* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2022-01-26 17:48 Andrew Ammerlaan
0 siblings, 0 replies; 29+ messages in thread
From: Andrew Ammerlaan @ 2022-01-26 17:48 UTC (permalink / raw
To: gentoo-commits
commit: a5362c2b5a6817a805335c0b3b4d6b883536b668
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 26 10:36:33 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Jan 26 10:36:33 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a5362c2b
sci-biology/samri: drop old and live
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/samri/samri-0.4.1.ebuild | 58 -----------------------------
sci-biology/samri/samri-9999.ebuild | 71 ------------------------------------
2 files changed, 129 deletions(-)
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 f94119541..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 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 -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="labbookdb test"
-KEYWORDS="~amd64"
-RESTRICT="!test? ( test )"
-
-DEPEND="
- test? (
- dev-python/pytest[${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 $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
-}
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
deleted file mode 100644
index 8dba8864c..000000000
--- a/sci-biology/samri/samri-9999.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..8} )
-
-inherit distutils-r1 prefix git-r3
-
-DESCRIPTION="Small Animal Magnetic Resonance Imaging"
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+atlases labbookdb test"
-KEYWORDS=""
-RESTRICT="!test? ( test )"
-
-DEPEND="
- test? (
- dev-python/pytest[${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[${PYTHON_USEDEP}]
- dev-python/scipy[${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[${PYTHON_USEDEP}]
- >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
- sci-libs/pybids[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${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/ 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:$PATH
- export PYTHONIOENCODING=utf-8
- ./test_scripts.sh || die "Test scripts failed."
- sed -i -e \
- "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
- samri/pipelines/tests/test_repos.py || die
- pytest -vv -k "not longtime" || die
-}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2024-02-16 2:11 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2024-02-16 2:11 UTC (permalink / raw
To: gentoo-commits
commit: 297ea3f7dcd4ee5fa24f0888703c15738c6732ef
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Feb 16 02:11:05 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Feb 16 02:11:05 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=297ea3f7
sci-biology/samri: updated sckikit-image package category
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.3.ebuild | 2 +-
sci-biology/samri/samri-0.5.4.ebuild | 2 +-
sci-biology/samri/samri-9999.ebuild | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/samri/samri-0.5.3.ebuild b/sci-biology/samri/samri-0.5.3.ebuild
index d6ffd5f1f..f632f83a8 100644
--- a/sci-biology/samri/samri-0.5.3.ebuild
+++ b/sci-biology/samri/samri-0.5.3.ebuild
@@ -48,7 +48,7 @@ RDEPEND="
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
+ dev-python/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
diff --git a/sci-biology/samri/samri-0.5.4.ebuild b/sci-biology/samri/samri-0.5.4.ebuild
index d6ffd5f1f..f632f83a8 100644
--- a/sci-biology/samri/samri-0.5.4.ebuild
+++ b/sci-biology/samri/samri-0.5.4.ebuild
@@ -48,7 +48,7 @@ RDEPEND="
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
+ dev-python/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index d6ffd5f1f..f632f83a8 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -48,7 +48,7 @@ RDEPEND="
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
+ dev-python/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2023-05-02 23:58 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2023-05-02 23:58 UTC (permalink / raw
To: gentoo-commits
commit: 43640a50ac9001267a0c8d2274213a6be0985ded
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue May 2 23:57:43 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue May 2 23:57:43 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=43640a50
sci-biology/samri: enable py3.11
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.3.ebuild | 2 +-
sci-biology/samri/samri-0.5.4.ebuild | 2 +-
sci-biology/samri/samri-9999.ebuild | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/samri/samri-0.5.3.ebuild b/sci-biology/samri/samri-0.5.3.ebuild
index d45474603..d6ffd5f1f 100644
--- a/sci-biology/samri/samri-0.5.3.ebuild
+++ b/sci-biology/samri/samri-0.5.3.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 prefix
diff --git a/sci-biology/samri/samri-0.5.4.ebuild b/sci-biology/samri/samri-0.5.4.ebuild
index d45474603..d6ffd5f1f 100644
--- a/sci-biology/samri/samri-0.5.4.ebuild
+++ b/sci-biology/samri/samri-0.5.4.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 prefix
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index d45474603..d6ffd5f1f 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 prefix
