[gentoo-commits] proj/sci:master commit in: dev-python/fusepy/
commit: ad581fd86bfffb1751ed69959f6d7b93d9dfdb8f
Author: Horea Christian chymera eu>
AuthorDate: Wed May 29 09:00:18 2024 +
Commit: Horea Christian gmail com>
CommitDate: Wed May 29 09:00:18 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ad581fd8
dev-python/fusepy: new package, add 3.0.1
Signed-off-by: Horea Christian chymera.eu>
dev-python/fusepy/fusepy-3.0.1.ebuild | 20
dev-python/fusepy/metadata.xml| 16
2 files changed, 36 insertions(+)
diff --git a/dev-python/fusepy/fusepy-3.0.1.ebuild
b/dev-python/fusepy/fusepy-3.0.1.ebuild
new file mode 100644
index 0..6e9b3de3c
--- /dev/null
+++ b/dev-python/fusepy/fusepy-3.0.1.ebuild
@@ -0,0 +1,20 @@
+# Copyright 2022-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..13} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Simple ctypes bindings for FUSE"
+HOMEPAGE="https://github.com/fusepy/fusepy;
+
+LICENSE="ISC"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+RESTRICT="test"# No usable test phases
+
+DEPEND="sys-fs/fuse:0"
+RDEPEND="${DEPEND}"
diff --git a/dev-python/fusepy/metadata.xml b/dev-python/fusepy/metadata.xml
new file mode 100644
index 0..53cf5c2f9
--- /dev/null
+++ b/dev-python/fusepy/metadata.xml
@@ -0,0 +1,16 @@
+
+https://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ gen...@chymera.eu
+ Horea Christian
+
+
+ fusepy
+ fusepy/fusepy
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/afni/
commit: 6d9b772f10ed51682604e5c1cb6f9c278a5c6c72
Author: Horea Christian chymera eu>
AuthorDate: Wed May 29 08:31:29 2024 +
Commit: Horea Christian gmail com>
CommitDate: Wed May 29 08:31:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6d9b772f
sci-biology/afni: correct version annotation
Signed-off-by: Horea Christian chymera.eu>
sci-biology/afni/afni-24.0.08-r3.ebuild | 125
1 file changed, 125 insertions(+)
diff --git a/sci-biology/afni/afni-24.0.08-r3.ebuild
b/sci-biology/afni/afni-24.0.08-r3.ebuild
new file mode 100644
index 0..12d6c8f87
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.08-r3.ebuild
@@ -0,0 +1,125 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/;
+SRC_URI="
+ https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz ->
${P}.gh.tar.gz
+
https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz ->
nifti-${NIFTI_HASH}.tar.gz
+
https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz ->
gifti-${GIFTI_HASH}.tar.gz
+ "
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-build/ninja
+ dev-libs/expat
+ dev-libs/glib:2
+ dev-libs/libf2c
+ media-libs/freeglut
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-biology/afni-datasets
+ sci-libs/gsl
+ sci-libs/gts
+ sys-devel/llvm:*
+ sys-libs/libomp
+ virtual/jpeg-compat:62
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXmu
+ x11-libs/libXpm
+ x11-libs/libXt
+ x11-libs/motif[-static-libs]
+ "
+DEPEND="
+ ${RDEPEND}
+ app-shells/tcsh
+ "
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+ #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
+src_prepare() {
+ tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+ tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+ cmake_src_prepare
+ default
+ }
+
+src_configure() {
+ if use !whirlgif; then
+ eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch"
+ fi
+ # Fix AFNI version, no better way seemed to work
+ sed -i -e "s/GIT_REPO_VERSION \"99\.99\.99\"/GIT_REPO_VERSION ${PV}/g"
cmake/get_git_repo_version.cmake
+ export CFLAGS="-pthread ${CFLAGS}"
+ local mycmakeargs=(
+ -DLIBDIR=/usr/$(get_libdir)
+ -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+ -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+ -DCOMP_COREBINARIES=ON
+ -DUSE_SYSTEM_NIFTI=OFF
+ -DUSE_SYSTEM_GIFTI=OFF
+ -DUSE_SYSTEM_XMHTML=OFF
+ -DUSE_SYSTEM_GTS=ON
+
-DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+
-DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+ -DCOMP_GUI=ON
+ -DCOMP_PLUGINS=ON
+ -DUSE_OMP=ON
+ -DCOMP_PYTHON=OFF
+ -DUSE_SYSTEM_F2C=ON
+ )
+ tc-export CC
+ cmake_src_configure
+}
+
+src_compile() {
+ cmake_src_compile
+ pushd src/python_scripts
+ distutils-r1_src_compile
+ popd
+}
+
+src_install() {
+ cmake_src_install
+ pushd src/python_scripts
+ distutils-r1_src_install
+ popd
+ cd "${D}"
+ rm usr/bin/mpeg_encode
+ doenvd "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+ echo
+ einfo "Please run the following commands if you"
+ einfo "intend to use afni binaries from an existing shell:"
+ einfo "source /etc/profile"
+ echo
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/afni/files/, sci-biology/afni/
commit: 0075b0aa4f9993e0bc54e9d627329332555d16e0
Author: Horea Christian chymera eu>
AuthorDate: Tue May 28 17:10:35 2024 +
Commit: Horea Christian gmail com>
CommitDate: Tue May 28 17:10:35 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0075b0aa
sci-biology/afni: env variable for AFNI data
Signed-off-by: Horea Christian chymera.eu>
sci-biology/afni/afni-24.0.08-r2.ebuild | 124
sci-biology/afni/files/97afni | 1 +
2 files changed, 125 insertions(+)
diff --git a/sci-biology/afni/afni-24.0.08-r2.ebuild
b/sci-biology/afni/afni-24.0.08-r2.ebuild
new file mode 100644
index 0..270100c0b
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.08-r2.ebuild
@@ -0,0 +1,124 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/;
+SRC_URI="
+ https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz ->
${P}.gh.tar.gz
+
https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz ->
nifti-${NIFTI_HASH}.tar.gz
+
https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz ->
gifti-${GIFTI_HASH}.tar.gz
+ "
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-build/ninja
+ dev-libs/expat
+ dev-libs/glib:2
+ dev-libs/libf2c
+ media-libs/freeglut
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-biology/afni-datasets
+ sci-libs/gsl
+ sci-libs/gts
+ sys-devel/llvm:*
+ sys-libs/libomp
+ virtual/jpeg-compat:62
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXmu
+ x11-libs/libXpm
+ x11-libs/libXt
+ x11-libs/motif[-static-libs]
+ "
+DEPEND="
+ ${RDEPEND}
+ app-shells/tcsh
+ "
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+ #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
+src_prepare() {
+ tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+ tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+ cmake_src_prepare
+ default
+ }
+
+src_configure() {
+ if use !whirlgif; then
+ eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch"
+ fi
+ export CFLAGS="-pthread ${CFLAGS}"
+ export GIT_REPO_VERSION=3.0.1.1
+ local mycmakeargs=(
+ -DLIBDIR=/usr/$(get_libdir)
+ -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+ -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+ -DCOMP_COREBINARIES=ON
+ -DUSE_SYSTEM_NIFTI=OFF
+ -DUSE_SYSTEM_GIFTI=OFF
+ -DUSE_SYSTEM_XMHTML=OFF
+ -DUSE_SYSTEM_GTS=ON
+
-DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+
-DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+ -DCOMP_GUI=ON
+ -DCOMP_PLUGINS=ON
+ -DUSE_OMP=ON
+ -DCOMP_PYTHON=OFF
+ -DUSE_SYSTEM_F2C=ON
+ )
+ tc-export CC
+ cmake_src_configure
+}
+
+src_compile() {
+ cmake_src_compile
+ pushd src/python_scripts
+ distutils-r1_src_compile
+ popd
+}
+
+src_install() {
+ cmake_src_install
+ pushd src/python_scripts
+ distutils-r1_src_install
+ popd
+ cd "${D}"
+ rm usr/bin/mpeg_encode
+ doenvd "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+ echo
+ einfo "Please run the following commands if you"
+ einfo "intend to use afni binaries from an existing shell:"
+ einfo "source /etc/profile"
+ echo
+}
diff --git a/sci-biology/afni/files/97afni b/sci-biology/afni/files/97afni
new file mode 100644
index 0..dbf463f47
--- /dev/null
+++ b/sci-biology/afni/files/97afni
@@ -0,0 +1 @@
+export AFNI_ATLAS_PATH=/usr/share/afni-datasets
[gentoo-commits] proj/sci:master commit in: sci-biology/afni-datasets/
commit: f3153dcbca91b2c127a05f04a8eec9db28ef7024
Author: Horea Christian chymera eu>
AuthorDate: Tue May 28 16:13:32 2024 +
Commit: Horea Christian gmail com>
CommitDate: Tue May 28 16:13:32 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f3153dcb
sci-biology/afni-datasets: new package, add 20240503
Signed-off-by: Horea Christian chymera.eu>
.../afni-datasets/afni-datasets-20240503.ebuild | 20
sci-biology/afni-datasets/metadata.xml | 12
2 files changed, 32 insertions(+)
diff --git a/sci-biology/afni-datasets/afni-datasets-20240503.ebuild
b/sci-biology/afni-datasets/afni-datasets-20240503.ebuild
new file mode 100644
index 0..4d554a633
--- /dev/null
+++ b/sci-biology/afni-datasets/afni-datasets-20240503.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_P="afni_atlases_dist_2024_0503"
+
+DESCRIPTION="Datasets for using and testing sci-biology/afni"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/;
+SRC_URI="https://afni.nimh.nih.gov/pub/dist/atlases/${MY_P}.tgz -> ${P}.tar.gz"
+
+S="${WORKDIR}/${MY_P}"
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_install() {
+ insinto /usr/share/${PN}
+ doins -r *
+}
diff --git a/sci-biology/afni-datasets/metadata.xml
b/sci-biology/afni-datasets/metadata.xml
new file mode 100644
index 0..cb6710311
--- /dev/null
+++ b/sci-biology/afni-datasets/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ gen...@chymera.eu
+ Horea Christian
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/afni/
commit: b5ce4a1154c05787fe20c3074b2bc91f5146bacf
Author: Horea Christian chymera eu>
AuthorDate: Fri May 24 13:49:20 2024 +
Commit: Horea Christian gmail com>
CommitDate: Fri May 24 13:49:20 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b5ce4a11
sci-biology/afni: update DESCRIPTION, HOMEPAGE
Signed-off-by: Horea Christian chymera.eu>
sci-biology/afni/afni-24.0.04-r1.ebuild | 12 ++--
sci-biology/afni/afni-24.0.08-r1.ebuild | 12 ++--
2 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/sci-biology/afni/afni-24.0.04-r1.ebuild
b/sci-biology/afni/afni-24.0.04-r1.ebuild
index 557fbd579..c5adfb6d8 100644
--- a/sci-biology/afni/afni-24.0.04-r1.ebuild
+++ b/sci-biology/afni/afni-24.0.04-r1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{10..13} )
DISTUTILS_USE_PEP517=setuptools
inherit cmake distutils-r1 toolchain-funcs
@@ -12,16 +12,18 @@ GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
-DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
-HOMEPAGE="http://stnava.github.io/ANTs/;
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/;
SRC_URI="
https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz ->
${P}.gh.tar.gz
https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz ->
nifti-${NIFTI_HASH}.tar.gz
https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz ->
gifti-${GIFTI_HASH}.tar.gz
"
-SLOT="0"
+S="${WORKDIR}/afni-AFNI_${PV}"
+
LICENSE="GPL-3+"
+SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="test whirlgif"
RESTRICT="!test? ( test )"
@@ -54,8 +56,6 @@ DEPEND="
app-shells/tcsh
"
-S="${WORKDIR}/afni-AFNI_${PV}"
-
src_prepare() {
tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
diff --git a/sci-biology/afni/afni-24.0.08-r1.ebuild
b/sci-biology/afni/afni-24.0.08-r1.ebuild
index 20293877f..21ecf81a1 100644
--- a/sci-biology/afni/afni-24.0.08-r1.ebuild
+++ b/sci-biology/afni/afni-24.0.08-r1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{10..13} )
DISTUTILS_USE_PEP517=setuptools
inherit cmake distutils-r1 toolchain-funcs
@@ -12,16 +12,18 @@ GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
-DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
-HOMEPAGE="http://stnava.github.io/ANTs/;
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/;
SRC_URI="
https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz ->
${P}.gh.tar.gz
https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz ->
nifti-${NIFTI_HASH}.tar.gz
https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz ->
gifti-${GIFTI_HASH}.tar.gz
"
-SLOT="0"
+S="${WORKDIR}/afni-AFNI_${PV}"
+
LICENSE="GPL-3+"
+SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="test whirlgif"
RESTRICT="!test? ( test )"
@@ -57,8 +59,6 @@ DEPEND="
#Update jpeg-compat to virtual/jpeg:0
# look for xmhtlm
-S="${WORKDIR}/afni-AFNI_${PV}"
-
#tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
src_prepare() {
tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
[gentoo-commits] proj/sci:master commit in: sci-biology/VelvetOptimiser/
commit: e120252601caa45b738cfc059a709d5d9ab9ec67
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Wed May 22 15:56:52 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Wed May 22 15:56:52 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e1202526
sci-biology/VelvetOptimiser: fix dependency on perl
Signed-off-by: Andrew Ammerlaan gentoo.org>
sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
index 49f2b6d9f..096349f5a 100644
--- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
@@ -16,7 +16,7 @@ KEYWORDS="~amd64"
RDEPEND="
>=sci-biology/bioperl-1.4
>=sci-biology/velvet-0.7.5.1
- dev-lang/perl[ithreads]" # actually >=5.8 but make sure 5.16 is
recognized as > 5.8, heh
+ dev-lang/perl[perl_features_ithreads]" # actually >=5.8 but make sure
5.16 is recognized as > 5.8, heh
src_install(){
dobin VelvetOptimiser.pl
[gentoo-commits] proj/sci:master commit in: sci-biology/nilearn/
commit: 397d1a5674eedf16770f86c6cfae9ba525fc94e9
Author: Horea Christian chymera eu>
AuthorDate: Wed May 22 11:27:36 2024 +
Commit: Horea Christian gmail com>
CommitDate: Wed May 22 11:27:36 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=397d1a56
sci-biology/nilearn: updated dependency name
Signed-off-by: Horea Christian chymera.eu>
sci-biology/nilearn/nilearn-0.8.1.ebuild | 2 +-
sci-biology/nilearn/nilearn-0.9.1.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/nilearn/nilearn-0.8.1.ebuild
b/sci-biology/nilearn/nilearn-0.8.1.ebuild
index 3064c0ba5..92c788f28 100644
--- a/sci-biology/nilearn/nilearn-0.8.1.ebuild
+++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild
@@ -27,7 +27,7 @@ BDEPEND="
RDEPEND="
>=dev-python/joblib-0.12[${PYTHON_USEDEP}]
>=dev-python/numpy-1.16[${PYTHON_USEDEP}]
- >=sci-libs/scikit-learn-0.21[${PYTHON_USEDEP}]
+ >=dev-python/scikit-learn-0.21[${PYTHON_USEDEP}]
>=dev-python/scipy-1.2[${PYTHON_USEDEP}]
>=sci-libs/nibabel-2.5[${PYTHON_USEDEP}]
>=dev-python/pandas-0.24.0[${PYTHON_USEDEP}]
diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild
b/sci-biology/nilearn/nilearn-0.9.1.ebuild
index 425e79444..4dbe5101e 100644
--- a/sci-biology/nilearn/nilearn-0.9.1.ebuild
+++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild
@@ -25,7 +25,7 @@ RDEPEND="
>=dev-python/requests-2[${PYTHON_USEDEP}]
>=dev-python/scipy-1.5[${PYTHON_USEDEP}]
>=sci-libs/nibabel-3[${PYTHON_USEDEP}]
- >=sci-libs/scikit-learn-0.22[${PYTHON_USEDEP}]
+ >=dev-python/scikit-learn-0.22[${PYTHON_USEDEP}]
"
PATCHES=( "${FILESDIR}/${P}-tests.patch" )
[gentoo-commits] proj/sci:master commit in: sci-physics/madgraph5/, sci-physics/madgraph5/files/
commit: f5adbcfabe52b1e36bc357dd54339905f776c3d8
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue May 7 18:44:35 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Thu May 16 14:01:53 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f5adbcfa
sci-physics/madgraph5: new package, add 3.5.3
Closes: https://github.com/gentoo/sci/pull/1270
Co-authored-by: Andrew Nowa Ammerlaan gentoo.org>
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/madgraph5/files/cuttools.patch | 44 +
sci-physics/madgraph5/madgraph5-3.5.3.ebuild | 93
sci-physics/madgraph5/metadata.xml | 32 ++
3 files changed, 169 insertions(+)
diff --git a/sci-physics/madgraph5/files/cuttools.patch
b/sci-physics/madgraph5/files/cuttools.patch
new file mode 100644
index 0..0d6249af8
--- /dev/null
+++ b/sci-physics/madgraph5/files/cuttools.patch
@@ -0,0 +1,44 @@
+diff -Naru MG5_aMC_v2_9_6.orig/vendor/CutTools/makefile
MG5_aMC_v2_9_6/vendor/CutTools/makefile
+--- MG5_aMC_v2_9_6.orig/vendor/CutTools/makefile 2022-04-13
11:13:28.277248753 +0200
MG5_aMC_v2_9_6/vendor/CutTools/makefile2022-04-13 11:13:43.702292725
+0200
+@@ -42,15 +42,15 @@
+ endif
+
+ cpmp:
+- cp -p ./src/cts/cts_mpr.in ./src/cts/cts_mpr.h
+- cp -p ./src/cts/cts_mpc.in ./src/cts/cts_mpc.h
+- cp -p ./src/cts/cts_mprec.in ./src/cts/cts_mprec.h
+- cp -p ./src/cts/cts_mpinit.in ./src/cts/cts_mpinit.h
++ cp ./src/cts/cts_mpr.in ./src/cts/cts_mpr.h
++ cp ./src/cts/cts_mpc.in ./src/cts/cts_mpc.h
++ cp ./src/cts/cts_mprec.in ./src/cts/cts_mprec.h
++ cp ./src/cts/cts_mpinit.in ./src/cts/cts_mpinit.h
+ cpqp:
+- cp -p ./src/cts/cts_qpr.in ./src/cts/cts_mpr.h
+- cp -p ./src/cts/cts_qpc.in ./src/cts/cts_mpc.h
+- cp -p ./src/cts/cts_qprec.in ./src/cts/cts_mprec.h
+- cp -p ./src/cts/cts_qpinit.in ./src/cts/cts_mpinit.h
++ cp ./src/cts/cts_qpr.in ./src/cts/cts_mpr.h
++ cp ./src/cts/cts_qpc.in ./src/cts/cts_mpc.h
++ cp ./src/cts/cts_qprec.in ./src/cts/cts_mprec.h
++ cp ./src/cts/cts_qpinit.in ./src/cts/cts_mpinit.h
+
+ clean$(BLD): default
+ rm -fr $(BLD)/*.f
+@@ -68,11 +68,11 @@
+
+ $(BLD)/version.h:
+ -mkdir -p $(BLD)
+- cp -p ./src/avh/* $(BLD)/
+- cp -p ./src/cts/* $(BLD)/
+- cp -p ./src/mpfun90/* $(BLD)/
+- cp -p ./src/qcdloop/* $(BLD)/
+- cp -p ./src/makefile $(BLD)/
++ cp ./src/avh/* $(BLD)/
++ cp ./src/cts/* $(BLD)/
++ cp ./src/mpfun90/* $(BLD)/
++ cp ./src/qcdloop/* $(BLD)/
++ cp ./src/makefile $(BLD)/
+
+ tar:
+ tar -czvf $(CTS_TAR) *
diff --git a/sci-physics/madgraph5/madgraph5-3.5.3.ebuild
b/sci-physics/madgraph5/madgraph5-3.5.3.ebuild
new file mode 100644
index 0..3ced7918c
--- /dev/null
+++ b/sci-physics/madgraph5/madgraph5-3.5.3.ebuild
@@ -0,0 +1,93 @@
+# Copyright 2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+# does not escape strings properly, so no python3_12 for now
+PYTHON_COMPAT=( python3_11 )
+inherit fortran-2 python-single-r1
+
+MY_PNN="MadGraph5"
+MY_PV=$(ver_rs 1-3 '_')
+MY_PN="MG5_aMC_v"
+MY_PF=${MY_PN}${MY_PV}
+
+DESCRIPTION="MadGraph5_aMC@NLO"
+HOMEPAGE="https://launchpad.net/mg5amcnlo;
+SRC_URI="https://launchpad.net/mg5amcnlo/$(ver_cut 1).0/$(ver_cut
1-2).x/+download/${MY_PN}${PV}.tar.gz -> ${MY_PNN}-${PV}.tar.gz"
+S="${WORKDIR}/${MY_PF}"
+
+LICENSE="UoI-NCSA"
+SLOT="3"
+KEYWORDS="~amd64"
+# TODO add pineapple, herwig, syscalc, pjfrym, pineappl
+IUSE="+hepmc2 +lhapdf +fastjet pythia collier thepeg" # td madanalysis5 ninja
samurai golem95
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+ ${PYTHON_DEPS}
+ sys-libs/zlib
+ sys-devel/gcc:*[fortran]
+ $(python_gen_cond_dep '
+ dev-python/numpy[${PYTHON_USEDEP}]
+ ')
+ lhapdf? ( sci-physics/lhapdf[${PYTHON_SINGLE_USEDEP}] )
+ fastjet? ( sci-physics/fastjet[${PYTHON_SINGLE_USEDEP}] )
+ pythia? ( sci-physics/pythia:8=[examples] )
+ hepmc2? ( sci-physics/hepmc:2 )
+ collier? ( sci-physics/collier[static-libs] )
+ thepeg? (
+ sci-physics/thepeg[hepmc3(-),fastjet?,lhapdf?]
