dev-python/astropy-helpers/metadata.xml
index 9f38fc355..bacda05a5 100644
--- a/dev-python/astropy-helpers/metadata.xml
+++ b/dev-python/astropy-helpers/metadata.xml
@@ -1,8 +1,8 @@
<?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">
+ <herd>sci-astronomy</herd>
+ <longdescription lang="en">
astropy-helpers is a collection of build tools used by astropy
that may be used by other projects.
</longdescription>
diff --git a/dev-python/astropy/ChangeLog b/dev-python/astropy/ChangeLog
index 8526d7c81..5b8636c22 100644
--- a/dev-python/astropy/ChangeLog
+++ b/dev-python/astropy/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for dev-python/astropy
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 15 Jan 2015; Justin Lecher <jlec@gentoo.org> ChangeLog:
+ Symlink
+
11 Aug 2014; Joseph Jon Booker <joe@neoturbine.net> astropy-9999.ebuild:
dev-python/astropy: Fix python deps
diff --git a/licenses/Mendeley-terms b/licenses/Mendeley-terms
new file mode 100644
index 000000000..e4e3e32c4
--- /dev/null
+++ b/licenses/Mendeley-terms
@@ -0,0 +1,220 @@
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diff --git a/sci-libs/arrayfire/arrayfire-9999.ebuild b/sci-libs/arrayfire/arrayfire-9999.ebuild
index f59d7e381..352a81483 100644
--- a/sci-libs/arrayfire/arrayfire-9999.ebuild
+++ b/sci-libs/arrayfire/arrayfire-9999.ebuild
@@ -82,5 +82,5 @@ src_configure() {
src_install() {
cmake-utils_src_install
- dobin "bin2cpp"
+ dobin "${BUILD_DIR}/bin2cpp"
}
diff --git a/sci-libs/dealii/ChangeLog b/sci-libs/dealii/ChangeLog
index 40e7c6894..47c62f19b 100644
--- a/sci-libs/dealii/ChangeLog
+++ b/sci-libs/dealii/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-libs/dealii
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*dealii-8.2.1 (14 Jan 2015)
+
+ 14 Jan 2015; Matthias Maier <tamiko@gentoo.org> +dealii-8.2.1.ebuild,
+ dealii-8.2.0.ebuild, dealii-9999.ebuild:
+ sci-libs/dealii - version bump; update live build
+
24 Dec 2014; Matthias Maier <tamiko@gentoo.org> dealii-9999.ebuild:
fix installation
diff --git a/sci-libs/dealii/Manifest b/sci-libs/dealii/Manifest
index 2d20fdf0c..bb7faf0be 100644
--- a/sci-libs/dealii/Manifest
+++ b/sci-libs/dealii/Manifest
@@ -2,3 +2,5 @@ DIST dealii-8.1.0-offline_documentation.tar.gz 96865280 SHA256 c39f309ff5296a05d
DIST dealii-8.1.0.tar.gz 13353502 SHA256 d666bbda2a17b41b80221d7029468246f2658051b8c00d9c5907cd6434c4df99 SHA512 9d6e913e7a8c54f386839d031f2931a74e8ac6e7db8693c201a11ec6ca34962626a42a57b727297c9f3d8b9efebddb4f2397c27bbee4212e726ce2714f1c3f70 WHIRLPOOL 8cd7aeb47c28bc473bb24d1632f6074de893b20d995d6077c80b88834693b8f9ad1aee181b7abda55a5567efa6c6d169da4c6061cd939b63351330f7e4b767c5
DIST dealii-8.2.0-offline_documentation.tar.gz 100812912 SHA256 90097f935731c418b4ab134063a186735cc9437f6a780bd3a640f093078082d6 SHA512 cb1b871a86d79cbaeba833c21ccfb80b362d0c7860397e94ca0dea62240ea18b70f28cc362a2c61021189ef08eea9fa0adf013d5c172e6551f0a5aacd8134fd7 WHIRLPOOL 0aba8d8ff27b4135e4b453049dd7d095634c559d89d6dd9dc24d5e77ca94955474df5ae490dbce83e7861c2e2d0760470998b14b266856e85b5462edd78a628a
