commit: 913f326e5bdf103886c972943d4cb078a2d79761 Author: Horea Christian <horea.christ <AT> yandex <DOT> com> AuthorDate: Tue Jun 26 13:53:29 2018 +0000 Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> CommitDate: Tue Jun 26 14:02:50 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=913f326e
sci-biology/samri: new package Package-Manager: Portage-2.3.40, Repoman-2.3.9 profiles/package.mask | 4 +++ sci-biology/samri/metadata.xml | 20 +++++++++++++ sci-biology/samri/samri-0.1.ebuild | 58 +++++++++++++++++++++++++++++++++++++ sci-biology/samri/samri-9999.ebuild | 57 ++++++++++++++++++++++++++++++++++++ 4 files changed, 139 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 9ea56c307..3b55d3b32 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,6 +30,10 @@ #--- END OF EXAMPLES --- +# Horea Christian <horea.chr...@gmail.com> (10 Mar 2012) +# All versions depend on hard-masked sci-biology/afni. +sci-biology/samri + # Horea Christian <horea.chr...@gmail.com> (10 Mar 2012) # Serious bundling issues, upstream does not support Gentoo # or more generally unbundling. Masked until unbundling diff --git a/sci-biology/samri/metadata.xml b/sci-biology/samri/metadata.xml new file mode 100644 index 000000000..a98f0b857 --- /dev/null +++ b/sci-biology/samri/metadata.xml @@ -0,0 +1,20 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>horea.chr...@gmail.com</email> + <name>Horea Christian</name> + </maintainer> + <longdescription lang="en"> + SAMRI provides fMRI preprocessing, metadata parsing, and data analysis functions + and pipelines. SAMRI integrates functionalities from a number of other packages + to create higher-level tools. + </longdescription> + <use> + <flag name="atlases">Include dependency on compatible anatomica atlases.</flag> + <flag name="labbookdb">Pipe data from LabbookDB databases.</flag> + </use> + <upstream> + <remote-id type="github">IBT-FMI/SAMRI</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/samri/samri-0.1.ebuild b/sci-biology/samri/samri-0.1.ebuild new file mode 100644 index 000000000..94598cb7c --- /dev/null +++ b/sci-biology/samri/samri-0.1.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python{2_7,3_4,3_5} ) + +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 -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="atlases labbookdb test" +KEYWORDS="~amd64 ~x86" + +# Numpy dependency to circumvent scikits_learn dependency bug: +# https://bugs.gentoo.org/653052 +DEPEND="test? ( sci-biology/samri_bindata )" +RDEPEND=" + dev-python/argh[${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[${PYTHON_USEDEP}] + dev-python/sqlalchemy[${PYTHON_USEDEP}] + dev-python/statsmodels[${PYTHON_USEDEP}] + >=sci-biology/fsl-5.0.9 + sci-biology/bru2nii + atlases? ( sci-biology/mouse-brain-atlases ) + labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) + sci-libs/nibabel[${PYTHON_USEDEP}] + >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] + >=sci-libs/nipype-0.14.0_pre20170830[${PYTHON_USEDEP}] + sci-libs/pybids[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + sci-biology/ants + sci-biology/afni + sci-biology/nilearn[${PYTHON_USEDEP}] + " + +S="${WORKDIR}/SAMRI-${PV}" + +python_test() { + distutils_install_for_testing + export MPLBACKEND="agg" + export PATH=${TEST_DIR}/scripts:$PATH + export PYTHONIOENCODING=utf-8 + pytest || die + for i in samri/examples/*.py; do + echo "Executing ${EPYTHON} ${i}" + ${EPYTHON} "$i" || die "Example Python script $i failed with ${EPYTHON}" + done + ./test_scripts.sh || die "Test scripts failed." +} diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild new file mode 100644 index 000000000..24078c41e --- /dev/null +++ b/sci-biology/samri/samri-9999.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python{2_7,3_4,3_5} ) + +inherit distutils-r1 git-r3 + +DESCRIPTION="Small Animal Magnetic Resonance Imaging" +HOMEPAGE="https://github.com/IBT-FMI/SAMRI"; +SRC_URI="" +EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI"; + +LICENSE="GPL-3" +SLOT="0" +IUSE="atlases labbookdb test" +KEYWORDS="" + +# Numpy dependency to circumvent scikits_learn dependency bug: +# https://bugs.gentoo.org/653052 +DEPEND="test? ( sci-biology/samri_bindata )" +RDEPEND=" + dev-python/argh[${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[${PYTHON_USEDEP}] + dev-python/sqlalchemy[${PYTHON_USEDEP}] + dev-python/statsmodels[${PYTHON_USEDEP}] + >=sci-biology/fsl-5.0.9 + sci-biology/bru2nii + atlases? ( sci-biology/mouse-brain-atlases ) + labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) + sci-libs/nibabel[${PYTHON_USEDEP}] + >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] + >=sci-libs/nipype-0.14.0_pre20170830[${PYTHON_USEDEP}] + sci-libs/pybids[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + sci-biology/ants + sci-biology/afni + sci-biology/nilearn[${PYTHON_USEDEP}] + " + +python_test() { + distutils_install_for_testing + export MPLBACKEND="agg" + export PATH=${TEST_DIR}/scripts:$PATH + export PYTHONIOENCODING=utf-8 + pytest || die + for i in examples/*.py; do + echo "Executing ${EPYTHON} ${i}" + ${EPYTHON} "$i" || die "Example Python script $i failed with ${EPYTHON}" + done + ./test_scripts.sh || die "Test scripts failed." +}