+ )
+"
+# madanalysis5? ( sci-physics/madanalysis5 )
+# td? ( sci-physics/topdrawer )
+# ninja? ( sci-physics/ninja[static-libs] )
+# samurai? ( sci-physics/samurai )
+# golem95? ( sci-physics/golem95 )
+DEPEND="${RDEPEND}"
+
+PATCHES=( "${FILESDIR}"/cuttools.patch )
+
+src_unpack() {
+ # Perserve permissions
+ tar xvzf "${DISTDIR}/${MY_PNN}-${PV}.tar.gz" -C "${WORKDIR}" || die
+}
+
+src_configure() {
+ cat <<-EOF >> input/mg5_configuration.txt || die
+ $(usex lhapdf "lhapdf_py3 = ${EPREFIX}/usr/bin/lhapdf-config" "")
+ $(usex fastjet
[gentoo-commits] proj/sci:master commit in: dev-vcs/datalad/
commit: f100ad37c1b21257197e2a4941a9074301c19fda
Author: Horea Christian chymera eu>
AuthorDate: Mon May 13 13:18:00 2024 +
Commit: Horea Christian gmail com>
CommitDate: Mon May 13 13:18:00 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f100ad37
dev-vcs/datalad: add 1.0.2
Signed-off-by: Horea Christian chymera.eu>
dev-vcs/datalad/datalad-1.0.2.ebuild | 79
1 file changed, 79 insertions(+)
diff --git a/dev-vcs/datalad/datalad-1.0.2.ebuild
b/dev-vcs/datalad/datalad-1.0.2.ebuild
new file mode 100644
index 0..de5b6cd6a
--- /dev/null
+++ b/dev-vcs/datalad/datalad-1.0.2.ebuild
@@ -0,0 +1,79 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Keep code, data, containers under control with git and git-annex"
+HOMEPAGE="https://github.com/datalad/datalad;
+#SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz ->
${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test +downloaders +metadata +publish misc"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
+ app-arch/p7zip
+ app-arch/patool[${PYTHON_USEDEP}]
+ dev-python/annexremote[${PYTHON_USEDEP}]
+ dev-python/distro[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ dev-python/humanize[${PYTHON_USEDEP}]
+ dev-python/iso8601[${PYTHON_USEDEP}]
+ dev-python/looseversion[${PYTHON_USEDEP}]
+ dev-python/platformdirs[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/wraps[${PYTHON_USEDEP}]
+ dev-vcs/git-annex
+ downloaders? (
+ dev-python/keyring[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ )
+ metadata? (
+ dev-python/simplejson[${PYTHON_USEDEP}]
+ dev-python/whoosh[${PYTHON_USEDEP}]
+ )
+ misc? (
+ dev-python/argcomplete[${PYTHON_USEDEP}]
+ dev-python/pyperclip[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ )
+ publish? (
+ dev-vcs/python-gitlab[${PYTHON_USEDEP}]
+ )
+"
+BDEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
+ test? (
+ ${RDEPEND}
+ dev-python/beautifulsoup4[${PYTHON_USEDEP}]
+ dev-python/httpretty[${PYTHON_USEDEP}]
+ dev-python/mypy[${PYTHON_USEDEP}]
+ dev-python/vcrpy[${PYTHON_USEDEP}]
+ )
+"
+# Also wants test dep:
+# dev-python/types-requests
+# dev-python/types-python-dateutil
+
+distutils_enable_tests pytest
+
+EPYTEST_DESELECT=(
+
tests/test_datetimes.py::TestUnitTestMethodDecorator::test_method_decorator_works_on_unittest_kwarg_frozen_time
+
tests/test_datetimes.py::TestUnitTestMethodDecorator::test_method_decorator_works_on_unittest_kwarg_frozen_time_with_func
+
tests/test_datetimes.py::TestUnitTestMethodDecorator::test_method_decorator_works_on_unittest_kwarg_hello
+)
+
+python_test() {
+ local -x DATALAD_TESTS_NONETWORK=1
+ # see test groups in "tox.ini"
+ epytest -k "not turtle and not slow and not usecase"
+}
[gentoo-commits] proj/sci:master commit in: dev-vcs/datalad-fuse/, dev-vcs/datalad-fuse/files/
commit: cf57569632902eee502e85ac0b8e3b81323f2e4c
Author: Horea Christian chymera eu>
AuthorDate: Fri May 10 09:18:29 2024 +
Commit: Horea Christian gmail com>
CommitDate: Fri May 10 09:18:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=cf575696
dev-vcs/datalad-fuse: new package, add 0.5.1
Signed-off-by: Horea Christian chymera.eu>
dev-vcs/datalad-fuse/datalad-fuse-0.5.1.ebuild | 43 ++
.../files/datalad-fuse-0.5.1-git_config.patch | 15
dev-vcs/datalad-fuse/metadata.xml | 16
3 files changed, 74 insertions(+)
diff --git a/dev-vcs/datalad-fuse/datalad-fuse-0.5.1.ebuild
b/dev-vcs/datalad-fuse/datalad-fuse-0.5.1.ebuild
new file mode 100644
index 0..1359f4e0d
--- /dev/null
+++ b/dev-vcs/datalad-fuse/datalad-fuse-0.5.1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Keep code, data, containers under control with git and git-annex"
+HOMEPAGE="https://github.com/datalad/datalad;
+SRC_URI="https://github.com/datalad/datalad-fuse/archive/refs/tags/${PV}.tar.gz
-> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/aiohttp-retry[${PYTHON_USEDEP}]
+ dev-python/fsspec[${PYTHON_USEDEP}]
+ dev-python/methodtools[${PYTHON_USEDEP}]
+ dev-python/linesep[${PYTHON_USEDEP}]
+ dev-vcs/datalad[${PYTHON_USEDEP}]
+ sys-fs/fuse
+"
+
+distutils_enable_tests pytest
+
+PATCHES=(
+ "${FILESDIR}/${P}-git_config.patch"
+)
+
+python_test() {
+ #git init -q || die
+ #git config --global user.email "placehol...@gentoo.org" || die
+ #git config --global user.name "Place Holder" || die
+ #git add . || die
+ #git commit -m "init" || die
+ ##GIT_AUTHOR_NAME="Place Holder"
GIT_AUTHOR_EMAIL="placehol...@gentoo.org" epytest
+ ##export GIT_AUTHOR_NAME="Place Holder"
+ ##export GIT_AUTHOR_EMAIL="placehol...@gentoo.org"
+ epytest
+}
diff --git a/dev-vcs/datalad-fuse/files/datalad-fuse-0.5.1-git_config.patch
b/dev-vcs/datalad-fuse/files/datalad-fuse-0.5.1-git_config.patch
new file mode 100644
index 0..f62fc412e
--- /dev/null
+++ b/dev-vcs/datalad-fuse/files/datalad-fuse-0.5.1-git_config.patch
@@ -0,0 +1,15 @@
+Upstreamed and perhaps removable for future releases:
+https://github.com/datalad/datalad-fuse/pull/113
+diff --git a/datalad_fuse/tests/test_fsspec_head.py
b/datalad_fuse/tests/test_fsspec_head.py
+index 75a6efc..1ffc60f 100644
+--- a/datalad_fuse/tests/test_fsspec_head.py
b/datalad_fuse/tests/test_fsspec_head.py
+@@ -131,6 +131,8 @@ def test_git_repo(tmp_path):
+ TEXT = (Path(__file__).with_name("data") / "text.txt").read_bytes()
+ (tmp_path / "text.txt").write_bytes(TEXT)
+ subprocess.run(["git", "add", "text.txt"], cwd=tmp_path, check=True)
++subprocess.run(["git", "config", "user.email", "pl...@holder.org"],
cwd=tmp_path, check=True)
++subprocess.run(["git", "config", "user.name", "Place Holder"],
cwd=tmp_path, check=True)
+ subprocess.run(["git", "commit", "-m", "Add a file"], cwd=tmp_path,
check=True)
+ ds = Dataset(tmp_path)
+ assert_in_results(
diff --git a/dev-vcs/datalad-fuse/metadata.xml
b/dev-vcs/datalad-fuse/metadata.xml
new file mode 100644
index 0..97f1a33f3
--- /dev/null
+++ b/dev-vcs/datalad-fuse/metadata.xml
@@ -0,0 +1,16 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ gen...@chymera.eu
+ Horea Christian
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ datalad/datalad-fuse
+ datalad-fuse
+
+
[gentoo-commits] proj/sci:master commit in: dev-python/aiohttp-retry/
commit: 39aa26e66beae16887de80286c1e97baf6432981
Author: Horea Christian chymera eu>
AuthorDate: Fri May 10 00:17:33 2024 +
Commit: Horea Christian gmail com>
CommitDate: Fri May 10 00:17:33 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=39aa26e6
dev-python/aiohttp-retry: new package, add 2.8.3
Signed-off-by: Horea Christian chymera.eu>
.../aiohttp-retry/aiohttp-retry-2.8.3.ebuild | 31 ++
dev-python/aiohttp-retry/metadata.xml | 16 +++
2 files changed, 47 insertions(+)
diff --git a/dev-python/aiohttp-retry/aiohttp-retry-2.8.3.ebuild
b/dev-python/aiohttp-retry/aiohttp-retry-2.8.3.ebuild
new file mode 100644
index 0..25df27ba6
--- /dev/null
+++ b/dev-python/aiohttp-retry/aiohttp-retry-2.8.3.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Simple retry client for aiohttp"
+HOMEPAGE="https://github.com/inyutin/aiohttp_retry;
+# Test suite missing from PyPI tarball, reported upstream:
+# https://github.com/inyutin/aiohttp_retry/issues/94
+SRC_URI="https://github.com/inyutin/aiohttp_retry/archive/refs/tags/v${PV}.tar.gz
-> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="dev-python/aiohttp[${PYTHON_USEDEP}]"
+
+BDEPEND="
+ test? (
+ dev-python/pytest-aiohttp[${PYTHON_USEDEP}]
+ dev-python/pytest-asyncio[${PYTHON_USEDEP}]
+ dev-python/pytest-tornasync[${PYTHON_USEDEP}]
+ )"
+
+distutils_enable_tests pytest
diff --git a/dev-python/aiohttp-retry/metadata.xml
b/dev-python/aiohttp-retry/metadata.xml
new file mode 100644
index 0..900a7e9f8
--- /dev/null
+++ b/dev-python/aiohttp-retry/metadata.xml
@@ -0,0 +1,16 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ gen...@chymera.eu
+ Horea Christian
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ inyutin/aiohttp_retry
+ aiohttp-retry
+
+
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 670b006885dabe96503628a52ddfc6d9a6635c57 Author: Horea Christian chymera eu> AuthorDate: Thu May 9 22:51:59 2024 + Commit: Horea Christian gmail com> CommitDate: Thu May 9 22:51:59 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=670b0068 profiles: unmasked nipype Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 2 -- 1 file changed, 2 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index efc64be51..09429792d 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -35,8 +35,6 @@ sci-biology/multiqc # Andrew Ammerlaan (2024-04-24) -# Dependencies dev-python/prov removed -sci-libs/nipype # reverse deps sci-biology/samri sci-biology/samri_bidsdata
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 1b90823136a7aa189484deb0f3769daf58d3c040 Author: Horea Christian chymera eu> AuthorDate: Thu May 9 23:02:28 2024 + Commit: Horea Christian gmail com> CommitDate: Thu May 9 23:02:28 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1b908231 profiles: unmasked samri, heudiconv Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 4 1 file changed, 4 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 09429792d..48068ccf9 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -36,7 +36,3 @@ sci-biology/multiqc # Andrew Ammerlaan (2024-04-24) # reverse deps -sci-biology/samri -sci-biology/samri_bidsdata -sci-biology/samri_bindata -dev-python/heudiconv
[gentoo-commits] proj/sci:master commit in: dev-python/prov/
commit: 024167b1e3f826ae32f4de09292733a499c8affa
Author: Horea Christian chymera eu>
AuthorDate: Thu May 9 22:47:56 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu May 9 22:48:45 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=024167b1
dev-python/prov: new package, add 2.0.0
Brought back here after deprecation from ::gentoo, fixed some of the
issues with it.
Signed-off-by: Horea Christian chymera.eu>
dev-python/prov/metadata.xml | 14 +
dev-python/prov/prov-2.0.0.ebuild | 43 +++
2 files changed, 57 insertions(+)
diff --git a/dev-python/prov/metadata.xml b/dev-python/prov/metadata.xml
new file mode 100644
index 0..d1559163d
--- /dev/null
+++ b/dev-python/prov/metadata.xml
@@ -0,0 +1,14 @@
+
+https://www.gentoo.org/dtd/metadata.dtd;>
+
+
+
+ A library for W3C Provenance Data Model supporting PROV-O
+ (RDF), PROV-XML, PROV-JSON import/export Interface to
+ Graphviz’s Dot language.
+
+
+ prov
+ trungdong/prov
+
+
diff --git a/dev-python/prov/prov-2.0.0.ebuild
b/dev-python/prov/prov-2.0.0.ebuild
new file mode 100644
index 0..a87b15c6f
--- /dev/null
+++ b/dev-python/prov/prov-2.0.0.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{9..12} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="W3C provenance data dodel library"
+HOMEPAGE="https://pypi.org/project/prov/;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/pydot[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/lxml[${PYTHON_USEDEP}]
+ >=dev-python/networkx-1.10[${PYTHON_USEDEP}]
+ dev-python/rdflib[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+
+# Reported upstream:
+# https://github.com/trungdong/prov/issues/156
+EPYTEST_DESELECT=(
+ src/prov/tests/test_model.py::TestAttributesBase
+ src/prov/tests/test_rdf.py::TestStatementsBase
+ src/prov/tests/test_rdf.py::TestAttributesBase2
+ src/prov/tests/test_rdf.py::TestQualifiedNamesBase
+ src/prov/tests/test_rdf.py::TestAttributesBase
+ src/prov/tests/test_model.py::TestStatementsBase
+ src/prov/tests/test_model.py::TestExamplesBase::test_all_examples
+ src/prov/tests/test_model.py::TestQualifiedNamesBase
+
src/prov/tests/test_rdf.py::RoundTripRDFTests::test_namespace_inheritance
+
src/prov/tests/test_rdf.py::RoundTripRDFTests::test_default_namespace_inheritance
+ src/prov/tests/test_rdf.py::TestRDFSerializer::test_json_to_ttl_match
+ src/prov/tests/test_rdf.py::TestJSONExamplesBase::test_all_examples
+ src/prov/tests/test_rdf.py::TestExamplesBase::test_all_examples
+)
[gentoo-commits] proj/sci:master commit in: dev-python/methodtools/, dev-python/methodtools/files/
commit: f373f8829169bcb92b7d80e2c8abfd36727b9622
Author: Horea Christian chymera eu>
AuthorDate: Thu May 9 22:07:11 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu May 9 22:07:11 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f373f882
dev-python/methodtools: new package, add 0.4.7
Signed-off-by: Horea Christian chymera.eu>
.../files/methodtools-0.4.7-nocov.patch| 9
dev-python/methodtools/metadata.xml| 16 +++
dev-python/methodtools/methodtools-0.4.7.ebuild| 24 ++
3 files changed, 49 insertions(+)
diff --git a/dev-python/methodtools/files/methodtools-0.4.7-nocov.patch
b/dev-python/methodtools/files/methodtools-0.4.7-nocov.patch
new file mode 100644
index 0..e2ff8a4c1
--- /dev/null
+++ b/dev-python/methodtools/files/methodtools-0.4.7-nocov.patch
@@ -0,0 +1,9 @@
+--- a/setup.cfg2023-02-05 08:15:17.0 -0500
b/setup.cfg2024-05-06 11:19:57.822360100 -0400
+@@ -35,6 +35,5 @@
+ [aliases]
+ test=pytest
+ [tool:pytest]
+-addopts=--verbose --cov-config .coveragerc --cov methodtools
+ python_files = tests/test*.py
+ norecursedirs=.git py ci
diff --git a/dev-python/methodtools/metadata.xml
b/dev-python/methodtools/metadata.xml
new file mode 100644
index 0..e85efd512
--- /dev/null
+++ b/dev-python/methodtools/metadata.xml
@@ -0,0 +1,16 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ gen...@chymera.eu
+ Horea Christian
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ youknowone/methodtools
+ methodtools
+
+
diff --git a/dev-python/methodtools/methodtools-0.4.7.ebuild
b/dev-python/methodtools/methodtools-0.4.7.ebuild
new file mode 100644
index 0..79e7739c5
--- /dev/null
+++ b/dev-python/methodtools/methodtools-0.4.7.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+inherit distutils-r1
+
+DESCRIPTION="Expand functools features to methods, classmethods, staticmethods"
+HOMEPAGE="https://github.com/youknowone/methodtools;
+# Not using PyPI archive because it misses test files:
+# https://github.com/youknowone/methodtools/issues/24
+SRC_URI="https://github.com/youknowone/methodtools/archive/refs/tags/${PV}.tar.gz
-> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/wirerope[${PYTHON_USEDEP}]"
+
+PATCHES=( "${FILESDIR}/${P}-nocov.patch" )
+
+distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: sci-biology/mrfast/, sci-biology/perlprimer/, sci-misc/jwnl/, sci-libs/gdcm/, ...