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2023-05-02 12:34 Andrew Ammerlaan
0 siblings, 0 replies; 29+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:34 UTC (permalink / raw
To: gentoo-commits
commit: 0388c0add0777d1811bf14fedb645b4d8de329db
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May 2 12:34:17 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May 2 12:34:17 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0388c0ad
sci-biology/samri: fix whitespace warnings
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/samri/samri-0.5.3.ebuild | 9 ++++-----
sci-biology/samri/samri-0.5.4.ebuild | 9 ++++-----
sci-biology/samri/samri-9999.ebuild | 9 ++++-----
3 files changed, 12 insertions(+), 15 deletions(-)
diff --git a/sci-biology/samri/samri-0.5.3.ebuild b/sci-biology/samri/samri-0.5.3.ebuild
index 56351ada3..d45474603 100644
--- a/sci-biology/samri/samri-0.5.3.ebuild
+++ b/sci-biology/samri/samri-0.5.3.ebuild
@@ -11,15 +11,14 @@ 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"
+ 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 -> ${P}.tar.gz"
- KEYWORDS="~amd64"
+ SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64"
S="${WORKDIR}/SAMRI-${PV}"
fi
-
LICENSE="GPL-3"
SLOT="0"
IUSE="+atlases labbookdb"
diff --git a/sci-biology/samri/samri-0.5.4.ebuild b/sci-biology/samri/samri-0.5.4.ebuild
index 56351ada3..d45474603 100644
--- a/sci-biology/samri/samri-0.5.4.ebuild
+++ b/sci-biology/samri/samri-0.5.4.ebuild
@@ -11,15 +11,14 @@ inherit distutils-r1 prefix
DESCRIPTION="Small Animal Magnetic Resonance Imaging"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
if [ "$PV" == "9999" ]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git"
+ 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 -> ${P}.tar.gz"
- KEYWORDS="~amd64"
+ SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64"
S="${WORKDIR}/SAMRI-${PV}"
fi
-
LICENSE="GPL-3"
SLOT="0"
IUSE="+atlases labbookdb"
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index 56351ada3..d45474603 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -11,15 +11,14 @@ inherit distutils-r1 prefix
DESCRIPTION="Small Animal Magnetic Resonance Imaging"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
if [ "$PV" == "9999" ]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git"
+ 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 -> ${P}.tar.gz"
- KEYWORDS="~amd64"
+ SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64"
S="${WORKDIR}/SAMRI-${PV}"
fi
-
LICENSE="GPL-3"
SLOT="0"
IUSE="+atlases labbookdb"
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2023-05-02 12:34 Andrew Ammerlaan
0 siblings, 0 replies; 29+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:34 UTC (permalink / raw
To: gentoo-commits
commit: 05c633669e6e478c73ecf3631a9e9abb25d37f84
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May 2 12:32:54 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May 2 12:32:54 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=05c63366
sci-biology/samri: drop 0.5.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/samri/samri-0.5.2.ebuild | 78 ------------------------------------
1 file changed, 78 deletions(-)
diff --git a/sci-biology/samri/samri-0.5.2.ebuild b/sci-biology/samri/samri-0.5.2.ebuild
deleted file mode 100644
index 56351ada3..000000000
--- a/sci-biology/samri/samri-0.5.2.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..10} )
-DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1 prefix
-
-DESCRIPTION="Small Animal Magnetic Resonance Imaging"
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-if [ "$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}]
- sci-libs/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:$PATH
- export PYTHONIOENCODING=utf-8
- ./test_scripts.sh || die "Test scripts failed."
- sed -i -e \
- "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
- samri/pipelines/tests/test_repos.py || die
- epytest -k "not longtime"
-}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2023-05-02 1:03 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2023-05-02 1:03 UTC (permalink / raw
To: gentoo-commits
commit: 3816342c4d4ad5da753dedcdcc7a50aaa27ac9be
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue May 2 01:03:16 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue May 2 01:03:16 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3816342c
sci-biology/samri: add 0.5.4
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.4.ebuild | 78 ++++++++++++++++++++++++++++++++++++
1 file changed, 78 insertions(+)
diff --git a/sci-biology/samri/samri-0.5.4.ebuild b/sci-biology/samri/samri-0.5.4.ebuild
new file mode 100644
index 000000000..56351ada3
--- /dev/null
+++ b/sci-biology/samri/samri-0.5.4.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 prefix
+
+DESCRIPTION="Small Animal Magnetic Resonance Imaging"
+HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
+if [ "$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}]
+ sci-libs/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:$PATH
+ export PYTHONIOENCODING=utf-8
+ ./test_scripts.sh || die "Test scripts failed."
