aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--sci-biology/samri/Manifest1
-rw-r--r--sci-biology/samri/samri-0.2.ebuild56
2 files changed, 57 insertions, 0 deletions
diff --git a/sci-biology/samri/Manifest b/sci-biology/samri/Manifest
index 1756e152f..8e2af4995 100644
--- a/sci-biology/samri/Manifest
+++ b/sci-biology/samri/Manifest
@@ -1 +1,2 @@
DIST samri-0.1.tar.gz 1767390 BLAKE2B 65fd268949b5e0e64d4f3aa9eef0fc7016a9404a468865634e1add74f4b8915f86bb7ee5ec9b8383b48ce0ab51624928cf4a6a65fda4595da67098cb72b00fdc SHA512 2d79a06455fae56edc1324a34186cfce2be4999733c502bbafcf6b310848ef4042012fd8f915f9a3ee7bf26f55398af19da93548d8d96453ba33a2ea22bfe775
+DIST samri-0.2.tar.gz 4091362 BLAKE2B 60cf74873027a0e033af946b48a3a3fe56462d3b7305a9a02bdded022af98bca50eb77b851b4d624816e90a18c18ed4ab17ddae22734de9ff404f5e26ed894b0 SHA512 85d0728bf44c62040d4d05736048a8a8d93ed580db763b07db65546de2891bbbb3036a661309cf37ac8ff256b0dcc28b47d4ce84a5a57bc95f3bcc3c24a5d989
diff --git a/sci-biology/samri/samri-0.2.ebuild b/sci-biology/samri/samri-0.2.ebuild
new file mode 100644
index 000000000..3b8f06a60
--- /dev/null
+++ b/sci-biology/samri/samri-0.2.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2019 Gentoo Authors
+# 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[${PYTHON_USEDEP}]
+ dev-python/statsmodels[${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
+ ./test_scripts.sh || die "Test scripts failed."
+ 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 || die
+}