DIST dealii-8.2.0.tar.gz 13666090 SHA256 a6f136c59a6b1c0789ea1692b7429a56e4fc3272a6e5079c08cdb3f5e24f982c SHA512 040056258f2c00d0ebae044011e851ab120432298dccda63a4853653c8c0839b7562e71a7ac37513d71f4eff319f57a61ed7189c564a9ba2936870266ac0470f WHIRLPOOL bcb1e0f478bb7baaa492b78e1d0062d84faef275cd0e82b1889867d6f6e49658fd6da5ec2ead8038f224562877166f778408e4462bb262038de4e2c7e95fe6ec
+DIST dealii-8.2.1-offline_documentation.tar.gz 98861605 SHA256 4622e8ef96c5105dc9cf6e35c54a6fd072956235320646c4f53b5def7748b2fd SHA512 721d963991d53f2c23010f6c398cddd9e058385375a3a77245fbe95b10dbfe1a452d1c2ead2cb8d8a0174b0b2262ed40832f100a545af49dc923d19f42e8e283 WHIRLPOOL 5a1d070d8336c9d9a3a582a73457fa1831f737ecd5def1787bcbffef30f718eef03c57c58ea80e79d6735b73d6f8c83d498a366f002fa5078ef51c71af74b2f9
+DIST dealii-8.2.1.tar.gz 13667634 SHA256 d75674e45fe63cd9fa294460fe45228904d51a68f744dbb99cd7b60720f3b2a0 SHA512 9cd3ed9a4330aa7464ecfe92677fcddae0aadcca7885c898eb8a746caa30fff587ccf5614cec61ffb6b27280c94b423d6370661a1791c601d7abce163502daeb WHIRLPOOL d7b86adcf7dc5dddf63aac4d37be6512aff9889279eb58f9d79cbc5d0c467a1ba50892a08495057f20a3352767f88a42bff7d82f9ba2b5567b02511cb806b7f5
diff --git a/sci-libs/dealii/dealii-8.2.0.ebuild b/sci-libs/dealii/dealii-8.2.0.ebuild
index 9860d7b9f..e7cf68128 120000
--- a/sci-libs/dealii/dealii-8.2.0.ebuild
+++ b/sci-libs/dealii/dealii-8.2.0.ebuild
@@ -1 +1 @@
-dealii-9999.ebuild \ No newline at end of file
+dealii-8.2.1.ebuild \ No newline at end of file
diff --git a/sci-libs/dealii/dealii-8.2.1.ebuild b/sci-libs/dealii/dealii-8.2.1.ebuild
new file mode 100644
index 000000000..2aff61972
--- /dev/null
+++ b/sci-libs/dealii/dealii-8.2.1.ebuild
@@ -0,0 +1,127 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils eutils multilib
+
+DESCRIPTION="Solving partial differential equations with the finite element method"
+HOMEPAGE="http://www.dealii.org/"
+
+if [[ ${PV} = *9999* ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="git://github.com/dealii/dealii.git"
+ SRC_URI=""
+ KEYWORDS=""
+else
+ MY_PV="${PV//0_rc/rc}"
+ MY_P="${PN}-${MY_PV}"
+ SRC_URI="https://github.com/dealii/dealii/archive/v${MY_PV}.tar.gz -> ${P}.tar.gz
+ doc? (
+ https://github.com/${PN}/${PN}/releases/download/v${MY_PV}/${MY_P}-offline_documentation.tar.gz
+ -> ${P}-offline_documentation.tar.gz
+ http://ganymed.iwr.uni-heidelberg.de/~maier/dealii/releases/${MY_P}-offline_documentation.tar.gz
+ -> ${P}-offline_documentation.tar.gz
+ )"
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+ S="${WORKDIR}/${PN}-${MY_PV}"
+fi
+
+LICENSE="LGPL-2.1+"
+SLOT="0"
+IUSE="
+ arpack avx c++11 +debug doc +examples hdf5 +lapack mesh_converter metis
+ mpi mumps muparser opencascade netcdf p4est parameter_gui petsc +sparse
+ sse2 static-libs +tbb trilinos
+"
+
+# TODO: add slepc use flag once slepc is packaged for gentoo-science
+REQUIRED_USE="
+ mumps? ( mpi lapack )
+ p4est? ( mpi )
+ trilinos? ( mpi )"
+
+RDEPEND="dev-libs/boost
+ app-arch/bzip2
+ sys-libs/zlib
+ arpack? ( sci-libs/arpack[mpi=] )
+ hdf5? ( sci-libs/hdf5[mpi=] )
+ lapack? ( virtual/lapack )
+ metis? ( >=sci-libs/parmetis-4 )
+ mpi? ( virtual/mpi )
+ mumps? ( sci-libs/mumps[mpi] )
+ muparser? ( dev-cpp/muParser )
+ netcdf? ( || ( <sci-libs/netcdf-4.2[cxx] sci-libs/netcdf-cxx ) )
+ opencascade? ( sci-libs/opencascade )
+ p4est? ( sci-libs/p4est[mpi] )
+ parameter_gui? ( dev-qt/qtgui )