commit: f1220d233b7ea8c04a84cb5efb241d074407f2c2
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue May 7 19:29:39 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue May 7 19:29:51 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f1220d23
*/*: drop sourceforge mirror
Signed-off-by: Andrew Ammerlaan gentoo.org>
sci-astronomy/libthesky/libthesky-0.4.2.ebuild | 4 ++--
sci-biology/codonw/codonw-1.4.4-r2.ebuild | 2 +-
sci-biology/mrfast/mrfast-2.6.0.1.ebuild| 2 +-
sci-biology/perlprimer/perlprimer-1.1.21.ebuild | 2 +-
sci-libs/gdcm/gdcm-3.0.14.ebuild| 4 ++--
sci-libs/libsufr/libsufr-0.7.7.ebuild | 2 +-
sci-libs/lwpr/lwpr-1.2.5.ebuild | 2 +-
sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild | 2 +-
sci-misc/jwnl/jwnl-1.4_rc2.ebuild | 2 +-
9 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/sci-astronomy/libthesky/libthesky-0.4.2.ebuild
b/sci-astronomy/libthesky/libthesky-0.4.2.ebuild
index 09f89265f..c7d2bd0c3 100644
--- a/sci-astronomy/libthesky/libthesky-0.4.2.ebuild
+++ b/sci-astronomy/libthesky/libthesky-0.4.2.ebuild
@@ -9,8 +9,8 @@ inherit cmake fortran-2
DESCRIPTION="Fortran library to compute positions of celestial bodies"
HOMEPAGE="http://libthesky.sourceforge.net/;
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz
- mirror://sourceforge/${PN}/libthesky-data-20160409.tar.bz2
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz
+ https://downloads.sourceforge.net/${PN}/libthesky-data-20160409.tar.bz2
"
LICENSE="GPL-3"
diff --git a/sci-biology/codonw/codonw-1.4.4-r2.ebuild
b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
index 49bf65452..56c76a408 100644
--- a/sci-biology/codonw/codonw-1.4.4-r2.ebuild
+++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
@@ -7,7 +7,7 @@ inherit toolchain-funcs
DESCRIPTION="Multivariate statistical analysis of codon and amino acid usage"
HOMEPAGE="https://codonw.sourceforge.net/;
-SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${PV//./_}.tar.gz
+SRC_URI="https://downloads.sourceforge.net/${PN}/CodonWSourceCode_${PV//./_}.tar.gz
https://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf;
LICENSE="GPL-2"
diff --git a/sci-biology/mrfast/mrfast-2.6.0.1.ebuild
b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild
index 5d89c0822..42fc0b62d 100644
--- a/sci-biology/mrfast/mrfast-2.6.0.1.ebuild
+++ b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild
@@ -7,7 +7,7 @@ inherit flag-o-matic toolchain-funcs
DESCRIPTION="Micro Read Fast Alignment Search Tool"
HOMEPAGE="http://mrfast.sourceforge.net/;
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz;
LICENSE="BSD"
SLOT="0"
diff --git a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
index bae672851..bc15bb8f4 100644
--- a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
+++ b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
@@ -5,7 +5,7 @@ EAPI=7
DESCRIPTION="Primers design for standard PCR, bisulphite PCR and Real-time PCR"
HOMEPAGE="http://perlprimer.sourceforge.net/;
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.bz2;
LICENSE="GPL-2"
SLOT="0"
diff --git a/sci-libs/gdcm/gdcm-3.0.14.ebuild b/sci-libs/gdcm/gdcm-3.0.14.ebuild
index c1000fea9..467fa623c 100644
--- a/sci-libs/gdcm/gdcm-3.0.14.ebuild
+++ b/sci-libs/gdcm/gdcm-3.0.14.ebuild
@@ -9,8 +9,8 @@ inherit cmake python-single-r1
DESCRIPTION="Cross-platform DICOM implementation"
HOMEPAGE="http://gdcm.sourceforge.net/;
-SRC_URI="mirror://sourceforge/gdcm/${P}.tar.bz2
- test? ( mirror://sourceforge/gdcm/gdcmData.tar.gz )" # 3.0.14: .bz2 is
broken, should be checked in next release
+SRC_URI="https://downloads.sourceforge.net/gdcm/${P}.tar.bz2
+ test? ( https://downloads.sourceforge.net/gdcm/gdcmData.tar.gz )" #
3.0.14: .bz2 is broken, should be checked in next release
LICENSE="BSD"
SLOT="0"
diff --git a/sci-libs/libsufr/libsufr-0.7.7.ebuild
b/sci-libs/libsufr/libsufr-0.7.7.ebuild
index 3515005bc..cd49de6b5 100644
--- a/sci-libs/libsufr/libsufr-0.7.7.ebuild
+++ b/sci-libs/libsufr/libsufr-0.7.7.ebuild
@@ -9,7 +9,7 @@ inherit cmake fortran-2
DESCRIPTION="LIBrary of Some Useful Fortran Routines"
HOMEPAGE="http://libsufr.sourceforge.net/;
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz;
LICENSE="GPL-3"
SLOT="0"
diff --git a/sci-libs/lwpr/lwpr-1.2.5.ebuild b/sci-libs/lwpr/lwpr-1.2.5.ebuild
index 3415656a9..2f040a86e 100644
--- a/sci-libs/lwpr/lwpr-1.2.5.ebuild
+++ b/sci-libs/lwpr/lwpr-1.2.5.ebuild
@@ -9,7 +9,7 @@ inherit docs
DESCRIPTION="The Locally Weighted Projection Regression Library"
HOMEPAGE="https://web.inf.ed.ac.uk/slmc;
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
[gentoo-commits] proj/sci:master commit in: dev-python/wirerope/, dev-python/wirerope/files/
commit: a713b317a1e583b970f6382a464603f100f269b8
Author: Horea Christian chymera eu>
AuthorDate: Mon May 6 15:10:45 2024 +
Commit: Horea Christian gmail com>
CommitDate: Mon May 6 15:10:45 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a713b317
dev-python/wirerope: new package, add 0.4.7
Signed-off-by: Horea Christian chymera.eu>
.../wirerope/files/wirerope-0.4.7-nocov.patch | 10 +
dev-python/wirerope/metadata.xml | 16 +
dev-python/wirerope/wirerope-0.4.7.ebuild | 26 ++
3 files changed, 52 insertions(+)
diff --git a/dev-python/wirerope/files/wirerope-0.4.7-nocov.patch
b/dev-python/wirerope/files/wirerope-0.4.7-nocov.patch
new file mode 100644
index 0..64d47d0b7
--- /dev/null
+++ b/dev-python/wirerope/files/wirerope-0.4.7-nocov.patch
@@ -0,0 +1,10 @@
+--- a/setup.cfg2023-02-05 08:00:42.0 -0500
b/setup.cfg2024-05-06 11:01:02.896234948 -0400
+@@ -33,7 +33,6 @@
+ sphinx
+
+ [tool:pytest]
+-addopts=--verbose --cov-config .coveragerc --cov wirerope
+ python_files = tests/test_*.py
+ norecursedirs=.git py ci
+ [flake8]
diff --git a/dev-python/wirerope/metadata.xml b/dev-python/wirerope/metadata.xml
new file mode 100644
index 0..6e39bae5d
--- /dev/null
+++ b/dev-python/wirerope/metadata.xml
@@ -0,0 +1,16 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ gen...@chymera.eu
+ Horea Christian
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ youknowone/wirerope
+ wirerope
+
+
diff --git a/dev-python/wirerope/wirerope-0.4.7.ebuild
b/dev-python/wirerope/wirerope-0.4.7.ebuild
new file mode 100644
index 0..74e7f40bd
--- /dev/null
+++ b/dev-python/wirerope/wirerope-0.4.7.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+inherit distutils-r1
+
+DESCRIPTION="A wrapper interface for python callables"
+HOMEPAGE="https://github.com/youknowone/wirerope;
+# Not using PyPI archive because it misses test files:
+# https://github.com/youknowone/wirerope/issues/20
+SRC_URI="https://github.com/youknowone/wirerope/archive/refs/tags/${PV}.tar.gz
-> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/six[${PYTHON_USEDEP}]
+"
+
+PATCHES=( "${FILESDIR}/${P}-nocov.patch" )
+
+distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: dev-python/linesep/, dev-python/linesep/files/
commit: 1794b33cc30fe3b533a39db20f9704843f5827e1
Author: Horea Christian chymera eu>
AuthorDate: Mon May 6 13:21:08 2024 +
Commit: Horea Christian gmail com>
CommitDate: Mon May 6 13:21:08 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1794b33c
dev-python/linesep: new package, add 0.5.0
Signed-off-by: Horea Christian chymera.eu>
dev-python/linesep/files/linesep-0.5.0-nocov.patch | 12 +++
dev-python/linesep/linesep-0.5.0.ebuild| 25 ++
dev-python/linesep/metadata.xml| 16 ++
3 files changed, 53 insertions(+)
diff --git a/dev-python/linesep/files/linesep-0.5.0-nocov.patch
b/dev-python/linesep/files/linesep-0.5.0-nocov.patch
new file mode 100644
index 0..a27bbd4b8
--- /dev/null
+++ b/dev-python/linesep/files/linesep-0.5.0-nocov.patch
@@ -0,0 +1,12 @@
+diff --git a/tox.ini b/tox.ini
+index 4d45597..cdd9e18 100644
+--- a/tox.ini
b/tox.ini
+@@ -31,7 +31,6 @@ commands =
+ mypy src test
+
+ [pytest]
+-addopts = --cov=linesep --no-cov-on-fail
+ asyncio_mode = strict
+ doctest_optionflags = IGNORE_EXCEPTION_DETAIL
+ filterwarnings = error
diff --git a/dev-python/linesep/linesep-0.5.0.ebuild
b/dev-python/linesep/linesep-0.5.0.ebuild
new file mode 100644
index 0..148ff0883
--- /dev/null
+++ b/dev-python/linesep/linesep-0.5.0.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Handling lines with arbitrary separators"
+HOMEPAGE="https://github.com/jwodder/linesep;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+BDEPEND="
+ test? (
+ dev-python/pytest-subtests[${PYTHON_USEDEP}]
+ )
+"
+
+PATCHES=( "${FILESDIR}/${P}-nocov.patch" )
+
+distutils_enable_tests pytest
diff --git a/dev-python/linesep/metadata.xml b/dev-python/linesep/metadata.xml
new file mode 100644
index 0..017856905
--- /dev/null
+++ b/dev-python/linesep/metadata.xml
@@ -0,0 +1,16 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ gen...@chymera.eu
+ Horea Christian
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ jwodder/linesep
+ linesep
+
+
[gentoo-commits] proj/sci:master commit in: sci-physics/jaxodraw-bin/
commit: 55493841dd75a1cdd15199aaf38337334fdc7d90
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Sun May 5 10:24:44 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Mon May 6 11:59:42 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=55493841
sci-physics/jaxodraw-bin: new package, add 2.1.0
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
Closes: https://github.com/gentoo/sci/pull/1269
sci-physics/jaxodraw-bin/jaxodraw-bin-2.1.0.ebuild | 54 ++
sci-physics/jaxodraw-bin/metadata.xml | 15 ++
2 files changed, 69 insertions(+)
diff --git a/sci-physics/jaxodraw-bin/jaxodraw-bin-2.1.0.ebuild
b/sci-physics/jaxodraw-bin/jaxodraw-bin-2.1.0.ebuild
new file mode 100644
index 0..e23381514
--- /dev/null
+++ b/sci-physics/jaxodraw-bin/jaxodraw-bin-2.1.0.ebuild
@@ -0,0 +1,54 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+JAVA_PKG_IUSE="doc source"
+
+inherit desktop java-pkg-2 latex-package
+
+MY_PN="jaxodraw"
+MY_PV=$(ver_rs 2 '-')
+MY_P=${MY_PN}-${MY_PV}
+
+DESCRIPTION="Java program for drawing Feynman diagrams"
+HOMEPAGE="
+ https://jaxodraw.sourceforge.io/index.html
+ http://jaxodraw.sourceforge.net/
+"
+SRC_URI="
+ https://${MY_PN}.sourceforge.net/download/pkgs/${MY_P}-bin.tar.gz
+ https://${MY_PN}.sourceforge.net/download/pkgs/${MY_P}-src.tar.gz
+ latex? (
https://downloads.sourceforge.net/${MY_PN}/axodraw4j_2008_11_19.tar.gz )
+"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+latex"
+
+DEPEND="
+ >=virtual/jdk-1.8
+ latex? ( dev-texlive/texlive-pstricks:0 )
+"
+
+RDEPEND=">=virtual/jre-1.8"
+
+src_install() {
+ java-pkg_newjar ${MY_P}.jar
+
+ newicon src/site/resources/images/favicon.ico jaxodraw.ico
+ make_desktop_entry jaxodraw JaxoDraw jaxodraw.ico
+
+ use source && java-pkg_dosrc src/main/java/net
+
+ dodoc src/doc/BUGS src/doc/CHANGELOG src/doc/README src/doc/TODO
+ use doc && java-pkg_dojavadoc build/javadoc
+
+ java-pkg_dolauncher "${MY_P}"
+
+ if use latex; then
+ cd "${WORKDIR}" || die "Failed to cd ${WORKDIR}"
+ latex-package_src_doinstall
+ fi
+}
diff --git a/sci-physics/jaxodraw-bin/metadata.xml
b/sci-physics/jaxodraw-bin/metadata.xml
new file mode 100644
index 0..7a665fa37
--- /dev/null
+++ b/sci-physics/jaxodraw-bin/metadata.xml
@@ -0,0 +1,15 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ sci-phys...@gentoo.org
+ Gentoo Physics Project
+
+
+ jaxodraw
+
+
[gentoo-commits] proj/sci:master commit in: dev-python/histoprint/
commit: 773b0fb36a5644343e8592ea6a34472524234e06
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Sun Mar 17 21:16:28 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Mon May 6 08:23:18 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=773b0fb3
dev-python/histoprint: new package, add 2.4.0
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
dev-python/histoprint/histoprint-2.4.0.ebuild | 20
dev-python/histoprint/metadata.xml| 19 +++
2 files changed, 39 insertions(+)
diff --git a/dev-python/histoprint/histoprint-2.4.0.ebuild
b/dev-python/histoprint/histoprint-2.4.0.ebuild
new file mode 100644
index 0..b6395b898
--- /dev/null
+++ b/dev-python/histoprint/histoprint-2.4.0.ebuild
@@ -0,0 +1,20 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Pretty print histograms to the console"
+HOMEPAGE="https://github.com/scikit-hep/histoprint;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ >=dev-python/click-7.0.0[${PYTHON_USEDEP}]
+ >=dev-python/uhi-0.2.1[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/histoprint/metadata.xml
b/dev-python/histoprint/metadata.xml
new file mode 100644
index 0..78373f05f
--- /dev/null
+++ b/dev-python/histoprint/metadata.xml
@@ -0,0 +1,19 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ Histoprint uses a mix of terminal color codes and Unicode trickery
(i.e. combining characters) to plot overlaying histograms. Some terminals are
not able to display Unicode combining characters correctly. Histoprint can
still be used in those terminals, but the character set needs to be constrained
to the non-combining ones (see below).
+
+
+ histoprint
+ scikit-hep/histoprint
+
+
[gentoo-commits] proj/sci:master commit in: dev-python/hist/
commit: 3a4aefebff189bf3eea674c215827925240f418f
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Sun Mar 17 21:18:32 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Mon May 6 08:23:31 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a4aefeb
dev-python/hist: new package, add 2.7.2
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
Closes: https://github.com/gentoo/sci/pull/1259
dev-python/hist/hist-2.7.2.ebuild | 26 ++
dev-python/hist/metadata.xml | 19 +++
2 files changed, 45 insertions(+)
diff --git a/dev-python/hist/hist-2.7.2.ebuild
b/dev-python/hist/hist-2.7.2.ebuild
new file mode 100644
index 0..082844a5f
--- /dev/null
+++ b/dev-python/hist/hist-2.7.2.ebuild
@@ -0,0 +1,26 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+inherit distutils-r1 pypi
+
+DESCRIPTION="Histogramming for analysis powered by boost-histogram "
+HOMEPAGE="https://github.com/scikit-hep/hist;
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/boost-histogram-1.3.1[${PYTHON_USEDEP}]
+ >=dev-python/histoprint-2.2.0[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.14.5[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+RESTRICT="test"
+# needs mplhep and dask_histogram ...
+#distutils_enable_tests pytest
diff --git a/dev-python/hist/metadata.xml b/dev-python/hist/metadata.xml
new file mode 100644
index 0..566083fe3
--- /dev/null
+++ b/dev-python/hist/metadata.xml
@@ -0,0 +1,19 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ Hist is an analyst-friendly front-end for boost-histogram, designed for
Python 3.7+ (3.6 users get version 2.4)
+
+
+ hist
+ scikit-hep/hist
+
+
[gentoo-commits] proj/sci:master commit in: sci-physics/pyhf/
commit: 7057468421337302f4dd9f9086c501496474402e
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Mon Apr 29 11:14:29 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Mon Apr 29 11:14:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=70574684
sci-physics/pyhf: add 0.7.5
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/pyhf/pyhf-0.7.5.ebuild | 37 +
1 file changed, 37 insertions(+)
diff --git a/sci-physics/pyhf/pyhf-0.7.5.ebuild
b/sci-physics/pyhf/pyhf-0.7.5.ebuild
new file mode 100644
index 0..22a36af7f
--- /dev/null
+++ b/sci-physics/pyhf/pyhf-0.7.5.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="pure-python fitting/limit-setting/interval estimation
HistFactory-style"
+HOMEPAGE="
+ https://github.com/scikit-hep/pyhf
+ https://doi.org/10.5281/zenodo.1169739
+ https://zenodo.org/record/8256635
+ https://doi.org/10.21105/joss.02823
+ https://inspirehep.net/literature/2598491
+ https://arxiv.org/abs/2211.15838
+ https://doi.org/10.22323/1.414.0245
+"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+# test needs missing scrapbook papermill pydocstyle ...
+RESTRICT="test"
+
+RDEPEND="
+ >=dev-python/click-8.0.0[${PYTHON_USEDEP}]
+ >=dev-python/jsonpatch-1.15[${PYTHON_USEDEP}]
+ >=dev-python/jsonschema-4.15.0[${PYTHON_USEDEP}]
+ >=dev-python/pyyaml-5.1[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.5.2[${PYTHON_USEDEP}]
+ >=dev-python/tqdm-4.56.0[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
[gentoo-commits] proj/sci:master commit in: dev-python/vector/
commit: 281eaa53826e68185d854a988365ca50503ceb5f
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Thu Apr 25 12:28:34 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Thu Apr 25 12:29:52 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=281eaa53
dev-python/vector: add 1.4.0
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
dev-python/vector/vector-1.4.0.ebuild | 34 ++
1 file changed, 34 insertions(+)
diff --git a/dev-python/vector/vector-1.4.0.ebuild
b/dev-python/vector/vector-1.4.0.ebuild
new file mode 100644
index 0..a57240b49
--- /dev/null
+++ b/dev-python/vector/vector-1.4.0.ebuild
@@ -0,0 +1,34 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1 pypi optfeature
+
+DESCRIPTION="Vector classes and utilities"
+HOMEPAGE="
+ https://github.com/scikit-hep/vector
+ https://vector.readthedocs.io/
+ https://doi.org/10.5281/zenodo.7054478
+"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+# tests need numba
+RESTRICT="test"
+
+RDEPEND="
+ >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+ >=dev-python/packaging-19[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+
+pkg_postinst() {
+ optfeature "awkward array support" dev-python/awkward
+ optfeature "sympy support" dev-python/sympy
+}
[gentoo-commits] proj/sci:master commit in: sci-physics/cernlib/
commit: 55da92a78fb0bf296acf20a2b09ae8290c53426d
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Apr 23 14:50:25 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Wed Apr 24 14:12:19 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=55da92a7
sci-physics/cernlib: Fix test failures
Closes: https://github.com/gentoo/sci/pull/1268
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
...-2023.10.31.0-r1.ebuild => cernlib-2023.10.31.0-r2.ebuild} | 11 +--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
b/sci-physics/cernlib/cernlib-2023.10.31.0-r2.ebuild
similarity index 82%
rename from sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
rename to sci-physics/cernlib/cernlib-2023.10.31.0-r2.ebuild
index c5c919678..93220dffb 100644
--- a/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
+++ b/sci-physics/cernlib/cernlib-2023.10.31.0-r2.ebuild
@@ -1,7 +1,7 @@
EAPI=8
CMAKE_MAKEFILE_GENERATOR="emake"
-inherit cmake fortran-2
+inherit cmake fortran-2 flag-o-matic
DESCRIPTION="CERN program library for High Energy Physics"
HOMEPAGE="https://cernlib.web.cern.ch/cernlib/;
@@ -16,7 +16,8 @@ LICENSE="
"
SLOT="0"
KEYWORDS="~amd64"
-IUSE="+free"
+# static-libs as default since otherwise test fail...