+ sed -i -e \
+ "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
+ samri/pipelines/tests/test_repos.py || die
+ epytest -k "not longtime"
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2023-04-11 2:06 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2023-04-11 2:06 UTC (permalink / raw
To: gentoo-commits
commit: b9b7ea94c0bf72b97d1313abe231d48e3ceaf440
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue Apr 11 02:04:51 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Apr 11 02:04:51 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b9b7ea94
sci-biology/samri: add 0.5.3
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.3.ebuild | 78 ++++++++++++++++++++++++++++++++++++
1 file changed, 78 insertions(+)
diff --git a/sci-biology/samri/samri-0.5.3.ebuild b/sci-biology/samri/samri-0.5.3.ebuild
new file mode 100644
index 000000000..56351ada3
--- /dev/null
+++ b/sci-biology/samri/samri-0.5.3.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 prefix
+
+DESCRIPTION="Small Animal Magnetic Resonance Imaging"
+HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
+if [ "$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}]
+ sci-libs/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:$PATH
+ export PYTHONIOENCODING=utf-8
+ ./test_scripts.sh || die "Test scripts failed."
+ sed -i -e \
+ "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
+ samri/pipelines/tests/test_repos.py || die
+ epytest -k "not longtime"
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2023-04-06 6:43 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2023-04-06 6:43 UTC (permalink / raw
To: gentoo-commits
commit: 30fcfb55431880f3525473433b4828862ab150d4
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Apr 6 06:42:46 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Apr 6 06:42:46 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=30fcfb55
sci-biology/samri: add 0.5.2
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.2.ebuild | 78 ++++++++++++++++++++++++++++++++++++
1 file changed, 78 insertions(+)
diff --git a/sci-biology/samri/samri-0.5.2.ebuild b/sci-biology/samri/samri-0.5.2.ebuild
new file mode 100644
index 000000000..56351ada3
--- /dev/null
+++ b/sci-biology/samri/samri-0.5.2.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 prefix
+
+DESCRIPTION="Small Animal Magnetic Resonance Imaging"
+HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
+if [ "$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}]
+ sci-libs/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:$PATH
+ export PYTHONIOENCODING=utf-8
+ ./test_scripts.sh || die "Test scripts failed."
+ sed -i -e \
+ "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
+ samri/pipelines/tests/test_repos.py || die
+ epytest -k "not longtime"
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2023-04-06 6:43 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2023-04-06 6:43 UTC (permalink / raw
To: gentoo-commits
commit: a1178bdeed13a9f087da91759e2c9b8bac0f065f
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Apr 6 06:43:04 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Apr 6 06:43:04 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a1178bde
sci-biology/samri: drop 0.5, 0.5.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.1.ebuild | 71 ------------------------------------
sci-biology/samri/samri-0.5.ebuild | 71 ------------------------------------
2 files changed, 142 deletions(-)
diff --git a/sci-biology/samri/samri-0.5.1.ebuild b/sci-biology/samri/samri-0.5.1.ebuild
deleted file mode 100644
index a20c63f61..000000000
--- a/sci-biology/samri/samri-0.5.1.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1 prefix
-
-DESCRIPTION="Small Animal Magnetic Resonance Imaging"
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/SAMRI-${PV}"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="+atlases labbookdb"
-REQUIRED_USE="test? ( atlases )"
-
-DEPEND="
- test? (
- sci-biology/samri_bidsdata
- sci-biology/samri_bindata
- )
- "
-RDEPEND="
- dev-python/argh[${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}]
- sci-libs/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:$PATH
- export PYTHONIOENCODING=utf-8
- ./test_scripts.sh || die "Test scripts failed."
- sed -i -e \
- "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
- samri/pipelines/tests/test_repos.py || die
- epytest -k "not longtime"
-}
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
deleted file mode 100644
index a20c63f61..000000000
--- a/sci-biology/samri/samri-0.5.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1 prefix
-
-DESCRIPTION="Small Animal Magnetic Resonance Imaging"
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/SAMRI-${PV}"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="+atlases labbookdb"
-REQUIRED_USE="test? ( atlases )"
-
-DEPEND="
- test? (
- sci-biology/samri_bidsdata
- sci-biology/samri_bindata
- )
- "
-RDEPEND="
- dev-python/argh[${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}]
- sci-libs/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:$PATH
- export PYTHONIOENCODING=utf-8
- ./test_scripts.sh || die "Test scripts failed."
- sed -i -e \
- "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
- samri/pipelines/tests/test_repos.py || die
- epytest -k "not longtime"
-}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2023-04-06 6:43 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2023-04-06 6:43 UTC (permalink / raw
To: gentoo-commits
commit: 2329ab7cb307b3f595e4e4d0117262c97157fec1
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Apr 6 06:42:28 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Apr 6 06:42:28 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2329ab7c
sci-biology/samri: add 9999
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-9999.ebuild | 78 +++++++++++++++++++++++++++++++++++++
1 file changed, 78 insertions(+)
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
new file mode 100644
index 000000000..56351ada3
--- /dev/null
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 prefix
+
+DESCRIPTION="Small Animal Magnetic Resonance Imaging"
+HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
+if [ "$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}]
+ sci-libs/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:$PATH
+ export PYTHONIOENCODING=utf-8
+ ./test_scripts.sh || die "Test scripts failed."
