diff options
Diffstat (limited to 'sci-biology/samri')
| -rw-r--r-- | sci-biology/samri/Manifest | 4 | ||||
| -rw-r--r-- | sci-biology/samri/samri-0.4.1.ebuild | 58 | ||||
| -rw-r--r-- | sci-biology/samri/samri-0.5.3.ebuild (renamed from sci-biology/samri/samri-0.5.ebuild) | 41 | ||||
| -rw-r--r-- | sci-biology/samri/samri-0.5.4.ebuild | 77 | ||||
| -rw-r--r-- | sci-biology/samri/samri-9999.ebuild | 40 |
5 files changed, 125 insertions, 95 deletions
diff --git a/sci-biology/samri/Manifest b/sci-biology/samri/Manifest index d8c689507..26d7dd5ed 100644 --- a/sci-biology/samri/Manifest +++ b/sci-biology/samri/Manifest @@ -1,2 +1,2 @@ -DIST samri-0.4.1.tar.gz 4115417 BLAKE2B 882b1fbf213f85919a790d669365498c06269a2cb37ba859606e0e4bd696116e954b6683dd636ff34406b2394b4ae3d743c1840a789a828ca3d535b27c0a80da SHA512 c2eef33e725d0d5b87f30ce8da51d9c46ce735a8d82e41f93eba8d225b58eead4777441db4be9078e7f29b3f92d12525d729dddea888fd7e9a66ba5e607d8caf -DIST samri-0.5.tar.gz 4117149 BLAKE2B 1767d6d07726431e43dad5f843eee04bd5111dde3174905b79b938aa94dbb340ca3f3d6316c6720bf01212b87c895df47c965738dff70ec1debbbd542bb77043 SHA512 94fb981adf78b2062e1beac8433bca34e3db90964f720918603e2b89d617b4dfe9f4bc1591b6953e060553ea0014ebca4db62aa0f5b264feb084bc785a48c367 +DIST samri-0.5.3.tar.gz 4122035 BLAKE2B 343dc6de7acf74b5fc169c1f07a4a7209483bee1d050021045a9582d13ea9ae2b8bd4dba0f7f876548e218863cd01bf6d12e571e2d83860366e88ceec7f8441c SHA512 fb9c98843477a35ec313d9284c1c23777af7c6c29fbaa3672b6aa7f7357a81ef874883e0f09f97f52a75febed11deb714343bdadc06708f3a5dcb12fea121a06 +DIST samri-0.5.4.tar.gz 4122057 BLAKE2B 3afdfe6198bc61697cac9ab80560d438d3c488b182d0da9b4a8321efca99d733c964bde000ef8a6a8b849df753f3369d8ea3ba984c8a9736fef466fe196dc003 SHA512 c783156b4eb66b146d039338381867d5683c2f90214d4451448da631609e1e0113f803851a04965b9e400ca5bc69910ec8cbaa1af4b023a89ded0ba6b38901b8 diff --git a/sci-biology/samri/samri-0.4.1.ebuild b/sci-biology/samri/samri-0.4.1.ebuild deleted file mode 100644 index 79c5949de..000000000 --- a/sci-biology/samri/samri-0.4.1.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..8} ) - -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 -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="labbookdb test" -KEYWORDS="~amd64" -RESTRICT="!test? ( test )" - -DEPEND=" - test? ( - dev-python/pytest[${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[${PYTHON_USEDEP}] - dev-python/seaborn[${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/scikit-image[${PYTHON_USEDEP}] - dev-python/scipy[${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 $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) -} diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.3.ebuild index 8faa270ab..f632f83a8 100644 --- a/sci-biology/samri/samri-0.5.ebuild +++ b/sci-biology/samri/samri-0.5.3.ebuild @@ -1,25 +1,31 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..8} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 prefix DESCRIPTION="Small Animal Magnetic Resonance Imaging" HOMEPAGE="https://github.com/IBT-FMI/SAMRI" -SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" +if [ "$PV" == "9999" ]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git" +else + SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" + S="${WORKDIR}/SAMRI-${PV}" +fi LICENSE="GPL-3" SLOT="0" -IUSE="+atlases labbookdb test" -KEYWORDS="~amd64" -RESTRICT="!test? ( test )" +IUSE="+atlases labbookdb" +REQUIRED_USE="test? ( atlases )" DEPEND=" test? ( - dev-python/pytest[${PYTHON_USEDEP}] sci-biology/samri_bidsdata sci-biology/samri_bindata ) @@ -36,26 +42,25 @@ RDEPEND=" >=media-gfx/blender-2.83.4 >=sci-biology/fsl-5.0.9 sci-biology/bru2nii - atlases? ( sci-biology/mouse-brain-atlases ) + atlases? ( sci-biology/mouse-brain-templates ) 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[${PYTHON_USEDEP}] - sci-libs/scikit-image[${PYTHON_USEDEP}] + <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] sci-biology/ants sci-biology/afni sci-biology/nilearn[${PYTHON_USEDEP}] " -REQUIRED_USE="test? ( atlases )" - -S="${WORKDIR}/SAMRI-${PV}" +distutils_enable_tests pytest +distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon 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` + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) } @@ -68,5 +73,5 @@ python_test() { sed -i -e \ "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ samri/pipelines/tests/test_repos.py || die - pytest -vv -k "not longtime" || die + epytest -k "not longtime" } diff --git a/sci-biology/samri/samri-0.5.4.ebuild b/sci-biology/samri/samri-0.5.4.ebuild new file mode 100644 index 000000000..f632f83a8 --- /dev/null +++ b/sci-biology/samri/samri-0.5.4.