+ petsc? ( sci-mathematics/petsc[mpi=] )
+ sparse? ( sci-libs/umfpack )
+ tbb? ( dev-cpp/tbb )
+ trilinos? ( sci-libs/trilinos )"
+
+DEPEND="${RDEPEND}
+ virtual/pkgconfig
+ doc? ( app-doc/doxygen[dot] dev-lang/perl )"
+
+src_configure() {
+ # deal.II needs a custom build type:
+ local CMAKE_BUILD_TYPE=$(usex debug DebugRelease Release)
+
+ local mycmakeargs=(
+ -DDEAL_II_ALLOW_AUTODETECTION=OFF
+ -DDEAL_II_ALLOW_BUNDLED=OFF
+ -DDEAL_II_ALLOW_PLATFORM_INTROSPECTION=OFF
+ -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=OFF
+ -DDEAL_II_COMPONENT_COMPAT_FILES=OFF
+ -DDEAL_II_CMAKE_MACROS_RELDIR=share/${PN}/cmake/macros
+ -DDEAL_II_DOCHTML_RELDIR=share/doc/${PF}/html
+ -DDEAL_II_DOCREADME_RELDIR=share/doc/${PF}/
+ -DDEAL_II_EXAMPLES_RELDIR=share/doc/${PF}/examples
+ -DDEAL_II_LIBRARY_RELDIR=$(get_libdir)
+ -DDEAL_II_WITH_BZIP2=ON
+ -DDEAL_II_WITH_ZLIB=ON
+ $(cmake-utils_use arpack DEAL_II_WITH_ARPACK)
+ $(cmake-utils_use avx DEAL_II_HAVE_AVX)
+ $(cmake-utils_use c++11 DEAL_II_WITH_CXX11)
+ $(cmake-utils_use doc DEAL_II_COMPONENT_DOCUMENTATION)
+ $(cmake-utils_use examples DEAL_II_COMPONENT_EXAMPLES)
+ $(cmake-utils_use hdf5 DEAL_II_WITH_HDF5)
+ $(cmake-utils_use lapack DEAL_II_WITH_LAPACK)
+ $(cmake-utils_use mesh_converter DEAL_II_COMPONENT_MESH_CONVERTER)
+ $(cmake-utils_use metis DEAL_II_WITH_METIS)
+ $(cmake-utils_use mpi DEAL_II_WITH_MPI)
+ $(cmake-utils_use mumps DEAL_II_WITH_MUMPS)
+ $(cmake-utils_use muparser DEAL_II_WITH_MUPARSER)
+ $(cmake-utils_use netcdf DEAL_II_WITH_NETCDF)
+ -DOPENCASCADE_DIR="${CASROOT}"
+ $(cmake-utils_use opencascade DEAL_II_WITH_OPENCASCADE)
+ $(cmake-utils_use p4est DEAL_II_WITH_P4EST)
+ $(cmake-utils_use parameter_gui DEAL_II_COMPONENT_PARAMETER_GUI)
+ $(cmake-utils_use petsc DEAL_II_WITH_PETSC)
+ $(cmake-utils_use sparse DEAL_II_WITH_UMFPACK)
+ $(cmake-utils_use sse2 DEAL_II_HAVE_SSE2)
+ $(cmake-utils_use !static-libs BUILD_SHARED_LIBS)
+ $(cmake-utils_use static-libs DEAL_II_PREFER_STATIC_LIBS)
+ $(cmake-utils_use tbb DEAL_II_WITH_THREADS)
+ $(cmake-utils_use trilinos DEAL_II_WITH_TRILINOS)
+ )
+ cmake-utils_src_configure
+}
+
+src_install() {
+ if use doc && [[ ${PV} != *9999* ]]; then
+ # copy missing images to the build directory:
+ cp -r "${WORKDIR}"/doc/doxygen/deal.II/images \
+ "${BUILD_DIR}"/doc/doxygen/deal.II || die
+ # replace links:
+ sed -i \
+ 's#"http://www.dealii.org/images/steps/developer/\(step-.*\)"#"images/\1"#g' \
+ "${BUILD_DIR}"/doc/doxygen/deal.II/step_*.html || die "sed failed"
+ fi
+ cmake-utils_src_install
+
+ # decompress the installed example sources:
+ use examples && docompress -x /usr/share/doc/${PF}/examples
+}
diff --git a/sci-libs/dealii/dealii-9999.ebuild b/sci-libs/dealii/dealii-9999.ebuild
index 09a86833f..5894b447e 100644
--- a/sci-libs/dealii/dealii-9999.ebuild
+++ b/sci-libs/dealii/dealii-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -32,13 +32,12 @@ LICENSE="LGPL-2.1+"
SLOT="0"
IUSE="
arpack avx c++11 +debug doc +examples hdf5 +lapack mesh_converter metis
- mpi mumps muparser opencascade netcdf p4est parameter_gui petsc +sparse
+ mpi muparser opencascade netcdf p4est parameter_gui petsc +sparse
sse2 static-libs +tbb trilinos
"
# TODO: add slepc use flag once slepc is packaged for gentoo-science
REQUIRED_USE="
