Merge branch 'master' of github.com:TheChymera/overlay

app-misc/repositorg/ChangeLog

@@ -0,0 +1,2 @@
+  12 May 2019;  <chymera@gentoo.org> +metadata.xml, repositorg-9999.ebuild:
+  app-misc/repositorg: Updated metadata and systemd   USE functionality

app-misc/repositorg/files/repositorg_uuid.service

@@ -0,0 +1,10 @@
+[Unit]
+Description=A repositorg service to check for UUID events
+After=local-fs.target
+ 
+[Service]
+ExecStart=/usr/bin/repositorg_uuid
+User=%i
+
+[Install]
+WantedBy=multi-user.target

app-misc/repositorg/metadata.xml

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>chr@chymer.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<longdescription lang="en">
+		Repositorg is Python module that lets you automatically reposit,
+		organize, rename, and process large collections of files (e.g.
+		pictures, or video). The package includes optional systemd support
+		which can trigger custom repositorg scripts based on hardware
+		events.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">TheChymera/repositorg</remote-id>
+	</upstream>
+</pkgmetadata>

app-misc/repositorg/repositorg-9999.ebuild

@@ -1,21 +1,40 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
-# $Header: $
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
+PYTHON_COMPAT=(python2_7 python3_{4,5,6})
 
-inherit distutils-r1 git-r3 multilib
+inherit distutils-r1 git-r3 systemd
 
-DESCRIPTION="Organize and rename large numbers of files"
+DESCRIPTION="Automatically reposit, organize, rename, and process large collections of files."
 HOMEPAGE="https://github.com/TheChymera/repositorg"
 SRC_URI=""
 EGIT_REPO_URI="https://github.com/TheChymera/repositorg"
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE=""
 KEYWORDS=""
+IUSE="systemd"
 
-DEPEND=""
+DEPEND="
+	>=dev-python/argh-0.26.2
+	media-libs/mutagen
+	systemd? ( sys-apps/systemd )
+"
+RDEPEND="${DEPEND}"
+
+python_install() {
+	distutils-r1_python_install
+	if use systemd; then
+		systemd_newunit "${FILESDIR}/${PN}_uuid.service" "${PN}_uuid@.service"
+	fi
+	dobin repositorg_uuid
+}
+
+src_test() {
+	cd test_scripts/
+	for i in *.sh; do
+		./"$i" || die "Test $i failed"
+	done
+}

drafts/nipype-1.1.7.ebuild

@@ -0,0 +1,56 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+PYTHON_REQ_USE="threads(+),sqlite"
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
+HOMEPAGE="http://nipy.sourceforge.net/nipype/"
+SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+DEPEND="
+	dev-python/future[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	~dev-python/prov-1.5.0[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	test? (
+		dev-python/mock[${PYTHON_USEDEP}]
+		dev-python/pytest[${PYTHON_USEDEP}]
+		dev-python/pytest-cov[${PYTHON_USEDEP}]
+		dev-python/pytest-xdist[${PYTHON_USEDEP}]
+		${RDEPEND}
+		)
+	$(python_gen_cond_dep 'dev-python/configparser[${PYTHON_USEDEP}]' python2_7)
+	"
+RDEPEND="
+	>=dev-python/click-6.6[${PYTHON_USEDEP}]
+	dev-python/networkx[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/pydot[${PYTHON_USEDEP}]
+	dev-python/pydotplus[${PYTHON_USEDEP}]
+	dev-python/pygraphviz[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	dev-python/simplejson[${PYTHON_USEDEP}]
+	dev-python/traits[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	virtual/python-funcsigs[${PYTHON_USEDEP}]
+	"
+
+python_test() {
+	py.test -v --cov nipype\
+		--cov-config .coveragerc\
+		--cov-report xml:cov.xml\
+		-c nipype/pytest.ini\
+		--doctest-modules nipype\
+		|| die
+}

