commit: e68c1eb1aea94ee2860d3b9feb079932114904ea
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Dec 8 14:54:04 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Dec 8 14:54:04 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e68c1eb1
sci-biology/samri: version bump 0.4.1
and old version deprecation
Package-Manager: Portage-2.3.78, Repoman-2.3.17
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.1.ebuild | 58 ----------------------
.../samri/{samri-0.2.ebuild => samri-0.4.1.ebuild} | 39 ++++++---------
2 files changed, 16 insertions(+), 81 deletions(-)
diff --git a/sci-biology/samri/samri-0.1.ebuild
b/sci-biology/samri/samri-0.1.ebuild
deleted file mode 100644
index 94598cb7c..000000000
--- a/sci-biology/samri/samri-0.1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# 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} )
-
-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 -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="atlases labbookdb test"
-KEYWORDS="~amd64 ~x86"
-
-# Numpy dependency to circumvent scikits_learn dependency bug:
-# https://bugs.gentoo.org/653052
-DEPEND="test? ( sci-biology/samri_bindata )"
-RDEPEND="
- dev-python/argh[${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/seaborn[${PYTHON_USEDEP}]
- dev-python/sqlalchemy[${PYTHON_USEDEP}]
- dev-python/statsmodels[${PYTHON_USEDEP}]
- >=sci-biology/fsl-5.0.9
- sci-biology/bru2nii
- atlases? ( sci-biology/mouse-brain-atlases )
- labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
- sci-libs/nibabel[${PYTHON_USEDEP}]
- >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
- >=sci-libs/nipype-0.14.0_pre20170830[${PYTHON_USEDEP}]
- sci-libs/pybids[${PYTHON_USEDEP}]
- sci-libs/scipy[${PYTHON_USEDEP}]
- sci-biology/ants
- sci-biology/afni
- sci-biology/nilearn[${PYTHON_USEDEP}]
- "
-
-S="${WORKDIR}/SAMRI-${PV}"
-
-python_test() {
- distutils_install_for_testing
- export MPLBACKEND="agg"
- export PATH=${TEST_DIR}/scripts:$PATH
- export PYTHONIOENCODING=utf-8
- pytest || die
- for i in samri/examples/*.py; do
- echo "Executing ${EPYTHON} ${i}"
- ${EPYTHON} "$i" || die "Example Python script $i failed with
${EPYTHON}"
- done
- ./test_scripts.sh || die "Test scripts failed."
-}
diff --git a/sci-biology/samri/samri-0.2.ebuild
b/sci-biology/samri/samri-0.4.1.ebuild
similarity index 58%
rename from sci-biology/samri/samri-0.2.ebuild
rename to sci-biology/samri/samri-0.4.1.ebuild
index 12c8d5e01..547b8e912 100644
--- a/sci-biology/samri/samri-0.2.ebuild
+++ b/sci-biology/samri/samri-0.4.1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+PYTHON_COMPAT=( python3_6 )
inherit distutils-r1
@@ -13,18 +13,16 @@
SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
-IUSE="+atlases labbookdb test"
-KEYWORDS="~amd64 ~x86"
+IUSE="labbookdb test"
+KEYWORDS="~amd64"
-# Numpy dependency to circumvent scikits_learn dependency bug:
-# https://bugs.gentoo.org/653052
DEPEND="
test? (
dev-python/pytest[${PYTHON_USEDEP}]
sci-biology/samri_bidsdata
sci-biology/samri_bindata
- )
- "
+ )
+"
RDEPEND="
dev-python/argh[${PYTHON_USEDEP}]
dev-python/joblib[${PYTHON_USEDEP}]
@@ -33,32 +31,27 @@ RDEPEND="
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/seaborn[${PYTHON_USEDEP}]
dev-python/statsmodels[${PYTHON_USEDEP}]
+ media-gfx/blender
>=sci-biology/fsl-5.0.9
sci-biology/bru2nii
- atlases? ( sci-biology/mouse-brain-atlases )
+ sci-biology/mouse-brain-atlases
labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
sci-libs/nibabel[${PYTHON_USEDEP}]
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
- >=sci-libs/nipype-0.14.0_pre20170830[${PYTHON_USEDEP}]
- sci-libs/pybids[${PYTHON_USEDEP}]
+ >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
+ <=sci-libs/pybids-0.6.5[${PYTHON_USEDEP}]
+ sci-libs/scikits_image[${PYTHON_USEDEP}]
sci-libs/scipy[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
- "
-
-REQUIRED_USE="test? ( atlases )"
+"
S="${WORKDIR}/SAMRI-${PV}"
-python_test() {
- distutils_install_for_testing
- export MPLBACKEND="agg"
- export PATH=${TEST_DIR}/scripts:$PATH
- export PYTHONIOENCODING=utf-8
- ./test_scripts.sh || die "Test scripts failed."
- sed -i -e \
- "/def test_bru2bids():/[email protected]('Removed in full
test suite, as this is already tested in `test_scripts.sh`')" \
- samri/pipelines/tests/test_repos.py || die
- pytest -vv || die
+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)
}