- mumps? ( mpi lapack )
p4est? ( mpi )
trilinos? ( mpi )"
@@ -50,7 +49,6 @@ RDEPEND="dev-libs/boost
lapack? ( virtual/lapack )
metis? ( >=sci-libs/parmetis-4 )
mpi? ( virtual/mpi )
- mumps? ( sci-libs/mumps[mpi] )
muparser? ( dev-cpp/muParser )
netcdf? ( || ( <sci-libs/netcdf-4.2[cxx] sci-libs/netcdf-cxx ) )
opencascade? ( sci-libs/opencascade )
@@ -92,7 +90,6 @@ src_configure() {
$(cmake-utils_use mesh_converter DEAL_II_COMPONENT_MESH_CONVERTER)
$(cmake-utils_use metis DEAL_II_WITH_METIS)
$(cmake-utils_use mpi DEAL_II_WITH_MPI)
- $(cmake-utils_use mumps DEAL_II_WITH_MUMPS)
$(cmake-utils_use muparser DEAL_II_WITH_MUPARSER)
$(cmake-utils_use netcdf DEAL_II_WITH_NETCDF)
-DOPENCASCADE_DIR="${CASROOT}"
diff --git a/sci-libs/libspatialindex/Manifest b/sci-libs/libspatialindex/Manifest
index 5150c659b..9b0e8058c 100644
--- a/sci-libs/libspatialindex/Manifest
+++ b/sci-libs/libspatialindex/Manifest
@@ -1 +1 @@
-DIST spatialindex-src-1.6.1.tar.bz2 346819 SHA256 42dc4149c04f7436632b3e15d5470fe80172e91f16a16665ffc5587b8c576fe4
+DIST spatialindex-src-1.8.5.tar.bz2 407871 SHA256 31ec0a9305c3bd6b4ad60a5261cba5402366dd7d1969a8846099717778e9a50a SHA512 d3e47982cc2809d04490fae27796b31cdb59675790010d8b45e1a98b5a23048a4a44e321a2470dd36c01aba6f6e7620cafc4988a02b55e4f59d1b7fa9b588b06 WHIRLPOOL 498fc14ff9aea93a362cf7719e20f77bd84b5f6be94e8b1bfb3bbb00bb04d2bf1e9cc1156090c8f7f37e0ca4b64ac5701e1c91476591f401bf9f738b0d6efa1f
diff --git a/sci-libs/libspatialindex/files/libspatialindex-1.8.1-QA.patch b/sci-libs/libspatialindex/files/libspatialindex-1.8.1-QA.patch
new file mode 100644
index 000000000..446452dc9
--- /dev/null
+++ b/sci-libs/libspatialindex/files/libspatialindex-1.8.1-QA.patch
@@ -0,0 +1,15 @@
+--- spatialindex-src-1.8.0/configure.ac
++++ spatialindex-src-1.8.0/configure.ac
+@@ -49,10 +49,10 @@
+ AC_ARG_ENABLE(debug, [ --enable-debug=[no/yes] turn on debugging [default=$debug_default]],, enable_debug=$debug_default)
+
+ if test "x$enable_debug" = "xyes"; then
+- CXXFLAGS="$CXXFLAGS -g -DDEBUG"
++ CXXFLAGS="$CXXFLAGS -DDEBUG"
+ AC_MSG_RESULT(checking wether debug information is enabled... yes)
+ else
+- CXXFLAGS="$CXXFLAGS -O2 -DNDEBUG"
++ CXXFLAGS="$CXXFLAGS -DNDEBUG"
+ AC_MSG_RESULT(checking wether debug information is enabled... no)
+ fi
+
diff --git a/sci-libs/libspatialindex/libspatialindex-1.6.1.ebuild b/sci-libs/libspatialindex/libspatialindex-1.6.1.ebuild
deleted file mode 100644
index cb5a9d9a2..000000000
--- a/sci-libs/libspatialindex/libspatialindex-1.6.1.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-MY_PN="spatialindex-src"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="General framework for developing spatial indices"
-HOMEPAGE="http://trac.gispython.org/spatialindex/wiki"
-SRC_URI="http://download.osgeo.org/libspatialindex/${MY_P}.tar.bz2"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-S="${WORKDIR}/${MY_P}"
diff --git a/sci-libs/libspatialindex/libspatialindex-1.8.5.ebuild b/sci-libs/libspatialindex/libspatialindex-1.8.5.ebuild
new file mode 100644
index 000000000..e6725933f
--- /dev/null
+++ b/sci-libs/libspatialindex/libspatialindex-1.8.5.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2014 Julian Ospald <hasufell@posteo.de>