drafts/nipype-1.1.9.ebuild

@@ -0,0 +1,57 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+PYTHON_REQ_USE="threads(+),sqlite"
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
+HOMEPAGE="http://nipy.sourceforge.net/nipype/"
+SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+DEPEND="
+	dev-python/future[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	~dev-python/prov-1.5.0[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	test? (
+		dev-python/mock[${PYTHON_USEDEP}]
+		dev-python/pytest[${PYTHON_USEDEP}]
+		dev-python/pytest-xdist[${PYTHON_USEDEP}]
+		${RDEPEND}
+		)
+	$(python_gen_cond_dep '
+		dev-python/futures[${PYTHON_USEDEP}]
+		dev-python/configparser[${PYTHON_USEDEP}]' python2_7)
+	"
+RDEPEND="
+	>=dev-python/click-6.6[${PYTHON_USEDEP}]
+	dev-python/networkx[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/pydot[${PYTHON_USEDEP}]
+	dev-python/pydotplus[${PYTHON_USEDEP}]
+	dev-python/pygraphviz[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	dev-python/simplejson[${PYTHON_USEDEP}]
+	dev-python/traits[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	virtual/python-funcsigs[${PYTHON_USEDEP}]
+	"
+
+python_test() {
+	py.test -v --cov nipype\
+		--cov-config .coveragerc\
+		--cov-report xml:cov.xml\
+		-c nipype/pytest.ini\
+		--doctest-modules nipype\
+		|| die
+}

sci-biology/psychopy/Manifest

@@ -0,0 +1 @@
+DIST psychopy-3.0.7.tar.gz 17200357 SHA256 6f40e3f430abd1f3fc90d00adbbfb6deeb283c29817df6a2d84fd6b3486b6b7c SHA512 9277c87cdf0add9ef827cc2eeea7a7d2b8c85ff4ce43fd3965119912cf648a99eec8a05c0cbb4ff601d173e433ae1bd03b7b081e63a315dd3b87ff5715f144d4 WHIRLPOOL c39270d3fe49e1dae09e878ac55bbe2db7a15c2f5494c90a29dbd563b72012dd485d7ed4c8082935b9e11a3178484b54daad67e027dff2f25245b3f4833bf583

sci-biology/psychopy/metadata.xml

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>horea.christ@gmail.com</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">psychopy/psychopy</remote-id>
+	</upstream>
+</pkgmetadata>

sci-biology/psychopy/psychopy-3.0.7.ebuild

@@ -0,0 +1,71 @@
+# Copyright 1999-2019 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python{2_7,3_5,3_6,3_7} )
+PYTHON_REQ_USE="threads(+)"
+
+inherit eutils gnome2-utils distutils-r1
+
+DESCRIPTION="Python experimental psychology toolkit"
+HOMEPAGE="http://www.psychopy.org/"
+SRC_URI="https://github.com/psychopy/psychopy/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+USE="qt5"
+
+DEPEND="
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	"
+RDEPEND="
+	dev-python/cffi[${PYTHON_USEDEP}]
+	dev-python/future[${PYTHON_USEDEP}]
+	dev-python/gevent[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/moviepy[${PYTHON_USEDEP}]
+	dev-python/msgpack[${PYTHON_USEDEP}]
+	dev-python/numpy[lapack,${PYTHON_USEDEP}]
+	dev-python/openpyxl[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/pillow[${PYTHON_USEDEP}]
+	dev-python/psutil[${PYTHON_USEDEP}]
+	dev-python/pytables[${PYTHON_USEDEP}]
+	dev-python/pyglet[${PYTHON_USEDEP}]
+	dev-python/pyopengl[${PYTHON_USEDEP}]
+	qt5? ( $(python_gen_cond_dep 'dev-python/PyQt5[${PYTHON_USEDEP}]' 'python3*') )
+	dev-python/pyserial[${PYTHON_USEDEP}]
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	dev-python/pyzmq[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	dev-python/wxpython:*[${PYTHON_USEDEP}]
+	dev-python/xlrd[${PYTHON_USEDEP}]
+	dev-vcs/python-gitlab[${PYTHON_USEDEP}]
+	media-libs/opencv[python,${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	"
+	#pyosf
+	#json_tricks
+	#soundfile
+	#sounddevice
+	#python-bidi
+	#arabic_reshaper
+	#gitpython
+	#astunparse
+	#esprima
+	#freetype-py
+	#pyparallel
+python_install_all() {
+	distutils-r1_python_install_all
+	newicon -s scalable psychopy/monitors/psychopy-icon.svg psychopy.svg
+	make_desktop_entry psychopyApp.py PsychoPy psychopy
+}
+
+pkg_postinst() {
+	gnome2_icon_cache_update
+}
+pkg_postrm() {
+	gnome2_icon_cache_update
+}