+ sed -i -e \
+ "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
+ samri/pipelines/tests/test_repos.py || die
+ epytest -k "not longtime"
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2023-04-05 21:42 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2023-04-05 21:42 UTC (permalink / raw
To: gentoo-commits
commit: be5fc54187e2e93f78cafd5dfd9a553fe76d4642
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed Apr 5 21:42:48 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed Apr 5 21:42:48 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=be5fc541
sci-biology/samri: add 0.5.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.1.ebuild | 71 ++++++++++++++++++++++++++++++++++++
1 file changed, 71 insertions(+)
diff --git a/sci-biology/samri/samri-0.5.1.ebuild b/sci-biology/samri/samri-0.5.1.ebuild
new file mode 100644
index 000000000..a20c63f61
--- /dev/null
+++ b/sci-biology/samri/samri-0.5.1.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+
+inherit distutils-r1 prefix
+
+DESCRIPTION="Small Animal Magnetic Resonance Imaging"
+HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
+SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/SAMRI-${PV}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="+atlases labbookdb"
+REQUIRED_USE="test? ( atlases )"
+
+DEPEND="
+ test? (
+ sci-biology/samri_bidsdata
+ sci-biology/samri_bindata
+ )
+ "
+RDEPEND="
+ dev-python/argh[${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}]
+ sci-libs/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"
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2023-01-12 10:22 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2023-01-12 10:22 UTC (permalink / raw
To: gentoo-commits
commit: 33a462e5acbaeb69527cdc781183ce9d24e5e1ab
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Jan 12 10:21:51 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jan 12 10:21:51 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=33a462e5
sci-biology/samri: disable py3.8, py3.9
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index aed6061e7..a20c63f61 100644
--- a/sci-biology/samri/samri-0.5.ebuild
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1 prefix
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2022-07-12 13:38 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2022-07-12 13:38 UTC (permalink / raw
To: gentoo-commits
commit: 7b5851d5cade32843e59bda9df9ab38ba7ef9072
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue Jul 12 13:37:56 2022 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Jul 12 13:37:56 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7b5851d5
sci-biology/samri: EAPI and PYTHON_COMPAT bump
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index 4cc90a0ef..aed6061e7 100644
--- a/sci-biology/samri/samri-0.5.ebuild
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -1,9 +1,9 @@
# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1 prefix
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2022-05-18 4:11 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2022-05-18 4:11 UTC (permalink / raw
To: gentoo-commits
commit: e59efb1f834bd94c49c3ef6afbfd91a932c23b89
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed May 18 04:11:21 2022 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed May 18 04:11:21 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e59efb1f
sci-biology/samri: dependency restriction
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index 7966ad16b..4cc90a0ef 100644
--- a/sci-biology/samri/samri-0.5.ebuild
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -41,7 +41,7 @@ RDEPEND="
sci-libs/nibabel[${PYTHON_USEDEP}]
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
- sci-libs/pybids[${PYTHON_USEDEP}]
+ <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
sci-libs/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2022-04-25 19:05 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2022-04-25 19:05 UTC (permalink / raw
To: gentoo-commits
commit: b68392e796daa3d8b1fe835b823cb8619e8213a9
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Apr 25 18:08:13 2022 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Apr 25 18:08:13 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b68392e7
sci-biology/samri: renamed dependency
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index 1633aa23f..7966ad16b 100644
--- a/sci-biology/samri/samri-0.5.ebuild
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -36,7 +36,7 @@ RDEPEND="
>=media-gfx/blender-2.83.4
>=sci-biology/fsl-5.0.9
sci-biology/bru2nii
- atlases? ( sci-biology/mouse-brain-atlases )
+ atlases? ( sci-biology/mouse-brain-templates )
labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
sci-libs/nibabel[${PYTHON_USEDEP}]
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2022-01-26 17:48 Andrew Ammerlaan
0 siblings, 0 replies; 29+ messages in thread
From: Andrew Ammerlaan @ 2022-01-26 17:48 UTC (permalink / raw
To: gentoo-commits
commit: 1d39e474755e118738efb60eb467eefdfe25c026
