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commit: 8b9cc8923541eccb9ebaca2ca5b996982f217c9a |
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Author: Horea Christian <chr <AT> chymera <DOT> eu> |
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AuthorDate: Sun Sep 27 08:32:42 2020 +0000 |
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Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> |
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CommitDate: Sun Sep 27 08:32:42 2020 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8b9cc892 |
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|
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sci-biology/samri: PYTHON_COMPAT and live ebuild update |
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|
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Package-Manager: Portage-3.0.8, Repoman-3.0.1 |
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Signed-off-by: Horea Christian <chr <AT> chymera.eu> |
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|
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sci-biology/samri/samri-0.4.1.ebuild | 4 ++-- |
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sci-biology/samri/samri-9999.ebuild | 31 +++++++++++++------------------ |
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2 files changed, 15 insertions(+), 20 deletions(-) |
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|
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diff --git a/sci-biology/samri/samri-0.4.1.ebuild b/sci-biology/samri/samri-0.4.1.ebuild |
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index 264e768dc..b3d3be34d 100644 |
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--- a/sci-biology/samri/samri-0.4.1.ebuild |
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+++ b/sci-biology/samri/samri-0.4.1.ebuild |
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@@ -1,9 +1,9 @@ |
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-# Copyright 1999-2019 Gentoo Authors |
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+# Copyright 1999-2020 Gentoo Authors |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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EAPI=7 |
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|
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-PYTHON_COMPAT=( python3_6 ) |
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+PYTHON_COMPAT=( python3_7 ) |
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|
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inherit distutils-r1 |
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|
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|
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diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild |
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index d9913f2f9..fc663fcbc 100644 |
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--- a/sci-biology/samri/samri-9999.ebuild |
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+++ b/sci-biology/samri/samri-9999.ebuild |
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@@ -1,11 +1,11 @@ |
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-# Copyright 1999-2019 Gentoo Authors |
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+# Copyright 1999-2020 Gentoo Authors |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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EAPI=7 |
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|
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-PYTHON_COMPAT=( python{3_4,3_5,3_6} ) |
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+PYTHON_COMPAT=( python3_7 ) |
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|
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-inherit distutils-r1 git-r3 prefix |
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+inherit distutils-r1 git-r3 |
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|
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DESCRIPTION="Small Animal Magnetic Resonance Imaging" |
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HOMEPAGE="https://github.com/IBT-FMI/SAMRI" |
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@@ -17,8 +17,6 @@ SLOT="0" |
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IUSE="+atlases labbookdb test" |
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KEYWORDS="" |
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|
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-# Numpy dependency to circumvent scikits_learn dependency bug: |
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-# https://bugs.gentoo.org/653052 |
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DEPEND=" |
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test? ( |
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dev-python/pytest[${PYTHON_USEDEP}] |
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@@ -32,28 +30,29 @@ RDEPEND=" |
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>=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}] |
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>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] |
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dev-python/pandas[${PYTHON_USEDEP}] |
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+ dev-python/scipy[${PYTHON_USEDEP}] |
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dev-python/seaborn[${PYTHON_USEDEP}] |
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dev-python/statsmodels[${PYTHON_USEDEP}] |
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+ >=media-gfx/blender-2.83.4 |
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>=sci-biology/fsl-5.0.9 |
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sci-biology/bru2nii |
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atlases? ( sci-biology/mouse-brain-atlases ) |
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labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) |
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sci-libs/nibabel[${PYTHON_USEDEP}] |
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>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] |
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- >=sci-libs/nipype-0.14.0_pre20170830[${PYTHON_USEDEP}] |
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+ >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] |
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sci-libs/pybids[${PYTHON_USEDEP}] |
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- dev-python/scipy[${PYTHON_USEDEP}] |
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+ sci-libs/scikits_image[${PYTHON_USEDEP}] |
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sci-biology/ants |
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sci-biology/afni |
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sci-biology/nilearn[${PYTHON_USEDEP}] |
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- " |
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+" |
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|
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REQUIRED_USE="test? ( atlases )" |
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|
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src_prepare() { |
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distutils-r1_src_prepare |
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- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ *` |
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- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \"/usr/ *` |
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+ sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` |
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sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` |
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eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) |
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} |
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@@ -64,12 +63,8 @@ python_test() { |
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export PATH=${TEST_DIR}/scripts:$PATH |
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export PYTHONIOENCODING=utf-8 |
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./test_scripts.sh || die "Test scripts failed." |
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- sed -i \ |
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- -e '1s/^/import pytest \n/' \ |
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- -e "/def test_bru2bids():/i@×××××××××××.skip('Skipped by Portage, as this was already tested in test_scripts.sh')" \ |
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- samri/pipelines/tests/test_reposit.py || die |
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- cd "${BUILD_DIR}" || die |
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- sed -i -e "s:'/tmp/:'$T/:g" `grep -rl "'/tmp/"` |
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- pytest -vv || die |
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- sed -i -e "s:'$T/:'/tmp/:g" `grep -rl "'$T/"` |
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+ sed -i -e \ |
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+ "/def test_bru2bids():/i@×××××××××××.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ |
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+ samri/pipelines/tests/test_repos.py || die |
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+ pytest -vv -k "not longtime" || die |
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} |
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