+IUSE="+free +static-libs"
RESTRICT="mirror"
RDEPEND="
@@ -59,6 +60,12 @@ src_configure() {
# docs follow rpm like spliting into packages cernlib, cernlib-devel,
etc.
# we move them into a folder that agrees with gentoo doc structure.
sed -i "s#/doc/#/doc/${PF}/#g" CMakeLists.txt || die
+ # with -O2 some tests fail
+ # let upstream decide on optimization (-O0) since code is fragile
+ filter-flags -O1 -O2 -O3 -Os -Oz -Og -Ofast
+ local mycmakeargs=(
+ -DBUILD_SHARED_LIBS=$(usex static-libs OFF ON)
+ )
cmake_src_configure
}
[gentoo-commits] proj/sci:master commit in: profiles/
commit: ca51d5147ba4ef27db118dffc07302eaac1bc7b9 Author: Andrew Ammerlaan gentoo org> AuthorDate: Wed Apr 24 09:34:43 2024 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Wed Apr 24 09:34:43 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca51d514 package.mask: mask multiqc and nipype Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 13 + 1 file changed, 13 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d39812beb..efc64be51 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,3 +29,16 @@ ## app-misc/some-package #--- END OF EXAMPLES --- + +# Andrew Ammerlaan (2024-04-24) +# Dependencies dev-python/future removed +sci-biology/multiqc + +# Andrew Ammerlaan (2024-04-24) +# Dependencies dev-python/prov removed +sci-libs/nipype +# reverse deps +sci-biology/samri +sci-biology/samri_bidsdata +sci-biology/samri_bindata +dev-python/heudiconv
[gentoo-commits] proj/sci:master commit in: sci-physics/particle/
commit: 0d6d40c476ef48c4e25a87f97426399dfb657438
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Apr 23 13:53:46 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Apr 23 13:53:46 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0d6d40c4
sci-physics/particle: add 0.24.0
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/particle/particle-0.24.0.ebuild | 44 +
1 file changed, 44 insertions(+)
diff --git a/sci-physics/particle/particle-0.24.0.ebuild
b/sci-physics/particle/particle-0.24.0.ebuild
new file mode 100644
index 0..43f1e67ca
--- /dev/null
+++ b/sci-physics/particle/particle-0.24.0.ebuild
@@ -0,0 +1,44 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1
+
+DESCRIPTION="PDG particle data and identification codes"
+HOMEPAGE="https://github.com/scikit-hep/particle;
+
+LICENSE="BSD"
+SLOT="0"
+
+if [[ ${PV} == ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scikit-hep/particle;
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=dev-python/attrs-19.2[${PYTHON_USEDEP}]
+ >=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}]
+ dev-python/deprecated[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ test? (
+ >=dev-python/pytest-6.0.0[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/tabulate[${PYTHON_USEDEP}]
+ )
+"
+distutils_enable_tests pytest
+
+src_prepare() {
+ default
+
+ sed -i -e 's:--benchmark-disable::' pyproject.toml || die
+}
+
+python_test() {
+ epytest --ignore tests/particle/test_performance.py
+}
[gentoo-commits] proj/sci:master commit in: sci-physics/cernlib/
commit: 76470804a085b752ebcae40c612f16fc32699379
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Apr 23 13:15:14 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Apr 23 13:15:14 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=76470804
sci-physics/cernlib: Drop var MY_P
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild | 1 -
1 file changed, 1 deletion(-)
diff --git a/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
b/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
index 326fadde3..c5c919678 100644
--- a/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
+++ b/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
@@ -3,7 +3,6 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="emake"
inherit cmake fortran-2
-MY_P="${P}"
DESCRIPTION="CERN program library for High Energy Physics"
HOMEPAGE="https://cernlib.web.cern.ch/cernlib/;
SRC_URI="
[gentoo-commits] proj/sci:master commit in: sci-physics/formcalc/
commit: 74771d4deed5bff927bf492fdc1d86bf2f099dce
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Wed Apr 10 19:17:08 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Wed Apr 17 10:20:18 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=74771d4d
sci-physics/formcalc: inherit fortran-2
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/formcalc/formcalc-9.10-r1.ebuild | 2 ++
sci-physics/formcalc/formcalc-9.9-r1.ebuild | 2 ++
2 files changed, 4 insertions(+)
diff --git a/sci-physics/formcalc/formcalc-9.10-r1.ebuild
b/sci-physics/formcalc/formcalc-9.10-r1.ebuild
index cefbd13bf..fb57ea648 100644
--- a/sci-physics/formcalc/formcalc-9.10-r1.ebuild
+++ b/sci-physics/formcalc/formcalc-9.10-r1.ebuild
@@ -3,6 +3,8 @@
EAPI=8
+inherit fortran-2
+
MY_PN=FormCalc
MY_P=${MY_PN}-${PV}
diff --git a/sci-physics/formcalc/formcalc-9.9-r1.ebuild
b/sci-physics/formcalc/formcalc-9.9-r1.ebuild
index 6ccb521fb..91d88dd99 100644
--- a/sci-physics/formcalc/formcalc-9.9-r1.ebuild
+++ b/sci-physics/formcalc/formcalc-9.9-r1.ebuild
@@ -3,6 +3,8 @@
EAPI=8
+inherit fortran-2
+
MY_PN=FormCalc
MY_P=${MY_PN}-${PV}
[gentoo-commits] proj/sci:master commit in: sci-physics/qcdloop/
commit: 21613b44a78c29aa0db553380a15ae494b19d314
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Wed Apr 10 19:16:41 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Wed Apr 17 10:20:17 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=21613b44
sci-physics/qcdloop: inherit fortran-2
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/qcdloop/qcdloop-2.0.5.ebuild | 8 +---
sci-physics/qcdloop/qcdloop-2.0.9.ebuild | 8 +---
2 files changed, 2 insertions(+), 14 deletions(-)
diff --git a/sci-physics/qcdloop/qcdloop-2.0.5.ebuild
b/sci-physics/qcdloop/qcdloop-2.0.5.ebuild
index 19a247ba2..672957c56 100644
--- a/sci-physics/qcdloop/qcdloop-2.0.5.ebuild
+++ b/sci-physics/qcdloop/qcdloop-2.0.5.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="emake"
-inherit cmake
+inherit cmake fortran-2
DESCRIPTION="An object-oriented one-loop scalar Feynman integrals framework"
HOMEPAGE="https://qcdloop.web.cern.ch/qcdloop/;
@@ -15,12 +15,6 @@ LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64"
-DEPEND=""
-RDEPEND="${DEPEND}"
-BDEPEND="
- virtual/fortran
-"
-
PATCHES=(
"${FILESDIR}"/${P}-cxx.patch
)
diff --git a/sci-physics/qcdloop/qcdloop-2.0.9.ebuild
b/sci-physics/qcdloop/qcdloop-2.0.9.ebuild
index ccea20aa5..6486e70b9 100644
--- a/sci-physics/qcdloop/qcdloop-2.0.9.ebuild
+++ b/sci-physics/qcdloop/qcdloop-2.0.9.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="emake"
-inherit cmake
+inherit cmake fortran-2
DESCRIPTION="An object-oriented one-loop scalar Feynman integrals framework"
HOMEPAGE="https://qcdloop.web.cern.ch/qcdloop/;
@@ -15,12 +15,6 @@ LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64"
-DEPEND=""
-RDEPEND="${DEPEND}"
-BDEPEND="
- virtual/fortran
-"
-
PATCHES=(
"${FILESDIR}"/${P}-cxx.patch
)
[gentoo-commits] proj/sci:master commit in: sci-physics/collier/
commit: 26fd6b8a5e827b48ef11d067c324f4c5fe5601c7
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Wed Apr 10 19:17:49 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Wed Apr 17 10:20:20 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=26fd6b8a
sci-physics/collier: drop virtual/fortran
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/collier/collier-1.2.8.ebuild | 6 ++
sci-physics/collier/metadata.xml | 3 ---
2 files changed, 2 insertions(+), 7 deletions(-)
diff --git a/sci-physics/collier/collier-1.2.8.ebuild
b/sci-physics/collier/collier-1.2.8.ebuild
index b50f9a279..c9410cf34 100644
--- a/sci-physics/collier/collier-1.2.8.ebuild
+++ b/sci-physics/collier/collier-1.2.8.ebuild
@@ -19,11 +19,9 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE="static-libs"
-BDEPEND="
- virtual/fortran
-"
+
PATCHES=(
-"${FILESDIR}/${PN}-1.2.7-mod.patch"
+ "${FILESDIR}/${PN}-1.2.7-mod.patch"
)
src_configure() {
diff --git a/sci-physics/collier/metadata.xml b/sci-physics/collier/metadata.xml
index f863d8237..72f8361a4 100644
--- a/sci-physics/collier/metadata.xml
+++ b/sci-physics/collier/metadata.xml
@@ -16,7 +16,4 @@
to the scalar one-loop functions of FF and in addition provides
the 2-, 3-, and 4-point tensor coefficient functions.
-
-Build static library
-
[gentoo-commits] proj/sci:master commit in: sci-physics/mcfm/
commit: 98c2b6d99ac3f38f22f7927b54f09527a2cf27a7
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Wed Apr 10 19:19:22 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Wed Apr 17 10:20:22 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=98c2b6d9
sci-physics/mcfm: inherit fortran-2
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/mcfm/mcfm-10.2.1.ebuild | 5 +
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/sci-physics/mcfm/mcfm-10.2.1.ebuild
b/sci-physics/mcfm/mcfm-10.2.1.ebuild
index 9a928e4c9..bfc795247 100644
--- a/sci-physics/mcfm/mcfm-10.2.1.ebuild
+++ b/sci-physics/mcfm/mcfm-10.2.1.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="emake"
-inherit cmake
+inherit cmake fortran-2
MY_PN=MCFM
MY_P=${MY_PN}-${PV}
@@ -29,9 +29,6 @@ DEPEND="
>=sci-libs/handyg-0.1.5
"
RDEPEND="${DEPEND}"
-BDEPEND="
- virtual/fortran
-"
PATCHES=(
"${FILESDIR}"/${P}-rest.patch
[gentoo-commits] proj/sci:master commit in: sci-physics/oneloop/
commit: 6d3d25d39b4f3ab569cc836491e3b3abf8994b49
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Wed Apr 10 19:19:59 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Wed Apr 17 10:20:23 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6d3d25d3
sci-physics/oneloop: add bitbucket upstream metadata
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/oneloop/metadata.xml | 3 +++
sci-physics/oneloop/oneloop-2020.07.31.ebuild | 5 +
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-physics/oneloop/metadata.xml b/sci-physics/oneloop/metadata.xml
index bdee6992b..35b6c2bd9 100644
--- a/sci-physics/oneloop/metadata.xml
+++ b/sci-physics/oneloop/metadata.xml
@@ -9,4 +9,7 @@
sci-phys...@gentoo.org
Gentoo Physics Project
+
+ hameren/oneloop
+
diff --git a/sci-physics/oneloop/oneloop-2020.07.31.ebuild
b/sci-physics/oneloop/oneloop-2020.07.31.ebuild
index 8b98d1e1d..9344d1513 100644
--- a/sci-physics/oneloop/oneloop-2020.07.31.ebuild
+++ b/sci-physics/oneloop/oneloop-2020.07.31.ebuild
@@ -5,7 +5,7 @@ EAPI=8
# python only needed for create.py to get binaries
PYTHON_COMPAT=( python3_{10..11} )
-inherit toolchain-funcs python-any-r1
+inherit toolchain-funcs python-any-r1 fortran-2
DESCRIPTION="Library of one-loop scalar functions"
HOMEPAGE="https://bitbucket.org/hameren/oneloop;
@@ -16,12 +16,9 @@ LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64"
-DEPEND=""
-RDEPEND="${DEPEND}"
BDEPEND="
${PYTHON_DEPS}
app-arch/unzip
- virtual/fortran
"
PATCHES=(
[gentoo-commits] proj/sci:master commit in: dev-python/MagnetoResistance-tool/
commit: 042352e58dc0a6e32777c28deeaacae1a0b382b4
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Thu Apr 11 12:49:14 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Thu Apr 11 12:49:28 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=042352e5
dev-python/MagnetoResistance-tool: enable py3.12
Signed-off-by: Andrew Ammerlaan gentoo.org>
dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git
a/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
index cb24f5d19..23e03adcf 100644
--- a/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
+++ b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
PYPI_NO_NORMALIZE=1
inherit distutils-r1 pypi
[gentoo-commits] proj/sci:master commit in: sci-physics/cernlib/
commit: d92a65a7066fd6bc6467e88a26c33e9e5a152a8e
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Mon Apr 8 11:32:34 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Apr 9 13:05:35 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d92a65a7
sci-physics/cernlib: split free and non-free
Closes: https://github.com/gentoo/sci/pull/1265
Co-authored-by: Andrew Nowa Ammerlaan gentoo.org>
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
31.0.ebuild => cernlib-2023.10.31.0-r1.ebuild} | 28 +-
sci-physics/cernlib/metadata.xml | 3 +++
2 files changed, 25 insertions(+), 6 deletions(-)
diff --git a/sci-physics/cernlib/cernlib-2023.10.31.0.ebuild
b/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
similarity index 70%
rename from sci-physics/cernlib/cernlib-2023.10.31.0.ebuild
rename to sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
index 697a25ef0..326fadde3 100644
--- a/sci-physics/cernlib/cernlib-2023.10.31.0.ebuild
+++ b/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
@@ -3,14 +3,22 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="emake"
inherit cmake fortran-2
+MY_P="${P}"
DESCRIPTION="CERN program library for High Energy Physics"
HOMEPAGE="https://cernlib.web.cern.ch/cernlib/;
-SRC_URI="https://cernlib.web.cern.ch/download/2023_source/tar/${P}-free.tar.gz;
-S="${WORKDIR}/${P}-free"
+SRC_URI="
+ free? (
https://cernlib.web.cern.ch/download/2023_source/tar/${P}-free.tar.gz )
+ !free? (
https://cernlib.web.cern.ch/download/2023_source/tar/${P}.tar.gz )
+"
-LICENSE="GPL-3"
+LICENSE="
+ free? ( BSD LGPL-2+ GPL-1+ )
+ !free? ( all-rights-reserved )
+"
SLOT="0"
KEYWORDS="~amd64"
+IUSE="+free"
+RESTRICT="mirror"
RDEPEND="
x11-libs/motif:0
@@ -28,10 +36,18 @@ BDEPEND="
"
PATCHES=(
- "${FILESDIR}"/$P-cfortran.patch
- "${FILESDIR}"/$P-ctest.patch
- "${FILESDIR}"/$P-man.patch
+ "${FILESDIR}"/${P}-cfortran.patch
+ "${FILESDIR}"/${P}-ctest.patch
+ "${FILESDIR}"/${P}-man.patch
)
+
+src_unpack() {
+ default
+ if use free; then
+ mv ${P}-free ${P} || die
+ fi
+}
+
src_prepare() {
cmake_src_prepare
# cfortran.patch
diff --git a/sci-physics/cernlib/metadata.xml b/sci-physics/cernlib/metadata.xml
index 887c950bc..dcbfb9b47 100644
--- a/sci-physics/cernlib/metadata.xml
+++ b/sci-physics/cernlib/metadata.xml
@@ -18,4 +18,7 @@
mathematics, data analysis, detectors simulation, data-handling
etc... applicable to a wide range of problems.