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 26 17:48:24 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Jan 26 17:48:24 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1d39e474
sci-biology/samri: bump python compat
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/samri/samri-0.5.ebuild | 21 ++++++++++-----------
1 file changed, 10 insertions(+), 11 deletions(-)
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index 84161f65f..1633aa23f 100644
--- a/sci-biology/samri/samri-0.5.ebuild
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -1,25 +1,25 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python3_{7..8} )
+PYTHON_COMPAT=( python3_{8..9} )
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 -> ${P}.tar.gz"
+S="${WORKDIR}/SAMRI-${PV}"
LICENSE="GPL-3"
SLOT="0"
-IUSE="+atlases labbookdb test"
KEYWORDS="~amd64"
-RESTRICT="!test? ( test )"
+IUSE="+atlases labbookdb"
+REQUIRED_USE="test? ( atlases )"
DEPEND="
test? (
- dev-python/pytest[${PYTHON_USEDEP}]
sci-biology/samri_bidsdata
sci-biology/samri_bindata
)
@@ -48,14 +48,13 @@ RDEPEND="
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 +67,5 @@ 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"
}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2021-01-03 5:22 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2021-01-03 5:22 UTC (permalink / raw
To: gentoo-commits
commit: 663642ba2433eb7748503f7f3eab2c0cd843a805
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Jan 3 05:22:31 2021 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Jan 3 05:22:31 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=663642ba
sci-biology/samri: PYTHON_COMPAT update
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.4.1.ebuild | 4 ++--
sci-biology/samri/samri-0.5.ebuild | 4 ++--
sci-biology/samri/samri-9999.ebuild | 4 ++--
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/sci-biology/samri/samri-0.4.1.ebuild b/sci-biology/samri/samri-0.4.1.ebuild
index 34d91def6..79c5949de 100644
--- a/sci-biology/samri/samri-0.4.1.ebuild
+++ b/sci-biology/samri/samri-0.4.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python3_7 )
+PYTHON_COMPAT=( python3_{7..8} )
inherit distutils-r1
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index d22909df2..8faa270ab 100644
--- a/sci-biology/samri/samri-0.5.ebuild
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python3_7 )
+PYTHON_COMPAT=( python3_{7..8} )
inherit distutils-r1
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index fb93fd9a0..507d6a53c 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python3_7 )
+PYTHON_COMPAT=( python3_{7..8} )
inherit distutils-r1 git-r3
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2020-12-24 11:00 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2020-12-24 11:00 UTC (permalink / raw
To: gentoo-commits
commit: dec35345ad7f0b8e049a33c417a9cef461a9a8e5
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Dec 24 10:56:49 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Dec 24 10:56:49 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=dec35345
sci-biology/samri: conditional test restriction
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.4.1.ebuild | 1 +
sci-biology/samri/samri-0.5.ebuild | 1 +
sci-biology/samri/samri-9999.ebuild | 1 +
3 files changed, 3 insertions(+)
diff --git a/sci-biology/samri/samri-0.4.1.ebuild b/sci-biology/samri/samri-0.4.1.ebuild
index d4b81f39e..34d91def6 100644
--- a/sci-biology/samri/samri-0.4.1.ebuild
+++ b/sci-biology/samri/samri-0.4.1.ebuild
@@ -15,6 +15,7 @@ LICENSE="GPL-3"
SLOT="0"
IUSE="labbookdb test"
KEYWORDS="~amd64"
+RESTRICT="!test? ( test )"
DEPEND="
test? (
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index 5cd5bb654..d22909df2 100644
--- a/sci-biology/samri/samri-0.5.ebuild
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -15,6 +15,7 @@ LICENSE="GPL-3"
SLOT="0"
IUSE="+atlases labbookdb test"
KEYWORDS="~amd64"
+RESTRICT="!test? ( test )"
DEPEND="
test? (
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index 3af34d615..fb93fd9a0 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -16,6 +16,7 @@ LICENSE="GPL-3"
SLOT="0"
IUSE="+atlases labbookdb test"
KEYWORDS=""
+RESTRICT="!test? ( test )"
DEPEND="
test? (
^ permalink raw reply related [flat|nested] 29+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2020-09-27 9:31 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2020-09-27 9:31 UTC (permalink / raw
To: gentoo-commits
commit: 8a9e478b567b41ec475344acf3f9e3f7d18e765a
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 09:27:43 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 09:27:43 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8a9e478b
sci-biology/samri: version bump 0.5
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.5.ebuild | 71 ++++++++++++++++++++++++++++++++++++++
1 file changed, 71 insertions(+)
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
new file mode 100644
index 000000000..24912c9c9
--- /dev/null
