[gentoo-commits] proj/sci:master commit in: sci-biology/nireg/, sci-biology/nilearn/

[gentoo-commits] proj/sci:master commit in: sci-biology/nireg/, sci-biology/nilearn/

[Horea Christian]

commit:     e8025d93b0c85cbfba9b4a6467e2b86f900cb499
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Mar 23 02:30:58 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Mar 23 02:33:02 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e8025d93

sci-biology/nireg: remove from tree.

Unmaintained as of 2016, not used by any packages

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/nilearn/nilearn-0.6.2.ebuild | 61 ++++++++++++++++++++++++++++++++
 sci-biology/nireg/metadata.xml           | 15 --------
 sci-biology/nireg/nireg-9999.ebuild      | 32 -----------------
 3 files changed, 61 insertions(+), 47 deletions(-)

diff --git a/sci-biology/nilearn/nilearn-0.6.2.ebuild b/sci-biology/nilearn/nilearn-0.6.2.ebuild
new file mode 100644
index 000000000..c532ab0ad
--- /dev/null
+++ b/sci-biology/nilearn/nilearn-0.6.2.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6,7} )
+
+inherit distutils-r1
+
+DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
+HOMEPAGE="http://nilearn.github.io/"
+SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+plot test"
+
+# Tests attempt to download external data.
+RESTRICT="test"
+
+DEPEND="
+	test? (
+		${RDEPEND}
+		dev-python/nose[${PYTHON_USEDEP}]
+		)
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	"
+RDEPEND="
+	dev-python/joblib[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/scikits_learn[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	plot? ( dev-python/matplotlib[${PYTHON_USEDEP}] )"
+
+# (Temporarily) commented out, since Gentoo sci-libs/scikits_learn decided it
+# is a mess to maintain system joblib usage
+#PATCHES=( "${FILESDIR}/0.4.1-bundled_joblib_test.patch" )
+
+python_prepare_all() {
+	# upstream is reluctant to *not* depend on bundled scikits_learn:
+	# https://github.com/nilearn/nilearn/pull/1398
+	# (Temporarily) commented out, since Gentoo sci-libs/scikits_learn decided it
+	# is a mess to maintain system joblib usage
+	#local f
+	#for f in nilearn/{*/*/,*/,}*.py; do
+	#	sed -r \
+	#		-e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \
+	#		-e 's/from (sklearn|\.|)\.externals import/import/' \
+	#	-i $f || die
+	#done
+
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	echo "backend: Agg" > matplotlibrc
+	#MPLCONFIGDIR=. nosetests -v || die
+	MPLCONFIGDIR=. pytest -vv || die
+}

diff --git a/sci-biology/nireg/metadata.xml b/sci-biology/nireg/metadata.xml
deleted file mode 100644
index d6592a893..000000000
--- a/sci-biology/nireg/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?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">
-Nireg is a package for nytive-python image registration.
-</longdescription>
-</pkgmetadata>

diff --git a/sci-biology/nireg/nireg-9999.ebuild b/sci-biology/nireg/nireg-9999.ebuild
deleted file mode 100644
index 980307fff..000000000
--- a/sci-biology/nireg/nireg-9999.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Image registration package for Python"
-HOMEPAGE="http://nipy.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/nipy/${PN}"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-KEYWORDS=""
-
-COMMONDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${COMMONDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? ( dev-python/nose[${PYTHON_USEDEP}] )"
-RDEPEND="${COMMONDEPEND}
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	"
-
-python_test() {
-	#nosetests -v || die
-	python -c "import nireg; nireg.test()" || die
-}