+
+ Use free sources
+
[gentoo-commits] proj/sci:master commit in: sci-physics/formcalc/
commit: 59675e1c7f9bdcc501e8be8ebfc13e3c6ca72029
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Apr 2 15:15:13 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Apr 9 13:03:16 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=59675e1c
sci-physics/formcalc: fix chmod cannot access
Closes: https://github.com/gentoo/sci/pull/1264
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/formcalc/formcalc-9.10-r1.ebuild | 9 ++---
sci-physics/formcalc/formcalc-9.9-r1.ebuild | 9 ++---
2 files changed, 4 insertions(+), 14 deletions(-)
diff --git a/sci-physics/formcalc/formcalc-9.10-r1.ebuild
b/sci-physics/formcalc/formcalc-9.10-r1.ebuild
index 6cee48279..cefbd13bf 100644
--- a/sci-physics/formcalc/formcalc-9.10-r1.ebuild
+++ b/sci-physics/formcalc/formcalc-9.10-r1.ebuild
@@ -36,14 +36,9 @@ src_compile() {
src_install() {
MMADIR=/usr/share/Mathematica/Applications
+ # unversioned directory
dosym ${MY_P} ${MMADIR}/${MY_PN}
- dodir ${MMADIR}/${MY_P}
- insinto ${MMADIR}
- doins -r "${S}"
- # Copy executable, etc. permissions
- for f in $(find * ! -type l); do
- fperms --reference="${S}/$f" ${MMADIR}/${MY_P}/$f
- done
+ mv "${WORKDIR}/${MY_P}" "${ED}${MMADIR}" || die
# switch to system form
dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/form
dosym `command -v tform` ${MMADIR}/${MY_P}/Linux-x86-64/tform
diff --git a/sci-physics/formcalc/formcalc-9.9-r1.ebuild
b/sci-physics/formcalc/formcalc-9.9-r1.ebuild
index a5cd57431..6ccb521fb 100644
--- a/sci-physics/formcalc/formcalc-9.9-r1.ebuild
+++ b/sci-physics/formcalc/formcalc-9.9-r1.ebuild
@@ -38,14 +38,9 @@ src_compile() {
src_install() {
MMADIR=/usr/share/Mathematica/Applications
+ # unversioned directory
dosym ${MY_P} ${MMADIR}/${MY_PN}
- dodir ${MMADIR}/${MY_P}
- insinto ${MMADIR}
- doins -r "${S}"
- # Copy executable, etc. permissions
- for f in $(find * ! -type l); do
- fperms --reference="${S}/$f" ${MMADIR}/${MY_P}/$f
- done
+ mv "${WORKDIR}/${MY_P}" "${ED}${MMADIR}" || die
# switch to system form
dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/form
dosym `command -v tform` ${MMADIR}/${MY_P}/Linux-x86-64/tform
[gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
commit: 73916dd3680ffd92e5bd3d32b262e5d78c86a448
Author: Horea Christian chymera eu>
AuthorDate: Tue Apr 2 23:56:26 2024 +
Commit: Horea Christian gmail com>
CommitDate: Wed Apr 3 00:00:03 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=73916dd3
sci-biology/neuroconv: dependency revbump
Signed-off-by: Horea Christian chymera.eu>
.../neuroconv/{neuroconv-0.4.8.ebuild => neuroconv-0.4.8-r1.ebuild} | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/sci-biology/neuroconv/neuroconv-0.4.8.ebuild
b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild
similarity index 97%
rename from sci-biology/neuroconv/neuroconv-0.4.8.ebuild
rename to sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild
index a3012611f..b21c2fd8e 100644
--- a/sci-biology/neuroconv/neuroconv-0.4.8.ebuild
+++ b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild
@@ -17,20 +17,21 @@ KEYWORDS="~amd64"
IUSE="+ecephys +icephys +ophys"
RDEPEND="
+ dev-python/docstring-parser[${PYTHON_USEDEP}]
dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/hdmf[${PYTHON_USEDEP}]
dev-python/hdmf-zarr[${PYTHON_USEDEP}]
+ dev-python/hdmf[${PYTHON_USEDEP}]
dev-python/jsonschema[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/nwbinspector[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/parse[${PYTHON_USEDEP}]
dev-python/psutil[${PYTHON_USEDEP}]
+ dev-python/pydantic[${PYTHON_USEDEP}]
dev-python/pynwb[${PYTHON_USEDEP}]
dev-python/pyyaml[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/pydantic[${PYTHON_USEDEP}]
ecephys? (
dev-python/spikeinterface[${PYTHON_USEDEP}]
)
[gentoo-commits] proj/sci:master commit in: sci-physics/qgraf/
commit: ea0d38d766e9a2c50c90a41b92e50c05e1075dc0
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Apr 2 10:07:33 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Apr 2 10:07:33 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea0d38d7
sci-physics/qgraf: explicit die on fortran compile
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/qgraf/qgraf-3.4.2.ebuild | 2 +-
sci-physics/qgraf/qgraf-3.5.2.ebuild | 2 +-
sci-physics/qgraf/qgraf-3.6.7.ebuild | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-physics/qgraf/qgraf-3.4.2.ebuild
b/sci-physics/qgraf/qgraf-3.4.2.ebuild
index 364198c4b..cdab94002 100644
--- a/sci-physics/qgraf/qgraf-3.4.2.ebuild
+++ b/sci-physics/qgraf/qgraf-3.4.2.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64"
IUSE="doc examples"
src_compile() {
- $(tc-getFC) ${P}.f -o ${PN} ${FFLAGS} ${LDFLAGS}
+ $(tc-getFC) ${P}.f -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to
compile"
}
src_install() {
diff --git a/sci-physics/qgraf/qgraf-3.5.2.ebuild
b/sci-physics/qgraf/qgraf-3.5.2.ebuild
index 7e9f88328..4194295a4 100644
--- a/sci-physics/qgraf/qgraf-3.5.2.ebuild
+++ b/sci-physics/qgraf/qgraf-3.5.2.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64"
IUSE="doc examples"
src_compile() {
- $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS}
+ $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to
compile"
}
src_install() {
diff --git a/sci-physics/qgraf/qgraf-3.6.7.ebuild
b/sci-physics/qgraf/qgraf-3.6.7.ebuild
index 7e9f88328..4194295a4 100644
--- a/sci-physics/qgraf/qgraf-3.6.7.ebuild
+++ b/sci-physics/qgraf/qgraf-3.6.7.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64"
IUSE="doc examples"
src_compile() {
- $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS}
+ $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to
compile"
}
src_install() {
[gentoo-commits] proj/sci:master commit in: dev-vcs/datalad/
commit: fa7b928d4a740e5f20dc701d0d5c26e4cda71c84
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue Apr 2 09:58:15 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue Apr 2 09:58:15 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=fa7b928d
dev-vcs/datalad: drop 0.18.1, 0.18.3
Signed-off-by: Andrew Ammerlaan gentoo.org>
dev-vcs/datalad/datalad-0.18.1.ebuild | 74 ---
dev-vcs/datalad/datalad-0.18.3.ebuild | 74 ---
2 files changed, 148 deletions(-)
diff --git a/dev-vcs/datalad/datalad-0.18.1.ebuild
b/dev-vcs/datalad/datalad-0.18.1.ebuild
deleted file mode 100644
index cd90c1db2..0
--- a/dev-vcs/datalad/datalad-0.18.1.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-DESCRIPTION="Keep code, data, containers under control with git and git-annex"
-HOMEPAGE="https://github.com/datalad/datalad;
-SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz ->
${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test +downloaders +metadata +publish misc"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
- app-arch/p7zip
- app-arch/patool[${PYTHON_USEDEP}]
- dev-python/annexremote[${PYTHON_USEDEP}]
- dev-python/distro[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/iso8601[${PYTHON_USEDEP}]
- dev-python/looseversion[${PYTHON_USEDEP}]
- dev-python/platformdirs[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/wraps[${PYTHON_USEDEP}]
- dev-vcs/git-annex
- downloaders? (
- dev-python/boto[${PYTHON_USEDEP}]
- dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings-alt[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- )
- metadata? (
- dev-python/simplejson[${PYTHON_USEDEP}]
- dev-python/whoosh[${PYTHON_USEDEP}]
- )
- misc? (
- dev-python/argcomplete[${PYTHON_USEDEP}]
- dev-python/pyperclip[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- )
- publish? (
- dev-vcs/python-gitlab[${PYTHON_USEDEP}]
- )
-"
-BDEPEND="
- dev-python/packaging[${PYTHON_USEDEP}]
- test? (
- ${RDEPEND}
- dev-python/beautifulsoup4[${PYTHON_USEDEP}]
- dev-python/httpretty[${PYTHON_USEDEP}]
- dev-python/mypy[${PYTHON_USEDEP}]
- dev-python/vcrpy[${PYTHON_USEDEP}]
- )
-"
-# Also wants test dep:
-# dev-python/types-requests
-# dev-python/types-python-dateutil
-
-distutils_enable_tests pytest
-
-python_test() {
- local -x DATALAD_TESTS_NONETWORK=1
- # see test groups in "tox.ini"
- epytest -k "not turtle and not slow and not usecase"
-}
diff --git a/dev-vcs/datalad/datalad-0.18.3.ebuild
b/dev-vcs/datalad/datalad-0.18.3.ebuild
deleted file mode 100644
index cd90c1db2..0
--- a/dev-vcs/datalad/datalad-0.18.3.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-DESCRIPTION="Keep code, data, containers under control with git and git-annex"
-HOMEPAGE="https://github.com/datalad/datalad;
-SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz ->
${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test +downloaders +metadata +publish misc"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
- app-arch/p7zip
- app-arch/patool[${PYTHON_USEDEP}]
- dev-python/annexremote[${PYTHON_USEDEP}]
- dev-python/distro[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/iso8601[${PYTHON_USEDEP}]
- dev-python/looseversion[${PYTHON_USEDEP}]
- dev-python/platformdirs[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/wraps[${PYTHON_USEDEP}]
- dev-vcs/git-annex
- downloaders? (
- dev-python/boto[${PYTHON_USEDEP}]
- dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings-alt[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- )
- metadata? (
- dev-python/simplejson[${PYTHON_USEDEP}]
-
[gentoo-commits] proj/sci:master commit in: sci-physics/qgraf/
commit: 5792303c3f9635dc69da36987634196975d1a6af
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Sun Mar 31 19:46:08 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Sun Mar 31 19:49:13 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5792303c
sci-physics/qgraf: add 3.4.2, 3.5.2, 3.6.7, drop 3.6.5, 3.6.6
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/qgraf/{qgraf-3.6.6.ebuild => qgraf-3.4.2.ebuild} | 2 +-
sci-physics/qgraf/{qgraf-3.6.5.ebuild => qgraf-3.5.2.ebuild} | 6 +-
sci-physics/qgraf/{qgraf-3.6.5.ebuild => qgraf-3.6.7.ebuild} | 6 +-
3 files changed, 3 insertions(+), 11 deletions(-)
diff --git a/sci-physics/qgraf/qgraf-3.6.6.ebuild
b/sci-physics/qgraf/qgraf-3.4.2.ebuild
similarity index 89%
rename from sci-physics/qgraf/qgraf-3.6.6.ebuild
rename to sci-physics/qgraf/qgraf-3.4.2.ebuild
index 4194295a4..364198c4b 100644
--- a/sci-physics/qgraf/qgraf-3.6.6.ebuild
+++ b/sci-physics/qgraf/qgraf-3.4.2.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64"
IUSE="doc examples"
src_compile() {
- $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to
compile"
+ $(tc-getFC) ${P}.f -o ${PN} ${FFLAGS} ${LDFLAGS}
}
src_install() {
diff --git a/sci-physics/qgraf/qgraf-3.6.5.ebuild
b/sci-physics/qgraf/qgraf-3.5.2.ebuild
similarity index 89%
copy from sci-physics/qgraf/qgraf-3.6.5.ebuild
copy to sci-physics/qgraf/qgraf-3.5.2.ebuild
index 68e0ebf97..7e9f88328 100644
--- a/sci-physics/qgraf/qgraf-3.6.5.ebuild
+++ b/sci-physics/qgraf/qgraf-3.5.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-inherit toolchain-funcs
+inherit toolchain-funcs fortran-2
DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models"
HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html;
@@ -16,10 +16,6 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE="doc examples"
-DEPEND="virtual/fortran"
-RDEPEND="${DEPEND}"
-BDEPEND=""
-
src_compile() {
$(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS}
}
diff --git a/sci-physics/qgraf/qgraf-3.6.5.ebuild
b/sci-physics/qgraf/qgraf-3.6.7.ebuild
similarity index 89%
rename from sci-physics/qgraf/qgraf-3.6.5.ebuild
rename to sci-physics/qgraf/qgraf-3.6.7.ebuild
index 68e0ebf97..7e9f88328 100644
--- a/sci-physics/qgraf/qgraf-3.6.5.ebuild
+++ b/sci-physics/qgraf/qgraf-3.6.7.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-inherit toolchain-funcs
+inherit toolchain-funcs fortran-2
DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models"
HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html;
@@ -16,10 +16,6 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE="doc examples"
-DEPEND="virtual/fortran"
-RDEPEND="${DEPEND}"
-BDEPEND=""
-
src_compile() {
$(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS}
}
[gentoo-commits] proj/sci:master commit in: dev-vcs/dandi-cli/
commit: 14882144687cbd9b4416ca35aa1ceabe6121922b
Author: Horea Christian chymera eu>
AuthorDate: Fri Mar 29 22:26:33 2024 +
Commit: Horea Christian gmail com>
CommitDate: Fri Mar 29 22:26:33 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=14882144
dev-vcs/dandi-cli: add 0.61.2
Signed-off-by: Horea Christian chymera.eu>
dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild | 81 +++
1 file changed, 81 insertions(+)
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild
b/dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild
new file mode 100644
index 0..760fb32b4
--- /dev/null
+++ b/dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+MY_PN="dandi"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="DANDI command line client to facilitate common operations"
+HOMEPAGE="https://github.com/dandi/dandi-cli;
+SRC_URI="$(pypi_sdist_url dandi)"
+
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test etelemetry"
+
+RDEPEND="
+ >=dev-python/dandi-schema-0.9.0[${PYTHON_USEDEP}]
+ >=dev-python/pydantic-2.0.0[${PYTHON_USEDEP}]
+ >=sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
+ >=dev-python/zarr_checksum-0.4.0[${PYTHON_USEDEP}]
+ dev-python/click-didyoumean[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ dev-python/fscacher[${PYTHON_USEDEP}]
+ dev-python/humanize[${PYTHON_USEDEP}]
+ dev-python/interleave[${PYTHON_USEDEP}]
+ dev-python/joblib[${PYTHON_USEDEP}]
+ dev-python/keyring[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
+ dev-python/nwbinspector[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/platformdirs[${PYTHON_USEDEP}]
+ dev-python/pycryptodome[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/pyout[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+ dev-python/semantic-version[${PYTHON_USEDEP}]
+ dev-python/tenacity[${PYTHON_USEDEP}]
+ dev-python/versioneer[${PYTHON_USEDEP}]
+ dev-python/wheel[${PYTHON_USEDEP}]
+ dev-python/yarl[${PYTHON_USEDEP}]
+ dev-python/zarr[${PYTHON_USEDEP}]
+"
+
+BDEPEND="
+ test? (
+ dev-python/anys[${PYTHON_USEDEP}]
+ dev-python/pyfakefs[${PYTHON_USEDEP}]
+ dev-python/pytest-mock[${PYTHON_USEDEP}]
+ dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
+ dev-python/responses[${PYTHON_USEDEP}]
+ dev-python/vcrpy[${PYTHON_USEDEP}]
+ media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
+ )
+"
+# Upstream might be amenable to dropping opencv:
+# https://github.com/dandi/dandi-cli/issues/944
+
+EPYTEST_DESELECT=(
+ # Reported upstream:
+ # https://github.com/dandi/dandi-cli/issues/1394
+ dandi/cli/tests/test_command.py::test_no_heavy_imports
+)
+
+distutils_enable_tests pytest
+
+python_test() {
+ export DANDI_TESTS_NONETWORK=1
+ epytest
+}
[gentoo-commits] proj/sci:master commit in: sci-libs/torchvision/, sci-libs/torchvision/files/
commit: 0e024beadac3ccaefb4a3961214eb74ee5853cf2
Author: Yiyang Wu gmail com>
AuthorDate: Mon Mar 25 07:30:51 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Wed Mar 27 10:12:48 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0e024bea
sci-libs/torchvision: add 0.17.1
Other changes compared to previous version:
1. Include a patch for ffmpeg 6.0 fix
2. Limit setuptools thread to 1, while ninja respect MAKEOPTS
3. revdump on ffmpeg because video_reader.so links to libavutil
libavcodec libavformat
4. Drop dev-qt/qtcore dependency since not needed
5. Drop test support: missing dependency expecttest, problematic import
issues: https://github.com/gentoo/sci/pull/1263#issuecomment-2021380600
Signed-off-by: Yiyang Wu gmail.com>
Closes: https://github.com/gentoo/sci/pull/1263
Signed-off-by: Andrew Ammerlaan gentoo.org>
.../files/torchvision-0.17.1-ffmpeg-6.patch| 36 +
sci-libs/torchvision/torchvision-0.17.1.ebuild | 45 ++
2 files changed, 81 insertions(+)
diff --git a/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch
b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch
new file mode 100644
index 0..7a3637f3a
--- /dev/null
+++ b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch
@@ -0,0 +1,36 @@
+From 86620bd84b872b76db0acafec167949dca03a29e Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Zolt=C3=A1n=20B=C3=B6sz=C3=B6rm=C3=A9nyi?=
+
+Date: Tue, 7 Nov 2023 10:43:11 +0100
+Subject: [PATCH] Fix build with ffmpeg 6.0
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+Signed-off-by: Zoltán Böszörményi
+---
+ torchvision/csrc/io/decoder/stream.cpp | 11 ++-
+ 1 file changed, 2 insertions(+), 9 deletions(-)
+
+diff --git a/torchvision/csrc/io/decoder/stream.cpp
b/torchvision/csrc/io/decoder/stream.cpp
+index 0d625ef211c..8c914050587 100644
+--- a/torchvision/csrc/io/decoder/stream.cpp
b/torchvision/csrc/io/decoder/stream.cpp
+@@ -63,15 +63,8 @@ int Stream::openCodec(std::vector*
metadata, int num_threads) {
+ codecCtx_->thread_count = num_threads;
+ } else {
+ // otherwise set sensible defaults
+-// with the special case for the different MPEG4 codecs
+-// that don't have threading context functions
+-if (codecCtx_->codec->capabilities & AV_CODEC_CAP_INTRA_ONLY) {
+- codecCtx_->thread_type = FF_THREAD_FRAME;
+- codecCtx_->thread_count = 2;
+-} else {
+- codecCtx_->thread_count = 8;
+- codecCtx_->thread_type = FF_THREAD_SLICE;
+-}
++codecCtx_->thread_count = 8;
++codecCtx_->thread_type = FF_THREAD_SLICE;
+ }
+
+ int ret;
diff --git a/sci-libs/torchvision/torchvision-0.17.1.ebuild
b/sci-libs/torchvision/torchvision-0.17.1.ebuild
new file mode 100644
index 0..e0c72684c
--- /dev/null
+++ b/sci-libs/torchvision/torchvision-0.17.1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 2020-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_SINGLE_IMPL=1
+DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_EXT=1
+inherit distutils-r1 multiprocessing
+
+DESCRIPTION="Datasets, transforms and models to specific to computer vision"
+HOMEPAGE="https://github.com/pytorch/vision;
+SRC_URI="https://github.com/pytorch/vision/archive/v${PV}.tar.gz ->
${P}.tar.gz"
+S="${WORKDIR}/vision-${PV}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+RESTRICT="test"
+
+RDEPEND="
+ $(python_gen_cond_dep '
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ dev-python/pillow[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ ')
+ sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}]
+ media-video/ffmpeg:=
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=( "${FILESDIR}/${PN}-0.17.1-ffmpeg-6.patch" )
+
+src_compile()
+{
+ export MAX_JOBS="$(makeopts_jobs)" # Let ninja respect MAKEOPTS
+
+ # Ensure some ext_module sources are compiled before linking
+ export MAKEOPTS="-j1"
+
+ distutils-r1_src_compile
+}
[gentoo-commits] proj/sci:master commit in: profiles/
commit: e3c9b1be480b74fa4b9d1b84002f8a2d261c6163 Author: Horea Christian chymera eu> AuthorDate: Fri Mar 22 21:19:03 2024 + Commit: Horea Christian gmail com> CommitDate: Fri Mar 22 21:19:03 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e3c9b1be profiles: unmasked packages with formerly missing deps Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 7 --- 1 file changed, 7 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 464a4005a..d39812beb 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,10 +29,3 @@ ## app-misc/some-package #--- END OF EXAMPLES --- - -# Andrew Ammerlaan (2024-03-15) -# Depends on unkeyworded dev-libs/libpthread-stubs -sci-biology/afni -sci-biology/samri -sci-biology/samri_bidsdata -sci-biology/samri_bindata
[gentoo-commits] proj/sci:master commit in: sci-biology/afni/
commit: bf635e42b9e981623432224920b21940f4feda56
Author: Horea Christian chymera eu>
AuthorDate: Fri Mar 22 21:18:40 2024 +
Commit: Horea Christian gmail com>
CommitDate: Fri Mar 22 21:18:40 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=bf635e42
sci-biology/afni: removed deprecated deps
Signed-off-by: Horea Christian chymera.eu>
sci-biology/afni/{afni-24.0.04.ebuild => afni-24.0.04-r1.ebuild} | 1 -
sci-biology/afni/{afni-24.0.08.ebuild => afni-24.0.08-r1.ebuild} | 1 -
2 files changed, 2 deletions(-)
diff --git a/sci-biology/afni/afni-24.0.04.ebuild
b/sci-biology/afni/afni-24.0.04-r1.ebuild
similarity index 98%
rename from sci-biology/afni/afni-24.0.04.ebuild
rename to sci-biology/afni/afni-24.0.04-r1.ebuild
index c00ef846f..557fbd579 100644
--- a/sci-biology/afni/afni-24.0.04.ebuild
+++ b/sci-biology/afni/afni-24.0.04-r1.ebuild
@@ -40,7 +40,6 @@ RDEPEND="
sci-libs/gts
sys-devel/llvm:*
sys-libs/libomp
- dev-libs/libpthread-stubs
virtual/jpeg-compat:62
x11-libs/libGLw
x11-libs/libXft
diff --git a/sci-biology/afni/afni-24.0.08.ebuild
b/sci-biology/afni/afni-24.0.08-r1.ebuild
similarity index 99%
rename from sci-biology/afni/afni-24.0.08.ebuild
rename to sci-biology/afni/afni-24.0.08-r1.ebuild
index 75ff5b6b6..20293877f 100644
--- a/sci-biology/afni/afni-24.0.08.ebuild
+++ b/sci-biology/afni/afni-24.0.08-r1.ebuild
@@ -40,7 +40,6 @@ RDEPEND="
sci-libs/gts
sys-devel/llvm:*
sys-libs/libomp
- dev-libs/libpthread-stubs
virtual/jpeg-compat:62
x11-libs/libGLw
x11-libs/libXft
[gentoo-commits] proj/sci:master commit in: sci-physics/cernlib/, sci-physics/cernlib/files/
commit: 2ba82f4414b79a0fd2473c45f0b6701e632e40bd
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Feb 27 13:34:57 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Fri Mar 22 16:37:26 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2ba82f44
sci-physics/cernlib: new package, add 2023.10.31.0
Closes: https://github.com/gentoo/sci/pull/1243
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/cernlib/cernlib-2023.10.31.0.ebuild| 57 ++
.../files/cernlib-2023.10.31.0-cfortran.patch | 21
.../cernlib/files/cernlib-2023.10.31.0-ctest.patch | 31
.../cernlib/files/cernlib-2023.10.31.0-man.patch | 22 +
sci-physics/cernlib/metadata.xml | 21
5 files changed, 152 insertions(+)
diff --git a/sci-physics/cernlib/cernlib-2023.10.31.0.ebuild
b/sci-physics/cernlib/cernlib-2023.10.31.0.ebuild
new file mode 100644
index 0..697a25ef0
--- /dev/null
+++ b/sci-physics/cernlib/cernlib-2023.10.31.0.ebuild
@@ -0,0 +1,57 @@
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+inherit cmake fortran-2
+
+DESCRIPTION="CERN program library for High Energy Physics"
+HOMEPAGE="https://cernlib.web.cern.ch/cernlib/;
+SRC_URI="https://cernlib.web.cern.ch/download/2023_source/tar/${P}-free.tar.gz;
+S="${WORKDIR}/${P}-free"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ x11-libs/motif:0
+ x11-libs/libXaw
+ x11-libs/libXau
+ virtual/lapack
+ dev-lang/cfortran
+ x11-libs/xbae
+ net-libs/libnsl
+ virtual/libcrypt:=
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ virtual/pkgconfig
+"
+
+PATCHES=(
+ "${FILESDIR}"/$P-cfortran.patch
+ "${FILESDIR}"/$P-ctest.patch
+ "${FILESDIR}"/$P-man.patch
+)
+src_prepare() {
+ cmake_src_prepare
+ # cfortran.patch
+ # Remove cfortran.h since it is already installed from dev-lang/cfortran
+ # thereby we avoid collisions if e.g. sci-physics/root[fortran] is
installed.