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_7 )
+
+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 -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="+atlases labbookdb test"
+KEYWORDS="~amd64"
+
+DEPEND="
+ test? (
+ dev-python/pytest[${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-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[${PYTHON_USEDEP}]
+ >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
+ sci-libs/pybids[${PYTHON_USEDEP}]
+ sci-libs/scikits_image[${PYTHON_USEDEP}]
+ sci-biology/ants
+ sci-biology/afni
+ sci-biology/nilearn[${PYTHON_USEDEP}]
+"
+
+REQUIRED_USE="test? ( atlases )"
+
+S="${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 -k "not longtime" || die
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2020-09-27 8:35 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2020-09-27 8:35 UTC (permalink / raw
To: gentoo-commits
commit: 8b9cc8923541eccb9ebaca2ca5b996982f217c9a
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 08:32:42 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> 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 <chr <AT> 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 "'$T/"`
+ sed -i -e \
+ "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
+ samri/pipelines/tests/test_repos.py || die
+ pytest -vv -k "not longtime" || die
}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2019-12-08 14:54 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2019-12-08 14:54 UTC (permalink / raw
To: gentoo-commits
commit: e68c1eb1aea94ee2860d3b9feb079932114904ea
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Dec 8 14:54:04 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Dec 8 14:54:04 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e68c1eb1
sci-biology/samri: version bump 0.4.1
and old version deprecation
Package-Manager: Portage-2.3.78, Repoman-2.3.17
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-0.1.ebuild | 58 ----------------------
.../samri/{samri-0.2.ebuild => samri-0.4.1.ebuild} | 39 ++++++---------
2 files changed, 16 insertions(+), 81 deletions(-)
diff --git a/sci-biology/samri/samri-0.1.ebuild b/sci-biology/samri/samri-0.1.ebuild
deleted file mode 100644
index 94598cb7c..000000000
--- a/sci-biology/samri/samri-0.1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Small Animal Magnetic Resonance Imaging"
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${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 ${EPYTHON}"
- done
- ./test_scripts.sh || die "Test scripts failed."
-}
diff --git a/sci-biology/samri/samri-0.2.ebuild b/sci-biology/samri/samri-0.4.1.ebuild
similarity index 58%
rename from sci-biology/samri/samri-0.2.ebuild
rename to sci-biology/samri/samri-0.4.1.ebuild
index 12c8d5e01..547b8e912 100644
--- a/sci-biology/samri/samri-0.2.ebuild
+++ b/sci-biology/samri/samri-0.4.1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+PYTHON_COMPAT=( python3_6 )
inherit distutils-r1
@@ -13,18 +13,16 @@ SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
-IUSE="+atlases labbookdb test"
-KEYWORDS="~amd64 ~x86"
+IUSE="labbookdb test"
+KEYWORDS="~amd64"
-# Numpy dependency to circumvent scikits_learn dependency bug:
-# https://bugs.gentoo.org/653052
DEPEND="
test? (
dev-python/pytest[${PYTHON_USEDEP}]
sci-biology/samri_bidsdata
sci-biology/samri_bindata
- )
- "
+ )
+"
RDEPEND="
dev-python/argh[${PYTHON_USEDEP}]
dev-python/joblib[${PYTHON_USEDEP}]
@@ -33,32 +31,27 @@ RDEPEND="
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/seaborn[${PYTHON_USEDEP}]
dev-python/statsmodels[${PYTHON_USEDEP}]
+ media-gfx/blender
>=sci-biology/fsl-5.0.9
sci-biology/bru2nii
- atlases? ( sci-biology/mouse-brain-atlases )
+ sci-biology/mouse-brain-atlases
labbookdb? ( sci-libs/labbookdb[${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/nipype-1.0.0[${PYTHON_USEDEP}]
+ <=sci-libs/pybids-0.6.5[${PYTHON_USEDEP}]
+ sci-libs/scikits_image[${PYTHON_USEDEP}]
sci-libs/scipy[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
- "
-
-REQUIRED_USE="test? ( atlases )"
+"
S="${WORKDIR}/SAMRI-${PV}"
-python_test() {
- distutils_install_for_testing
- export MPLBACKEND="agg"
- export PATH=${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
+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 $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2019-04-28 2:00 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2019-04-28 2:00 UTC (permalink / raw
To: gentoo-commits
commit: 821a0d0ad237cc05b5e5e3ba5cc7e36c463f0ff0
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Apr 28 01:55:41 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Apr 28 01:59:53 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=821a0d0a
sci-biology/samri: updated tests
Package-Manager: Portage-2.3.65, Repoman-2.3.12
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/samri/samri-9999.ebuild | 2 ++
1 file changed, 2 insertions(+)
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index 758eed180..a73f94a95 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -69,5 +69,7 @@ python_test() {