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit autotools eutils
+
+MY_PN="spatialindex-src"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="General framework for developing spatial indices"
+HOMEPAGE="http://libspatialindex.github.com/"
+SRC_URI="http://download.osgeo.org/libspatialindex/${MY_P}.tar.bz2"
+LICENSE="MIT"
+
+KEYWORDS="~amd64 ~x86"
+SLOT="0/4"
+IUSE="debug static-libs"
+
+S=${WORKDIR}/${MY_P}
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PN}-1.8.1-QA.patch
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ $(use_enable static-libs static) \
+ $(use_enable debug)
+}
+
+src_install() {
+ default
+ use static-libs || prune_libtool_files
+}
diff --git a/sci-libs/libspatialindex/metadata.xml b/sci-libs/libspatialindex/metadata.xml
index 5f27678c1..8d63d2790 100644
--- a/sci-libs/libspatialindex/metadata.xml
+++ b/sci-libs/libspatialindex/metadata.xml
@@ -1,5 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-geosciences</herd>
+ <herd>sci-geosciences</herd>
+ <maintainer>
+ <email>hasufell@posteo.de</email>
+ <name>Julian Ospald</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-misc/kaldi/ChangeLog b/sci-misc/kaldi/ChangeLog
new file mode 100644
index 000000000..f7406faf9
--- /dev/null
+++ b/sci-misc/kaldi/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-misc/kaldi
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*kaldi-0_p20150101 (11 Jan 2015)
+
+ 11 Jan 2015; Pavel Denisov <pavel.a.denisov@gmail.com> +files/Makefile.patch,
+ +files/configure.patch, +files/default_rules.mk.patch,
+ +kaldi-0_p20150101.ebuild, +metadata.xml:
+ sci-misc/kaldi: New package
diff --git a/sci-misc/kaldi/files/Makefile.patch b/sci-misc/kaldi/files/Makefile.patch
new file mode 100644
index 000000000..07302d6d4
--- /dev/null
+++ b/sci-misc/kaldi/files/Makefile.patch
@@ -0,0 +1,19 @@
+--- Makefile.orig 2015-01-01 21:51:30.999356027 -0400
++++ Makefile 2015-01-04 16:54:02.527824499 -0400
+@@ -131,6 +131,16 @@
+ ext_depend: check_portaudio
+ -for x in $(EXT_SUBDIRS); do $(MAKE) -C $$x depend; done
+
++print-binfiles: $(addsuffix /print-binfiles, $(SUBDIRS))
++
++%/print-binfiles:
++ @$(MAKE) --no-print-directory -C $(dir $@) print-binfiles
++
++print-libfiles: $(addsuffix /print-libfiles, $(SUBDIRS))
++
++%/print-libfiles:
++ @$(MAKE) --no-print-directory -C $(dir $@) print-libfiles
++
+
+ .PHONY: $(SUBDIRS)
+ $(SUBDIRS) : mklibdir
diff --git a/sci-misc/kaldi/files/configure.patch b/sci-misc/kaldi/files/configure.patch
new file mode 100644
index 000000000..07d663e93
--- /dev/null
+++ b/sci-misc/kaldi/files/configure.patch
@@ -0,0 +1,71 @@
+--- configure.orig 2015-01-01 21:51:05.611960184 -0400
++++ configure 2015-01-01 22:06:11.027064734 -0400
+@@ -45,15 +45,6 @@
+ fi
+ }
+
+-
+-
+-## First do some checks. These verify that all the things are
+-## here that should be here.
+-if [ "`basename $PWD`" != "src" ]; then
+- echo 'You must run "configure" from the src/ directory.'
+- exit 1
+-fi
+-
+ ## Default locations for FST and linear algebra libraries.
+ MATHLIB='ATLAS'
+ ATLASROOT=`rel2abs ../tools/ATLAS/`
+@@ -473,6 +464,23 @@
+ exit_success;
+ }
+
++function linux_configure_gentoo {
++ m=$1 # 64 or empty.
