sci-biology/samri: superseded by Gentoo Science
Signed-off-by: Horea Christian <chr@chymera.eu>
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Horea Christian
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25 Sep 2020; <chymera@gentoo.org> samri-0.4.2.ebuild, samri-9999.ebuild:
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sci-biology/samri: updated scipy dependency category
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*samri-0.4.2 (10 Jan 2020)
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10 Jan 2020; <chymera@gentoo.org> +samri-0.4.2.ebuild:
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sci-biology/samri: version bump 0.4.2 ahead of Gentoo Science
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08 Dec 2019; <chymera@gentoo.org> -Manifest, -samri-0.4.1.ebuild:
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sci-biology/samri: migrated version to Gentoo Science https://gitweb.gentoo.o
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rg/proj/sci.git/commit/?id=e68c1eb1aea94ee2860d3b9feb079932114904ea
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*samri-0.4.1 (08 Dec 2019)
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08 Dec 2019; <chymera@gentoo.org> +samri-0.4.1.ebuild, -samri-0.4.ebuild:
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sci-biology/samri: version bump 0.4.1 ahead of Gentoo Science
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*samri-9999 (12 Nov 2019)
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12 Nov 2019; <chymera@gentoo.org> +samri-9999.ebuild:
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sci-biology/samri: live package with test suite
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12 Nov 2019; <chymera@gentoo.org> metadata.xml, samri-0.4.ebuild:
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sci-biology/samri:
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DIST samri-0.4.2.tar.gz 4115783 SHA256 bf2d14a57e153d1dbfdb6471434412a1ab00c92dd8cd4a858fa9c9b7703dfae6 SHA512 cb5853ea0d47a3cfd61a0064a1ab776f34dc5178fbe53d515452c03b5b3b24e39d1fe22f6f75e3918c86aaac7517aac05bc911ea8ffdb5a4c3ef07b5cff63880 WHIRLPOOL dd9f42ec3b5d3280968560f5d81bb8db252f9256ad42f888af1b8ceaed57946febe69d3e6dc11824a9713fa5ae51d62f38e7ee1b333d6f2c7279c76af9b18e32
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<?xml version='1.0' encoding='UTF-8'?>
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="person">
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<email>chr@chymera.eu</email>
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<name>Horea Christian</name>
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</maintainer>
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<longdescription lang="en">
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SAMRI (Small Animal Magnetic Resonance Imaging) — pronounced "Sam-rye" — provides
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fMRI preprocessing, metadata parsing, and data analysis functions and workflows.
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SAMRI integrates functionalities from a number of other packages to create
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higher-level tools. The resulting interfaces aim to maximize reproducibility,
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simplify batch processing, and minimize the number of function calls required to
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generate figures and statistical summaries from the raw data.
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</longdescription>
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<use>
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<flag name="labbookdb">Pipe data from LabbookDB databases.</flag>
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</use>
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<upstream>
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<remote-id type="github">IBT-FMI/SAMRI</remote-id>
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</upstream>
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</pkgmetadata>
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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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EAPI=7
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PYTHON_COMPAT=( python3_6 )
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inherit distutils-r1
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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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SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
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LICENSE="GPL-3"
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SLOT="0"
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IUSE="labbookdb test"
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KEYWORDS="~amd64"
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DEPEND="
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test? (
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dev-python/pytest[${PYTHON_USEDEP}]
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sci-biology/samri_bidsdata
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sci-biology/samri_bindata
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)
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"
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RDEPEND="
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dev-python/argh[${PYTHON_USEDEP}]
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dev-python/joblib[${PYTHON_USEDEP}]
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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
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>=sci-biology/fsl-5.0.9
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sci-biology/bru2nii
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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[${PYTHON_USEDEP}]
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>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
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<=sci-libs/pybids-0.6.5[${PYTHON_USEDEP}]
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sci-libs/scikits_image[${PYTHON_USEDEP}]
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sci-biology/ants
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sci-biology/afni
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sci-biology/nilearn[${PYTHON_USEDEP}]
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"
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S="${WORKDIR}/SAMRI-${PV}"
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src_prepare() {
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sed -i -e "s:/usr:${EPREFIX}/usr:g" `grep -rlI \'/usr/ samri` || die
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sed -i -e "s:/usr:${EPREFIX}/usr:g" `grep -rlI /usr/ test_scripts.sh` || die
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distutils-r1_src_prepare
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}
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# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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PYTHON_COMPAT=( python3_{5,6} )
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inherit distutils-r1 git-r3
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DESCRIPTION="Small Animal Magnetic Resonance Imaging"
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HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
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SRC_URI=""
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EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI"
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LICENSE="GPL-3"
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SLOT="0"
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IUSE="labbookdb test"
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KEYWORDS=""
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DEPEND="
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test? (
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dev-python/pytest[${PYTHON_USEDEP}]
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sci-biology/samri_bidsdata
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sci-biology/samri_bindata
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)
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"
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RDEPEND="
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dev-python/argh[${PYTHON_USEDEP}]
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dev-python/joblib[${PYTHON_USEDEP}]
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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
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>=sci-biology/fsl-5.0.9
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sci-biology/bru2nii
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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[${PYTHON_USEDEP}]
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>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
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<=sci-libs/pybids-0.6.5[${PYTHON_USEDEP}]
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sci-libs/scikits_image[${PYTHON_USEDEP}]
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sci-biology/ants
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sci-biology/afni
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sci-biology/nilearn[${PYTHON_USEDEP}]
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"
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#S="${WORKDIR}/SAMRI-${PV}"
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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/ 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 $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
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}
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python_test() {
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distutils_install_for_testing
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export MPLBACKEND="agg"
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export PATH=${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 -e \
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"/def test_bru2bids():/i@pytest.mark.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 || die
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}
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