-e "/def test_bru2bids():/i@pytest.mark.skip('Skipped by Portage, as this was already tested in test_scripts.sh')" \
samri/pipelines/tests/test_reposit.py || die
cd "${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/"`
}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2019-01-17 21:24 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2019-01-17 21:24 UTC (permalink / raw
To: gentoo-commits
commit: affa20f37f1ea573d97109a36e9b67485b24910b
Author: Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Thu Jan 17 21:23:54 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jan 17 21:23:54 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=affa20f3
sci-biology/samri: dropped python2 support
Package-Manager: Portage-2.3.56, Repoman-2.3.12
Signed-off-by: Horea Christian <horea.christ <AT> yandex.com>
sci-biology/samri/samri-9999.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index 8a6bc65ae..758eed180 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+PYTHON_COMPAT=( python{3_4,3_5,3_6} )
inherit distutils-r1 git-r3 prefix
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2019-01-17 21:23 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2019-01-17 21:23 UTC (permalink / raw
To: gentoo-commits
commit: 1ac50c41899fc23bf770661caca378dcd6457a64
Author: Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Thu Jan 17 21:21:13 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jan 17 21:23:01 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ac50c41
sci-biology/samri: added prefix support
Package-Manager: Portage-2.3.56, Repoman-2.3.12
Signed-off-by: Horea Christian <horea.christ <AT> yandex.com>
sci-biology/samri/samri-9999.ebuild | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index 4f2c64bc7..8a6bc65ae 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-inherit distutils-r1 git-r3
+inherit distutils-r1 git-r3 prefix
DESCRIPTION="Small Animal Magnetic Resonance Imaging"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
@@ -50,14 +50,24 @@ RDEPEND="
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/ 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:$PATH
export PYTHONIOENCODING=utf-8
./test_scripts.sh || die "Test scripts failed."
- sed -i -e \
- "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
- samri/pipelines/tests/test_repos.py || die
+ sed -i \
+ -e '1s/^/import pytest \n/' \
+ -e "/def test_bru2bids():/i@pytest.mark.skip('Skipped by Portage, as this was already tested in test_scripts.sh')" \
+ samri/pipelines/tests/test_reposit.py || die
+ cd "${BUILD_DIR}" || die
pytest -vv || die
}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2019-01-14 17:39 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2019-01-14 17:39 UTC (permalink / raw
To: gentoo-commits
commit: 9b73be5982c6c1dffb122a1cd10f5997d4d50731
Author: Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Mon Jan 14 17:36:42 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 14 17:38:55 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9b73be59
sci-biology/samri: testing required atlases
Package-Manager: Portage-2.3.55, Repoman-2.3.12
Signed-off-by: Horea Christian <horea.christ <AT> yandex.com>
sci-biology/samri/samri-0.2.ebuild | 4 +++-
sci-biology/samri/samri-9999.ebuild | 4 +++-
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-biology/samri/samri-0.2.ebuild b/sci-biology/samri/samri-0.2.ebuild
index af8210de2..12c8d5e01 100644
--- a/sci-biology/samri/samri-0.2.ebuild
+++ b/sci-biology/samri/samri-0.2.ebuild
@@ -13,7 +13,7 @@ SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
-IUSE="atlases labbookdb test"
+IUSE="+atlases labbookdb test"
KEYWORDS="~amd64 ~x86"
# Numpy dependency to circumvent scikits_learn dependency bug:
@@ -47,6 +47,8 @@ RDEPEND="
sci-biology/nilearn[${PYTHON_USEDEP}]
"
+REQUIRED_USE="test? ( atlases )"
+
S="${WORKDIR}/SAMRI-${PV}"
python_test() {
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index ad9b6a35c..4f2c64bc7 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -14,7 +14,7 @@ EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI"
LICENSE="GPL-3"
SLOT="0"
-IUSE="atlases labbookdb test"
+IUSE="+atlases labbookdb test"
KEYWORDS=""
# Numpy dependency to circumvent scikits_learn dependency bug:
@@ -48,6 +48,8 @@ RDEPEND="
sci-biology/nilearn[${PYTHON_USEDEP}]
"
+REQUIRED_USE="test? ( atlases )"
+
python_test() {
distutils_install_for_testing
export MPLBACKEND="agg"
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2019-01-12 12:43 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2019-01-12 12:43 UTC (permalink / raw
To: gentoo-commits
commit: d74e2a1c91b6f02109d0bb2778bf3a9e05ce61f0
Author: Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Sat Jan 12 10:35:39 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Jan 12 12:43:03 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d74e2a1c
sci-biology/samri: PYTHON_COMPAT bump
and testing dependency update