++ ATLASLIBS="/usr/lib$m/libatlas.so.3 /usr/lib$m/libf77blas.so.3 /usr/lib$m/libatlcblas.so.3 /usr/lib$m/libatlclapack.so.3"
++ for f in $ATLASLIBS; do
++ [ ! -f $f ] && return 1;
++ done
++ libdir=$(dirname $(echo $ATLASLIBS | awk '{print $1}'))
++ [ -z "$libdir" ] && echo "Error getting libdir in linux_configure_gentoo" && exit 1;
++ echo ATLASINC = $ATLASROOT >> kaldi.mk
++ echo ATLASLIBS = $ATLASLIBS -Wl,-rpath=$libdir >> kaldi.mk
++ echo
++ cat makefiles/linux_atlas.mk >> kaldi.mk
++ fix_cxx_flag
++ echo "Successfully configured for gentoo [dynamic libraries] with ATLASLIBS =$ATLASLIBS"
++ $use_cuda && linux_configure_cuda
++ exit_success;
++}
+
+ function linux_configure_static {
+ if $threaded_atlas; then pt=pt; else pt=""; fi
+@@ -716,8 +724,8 @@
+
+ echo "On Linux: Checking for linear algebra header files ..."
+ if [ "$MATHLIB" == "ATLAS" ]; then
+- if [ ! -f $ATLASROOT/include/cblas.h ] || [ ! -f $ATLASROOT/include/clapack.h ] ; then
+- failure "Could not find required header files cblas.h or clapack.h in ATLAS dir '$ATLASROOT/include'"
++ if ( [ ! -f $ATLASROOT/include/cblas.h ] || [ ! -f $ATLASROOT/include/clapack.h ] ) && ( [ ! -f $ATLASROOT/cblas.h ] || [ ! -f $ATLASROOT/clapack.h ] ) ; then
++ failure "Could not find required header files cblas.h or clapack.h in ATLAS dirs '$ATLASROOT/include' or '$ATLASROOT'"
+ fi
+ echo "Using ATLAS as the linear algebra library."
+
+@@ -741,6 +749,8 @@
+ linux_configure_debian7 || \
+ linux_configure_redhat 64 || \
+ linux_configure_redhat || \
++ linux_configure_gentoo 64 || \
++ linux_configure_gentoo || \
+ linux_atlas_failure "Failed to configure ATLAS lbiraries";
+ else
+ # Prefer dynamic to static math.
+@@ -751,6 +761,8 @@
+ linux_configure_debian7 || \
+ linux_configure_redhat 64 || \
+ linux_configure_redhat || \
++ linux_configure_gentoo 64 || \
++ linux_configure_gentoo || \
+ linux_atlas_failure "Failed to configure ATLAS lbiraries";
+ fi
+
diff --git a/sci-misc/kaldi/files/default_rules.mk.patch b/sci-misc/kaldi/files/default_rules.mk.patch
new file mode 100644
index 000000000..26c7f3616
--- /dev/null
+++ b/sci-misc/kaldi/files/default_rules.mk.patch
@@ -0,0 +1,20 @@
+--- makefiles/default_rules.mk.orig 2015-01-10 19:56:03.918751769 -0400
++++ makefiles/default_rules.mk 2015-01-11 13:34:14.596055674 -0400
+@@ -14,7 +14,7 @@
+ LIBFILE = lib$(LIBNAME).so
+ #LDLIBS += -l$(LIBNAME)
+ endif
+- LDFLAGS += -Wl,-rpath=$(shell readlink -f $(KALDILIBDIR)) -L.
++ LDFLAGS += -L.
