[gentoo-commits] proj/sci:master commit in: sci-biology/samri/

[Horea Christian]

commit:     8a9e478b567b41ec475344acf3f9e3f7d18e765a
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 09:27:43 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 09:27:43 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8a9e478b

sci-biology/samri: version bump 0.5

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/samri/samri-0.5.ebuild | 71 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)

diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
new file mode 100644
index 000000000..24912c9c9
--- /dev/null
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="Small Animal Magnetic Resonance Imaging"
+HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
+SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="+atlases labbookdb test"
+KEYWORDS="~amd64"
+
+DEPEND="
+	test? (
+		dev-python/pytest[${PYTHON_USEDEP}]
+		sci-biology/samri_bidsdata
+		sci-biology/samri_bindata
+		)
+	"
+RDEPEND="
+	dev-python/argh[${PYTHON_USEDEP}]
+	dev-python/joblib[${PYTHON_USEDEP}]
+	>=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dev-python/seaborn[${PYTHON_USEDEP}]
+	dev-python/statsmodels[${PYTHON_USEDEP}]
+	>=media-gfx/blender-2.83.4
+	>=sci-biology/fsl-5.0.9
+	sci-biology/bru2nii
+	atlases? ( sci-biology/mouse-brain-atlases )
+	labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
+	>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
+	sci-libs/pybids[${PYTHON_USEDEP}]
+	sci-libs/scikits_image[${PYTHON_USEDEP}]
+	sci-biology/ants
+	sci-biology/afni
+	sci-biology/nilearn[${PYTHON_USEDEP}]
+"
+
+REQUIRED_USE="test? ( atlases )"
+
+S="${WORKDIR}/SAMRI-${PV}"
+
+src_prepare() {
+	distutils-r1_src_prepare
+	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri`
+	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh`
+	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
+}
+
+python_test() {
+	distutils_install_for_testing
+	export MPLBACKEND="agg"
+	export PATH=${TEST_DIR}/scripts:$PATH
+	export PYTHONIOENCODING=utf-8
+	./test_scripts.sh || die "Test scripts failed."
+	sed -i -e \
+		"/def test_bru2bids():/i@×××××××××××.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
+		samri/pipelines/tests/test_repos.py || die
+	pytest -vv -k "not longtime" || die
+}