diff --git a/sci-biology/samri/ChangeLog b/sci-biology/samri/ChangeLog index 2bd93f1..a6b3459 100644 --- a/sci-biology/samri/ChangeLog +++ b/sci-biology/samri/ChangeLog @@ -1,2 +1,7 @@ +*samri-9999 (12 Nov 2019) + + 12 Nov 2019; +samri-9999.ebuild: + sci-biology/samri: live package with test suite + 12 Nov 2019; metadata.xml, samri-0.4.ebuild: sci-biology/samri: diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild new file mode 100644 index 0000000..96ad85c --- /dev/null +++ b/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 +}