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 prefix + +DESCRIPTION="Small Animal Magnetic Resonance Imaging" +HOMEPAGE="https://github.com/IBT-FMI/SAMRI" +if [ "$PV" == "9999" ]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git" +else + SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" + S="${WORKDIR}/SAMRI-${PV}" +fi + +LICENSE="GPL-3" +SLOT="0" +IUSE="+atlases labbookdb" +REQUIRED_USE="test? ( atlases )" + +DEPEND=" + test? ( + sci-biology/samri_bidsdata + sci-biology/samri_bindata + ) + " +RDEPEND=" + dev-python/argh[${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[${PYTHON_USEDEP}] + >=media-gfx/blender-2.83.4 + >=sci-biology/fsl-5.0.9 + sci-biology/bru2nii + atlases? ( sci-biology/mouse-brain-templates ) + labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) + sci-libs/nibabel[${PYTHON_USEDEP}] + >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] + >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] + <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] + sci-biology/ants + sci-biology/afni + sci-biology/nilearn[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest +distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon + +src_prepare() { + distutils-r1_src_prepare + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die + eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) +} + +python_test() { + distutils_install_for_testing + export MPLBACKEND="agg" + export PATH=${TEST_DIR}/scripts:$PATH + export PYTHONIOENCODING=utf-8 + ./test_scripts.sh || die "Test scripts failed." + sed -i -e \ + "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ + samri/pipelines/tests/test_repos.py || die + epytest -k "not longtime" +} diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild index 507d6a53c..f632f83a8 100644 --- a/sci-biology/samri/samri-9999.ebuild +++ b/sci-biology/samri/samri-9999.ebuild @@ -1,26 +1,31 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..8} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 git-r3 +inherit distutils-r1 prefix DESCRIPTION="Small Animal Magnetic Resonance Imaging" HOMEPAGE="https://github.com/IBT-FMI/SAMRI" -SRC_URI="" -EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI" +if [ "$PV" == "9999" ]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git" +else + SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" + S="${WORKDIR}/SAMRI-${PV}" +fi LICENSE="GPL-3" SLOT="0" -IUSE="+atlases labbookdb test" -KEYWORDS="" -RESTRICT="!test? ( test )" +IUSE="+atlases labbookdb" +REQUIRED_USE="test? ( atlases )" DEPEND=" test? ( - dev-python/pytest[${PYTHON_USEDEP}] sci-biology/samri_bidsdata sci-biology/samri_bindata ) @@ -37,24 +42,25 @@ RDEPEND=" >=media-gfx/blender-2.83.4 >=sci-biology/fsl-5.0.9 sci-biology/bru2nii - atlases? ( sci-biology/mouse-brain-atlases ) + atlases? ( sci-biology/mouse-brain-templates ) 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[${PYTHON_USEDEP}] - sci-libs/scikit-image[${PYTHON_USEDEP}] + <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] sci-biology/ants sci-biology/afni sci-biology/nilearn[${PYTHON_USEDEP}] " -REQUIRED_USE="test? ( atlases )" +distutils_enable_tests pytest +distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon 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` + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) } @@ -67,5 +73,5 @@ python_test() { 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 + epytest -k "not longtime" } |