+ rm cfortran/cfortran.h || die
+}
+
+src_configure() {
+ # docs follow rpm like spliting into packages cernlib, cernlib-devel,
etc.
+ # we move them into a folder that agrees with gentoo doc structure.
+ sed -i "s#/doc/#/doc/${PF}/#g" CMakeLists.txt || die
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+ # man.patch
+ # The CMakeLists.txt already compresses the manual before install
+ # therefore we install it manually and avoid QA problems.
+ doman contrib/man/man1/*.1
+ doman contrib/man/man8/*.8
+}
diff --git a/sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch
b/sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch
new file mode 100644
index 0..b4426b3eb
--- /dev/null
+++ b/sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch
@@ -0,0 +1,21 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 0b56fc85..ead47c54 100644
+--- a/CMakeLists.txt
b/CMakeLists.txt
+@@ -735,7 +735,6 @@ add_subdirectory(code_motif)
+
+ set(CERNLIB_MMAP 1)
+ install(FILES
+-${CMAKE_CURRENT_SOURCE_DIR}/cfortran/cfortran.h
+ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/comis.h
+ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/cspack.h
+ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/geant315.h
+@@ -757,7 +756,7 @@ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/paw.h
+ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/zebra.h
+ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/ COMPONENT libs )
+
+-set(head cfortran.h comis.h cspack.h geant315.h geant321.h gen.h graflib.h
hbook.h hbook_94b.h higz.h hplot.h jetset74.h kernlib.h kuip.h lapack.h
lepto62.h minuit.h packlib.h paw.h zebra.h )
++set(head comis.h cspack.h geant315.h geant321.h gen.h graflib.h hbook.h
hbook_94b.h higz.h hplot.h jetset74.h kernlib.h kuip.h lapack.h lepto62.h
minuit.h packlib.h paw.h zebra.h )
+
+ install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E make_directory
${CMAKE_INSTALL_INCLUDEDIR}/cfortran/)")
+ foreach ( m ${head} )
diff --git a/sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch
b/sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch
new file mode 100644
index 0..b329bb900
--- /dev/null
+++ b/sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch
@@ -0,0 +1,31 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 0b56fc85..78a28e11 100644
+--- a/CMakeLists.txt
b/CMakeLists.txt
+@@ -162,9 +162,10 @@ macro(CLATestTarget ast)
+ list(FIND a "<" NEEDSHELL)
+ list(JOIN a " " MYCMD)
+ if (NEEDSHELL STREQUAL "-1")
+-add_test(NAME test${exec} COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${exec}
{MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
++add_test(NAME test${exec} COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${exec}
${MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: 7f1649f287ef810d3ad4745e0736501d329ff744
Author: Horea Christian chymera eu>
AuthorDate: Thu Mar 21 16:55:56 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Mar 21 22:15:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f1649f2
dev-python/pynwb: add 2.6.0, drop 2.3.2
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/{pynwb-2.3.2.ebuild => pynwb-2.6.0.ebuild} | 11 +--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/dev-python/pynwb/pynwb-2.3.2.ebuild
b/dev-python/pynwb/pynwb-2.6.0.ebuild
similarity index 81%
rename from dev-python/pynwb/pynwb-2.3.2.ebuild
rename to dev-python/pynwb/pynwb-2.6.0.ebuild
index 6599fbf8f..2f403981c 100644
--- a/dev-python/pynwb/pynwb-2.3.2.ebuild
+++ b/dev-python/pynwb/pynwb-2.6.0.ebuild
@@ -15,14 +15,14 @@ LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- >=sci-libs/hdf5-1.12.2
>=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+ >=sci-libs/hdf5-1.12.2
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
"
-BDEPEND=""
EPYTEST_DESELECT=(
# Reported upsream:
@@ -39,6 +39,13 @@ EPYTEST_DESELECT=(
tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension
tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache
tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns
+ # Reported upstream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+ tests/unit/test_file.py::TestNoCacheSpec::test_simple
+ # Not sandboxed, reported upstream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+
tests/read_dandi/test_read_dandi.py::TestReadNWBDandisets::test_read_first_nwb_asset
+ tests/unit/test_base.py::TestTimeSeries::test_repr_html
)
distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
commit: 597997e35db5451deb6079df099686bc085b732a
Author: Horea Christian chymera eu>
AuthorDate: Thu Mar 21 22:10:03 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Mar 21 22:15:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=597997e3
sci-biology/neuroconv: version bump, treeclean
Signed-off-by: Horea Christian chymera.eu>
sci-biology/neuroconv/neuroconv-0.2.4.ebuild | 56 --
...conv-0.4.6-r1.ebuild => neuroconv-0.4.8.ebuild} | 6 +++
2 files changed, 6 insertions(+), 56 deletions(-)
diff --git a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild
b/sci-biology/neuroconv/neuroconv-0.2.4.ebuild
deleted file mode 100644
index c554ce791..0
--- a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 2021-2023 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
-
-DESCRIPTION="Create NWB files from proprietary formats."
-HOMEPAGE="https://github.com/catalystneuro/neuroconv;
-SRC_URI="https://github.com/catalystneuro/neuroconv/archive/refs/tags/v${PV}.tar.gz
-> ${P}.gh.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="+ecephys +icephys +ophys"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/hdmf[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/psutil[${PYTHON_USEDEP}]
- dev-python/pynwb[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-vcs/dandi-cli[${PYTHON_USEDEP}]
- ecephys? (
- dev-python/spikeinterface[${PYTHON_USEDEP}]
- )
- icephys? (
- dev-python/neo[${PYTHON_USEDEP}]
- )
- ophys? (
- sci-biology/roiextractors[${PYTHON_USEDEP}]
- )
-"
-BDEPEND="
- test? (
- dev-python/parameterized[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-python_test() {
- # Additional tests require complex data getting infrastructure, ophys
tests still have issues:
- # https://github.com/catalystneuro/neuroconv/issues/305
- local my_tests=( "tests/test_minimal" )
- use ecephys && my_tests+=( "tests/test_ecephys" )
- #use ophys && my_tests+=( "tests/test_ophys" )
- epytest ${my_tests[*]// /|}
-}
diff --git a/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild
b/sci-biology/neuroconv/neuroconv-0.4.8.ebuild
similarity index 88%
rename from sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild
rename to sci-biology/neuroconv/neuroconv-0.4.8.ebuild
index 1676aa6b7..a3012611f 100644
--- a/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild
+++ b/sci-biology/neuroconv/neuroconv-0.4.8.ebuild
@@ -49,6 +49,12 @@ BDEPEND="
distutils_enable_tests pytest
+# Reported upstream:
+# https://github.com/catalystneuro/neuroconv/issues/785
+EPYTEST_DESELECT=(
+
tests/test_ecephys/test_mock_recording_interface.py::TestMockRecordingInterface::test_conversion_as_lone_interface
+)
+
python_test() {
# Additional tests require complex data getting infrastructure, ophys
tests still have issues:
# https://github.com/catalystneuro/neuroconv/issues/305
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/
commit: 660cac741c12de9ea6e4b98195b2be6a07821f0e
Author: Horea Christian chymera eu>
AuthorDate: Thu Mar 21 21:34:50 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Mar 21 22:15:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=660cac74
dev-python/hdmf: version and PYTHON_COMPAT bump, treeclean
Signed-off-by: Horea Christian chymera.eu>
.../{hdmf-3.11.0.ebuild => hdmf-3.13.0.ebuild} | 4 +--
dev-python/hdmf/hdmf-3.5.1.ebuild | 28 -
dev-python/hdmf/hdmf-3.5.2.ebuild | 29 --
3 files changed, 2 insertions(+), 59 deletions(-)
diff --git a/dev-python/hdmf/hdmf-3.11.0.ebuild
b/dev-python/hdmf/hdmf-3.13.0.ebuild
similarity index 88%
rename from dev-python/hdmf/hdmf-3.11.0.ebuild
rename to dev-python/hdmf/hdmf-3.13.0.ebuild
index 2463ccc1a..7068afb01 100644
--- a/dev-python/hdmf/hdmf-3.11.0.ebuild
+++ b/dev-python/hdmf/hdmf-3.13.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=hatchling
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit distutils-r1 pypi
DESCRIPTION="The Hierarchical Data Modeling Framework"
@@ -25,7 +25,7 @@ RDEPEND="
"
PATCHES=(
- "${FILESDIR}/${P}-no_test_coverage.patch"
+ "${FILESDIR}/${PN}-3.11.0-no_test_coverage.patch"
)
distutils_enable_tests pytest
diff --git a/dev-python/hdmf/hdmf-3.5.1.ebuild
b/dev-python/hdmf/hdmf-3.5.1.ebuild
deleted file mode 100644
index 883b5b95b..0
--- a/dev-python/hdmf/hdmf-3.5.1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-DESCRIPTION="The Hierarchical Data Modeling Framework"
-HOMEPAGE="https://github.com/hdmf-dev/hdmf;
-SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz;
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-distutils_enable_tests pytest
diff --git a/dev-python/hdmf/hdmf-3.5.2.ebuild
b/dev-python/hdmf/hdmf-3.5.2.ebuild
deleted file mode 100644
index ee978516e..0
--- a/dev-python/hdmf/hdmf-3.5.2.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1 pypi
-
-DESCRIPTION="The Hierarchical Data Modeling Framework"
-HOMEPAGE="https://github.com/hdmf-dev/hdmf;
-SRC_URI="$(pypi_sdist_url hdmf)"
-#SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz;
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: dev-python/docstring-parser/
commit: fe2376ff6b4bbf3759f189c2f71e5d9817487ac3
Author: Horea Christian chymera eu>
AuthorDate: Wed Mar 20 21:50:28 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Mar 21 22:15:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=fe2376ff
dev-python/docstring-parser: new package, add 0.16
Signed-off-by: Horea Christian chymera.eu>
.../docstring-parser/docstring-parser-0.16.ebuild | 18 ++
dev-python/docstring-parser/metadata.xml | 16
2 files changed, 34 insertions(+)
diff --git a/dev-python/docstring-parser/docstring-parser-0.16.ebuild
b/dev-python/docstring-parser/docstring-parser-0.16.ebuild
new file mode 100644
index 0..1d82de77c
--- /dev/null
+++ b/dev-python/docstring-parser/docstring-parser-0.16.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Parse Python docstrings in various flavors"
+HOMEPAGE="https://github.com/rr-/docstring_parser;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+distutils_enable_tests pytest
diff --git a/dev-python/docstring-parser/metadata.xml
b/dev-python/docstring-parser/metadata.xml
new file mode 100644
index 0..140ee785a
--- /dev/null
+++ b/dev-python/docstring-parser/metadata.xml
@@ -0,0 +1,16 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ gen...@chymera.eu
+ Horea Christian
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ docstring-parser
+ rr-/docstring_parser
+
+
[gentoo-commits] proj/sci:master commit in: profiles/
commit: b846f5dfcb198edc40f2061b2e8bbf2cd3f555ad Author: Horea Christian chymera eu> AuthorDate: Thu Mar 21 22:11:32 2024 + Commit: Horea Christian gmail com> CommitDate: Thu Mar 21 22:15:29 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b846f5df profiles: unmasked packages with formerly missing deps Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 4 1 file changed, 4 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index b908c0a3e..464a4005a 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -31,10 +31,6 @@ #--- END OF EXAMPLES --- # Andrew Ammerlaan (2024-03-15) -# Depends on removed dev-python/pydantic -dev-python/dandi-schema -dev-vcs/dandi-cli -sci-biology/neuroconv # Depends on unkeyworded dev-libs/libpthread-stubs sci-biology/afni sci-biology/samri
[gentoo-commits] proj/sci:master commit in: dev-vcs/dandi-cli/
commit: 5921d0badd2028076883c6742f7524cd8e0724b9
Author: Horea Christian chymera eu>
AuthorDate: Wed Mar 20 21:36:51 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Mar 21 22:15:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5921d0ba
dev-vcs/dandi-cli: version bump, dropped versions with removed deps
Signed-off-by: Horea Christian chymera.eu>
dev-vcs/dandi-cli/dandi-cli-0.55.1.ebuild | 87 -
dev-vcs/dandi-cli/dandi-cli-0.59.0.ebuild | 89 --
...i-cli-0.59.1.ebuild => dandi-cli-0.61.0.ebuild} | 6 +-
3 files changed, 3 insertions(+), 179 deletions(-)
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.55.1.ebuild
b/dev-vcs/dandi-cli/dandi-cli-0.55.1.ebuild
deleted file mode 100644
index beb2ffcc7..0
--- a/dev-vcs/dandi-cli/dandi-cli-0.55.1.ebuild
+++ /dev/null
@@ -1,87 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1 pypi
-
-MY_PN="dandi"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="DANDI command line client to facilitate common operations"
-HOMEPAGE="https://github.com/dandi/dandi-cli;
-SRC_URI="$(pypi_sdist_url dandi)"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test etelemetry"
-
-RDEPEND="
- =dev-python/dandi-schema-0.8*[${PYTHON_USEDEP}]
- >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
- >=sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
- dev-python/appdirs[${PYTHON_USEDEP}]
- dev-python/click-didyoumean[${PYTHON_USEDEP}]
- dev-python/click[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- dev-python/fscacher[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/interleave[${PYTHON_USEDEP}]
- dev-python/joblib[${PYTHON_USEDEP}]
- dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings-alt[${PYTHON_USEDEP}]
- dev-python/nwbinspector[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/pycryptodome[${PYTHON_USEDEP}]
- dev-python/pynwb[${PYTHON_USEDEP}]
- dev-python/pyout[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/semantic-version[${PYTHON_USEDEP}]
- dev-python/tenacity[${PYTHON_USEDEP}]
- dev-python/wheel[${PYTHON_USEDEP}]
- dev-python/zarr[${PYTHON_USEDEP}]
- dev-python/zarr_checksum[${PYTHON_USEDEP}]
-"
-
-BDEPEND="
- test? (
- dev-python/anys[${PYTHON_USEDEP}]
- dev-python/pyfakefs[${PYTHON_USEDEP}]
- dev-python/pytest-mock[${PYTHON_USEDEP}]
- dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
- dev-python/responses[${PYTHON_USEDEP}]
- dev-python/vcrpy[${PYTHON_USEDEP}]
- media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
- )
-"
-# Upstream might be amenable to dropping opencv:
-# https://github.com/dandi/dandi-cli/issues/944
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.55.0-hdf5.patch"
-)
-
-distutils_enable_tests pytest
-
-src_prepare() {
- if use etelemetry; then
- default
- else
- eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch"
- default
- sed -i "/etelemetry/d" setup.cfg
- fi
-}
-
-python_test() {
- export DANDI_TESTS_NONETWORK=1
- epytest
-}
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.59.0.ebuild
b/dev-vcs/dandi-cli/dandi-cli-0.59.0.ebuild
deleted file mode 100644
index df160ad23..0
--- a/dev-vcs/dandi-cli/dandi-cli-0.59.0.ebuild
+++ /dev/null
@@ -1,89 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1 pypi
-
-MY_PN="dandi"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="DANDI command line client to facilitate common operations"
-HOMEPAGE="https://github.com/dandi/dandi-cli;
-SRC_URI="$(pypi_sdist_url dandi)"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test etelemetry"
-
-RDEPEND="
- =dev-python/dandi-schema-0.8*[${PYTHON_USEDEP}]
- >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
- >=sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
- dev-python/click-didyoumean[${PYTHON_USEDEP}]
- dev-python/click[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- dev-python/fscacher[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/interleave[${PYTHON_USEDEP}]
- dev-python/joblib[${PYTHON_USEDEP}]
- dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings-alt[${PYTHON_USEDEP}]
-
[gentoo-commits] proj/sci:master commit in: dev-python/dandi-schema/
commit: 43d8c443869bc8f51d3e03ede300ae7bfd573bc8
Author: Horea Christian chymera eu>
AuthorDate: Wed Mar 20 20:16:06 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Mar 21 22:15:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=43d8c443
dev-python/dandi-schema: drop 0.8.3-r1, 0.8.4
Signed-off-by: Horea Christian chymera.eu>
.../dandi-schema/dandi-schema-0.8.3-r1.ebuild | 42 --
dev-python/dandi-schema/dandi-schema-0.8.4.ebuild | 42 --
2 files changed, 84 deletions(-)
diff --git a/dev-python/dandi-schema/dandi-schema-0.8.3-r1.ebuild
b/dev-python/dandi-schema/dandi-schema-0.8.3-r1.ebuild
deleted file mode 100644
index 8a2978c99..0
--- a/dev-python/dandi-schema/dandi-schema-0.8.3-r1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..12} )
-
-inherit distutils-r1
-
-DESCRIPTION="Schemata for DANDI archive project"
-HOMEPAGE="https://github.com/dandi/dandi-schema;
-SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz
-> ${P}.gh.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/wheel[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- > dandischema/_version.py
-}
-
-distutils_enable_tests pytest
-
-python_test() {
- export DANDI_TESTS_NONETWORK=1
- pushd dandischema || die
- epytest tests
- popd
-}
diff --git a/dev-python/dandi-schema/dandi-schema-0.8.4.ebuild
b/dev-python/dandi-schema/dandi-schema-0.8.4.ebuild
deleted file mode 100644
index 8a2978c99..0
--- a/dev-python/dandi-schema/dandi-schema-0.8.4.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..12} )
-
-inherit distutils-r1
-
-DESCRIPTION="Schemata for DANDI archive project"
-HOMEPAGE="https://github.com/dandi/dandi-schema;
-SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz
-> ${P}.gh.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/wheel[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- > dandischema/_version.py
-}
-
-distutils_enable_tests pytest
-
-python_test() {
- export DANDI_TESTS_NONETWORK=1
- pushd dandischema || die
- epytest tests
- popd
-}
[gentoo-commits] proj/sci:master commit in: dev-vcs/datalad/
commit: ce6f7cbc60fe2f903dc7ed467383f8f583d35cbd
Author: Horea Christian chymera eu>
AuthorDate: Wed Mar 20 21:09:44 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Mar 21 22:15:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ce6f7cbc
dev-vcs/datalad: dropped boto dependency
Signed-off-by: Horea Christian chymera.eu>
dev-vcs/datalad/{datalad-0.19.6.ebuild => datalad-0.19.6-r1.ebuild} | 1 -