sci-libs/libxc/Manifest

@@ -0,0 +1 @@
+DIST libxc-4.3.4.tar.gz 15602575 BLAKE2B 07d1b9be62344727b2b364ea7b6eb7abcb62a76cb5b17c3601847d0528a86d23762f17cdde383611b842b65342c81467af1896dbcf55569165e2be26aa348616 SHA512 9e364b27fe0bf903e5d08f5814130e2059a001a6ea08938221e20d87d0072d51177d0d21217a744c8f5828a7c88437dc624a9cf173a203783c96d2d681b71e82

sci-libs/libxc/libxc-4.3.4.ebuild

@@ -0,0 +1,52 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools fortran-2
+
+DESCRIPTION="A library of exchange-correlation functionals for use in DFT"
+HOMEPAGE="http://octopus-code.org/wiki/Libxc"
+SRC_URI="http://www.tddft.org/programs/octopus/down.php?file=libxc/${PV}/${P}.tar.gz"
+
+LICENSE="MPL-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="fortran static-libs -test"
+
+pkg_setup() {
+	use fortran && fortran-2_pkg_setup
+}
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	econf --enable-shared \
+		$(use_enable fortran) \
+		$(use_enable static-libs static)
+}
+
+## Upstream recommends not running the test suite because it requires
+## human expert interpretation to determine whether output is an error or
+## expected under certain circumstances. Nevertheless, experts might want the option.
+# The autotools src_test function modified not to die. Runs emake check in build directory.
+src_test() {
+	debug-print-function ${FUNCNAME} "$@"
+
+	_check_build_dir
+	pushd "${BUILD_DIR}" > /dev/null || die
+	make check || ewarn "Make check failed. See above for details."
+	einfo "emake check done"
+	popd > /dev/null || die
+}
+
+src_install() {
+	default
+	find "${ED%/}" -name '*.la' -type f -delete || die
+	if ! use fortran; then
+		rm "${ED%/}"/usr/$(get_libdir)/pkgconfig/libxcf{03,90}.pc || die
+	fi
+}

sci-libs/libxc/metadata.xml

@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>Hloupy.Honza@centrum.cz</email>
+		<name>Honza Macháček</name>
+	</maintainer>
+	<longdescription lang="en">
+		Libxc is a library of exchange-correlation functionals for density-functional theory.
+		The aim is to provide a portable, well tested and reliable set of exchange and correlation
+		functionals that can be used by all the ETSF codes and also other codes.
+
+		In Libxc you can find different types of functionals: LDA, GGA, hybrids, and mGGA (experimental).
+		These functionals depend on local information, in the sense that the value of the potential
+		at a given point depends only on the values of the density -- and the gradient of the density
+		and the kinetic energy density, for the GGA and mGGA cases.
+
+		It can calculate the functional itself and its derivative; for some functionals,
+		higher-order derivatives are available.
+
+		Libxc is written in C and has Fortran bindings. It is released under the MPL2 license.
+		Contributions are welcome.
+	</longdescription>
+	<upstream>
+		<doc>http://octopus-code.org/wiki/Libxc:manual</doc>
+	</upstream>
+</pkgmetadata>

sci-libs/nipype/metadata.xml

@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>horea.christ@gmail.com</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</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>
+	<upstream>
+		<remote-id type="github">nipy/nipype</remote-id>
+		<remote-id type="sourceforge">nipy</remote-id>
+	</upstream>
+</pkgmetadata>