Merge branch 'master' of github.com:TheChymera/overlay

sci-biology/samri/ChangeLog

@@ -1,2 +1,7 @@
+*samri-9999 (12 Nov 2019)
+
+  12 Nov 2019;  <chymera@gentoo.org> +samri-9999.ebuild:
+  sci-biology/samri: live package with test suite
+
   12 Nov 2019;  <chymera@gentoo.org> metadata.xml, samri-0.4.ebuild:
   sci-biology/samri:

sci-biology/samri/samri-9999.ebuild

@@ -0,0 +1,70 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{5,6} )
+
+inherit distutils-r1 git-r3
+
+DESCRIPTION="Small Animal Magnetic Resonance Imaging"
+HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
+SRC_URI=""
+EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="labbookdb test"
+KEYWORDS=""
+
+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/seaborn[${PYTHON_USEDEP}]
+	dev-python/statsmodels[${PYTHON_USEDEP}]
+	media-gfx/blender
+	>=sci-biology/fsl-5.0.9
+	sci-biology/bru2nii
+	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-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}]
+"
+
+#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@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
+}