1 file changed, 1 deletion(-)
diff --git a/dev-vcs/datalad/datalad-0.19.6.ebuild
b/dev-vcs/datalad/datalad-0.19.6-r1.ebuild
similarity index 98%
rename from dev-vcs/datalad/datalad-0.19.6.ebuild
rename to dev-vcs/datalad/datalad-0.19.6-r1.ebuild
index 3416c0485..c95bc935f 100644
--- a/dev-vcs/datalad/datalad-0.19.6.ebuild
+++ b/dev-vcs/datalad/datalad-0.19.6-r1.ebuild
@@ -32,7 +32,6 @@ RDEPEND="
dev-python/wraps[${PYTHON_USEDEP}]
dev-vcs/git-annex
downloaders? (
- dev-python/boto[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/msgpack[${PYTHON_USEDEP}]
[gentoo-commits] proj/sci:master commit in: dev-python/zarr_checksum/
commit: b867c41e05c08fdd66e803e1c48a1bc5f10e6d9a
Author: Horea Christian chymera eu>
AuthorDate: Wed Mar 20 21:34:35 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Mar 21 22:15:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b867c41e
dev-python/zarr_checksum: add 0.4.0
Signed-off-by: Horea Christian chymera.eu>
.../zarr_checksum/zarr_checksum-0.4.0.ebuild | 26 ++
1 file changed, 26 insertions(+)
diff --git a/dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild
b/dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild
new file mode 100644
index 0..58cb87329
--- /dev/null
+++ b/dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild
@@ -0,0 +1,26 @@
+# 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=poetry
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Calculatine zarr checksums from local or cloud storage"
+HOMEPAGE="https://github.com/dandi/zarr_checksum;
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/boto3[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/pydantic[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/zarr[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: sci-physics/rivet/files/, sci-physics/rivet/
commit: 3d907e4302c89f4b9f1240e2b0e9af6c2f2a37ef Author: Andrew Ammerlaan gentoo org> AuthorDate: Wed Mar 20 19:50:37 2024 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Wed Mar 20 19:57:55 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3d907e43 sci-physics/rivet: moved to ::gentoo Signed-off-by: Andrew Ammerlaan gentoo.org> sci-physics/rivet/files/rivet-3.1.5-doc.patch | 38 --- sci-physics/rivet/files/rivet-3.1.5-test.patch | 11 --- sci-physics/rivet/files/rivet-3.1.6-binreloc.patch | 12 sci-physics/rivet/metadata.xml | 20 -- sci-physics/rivet/rivet-3.1.5.ebuild | 75 - sci-physics/rivet/rivet-3.1.6.ebuild | 75 - sci-physics/rivet/rivet-3.1.7.ebuild | 78 -- 7 files changed, 309 deletions(-) diff --git a/sci-physics/rivet/files/rivet-3.1.5-doc.patch b/sci-physics/rivet/files/rivet-3.1.5-doc.patch deleted file mode 100644 index ae01b1812..0 --- a/sci-physics/rivet/files/rivet-3.1.5-doc.patch +++ /dev/null @@ -1,38 +0,0 @@ a/doc/Makefile.am -+++ b/doc/Makefile.am -@@ -11,7 +11,7 @@ - $(mkdir_p) analists && cd analists && \ - LD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(LD_LIBRARY_PATH) \ - DYLD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(DYLD_LIBRARY_PATH) \ --PYTHONPATH=$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \ -+PYTHONPATH=$(shell realpath $(abs_top_builddir)/pyext/build/lib*):$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \ - RIVET_ANALYSIS_PATH=$(abs_top_builddir)/analyses:: \ - $(PYTHON) $(abs_srcdir)/analists/mk-analysis-html || true - -@@ -21,7 +21,7 @@ - $(mkdir_p) analists && cd analists && \ - LD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(LD_LIBRARY_PATH) \ - DYLD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(DYLD_LIBRARY_PATH) \ --PYTHONPATH=$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \ -+PYTHONPATH=$(shell realpath $(abs_top_builddir)/pyext/build/lib*):$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \ - RIVET_ANALYSIS_PATH=$(abs_top_builddir)/analyses:: \ - $(PYTHON) $(abs_srcdir)/analists/mk-analysis-json || true - -@@ -31,7 +31,7 @@ - $(mkdir_p) analists && cd analists && \ - LD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(LD_LIBRARY_PATH) \ - DYLD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(DYLD_LIBRARY_PATH) \ --PYTHONPATH=$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \ -+PYTHONPATH=$(shell realpath $(abs_top_builddir)/pyext/build/lib*):$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \ - RIVET_ANALYSIS_PATH=$(abs_top_builddir)/analyses:: \ - $(PYTHON) $(abs_srcdir)/analists/mk-analysis-txt || true - -@@ -46,7 +46,7 @@ - $(mkdir_p) coverage && cd coverage && \ - LD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(LD_LIBRARY_PATH):$(LD_LIBRARY_PATH) \ - DYLD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(DYLD_LIBRARY_PATH):$(DYLD_LIBRARY_PATH) \ --PYTHONPATH=$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \ -+PYTHONPATH=$(shell realpath $(abs_top_builddir)/pyext/build/lib*):$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \ - RIVET_ANALYSIS_PATH=$(abs_top_builddir)/analyses:: \ - $(abs_srcdir)/coverage/mk-coverage-htmls || true - diff --git a/sci-physics/rivet/files/rivet-3.1.5-test.patch b/sci-physics/rivet/files/rivet-3.1.5-test.patch deleted file mode 100644 index 915473eb1..0 --- a/sci-physics/rivet/files/rivet-3.1.5-test.patch +++ /dev/null @@ -1,11 +0,0 @@ a/test/Makefile.am -+++ b/test/Makefile.am -@@ -26,7 +26,7 @@ - LIBLOCATION=$(top_builddir)/src/.libs \ - LD_LIBRARY_PATH=$(top_builddir)/src/.libs:$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH) \ - DYLD_LIBRARY_PATH=$(top_builddir)/src/.libs:$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH) \ -- PYTHONPATH=$(top_builddir)/pyext/build/$(RIVET_SETUP_PY_PATH):$(PYTHONPATH) \ -+ PYTHONPATH=$(shell realpath $(top_builddir)/pyext/build/lib*):$(top_builddir)/pyext/build/$(RIVET_SETUP_PY_PATH):$(PYTHONPATH) \ - PATH=$(top_builddir)/bin:$(top_srcdir)/bin:$(PATH) \ - PYTHON=$(PYTHON) \ - RIVET_TESTS_SRC=$(srcdir) diff --git a/sci-physics/rivet/files/rivet-3.1.6-binreloc.patch
[gentoo-commits] proj/sci:master commit in: sci-physics/scikit-hep-testdata/
commit: a00db1fc41fc8e3850be968e1f3b1907e3920eaf
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Wed Mar 20 07:08:31 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Wed Mar 20 10:22:16 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a00db1fc
sci-physics/scikit-hep-testdata: new package, add 0.4.39
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/scikit-hep-testdata/metadata.xml | 19 ++
.../scikit-hep-testdata-0.4.39.ebuild | 30 ++
2 files changed, 49 insertions(+)
diff --git a/sci-physics/scikit-hep-testdata/metadata.xml
b/sci-physics/scikit-hep-testdata/metadata.xml
new file mode 100644
index 0..ea2e37599
--- /dev/null
+++ b/sci-physics/scikit-hep-testdata/metadata.xml
@@ -0,0 +1,19 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ A common package to provide example files (e.g. ROOT) for testing and
developing packages against. The sample of files is representative of typical
files found "in the wild".
+
+
+ scikit-hep-testdata
+ scikit-hep/scikit-hep-testdata
+
+
diff --git a/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild
b/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild
new file mode 100644
index 0..47d0f0bbd
--- /dev/null
+++ b/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild
@@ -0,0 +1,30 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="A package to provide example files for testing and developing
packages against."
+HOMEPAGE="https://github.com/scikit-hep/scikit-hep-testdata;
+# pypi does not include the data nor tests
+SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz
-> ${P}.gh.tar.gz"
+S="${WORKDIR}/${P}"
+# export is needed here!
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+# otherwise we don't install the data
+export SKHEP_DATA=1
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/setuptools-scm[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: sci-physics/pylhe/, sci-physics/pylhe/files/
commit: c1dc06bee3b7aa287ba0d417a5676ad63c07d57e
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Wed Mar 20 07:10:54 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Wed Mar 20 10:22:27 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c1dc06be
sci-physics/pylhe: new package, add 0.7.0, 0.8.0
Closes: https://github.com/gentoo/sci/pull/1262
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch | 8 +
sci-physics/pylhe/metadata.xml | 19
sci-physics/pylhe/pylhe-0.7.0.ebuild | 35 ++
sci-physics/pylhe/pylhe-0.8.0.ebuild | 35 ++
4 files changed, 97 insertions(+)
diff --git a/sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch
b/sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch
new file mode 100644
index 0..ea678ce8c
--- /dev/null
+++ b/sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch
@@ -0,0 +1,8 @@
+--- a/pytest.ini 2024-03-20 07:36:32.600030197 +0100
b/pytest.ini 2024-03-20 07:36:45.896874886 +0100
+@@ -1,4 +1,4 @@
+ [pytest]
+ docstyle_convention = numpy
+ junit_family = xunit2
+-addopts = --ignore=setup.py --ignore=binder/ --ignore=docs/ --cov=pylhe
--cov-report=term-missing --cov-config=.coveragerc --cov-report xml
--doctest-modules --doctest-glob='*.rst'
++addopts = --ignore=setup.py --ignore=binder/ --ignore=docs/ --doctest-modules
--doctest-glob='*.rst'
diff --git a/sci-physics/pylhe/metadata.xml b/sci-physics/pylhe/metadata.xml
new file mode 100644
index 0..86ede8deb
--- /dev/null
+++ b/sci-physics/pylhe/metadata.xml
@@ -0,0 +1,19 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ Small and thin Python interface to read Les Houches Event (LHE) files.
+
+
+ pylhe
+ scikit-hep/pylhe
+
+
diff --git a/sci-physics/pylhe/pylhe-0.7.0.ebuild
b/sci-physics/pylhe/pylhe-0.7.0.ebuild
new file mode 100644
index 0..45ef91695
--- /dev/null
+++ b/sci-physics/pylhe/pylhe-0.7.0.ebuild
@@ -0,0 +1,35 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Lightweight Python interface to read Les Houches Event (LHE)
files"
+HOMEPAGE="https://github.com/scikit-hep/pylhe;
+# pypi does not include tests
+SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz
-> ${P}.gh.tar.gz"
+# export is needed here!
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/graphviz-0.12.0[${PYTHON_USEDEP}]
+ >=sci-physics/particle-0.16[${PYTHON_USEDEP}]
+ >=dev-python/awkward-1.2.0[${PYTHON_USEDEP}]
+ >=dev-python/vector-0.8.1[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/setuptools-scm[${PYTHON_USEDEP}]
+ test? (
+ >=sci-physics/scikit-hep-testdata-0.4.36[${PYTHON_USEDEP}]
+ )
+"
+PATCHES=(
+ "${FILESDIR}/${PN}"-0.7.0-coverage.patch
+)
+
+distutils_enable_tests pytest
diff --git a/sci-physics/pylhe/pylhe-0.8.0.ebuild
b/sci-physics/pylhe/pylhe-0.8.0.ebuild
new file mode 100644
index 0..45ef91695
--- /dev/null
+++ b/sci-physics/pylhe/pylhe-0.8.0.ebuild
@@ -0,0 +1,35 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Lightweight Python interface to read Les Houches Event (LHE)
files"
+HOMEPAGE="https://github.com/scikit-hep/pylhe;
+# pypi does not include tests
+SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz
-> ${P}.gh.tar.gz"
+# export is needed here!
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/graphviz-0.12.0[${PYTHON_USEDEP}]
+ >=sci-physics/particle-0.16[${PYTHON_USEDEP}]
+ >=dev-python/awkward-1.2.0[${PYTHON_USEDEP}]
+ >=dev-python/vector-0.8.1[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/setuptools-scm[${PYTHON_USEDEP}]
+ test? (
+ >=sci-physics/scikit-hep-testdata-0.4.36[${PYTHON_USEDEP}]
+ )
+"
+PATCHES=(
+ "${FILESDIR}/${PN}"-0.7.0-coverage.patch
+)
+
+distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: sci-physics/uproot/
commit: c765189268610d7516a1a83d82f7e8bd482ce84b
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Mar 19 19:30:45 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Wed Mar 20 10:21:24 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c7651892
sci-physics/uproot: new package, add 5.3.1
Closes: https://github.com/gentoo/sci/pull/1261
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/uproot/metadata.xml| 21 +
sci-physics/uproot/uproot-5.3.1.ebuild | 28
2 files changed, 49 insertions(+)
diff --git a/sci-physics/uproot/metadata.xml b/sci-physics/uproot/metadata.xml
new file mode 100644
index 0..1b293facb
--- /dev/null
+++ b/sci-physics/uproot/metadata.xml
@@ -0,0 +1,21 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ Uproot is a library for reading and writing ROOT files in pure
Python and NumPy.
+
+ Unlike the standard C++ ROOT implementation, Uproot is only an
I/O library, primarily intended to stream data into machine learning libraries
in Python. Unlike PyROOT and root_numpy, Uproot does not depend on C++ ROOT.
Instead, it uses Numpy to cast blocks of data from the ROOT file as Numpy
arrays.
+
+
+ uproot
+ scikit-hep/uproot5
+
+
diff --git a/sci-physics/uproot/uproot-5.3.1.ebuild
b/sci-physics/uproot/uproot-5.3.1.ebuild
new file mode 100644
index 0..cfc3880e9
--- /dev/null
+++ b/sci-physics/uproot/uproot-5.3.1.ebuild
@@ -0,0 +1,28 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+inherit distutils-r1 pypi
+
+DESCRIPTION="ROOT I/O in pure Python and Numpy."
+HOMEPAGE="https://github.com/scikit-hep/uproot;
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/awkward-2.4.6[${PYTHON_USEDEP}]
+ >=dev-python/cramjam-2.5.0[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/fsspec[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+# way too many missing packages, isal, deflate, xxhash, http servers etc
+# distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: dev-python/awkward/
commit: 0d7ad5db16dcdab71f94d4b39fc3599aaffa
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Mar 19 20:59:06 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Mar 19 20:59:06 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0d7ad5db
dev-python/awkward: add missing test dependency
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
dev-python/awkward/awkward-2.5.2.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/dev-python/awkward/awkward-2.5.2.ebuild
b/dev-python/awkward/awkward-2.5.2.ebuild
index 75c754dda..c11095214 100644
--- a/dev-python/awkward/awkward-2.5.2.ebuild
+++ b/dev-python/awkward/awkward-2.5.2.ebuild
@@ -22,6 +22,7 @@ BDEPEND="
dev-python/hatch-vcs[${PYTHON_USEDEP}]
dev-python/hatch-fancy-pypi-readme[${PYTHON_USEDEP}]
test? (
+ dev-libs/apache-arrow[zstd]
dev-python/pyarrow[${PYTHON_USEDEP}]
dev-python/fsspec[${PYTHON_USEDEP}]
dev-python/numexpr[${PYTHON_USEDEP}]
[gentoo-commits] proj/sci:master commit in: sci-physics/particle/
commit: d41f019755193ba78fdffe64e1d6bd726d810b7e
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Mar 19 19:42:10 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Mar 19 19:42:10 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d41f0197
sci-physics/particle: add 0.23.1, enable py3.12
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/particle/{particle-.ebuild => particle-0.23.1.ebuild} | 2 +-
sci-physics/particle/particle-.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-physics/particle/particle-.ebuild
b/sci-physics/particle/particle-0.23.1.ebuild
similarity index 95%
copy from sci-physics/particle/particle-.ebuild
copy to sci-physics/particle/particle-0.23.1.ebuild
index 88da33c3e..43f1e67ca 100644
--- a/sci-physics/particle/particle-.ebuild
+++ b/sci-physics/particle/particle-0.23.1.ebuild
@@ -1,6 +1,6 @@
EAPI=8
-PYTHON_COMPAT=( python3_11 )
+PYTHON_COMPAT=( python3_{11..12} )
DISTUTILS_USE_PEP517=hatchling
inherit distutils-r1
diff --git a/sci-physics/particle/particle-.ebuild
b/sci-physics/particle/particle-.ebuild
index 88da33c3e..43f1e67ca 100644
--- a/sci-physics/particle/particle-.ebuild
+++ b/sci-physics/particle/particle-.ebuild
@@ -1,6 +1,6 @@
EAPI=8
-PYTHON_COMPAT=( python3_11 )
+PYTHON_COMPAT=( python3_{11..12} )
DISTUTILS_USE_PEP517=hatchling
inherit distutils-r1
[gentoo-commits] proj/sci:master commit in: sci-libs/vegas/
commit: 071a47e6cd9c931e84da4fc67dbc35903f5f0750
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Sat Mar 16 09:33:21 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Mar 19 17:02:45 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=071a47e6
sci-libs/vegas: new package, add 6.0.1
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-libs/vegas/metadata.xml | 19 +++
sci-libs/vegas/vegas-6.0.1.ebuild | 24
2 files changed, 43 insertions(+)
diff --git a/sci-libs/vegas/metadata.xml b/sci-libs/vegas/metadata.xml
new file mode 100644
index 0..8ae183900
--- /dev/null
+++ b/sci-libs/vegas/metadata.xml
@@ -0,0 +1,19 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ The vegas package is for evaluating multidimensional integrals using an
improved version of the adaptive Monte Carlo vegas algorithm (G. P. Lepage, J.
Comput. Phys. 27(1978) 192).
+
+
+ vegas
+ gplepage/vegas
+
+
diff --git a/sci-libs/vegas/vegas-6.0.1.ebuild
b/sci-libs/vegas/vegas-6.0.1.ebuild
new file mode 100644
index 0..7654563e4
--- /dev/null
+++ b/sci-libs/vegas/vegas-6.0.1.ebuild
@@ -0,0 +1,24 @@
+EAPI=8
+
+DISTUTILS_EXT=1
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Adaptive multidimensional Monte Carlo integration."
+HOMEPAGE="https://github.com/gplepage/vegas;
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~arm64"
+
+RDEPEND="
+ >=dev-python/numpy-1.16[${PYTHON_USEDEP}]
+ >=sci-libs/gvar-13.0.2[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ >=dev-python/cython-0.17[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests unittest
[gentoo-commits] proj/sci:master commit in: sci-libs/gvar/
commit: c511ece6ebd84adcb0e5211b587c9196f3f43fed
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Sat Mar 16 08:12:33 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Mar 19 17:02:43 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c511ece6
sci-libs/gvar: new package, add 13.0.2
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-libs/gvar/gvar-13.0.2.ebuild | 22 ++
sci-libs/gvar/metadata.xml | 19 +++
2 files changed, 41 insertions(+)
diff --git a/sci-libs/gvar/gvar-13.0.2.ebuild b/sci-libs/gvar/gvar-13.0.2.ebuild
new file mode 100644
index 0..b9d9121e4
--- /dev/null
+++ b/sci-libs/gvar/gvar-13.0.2.ebuild
@@ -0,0 +1,22 @@
+EAPI=8
+
+DISTUTILS_EXT=1
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Gaussian random variables."
