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

["Horea Christian" <horea.christ@gmail.com>]

commit:     8b9cc8923541eccb9ebaca2ca5b996982f217c9a
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 08:32:42 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 08:32:42 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8b9cc892

sci-biology/samri: PYTHON_COMPAT and live ebuild update

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

 sci-biology/samri/samri-0.4.1.ebuild |  4 ++--
 sci-biology/samri/samri-9999.ebuild  | 31 +++++++++++++------------------
 2 files changed, 15 insertions(+), 20 deletions(-)

diff --git a/sci-biology/samri/samri-0.4.1.ebuild b/sci-biology/samri/samri-0.4.1.ebuild
index 264e768dc..b3d3be34d 100644
--- a/sci-biology/samri/samri-0.4.1.ebuild
+++ b/sci-biology/samri/samri-0.4.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_6 )
+PYTHON_COMPAT=( python3_7 )
 
 inherit distutils-r1
 

diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index d9913f2f9..fc663fcbc 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python{3_4,3_5,3_6} )
+PYTHON_COMPAT=( python3_7 )
 
-inherit distutils-r1 git-r3 prefix
+inherit distutils-r1 git-r3
 
 DESCRIPTION="Small Animal Magnetic Resonance Imaging"
 HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
@@ -17,8 +17,6 @@ SLOT="0"
 IUSE="+atlases labbookdb test"
 KEYWORDS=""
 
-# Numpy dependency to circumvent scikits_learn dependency bug:
-# https://bugs.gentoo.org/653052
 DEPEND="
 	test? (
 		dev-python/pytest[${PYTHON_USEDEP}]
@@ -32,28 +30,29 @@ RDEPEND="
 	>=dev-python/matplotlib-2.0.2[${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-0.14.0_pre20170830[${PYTHON_USEDEP}]
+	>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
 	sci-libs/pybids[${PYTHON_USEDEP}]
-	dev-python/scipy[${PYTHON_USEDEP}]
+	sci-libs/scikits_image[${PYTHON_USEDEP}]
 	sci-biology/ants
 	sci-biology/afni
 	sci-biology/nilearn[${PYTHON_USEDEP}]
-	"
+"
 
 REQUIRED_USE="test? ( atlases )"
 
 src_prepare() {
 	distutils-r1_src_prepare
-	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ *`
-	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \"/usr/ *`
+	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 $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
 }
@@ -64,12 +63,8 @@ python_test() {
 	export PATH=${TEST_DIR}/scripts:$PATH
 	export PYTHONIOENCODING=utf-8
 	./test_scripts.sh || die "Test scripts failed."
-	sed -i \
-		-e '1s/^/import pytest \n/' \
-		-e "/def test_bru2bids():/i@pytest.mark.skip('Skipped by Portage, as this was already tested in test_scripts.sh')" \
-		samri/pipelines/tests/test_reposit.py || die
-	cd "${BUILD_DIR}" || die
-	sed -i -e "s:'/tmp/:'$T/:g" `grep -rl "'/tmp/"`
-	pytest -vv || die
-	sed -i -e "s:'$T/:'/tmp/:g" `grep -rl "'$T/"`
+	sed -i -e \
+		"/def test_bru2bids():/i@pytest.mark.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
 }