From aff4737d9c21233bc0ec5295460306d9da038800 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sun, 3 Jan 2021 00:21:55 -0500 Subject: [PATCH] sci-biology/samri: superseded by Gentoo Science Signed-off-by: Horea Christian --- sci-biology/samri/ChangeLog | 24 ---------- sci-biology/samri/Manifest | 1 - sci-biology/samri/metadata.xml | 22 --------- sci-biology/samri/samri-0.4.2.ebuild | 56 ---------------------- sci-biology/samri/samri-9999.ebuild | 70 ---------------------------- 5 files changed, 173 deletions(-) delete mode 100644 sci-biology/samri/ChangeLog delete mode 100644 sci-biology/samri/Manifest delete mode 100644 sci-biology/samri/metadata.xml delete mode 100644 sci-biology/samri/samri-0.4.2.ebuild delete mode 100644 sci-biology/samri/samri-9999.ebuild diff --git a/sci-biology/samri/ChangeLog b/sci-biology/samri/ChangeLog deleted file mode 100644 index 345d9b5..0000000 --- a/sci-biology/samri/ChangeLog +++ /dev/null @@ -1,24 +0,0 @@ - 25 Sep 2020; samri-0.4.2.ebuild, samri-9999.ebuild: - sci-biology/samri: updated scipy dependency category - -*samri-0.4.2 (10 Jan 2020) - - 10 Jan 2020; +samri-0.4.2.ebuild: - sci-biology/samri: version bump 0.4.2 ahead of Gentoo Science - - 08 Dec 2019; -Manifest, -samri-0.4.1.ebuild: - sci-biology/samri: migrated version to Gentoo Science https://gitweb.gentoo.o - rg/proj/sci.git/commit/?id=e68c1eb1aea94ee2860d3b9feb079932114904ea - -*samri-0.4.1 (08 Dec 2019) - - 08 Dec 2019; +samri-0.4.1.ebuild, -samri-0.4.ebuild: - sci-biology/samri: version bump 0.4.1 ahead of Gentoo Science - -*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/Manifest b/sci-biology/samri/Manifest deleted file mode 100644 index 69cc282..0000000 --- a/sci-biology/samri/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST samri-0.4.2.tar.gz 4115783 SHA256 bf2d14a57e153d1dbfdb6471434412a1ab00c92dd8cd4a858fa9c9b7703dfae6 SHA512 cb5853ea0d47a3cfd61a0064a1ab776f34dc5178fbe53d515452c03b5b3b24e39d1fe22f6f75e3918c86aaac7517aac05bc911ea8ffdb5a4c3ef07b5cff63880 WHIRLPOOL dd9f42ec3b5d3280968560f5d81bb8db252f9256ad42f888af1b8ceaed57946febe69d3e6dc11824a9713fa5ae51d62f38e7ee1b333d6f2c7279c76af9b18e32 diff --git a/sci-biology/samri/metadata.xml b/sci-biology/samri/metadata.xml deleted file mode 100644 index 4203e6f..0000000 --- a/sci-biology/samri/metadata.xml +++ /dev/null @@ -1,22 +0,0 @@ - - - - - chr@chymera.eu - Horea Christian - - - SAMRI (Small Animal Magnetic Resonance Imaging) — pronounced "Sam-rye" — provides - fMRI preprocessing, metadata parsing, and data analysis functions and workflows. - SAMRI integrates functionalities from a number of other packages to create - higher-level tools. The resulting interfaces aim to maximize reproducibility, - simplify batch processing, and minimize the number of function calls required to - generate figures and statistical summaries from the raw data. - - - Pipe data from LabbookDB databases. - - - IBT-FMI/SAMRI - - diff --git a/sci-biology/samri/samri-0.4.2.ebuild b/sci-biology/samri/samri-0.4.2.ebuild deleted file mode 100644 index c896fb1..0000000 --- a/sci-biology/samri/samri-0.4.2.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_6 ) - -inherit distutils-r1 - -DESCRIPTION="Small Animal Magnetic Resonance Imaging" -HOMEPAGE="https://github.com/IBT-FMI/SAMRI" -SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="labbookdb test" -KEYWORDS="~amd64" - -DEPEND=" - test? ( - dev-python/pytest[${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[${PYTHON_USEDEP}] - dev-python/scipy[${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-biology/ants - sci-biology/afni - sci-biology/nilearn[${PYTHON_USEDEP}] -" - -S="${WORKDIR}/SAMRI-${PV}" - -src_prepare() { - sed -i -e "s:/usr:${EPREFIX}/usr:g" `grep -rlI \'/usr/ samri` || die - sed -i -e "s:/usr:${EPREFIX}/usr:g" `grep -rlI /usr/ test_scripts.sh` || die - distutils-r1_src_prepare -} diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild deleted file mode 100644 index 77904f5..0000000 --- a/sci-biology/samri/samri-9999.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{5,6} ) - -inherit distutils-r1 git-r3 - -DESCRIPTION="Small Animal Magnetic Resonance Imaging" -HOMEPAGE="https://github.com/IBT-FMI/SAMRI" -SRC_URI="" -EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI" - -LICENSE="GPL-3" -SLOT="0" -IUSE="labbookdb test" -KEYWORDS="" - -DEPEND=" - test? ( - dev-python/pytest[${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[${PYTHON_USEDEP}] - dev-python/scipy[${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-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 -}