commit: 3816342c4d4ad5da753dedcdcc7a50aaa27ac9be
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue May 2 01:03:16 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue May 2 01:03:16 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3816342c
sci-biology/samri: add 0.5.4
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.4.ebuild | 78 ++++++++++++++++++++++++++++++++++++
1 file changed, 78 insertions(+)
diff --git a/sci-biology/samri/samri-0.5.4.ebuild
b/sci-biology/samri/samri-0.5.4.ebuild
new file mode 100644
index 000000000..56351ada3
--- /dev/null
+++ b/sci-biology/samri/samri-0.5.4.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 prefix
+
+DESCRIPTION="Small Animal Magnetic Resonance Imaging"
+HOMEPAGE="https://github.com/IBT-FMI/SAMRI";
+if [ "$PV" == "9999" ]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git";
+else
+ SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz ->
${P}.tar.gz"
+ KEYWORDS="~amd64"
+ S="${WORKDIR}/SAMRI-${PV}"
+fi
+
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="+atlases labbookdb"
+REQUIRED_USE="test? ( atlases )"
+
+DEPEND="
+ test? (
+ sci-biology/samri_bidsdata
+ sci-biology/samri_bindata
+ )
+ "
+RDEPEND="
+ dev-python/argh[${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[${PYTHON_USEDEP}]
+ >=media-gfx/blender-2.83.4
+ >=sci-biology/fsl-5.0.9
+ sci-biology/bru2nii
+ atlases? ( sci-biology/mouse-brain-templates )
+ labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
+ sci-libs/nibabel[${PYTHON_USEDEP}]
+ >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
+ >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
+ <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
+ sci-libs/scikit-image[${PYTHON_USEDEP}]
+ sci-biology/ants
+ sci-biology/afni
+ sci-biology/nilearn[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon
+
+src_prepare() {
+ distutils-r1_src_prepare
+ sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/
samri` || die
+ sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/
test_scripts.sh` || die
+ 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():/[email protected]('Removed in full
test suite, as this is already tested in `test_scripts.sh`')" \
+ samri/pipelines/tests/test_repos.py || die
+ epytest -k "not longtime"
+}