+ LDFLAGS += $(foreach dep,$(ADDLIBS), -L$(dir $(dep)) )
+ XDEPENDS = $(foreach dep,$(ADDLIBS), $(dir $(dep))/lib$(notdir $(basename $(dep))).so )
+ else # Platform not supported
+@@ -84,3 +84,8 @@
+ #.depend.mk: depend
+ -include .depend.mk
+
++print-binfiles:
++ @echo $(addprefix $(shell pwd)/, $(BINFILES))
++
++print-libfiles:
++ @echo $(addsuffix .so, $(addprefix $(shell pwd)/lib, $(LIBNAME)))
diff --git a/sci-misc/kaldi/kaldi-0_p20150101.ebuild b/sci-misc/kaldi/kaldi-0_p20150101.ebuild
new file mode 100644
index 000000000..9ef57039e
--- /dev/null
+++ b/sci-misc/kaldi/kaldi-0_p20150101.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="5"
+
+inherit eutils flag-o-matic subversion
+
+DESCRIPTION="A toolkit for speech recognition"
+HOMEPAGE="http://kaldi.sourceforge.net/"
+ESVN_REPO_URI="https://svn.code.sf.net/p/kaldi/code/trunk/src@4735"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+IUSE="doc test threads"
+KEYWORDS=""
+
+RDEPEND="
+ media-libs/speex
+ sci-libs/atlas[lapack,threads=]
+ ~sci-misc/openfst-1.3.4"
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen )"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/configure.patch \
+ "${FILESDIR}"/Makefile.patch \
+ "${FILESDIR}"/default_rules.mk.patch
+}
+
+src_configure() {
+ # Upstream's configure script is "hand-generated" and not autotools compatible,
+ # for this reason econf can not be used
+ ./configure \
+ --shared \
+ --fst-root="${EPREFIX}/usr" \
+ $(use threads && echo --threaded-atlas=yes) \
+ --atlas-root="${EPREFIX}/usr/include/atlas" || die "failed to run configure"
+
+ use test || append-cxxflags -DNDEBUG
+
+ sed -i \
+ -e 's/OPENFST_VER =/OPENFST_VER = 1.3.4#/' \
+ -e "s:-g :-DHAVE_SPEEX ${CXXFLAGS} :" \
+ -e "s:-lm -lpthread -ldl:-lm -lpthread -ldl -lspeex ${LDFLAGS}:" \
+ kaldi.mk || die "sed unix/kaldi.mk failed"
+}
+
+src_compile() {
+ emake
+ use doc && doxygen
+}
+
+src_install() {
+ dolib.so $(make print-libfiles)
+ dobin $(make print-binfiles)
+ use doc && dohtml -r html/*
+}
diff --git a/sci-misc/kaldi/metadata.xml b/sci-misc/kaldi/metadata.xml
new file mode 100644
index 000000000..9e25ae0bb
--- /dev/null
+++ b/sci-misc/kaldi/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>pavel.a.denisov@gmail.com</email>
+ </maintainer>
+ <longdescription lang="en">
+ Kaldi is a toolkit for speech recognition written
+ in C++ and licensed under the Apache License v2.0.
+ Kaldi is intended for use by speech recognition researchers.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-misc/mendeleydesktop/ChangeLog b/sci-misc/mendeleydesktop/ChangeLog
new file mode 100644
index 000000000..18821b652
--- /dev/null
+++ b/sci-misc/mendeleydesktop/ChangeLog
@@ -0,0 +1,14 @@
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*mendeleydesktop-1.13.1 (14 Jan 2015)
+
+ 14 Jan 2015; Marius Brehler <marbre@linux.sungazer.de>,
+ -mendeleydesktop-1.13.ebuild, +mendeleydesktop-1.13.1.ebuild:
+ Version bump; Drop old
+
+*mendeleydesktop-1.13 (13 Jan 2015)
+
+ 13 Jan 2015; Marius Brehler <marbre@linux.sungazer.de>,
+ +mendeleydesktop-1.13.ebuild, metadata.xml:
+ Add version bumped ebuild
diff --git a/sci-misc/mendeleydesktop/Manifest b/sci-misc/mendeleydesktop/Manifest
new file mode 100644
index 000000000..9a90938f2
--- /dev/null
+++ b/sci-misc/mendeleydesktop/Manifest
@@ -0,0 +1,2 @@
+DIST mendeleydesktop-1.13.1-linux-i486.tar.bz2 32918387 SHA256 6eb2026a592ab4a5fdc3184ff9b099a37fab559eee10e9f85e0aade61608c28b SHA512 f8bb3b3c2668a713d1f768ea8c45873028b1bb0c7beef3b8c59aed5997562585da57b754f61fd3ad0a9a0bd1fd49c069296994f5e387f8568f7a1c48fc146bc8 WHIRLPOOL 7b66e44d5625c1878e4602b8050fecdb953ccd286c4d3997625feb2be4c8989915bf2797cc77d1f50c2d2330791d3b3003cd4622a2911f6a616ac03dde6af01c