Package-Manager: Portage-2.3.55, Repoman-2.3.12
Signed-off-by: Horea Christian <horea.christ <AT> yandex.com>
sci-biology/samri/samri-0.2.ebuild | 10 ++++++++--
sci-biology/samri/samri-9999.ebuild | 8 +++++++-
2 files changed, 15 insertions(+), 3 deletions(-)
diff --git a/sci-biology/samri/samri-0.2.ebuild b/sci-biology/samri/samri-0.2.ebuild
index 3b8f06a60..af8210de2 100644
--- a/sci-biology/samri/samri-0.2.ebuild
+++ b/sci-biology/samri/samri-0.2.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
+PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
inherit distutils-r1
@@ -18,7 +18,13 @@ KEYWORDS="~amd64 ~x86"
# Numpy dependency to circumvent scikits_learn dependency bug:
# https://bugs.gentoo.org/653052
-DEPEND="test? ( sci-biology/samri_bindata )"
+DEPEND="
+ test? (
+ dev-python/pytest[${PYTHON_USEDEP}]
+ sci-biology/samri_bidsdata
+ sci-biology/samri_bindata
+ )
+ "
RDEPEND="
dev-python/argh[${PYTHON_USEDEP}]
dev-python/joblib[${PYTHON_USEDEP}]
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index 1cc0f87a3..ad9b6a35c 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -19,7 +19,13 @@ KEYWORDS=""
# Numpy dependency to circumvent scikits_learn dependency bug:
# https://bugs.gentoo.org/653052
-DEPEND="test? ( sci-biology/samri_bindata )"
+DEPEND="
+ test? (
+ dev-python/pytest[${PYTHON_USEDEP}]
+ sci-biology/samri_bidsdata
+ sci-biology/samri_bindata
+ )
+ "
RDEPEND="
dev-python/argh[${PYTHON_USEDEP}]
dev-python/joblib[${PYTHON_USEDEP}]
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2019-01-06 15:52 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2019-01-06 15:52 UTC (permalink / raw
To: gentoo-commits
commit: 3f38251efe059ee10779bcc12ab4be8eed628902
Author: Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Sun Jan 6 15:47:56 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Jan 6 15:52:20 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f38251e
sci-biology/samri: dependency update
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Horea Christian <horea.christ <AT> yandex.com>
sci-biology/samri/samri-9999.ebuild | 1 -
1 file changed, 1 deletion(-)
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index df5845e98..1cc0f87a3 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -27,7 +27,6 @@ RDEPEND="
>=dev-python/numpy-1.13.3[${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
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2019-01-06 15:09 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2019-01-06 15:09 UTC (permalink / raw
To: gentoo-commits
commit: 35b70ea666aeb1b55743d6c6d57e5cb7118cab58
Author: Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Sun Jan 6 15:07:30 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Jan 6 15:08:55 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=35b70ea6
sci-biology/samri: version bump
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Horea Christian <horea.christ <AT> yandex.com>
sci-biology/samri/samri-0.2.ebuild | 56 ++++++++++++++++++++++++++++++++++++++
1 file changed, 56 insertions(+)
diff --git a/sci-biology/samri/samri-0.2.ebuild b/sci-biology/samri/samri-0.2.ebuild
new file mode 100644
index 000000000..3b8f06a60
--- /dev/null
+++ b/sci-biology/samri/samri-0.2.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2019 Gentoo Authors
+# 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[${PYTHON_USEDEP}]
+ dev-python/statsmodels[${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:$PATH
+ export PYTHONIOENCODING=utf-8
+ ./test_scripts.sh || die "Test scripts failed."
+ sed -i -e \
+ "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
+ samri/pipelines/tests/test_repos.py || die
+ pytest -vv || die
+}
^ permalink raw reply related [flat|nested] 29+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/samri/
@ 2019-01-06 14:52 Horea Christian
0 siblings, 0 replies; 29+ messages in thread
From: Horea Christian @ 2019-01-06 14:52 UTC (permalink / raw
To: gentoo-commits
commit: 3deb3266cc23db1815042c373997195ee6f9c93b
Author: Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Sun Jan 6 14:51:18 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Jan 6 14:51:54 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3deb3266
sci-biology/samri: updated ebuild
including test suite, EAPI, and PYTHON_COMPAT bump
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Horea Christian <horea.christ <AT> yandex.com>
sci-biology/samri/samri-9999.ebuild | 15 +++++++--------
1 file changed, 7 insertions(+), 8 deletions(-)
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index 24078c41e..df5845e98 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
+PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
inherit distutils-r1 git-r3
@@ -48,10 +48,9 @@ python_test() {
export MPLBACKEND="agg"
export PATH=${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."
+ 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
}
^ permalink raw reply related [flat|nested] 29+ messages in thread
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