From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id EA674138359 for ; Sun, 27 Sep 2020 08:36:02 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id E1426E0819; Sun, 27 Sep 2020 08:36:01 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id C3C98E0819 for ; Sun, 27 Sep 2020 08:36:01 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 7D000335DA3 for ; Sun, 27 Sep 2020 08:36:00 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 0440E37B for ; Sun, 27 Sep 2020 08:35:59 +0000 (UTC) From: "Horea Christian" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Horea Christian" Message-ID: <1601195562.8b9cc8923541eccb9ebaca2ca5b996982f217c9a.chymera@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/samri/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/samri/samri-0.4.1.ebuild sci-biology/samri/samri-9999.ebuild X-VCS-Directories: sci-biology/samri/ X-VCS-Committer: chymera X-VCS-Committer-Name: Horea Christian X-VCS-Revision: 8b9cc8923541eccb9ebaca2ca5b996982f217c9a X-VCS-Branch: master Date: Sun, 27 Sep 2020 08:35:59 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 49bb6054-b069-488a-9c6a-388828ff33cb X-Archives-Hash: a47fe346261dfdbb759dafd84d2b0a86 commit: 8b9cc8923541eccb9ebaca2ca5b996982f217c9a Author: Horea Christian chymera eu> AuthorDate: Sun Sep 27 08:32:42 2020 +0000 Commit: Horea Christian gmail com> CommitDate: Sun Sep 27 08:32:42 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8b9cc892 sci-biology/samri: PYTHON_COMPAT and live ebuild update Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: Horea Christian chymera.eu> sci-biology/samri/samri-0.4.1.ebuild | 4 ++-- sci-biology/samri/samri-9999.ebuild | 31 +++++++++++++------------------ 2 files changed, 15 insertions(+), 20 deletions(-) diff --git a/sci-biology/samri/samri-0.4.1.ebuild b/sci-biology/samri/samri-0.4.1.ebuild index 264e768dc..b3d3be34d 100644 --- a/sci-biology/samri/samri-0.4.1.ebuild +++ b/sci-biology/samri/samri-0.4.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -PYTHON_COMPAT=( python3_6 ) +PYTHON_COMPAT=( python3_7 ) inherit distutils-r1 diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild index d9913f2f9..fc663fcbc 100644 --- a/sci-biology/samri/samri-9999.ebuild +++ b/sci-biology/samri/samri-9999.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -PYTHON_COMPAT=( python{3_4,3_5,3_6} ) +PYTHON_COMPAT=( python3_7 ) -inherit distutils-r1 git-r3 prefix +inherit distutils-r1 git-r3 DESCRIPTION="Small Animal Magnetic Resonance Imaging" HOMEPAGE="https://github.com/IBT-FMI/SAMRI" @@ -17,8 +17,6 @@ SLOT="0" IUSE="+atlases labbookdb test" KEYWORDS="" -# Numpy dependency to circumvent scikits_learn dependency bug: -# https://bugs.gentoo.org/653052 DEPEND=" test? ( dev-python/pytest[${PYTHON_USEDEP}] @@ -32,28 +30,29 @@ RDEPEND=" >=dev-python/matplotlib-2.0.2[${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[${PYTHON_USEDEP}] + >=media-gfx/blender-2.83.4 >=sci-biology/fsl-5.0.9 sci-biology/bru2nii atlases? ( sci-biology/mouse-brain-atlases ) labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) sci-libs/nibabel[${PYTHON_USEDEP}] >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] - >=sci-libs/nipype-0.14.0_pre20170830[${PYTHON_USEDEP}] + >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] sci-libs/pybids[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] + sci-libs/scikits_image[${PYTHON_USEDEP}] sci-biology/ants sci-biology/afni sci-biology/nilearn[${PYTHON_USEDEP}] - " +" REQUIRED_USE="test? ( atlases )" src_prepare() { distutils-r1_src_prepare - sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ *` - sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \"/usr/ *` + 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 $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) } @@ -64,12 +63,8 @@ python_test() { export PATH=${TEST_DIR}/scripts:$PATH export PYTHONIOENCODING=utf-8 ./test_scripts.sh || die "Test scripts failed." - sed -i \ - -e '1s/^/import pytest \n/' \ - -e "/def test_bru2bids():/i@pytest.mark.skip('Skipped by Portage, as this was already tested in test_scripts.sh')" \ - samri/pipelines/tests/test_reposit.py || die - cd "${BUILD_DIR}" || die - sed -i -e "s:'/tmp/:'$T/:g" `grep -rl "'/tmp/"` - pytest -vv || die - sed -i -e "s:'$T/:'/tmp/:g" `grep -rl "'$T/"` + 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 -k "not longtime" || die }