+DIST mendeleydesktop-1.13.1-linux-x86_64.tar.bz2 32610864 SHA256 2c0c40bf64988fb77bc0847fedb8bfcd4e89ca6577cdf1fe2a126d33ab052bd1 SHA512 682e2745bfb2d767d17ce7cf27720d0210e606ff7e81caea6201a62858c0b6365812479e4b256194fafbf5239aee2cb4ee7813ea2724c9f2c1774a8e6b72812b WHIRLPOOL 67247134b54e62d0969fc1da433b7b5e6f24c6035461ff4bf37fda3cb1e2a285713e3d66640f455fda2ecc2ae1ff308dd5e858b94a196a45917b112c7d16d370
diff --git a/sci-misc/mendeleydesktop/mendeleydesktop-1.13.1.ebuild b/sci-misc/mendeleydesktop/mendeleydesktop-1.13.1.ebuild
new file mode 100644
index 000000000..8855f7558
--- /dev/null
+++ b/sci-misc/mendeleydesktop/mendeleydesktop-1.13.1.ebuild
@@ -0,0 +1,114 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils fdo-mime multilib
+
+MY_P_AMD64="${P}-linux-x86_64"
+MY_P_X86="${P}-linux-i486"
+
+DESCRIPTION="A free research management tool for desktop and web"
+HOMEPAGE="http://www.mendeley.com/"
+SRC_URI="amd64? ( ${MY_P_AMD64}.tar.bz2 )
+ x86? ( ${MY_P_X86}.tar.bz2 )
+ amd64-linux? ( ${MY_P_AMD64}.tar.bz2 )
+ x86-linux? ( ${MY_P_X86}.tar.bz2 )"
+
+LICENSE="Mendeley-terms"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RESTRICT="fetch"
+
+DEPEND=""
+RDEPEND="
+ dev-qt/qtcore:4
+ dev-qt/qtgui:4
+ dev-qt/qtsvg:4
+ dev-qt/qtwebkit:4
+ dev-qt/qtxmlpatterns:4"
+
+QA_PREBUILT="/opt/mendeleydesktop/.*"
+
+pkg_nofetch() {
+ elog "Please download ${A} from:"
+ elog "http://www.mendeley.com/download-mendeley-desktop/"
+ elog "and move it to ${DISTDIR}"
+}
+
+src_unpack() {
+ unpack ${A}
+
+ cd "${WORKDIR}" || die
+
+ if use amd64 || use amd64-linux ; then
+ mv -f "${MY_P_AMD64}" "${P}" || die
+ else
+ mv -f "${MY_P_X86}" "${P}" || die
+ fi
+}
+
+src_prepare() {
+ # remove bundled Qt libraries
+ rm -r lib/mendeleydesktop/plugins \
+ || die "failed to remove plugin directory"
+ rm -r lib/qt || die "failed to remove qt libraries"
+
+ # force use of system Qt libraries
+ sed -i "s:sys\.argv\.count(\"--force-system-qt\") > 0:True:" \
+ bin/mendeleydesktop || die "failed to patch startup script"
+
+ # fix library paths
+ sed -i \
+ -e "s:lib/mendeleydesktop:$(get_libdir)/mendeleydesktop:g" \
+ -e "s:MENDELEY_BASE_PATH + \"/lib/\":MENDELEY_BASE_PATH + \"/$(get_libdir)/\":g" \
+ bin/mendeleydesktop || die "failed to patch library path"
+}
+
+src_install() {
+ # install menu
+ domenu share/applications/${PN}.desktop
+
+ # install application icons
+ insinto /usr/share/icons
+ doins -r share/icons/hicolor
+
+ # install default icon
+ insinto /usr/share/pixmaps
+ doins share/icons/hicolor/48x48/apps/${PN}.png
+
+ # install documentation, but no license file
+ dodoc share/doc/${PN}/Readme.txt
+
+ # install binary
+ into /opt/${PN}
+ dobin bin/*
+
+ # install libraries
+ dolib.so lib/lib*.so*
+
+ # install programs
+ exeinto /opt/mendeleydesktop/$(get_libdir)/mendeleydesktop/libexec
+ doexe lib/mendeleydesktop/libexec/*
+
+ # install shared files
+ insinto /opt/${PN}/share
+ doins -r share/mendeleydesktop
+
+ # install launch script
+ into /opt
+ make_wrapper ${PN} "/opt/${PN}/bin/${PN} --unix-distro-build"
+}
+
+pkg_postinst() {
+ fdo-mime_desktop_database_update
+ fdo-mime_mime_database_update
+}
+
+pkg_postrm() {
+ fdo-mime_desktop_database_update
+ fdo-mime_mime_database_update
+}
diff --git a/sci-misc/mendeleydesktop/metadata.xml b/sci-misc/mendeleydesktop/metadata.xml
new file mode 100644
index 000000000..067828793
--- /dev/null
+++ b/sci-misc/mendeleydesktop/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <longdescription>
+Mendeley(TM) is a free reference manager and academic social network that can
+help you organize your research, collaborate with others online, and discover
+the latest research.
+</longdescription>
+</pkgmetadata>