+HOMEPAGE="https://github.com/gplepage/gvar;
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~arm64"
+
+RDEPEND="
+ >=dev-python/cython-0.17[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.16[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+distutils_enable_tests unittest
diff --git a/sci-libs/gvar/metadata.xml b/sci-libs/gvar/metadata.xml
new file mode 100644
index 0..31346f0dd
--- /dev/null
+++ b/sci-libs/gvar/metadata.xml
@@ -0,0 +1,19 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ This package facilitates the creation and manipulation of arbitrarily
complicated (correlated) multi-dimensional Gaussian random variables. The
random variables are represented by a new data type (gvar.GVar) that can be
used in arithmetic expressions and pure Python functions. Such
expressions/functions create new Gaussian random variables while automatically
tracking statistical correlations between the new and old variables. This data
type is useful for simple error propagation, but also is heavily used by the
Bayesian least-squares fitting module lsqfit.py to define priors and specify
fit results, while accounting for correlations between all variables.
+
+
+ gvar
+ gplepage/gvar
+
+
[gentoo-commits] proj/sci:master commit in: dev-python/awkward/
commit: 0a7d66b3d22bf305ebf01ba53239c9d9ed2caa46
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Sat Mar 16 12:07:34 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Mar 19 16:33:24 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0a7d66b3
dev-python/awkward: new package, add 2.5.2
Closes: https://github.com/gentoo/sci/pull/1257
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
dev-python/awkward/awkward-2.5.2.ebuild | 37 +
dev-python/awkward/metadata.xml | 19 +
2 files changed, 56 insertions(+)
diff --git a/dev-python/awkward/awkward-2.5.2.ebuild
b/dev-python/awkward/awkward-2.5.2.ebuild
new file mode 100644
index 0..75c754dda
--- /dev/null
+++ b/dev-python/awkward/awkward-2.5.2.ebuild
@@ -0,0 +1,37 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+inherit distutils-r1 pypi
+
+DESCRIPTION="Manipulate JSON-like data with NumPy-like idioms."
+HOMEPAGE="https://github.com/scikit-hep/awkward;
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
+ ~dev-python/awkward-cpp-28[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+ dev-python/hatch-fancy-pypi-readme[${PYTHON_USEDEP}]
+ test? (
+ dev-python/pyarrow[${PYTHON_USEDEP}]
+ dev-python/fsspec[${PYTHON_USEDEP}]
+ dev-python/numexpr[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_IGNORE=(
+ tests-cuda/
+ tests-cuda-kernels/
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/awkward/metadata.xml b/dev-python/awkward/metadata.xml
new file mode 100644
index 0..b3ac679d3
--- /dev/null
+++ b/dev-python/awkward/metadata.xml
@@ -0,0 +1,19 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ Awkward Array is a library for nested, variable-sized data,
including arbitrary-length lists, records, mixed types, and missing data, using
NumPy-like idioms.
+
+
+ awkward
+ scikit-hep/awkward
+
+
[gentoo-commits] proj/sci:master commit in: dev-python/pyerfa/, dev-python/jacobi/, sci-physics/pyhf/, dev-python/astropy/, ...
commit: e6d660269eebd2767ec6d66c123a77f39f4b74f5
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Mon Mar 18 19:40:53 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Mon Mar 18 21:01:35 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e6d66026
*/*: fix BDEPEND -> DEPEND
Closes: https://github.com/gentoo/sci/pull/1260
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
dev-python/archspec/archspec-0.1.4.ebuild| 2 +-
dev-python/astropy/astropy-5.2.1.ebuild | 3 ++-
dev-python/jacobi/jacobi-0.8.1.ebuild| 2 +-
dev-python/jacobi/jacobi-0.9.2.ebuild| 2 +-
dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild | 3 ++-
dev-python/vector/vector-1.1.1.ebuild| 4 +++-
dev-python/vector/vector-1.3.1.ebuild| 4 +++-
sci-mathematics/lie/lie-2.2.2.ebuild | 2 +-
sci-physics/hepunits/hepunits-2.3.2.ebuild | 2 +-
sci-physics/hepunits/hepunits-2.3.3.ebuild | 2 +-
sci-physics/hepunits/hepunits-.ebuild| 2 +-
sci-physics/particle/particle-0.23.0.ebuild | 4 +++-
sci-physics/particle/particle-.ebuild| 4 +++-
sci-physics/pyhf/pyhf-0.7.3.ebuild | 2 +-
sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild | 2 +-
sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild | 2 +-
sys-cluster/easybuild-easyblocks/easybuild-easyblocks-.ebuild| 2 +-
sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild | 2 +-
sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild | 2 +-
sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-.ebuild | 2 +-
sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild | 2 +-
sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild | 2 +-
sys-cluster/easybuild-framework/easybuild-framework-.ebuild | 2 +-
sys-cluster/easybuild/easybuild-4.6.2.ebuild | 2 +-
sys-cluster/easybuild/easybuild-4.9.0.ebuild | 2 +-
sys-cluster/easybuild/easybuild-.ebuild | 2 +-
26 files changed, 36 insertions(+), 26 deletions(-)
diff --git a/dev-python/archspec/archspec-0.1.4.ebuild
b/dev-python/archspec/archspec-0.1.4.ebuild
index f1b1cb0f1..35500e00d 100644
--- a/dev-python/archspec/archspec-0.1.4.ebuild
+++ b/dev-python/archspec/archspec-0.1.4.ebuild
@@ -16,4 +16,4 @@ RDEPEND="
<=dev-python/six-2.0.0[${PYTHON_USEDEP}]
>=dev-python/click-7.1.2[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}"
diff --git a/dev-python/astropy/astropy-5.2.1.ebuild
b/dev-python/astropy/astropy-5.2.1.ebuild
index ac5c388b0..b52d1e6f5 100644
--- a/dev-python/astropy/astropy-5.2.1.ebuild
+++ b/dev-python/astropy/astropy-5.2.1.ebuild
@@ -33,7 +33,8 @@ RDEPEND="
>=sci-libs/cfitsio-3.350:0=
sys-libs/zlib:0=
"
-BDEPEND="${RDEPEND}
+DEPEND="${RDEPEND}"
+BDEPEND="
dev-python/astropy-helpers[${PYTHON_USEDEP}]
dev-python/extension-helpers[${PYTHON_USEDEP}]
dev-python/cython[${PYTHON_USEDEP}]
diff --git a/dev-python/jacobi/jacobi-0.8.1.ebuild
b/dev-python/jacobi/jacobi-0.8.1.ebuild
index 404e8c2ca..93afcbf16 100644
--- a/dev-python/jacobi/jacobi-0.8.1.ebuild
+++ b/dev-python/jacobi/jacobi-0.8.1.ebuild
@@ -14,7 +14,7 @@ KEYWORDS="~amd64"
RDEPEND="
>=dev-python/numpy-1.10[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}"
distutils_enable_tests pytest
diff --git a/dev-python/jacobi/jacobi-0.9.2.ebuild
b/dev-python/jacobi/jacobi-0.9.2.ebuild
index f8605063c..806967a38 100644
--- a/dev-python/jacobi/jacobi-0.9.2.ebuild
+++ b/dev-python/jacobi/jacobi-0.9.2.ebuild
@@ -14,7 +14,7 @@ KEYWORDS="~amd64"
RDEPEND="
>=dev-python/numpy-1.10[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}"
distutils_enable_tests pytest
diff --git a/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild
b/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild
index b52026473..11a68c169 100644
--- a/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild
+++ b/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild
@@ -22,7 +22,8 @@ RDEPEND="
sci-astronomy/erfa:0=
>=dev-python/numpy-1.17[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}
+DEPEND="${RDEPEND}"
+BDEPEND="
dev-python/setuptools-scm[${PYTHON_USEDEP}]
test? (
dev-python/pytest-doctestplus[${PYTHON_USEDEP}]
diff --git a/dev-python/vector/vector-1.1.1.ebuild
b/dev-python/vector/vector-1.1.1.ebuild
index 936578e50..8b5a45c3d 100644
--- a/dev-python/vector/vector-1.1.1.ebuild
+++
[gentoo-commits] proj/sci:master commit in: dev-python/vector/
commit: 26a7c9da38c6e72435e63e70cc559d461232d467
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Sun Mar 17 16:00:37 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Sun Mar 17 16:00:37 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=26a7c9da
dev-python/vector: add 1.3.1
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
dev-python/vector/vector-1.3.1.ebuild | 20
1 file changed, 20 insertions(+)
diff --git a/dev-python/vector/vector-1.3.1.ebuild
b/dev-python/vector/vector-1.3.1.ebuild
new file mode 100644
index 0..936578e50
--- /dev/null
+++ b/dev-python/vector/vector-1.3.1.ebuild
@@ -0,0 +1,20 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1 pypi
+
+DESCRIPTION="Vector classes and utilities"
+HOMEPAGE="https://github.com/scikit-hep/vector;
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
[gentoo-commits] proj/sci:master commit in: dev-python/uhi/
commit: fefc0c6312315941eb86943101f0655f9c692f30
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Sun Mar 17 15:59:19 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Sun Mar 17 15:59:19 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=fefc0c63
dev-python/uhi: enable py3.12
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
dev-python/uhi/uhi-0.4.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/dev-python/uhi/uhi-0.4.0.ebuild b/dev-python/uhi/uhi-0.4.0.ebuild
index 89db57b1c..380e3bdbd 100644
--- a/dev-python/uhi/uhi-0.4.0.ebuild
+++ b/dev-python/uhi/uhi-0.4.0.ebuild
@@ -1,6 +1,6 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=hatchling
SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
inherit distutils-r1 pypi
[gentoo-commits] proj/sci:master commit in: dev-python/boost-histogram/
commit: c08d995df501ca71f6150272ad36908c97a4adfe
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Sun Mar 17 15:59:07 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Sun Mar 17 15:59:07 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c08d995d
dev-python/boost-histogram: enable py3.12
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
dev-python/boost-histogram/boost-histogram-1.4.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild
b/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild
index 0336c4e87..96950ebe5 100644
--- a/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild
+++ b/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild
@@ -1,6 +1,6 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 pypi
[gentoo-commits] proj/sci:master commit in: dev-python/jacobi/
commit: ef9974941a17891d7023b2a1bff931ff60a198bc
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Sat Mar 16 18:46:20 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Sat Mar 16 18:59:16 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ef997494
dev-python/jacobi: add 0.9.2
Closes: https://github.com/gentoo/sci/pull/1258
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
dev-python/jacobi/jacobi-0.9.2.ebuild | 26 ++
1 file changed, 26 insertions(+)
diff --git a/dev-python/jacobi/jacobi-0.9.2.ebuild
b/dev-python/jacobi/jacobi-0.9.2.ebuild
new file mode 100644
index 0..f8605063c
--- /dev/null
+++ b/dev-python/jacobi/jacobi-0.9.2.ebuild
@@ -0,0 +1,26 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Numerical derivatives for analytic functions with arbitrary
precision."
+HOMEPAGE="https://github.com/HDembinski/jacobi;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.10[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+python_test() {
+ local EPYTEST_IGNORE=(
+ tests/bench.py
+ )
+ epytest
+}
[gentoo-commits] proj/sci:master commit in: dev-python/awkward-cpp/
commit: b7335c04383c2c65bf7601cce8795d0672be3f94
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Feb 27 14:05:19 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Sat Mar 16 11:58:43 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b7335c04
dev-python/awkward-cpp: new package, add 28
Co-authored-by: Andrew Nowa Ammerlaan gentoo.org>
Closes: https://github.com/gentoo/sci/pull/1246
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
dev-python/awkward-cpp/awkward-cpp-28.ebuild | 26 ++
dev-python/awkward-cpp/metadata.xml | 19 +++
2 files changed, 45 insertions(+)
diff --git a/dev-python/awkward-cpp/awkward-cpp-28.ebuild
b/dev-python/awkward-cpp/awkward-cpp-28.ebuild
new file mode 100644
index 0..57634d120
--- /dev/null
+++ b/dev-python/awkward-cpp/awkward-cpp-28.ebuild
@@ -0,0 +1,26 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+DISTUTILS_USE_PEP517=scikit-build-core
+PYPI_NO_NORMALIZE=1
+
+inherit pypi distutils-r1
+
+DESCRIPTION="awkward-cpp bindings for Python"
+HOMEPAGE="https://github.com/scikit-hep/awkward/;
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="
+ >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+ >=dev-python/scikit-build-core-0.2.0[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/awkward-cpp/metadata.xml
b/dev-python/awkward-cpp/metadata.xml
new file mode 100644
index 0..a94e99f4b
--- /dev/null
+++ b/dev-python/awkward-cpp/metadata.xml
@@ -0,0 +1,19 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ awkward-cpp provides precompiled routines for the awkward package. It
is not useful on its own, only as a dependency for awkward .
+
+
+ awkward
+ scikit-hep/awkward
+
+
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 481cfc5b24936c3b6d9216861e6a438a8db9c7c6 Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Mar 15 11:28:27 2024 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Mar 15 11:28:27 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=481cfc5b mask packs with incomp deps Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 3 +++ 1 file changed, 3 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 9384fafc7..b908c0a3e 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -37,3 +37,6 @@ dev-vcs/dandi-cli sci-biology/neuroconv # Depends on unkeyworded dev-libs/libpthread-stubs sci-biology/afni +sci-biology/samri +sci-biology/samri_bidsdata +sci-biology/samri_bindata
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 557d3b57a23fc54c993f0296b1935a06bc99bf8e Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Mar 15 11:25:41 2024 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Mar 15 11:25:41 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=557d3b57 mask packs with incomp deps Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 8 1 file changed, 8 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d39812beb..9384fafc7 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,3 +29,11 @@ ## app-misc/some-package #--- END OF EXAMPLES --- + +# Andrew Ammerlaan (2024-03-15) +# Depends on removed dev-python/pydantic +dev-python/dandi-schema +dev-vcs/dandi-cli +sci-biology/neuroconv +# Depends on unkeyworded dev-libs/libpthread-stubs +sci-biology/afni
[gentoo-commits] proj/sci:master commit in: sci-physics/qgraf/
commit: 7c3c47e94fcbdc3b4abddcbb4bf005ab5cd48a39
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Mar 12 20:41:41 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Thu Mar 14 12:32:11 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7c3c47e9
sci-physics/qgraf: add 3.6.6
Co-authored-by: Andrew Nowa Ammerlaan gentoo.org>
Closes: https://github.com/gentoo/sci/pull/1253
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/qgraf/qgraf-3.6.6.ebuild | 32
1 file changed, 32 insertions(+)
diff --git a/sci-physics/qgraf/qgraf-3.6.6.ebuild
b/sci-physics/qgraf/qgraf-3.6.6.ebuild
new file mode 100644
index 0..4194295a4
--- /dev/null
+++ b/sci-physics/qgraf/qgraf-3.6.6.ebuild
@@ -0,0 +1,32 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs fortran-2
+
+DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models"
+HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html;
+SRC_URI="http://anonymous:anonym...@qgraf.tecnico.ulisboa.pt/v$(ver_cut
1-2)/qgraf-${PV}.tgz"
+S="${WORKDIR}"
+
+LICENSE="all-rights-reserved"
+RESTRICT="bindist mirror"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="doc examples"
+
+src_compile() {
+ $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to
compile"
+}
+
+src_install() {
+ dobin ${PN}
+
+ use doc && dodoc *.pdf
+ if use examples; then
+ docinto examples
+ dodoc phi3 qed qcd *.sty *.dat
+ docompress -x /usr/share/doc/${PF}/examples
+ fi
+}
[gentoo-commits] proj/sci:master commit in: sci-physics/spheno/files/, sci-physics/spheno/
commit: f582ca64c1dff0d61b9b012515f84887cc227959
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Mar 12 22:05:26 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Thu Mar 14 12:29:46 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f582ca64
sci-physics/spheno: add 4.0.5
Closes: https://github.com/gentoo/sci/pull/1254
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
.../spheno/files/spheno-4.0.5-gfortran.patch | 29 ++
...{spheno-3.3.8.ebuild => spheno-3.3.8-r1.ebuild} | 14 ---
.../{spheno-3.3.8.ebuild => spheno-4.0.5.ebuild} | 14 ---
3 files changed, 39 insertions(+), 18 deletions(-)
diff --git a/sci-physics/spheno/files/spheno-4.0.5-gfortran.patch
b/sci-physics/spheno/files/spheno-4.0.5-gfortran.patch
new file mode 100644
index 0..1abf36367
--- /dev/null
+++ b/sci-physics/spheno/files/spheno-4.0.5-gfortran.patch
@@ -0,0 +1,29 @@
+--- a/src/Makefile 2023-05-04 12:33:44.804394098 +0200
b/src/Makefile 2023-05-04 12:34:37.023776033 +0200
+@@ -21,9 +21,9 @@
+ #
+
+ # Intels ifort, default in optimized mode
+-F90 = ifort
+-comp = -c -O -module ${Mdir} -I${InDir}
+-LFlagsB = -O
++F90 = ${F90}
++comp = -c -O -J${Mdir} -I${InDir} ${FFLAGS} ${FCFLAGS} ${CFLAGS}
++LFlagsB = -O ${LDFLAGS}
+
+ # Intels ifort, debug modus
+ ifeq (${F90},ifortg)
+@@ -81,11 +81,11 @@
+ #
+ .f90.a:
+ ${F90} ${comp} $<
+- ar ${linker} $@ $*.o
++ $(AR) ${linker} $@ $*.o
+ rm -f $*.o
+ .F90.a:
+ ${F90} ${comp} ${PreDef} $<
+- ar ${linker} $@ $*.o
++ $(AR) ${linker} $@ $*.o
+ rm -f $*.o
+ .f90.o:
+ ${F90} ${comp} $<
diff --git a/sci-physics/spheno/spheno-3.3.8.ebuild
b/sci-physics/spheno/spheno-3.3.8-r1.ebuild
similarity index 84%
copy from sci-physics/spheno/spheno-3.3.8.ebuild
copy to sci-physics/spheno/spheno-3.3.8-r1.ebuild
index 9a740b89e..7ed53c4c7 100644
--- a/sci-physics/spheno/spheno-3.3.8.ebuild
+++ b/sci-physics/spheno/spheno-3.3.8-r1.ebuild
@@ -3,14 +3,14 @@
EAPI=8
-inherit toolchain-funcs
+inherit fortran-2
MY_PN=SPheno
MY_P=${MY_PN}-${PV}
DESCRIPTION="SPheno stands for S(upersymmetric) Pheno(menology)"
HOMEPAGE="https://spheno.hepforge.org/;
-SRC_URI="https://spheno.hepforge.org/downloads/?f=${MY_P}.tar.gz;
+SRC_URI="https://spheno.hepforge.org/downloads/?f=${MY_P}.tar.gz ->
${P}.tar.gz"
S="${WORKDIR}/${MY_P}"
LICENSE="all-rights-reserved"
@@ -18,16 +18,11 @@ RESTRICT="bindist mirror"
SLOT="0"
KEYWORDS="~amd64"
-DEPEND="virtual/fortran"
-RDEPEND="${DEPEND}"
-
PATCHES=( "${FILESDIR}"/${P}-gfortran.patch )
src_compile() {
# single thread force needed since fortan mods depend on each other
- export MAKEOPTS=-j1
- tc-export FC AR
- emake AR="${AR}" F90="${FC}"
+ emake -j1 F90="${FC}"
}
src_install() {
@@ -35,7 +30,8 @@ src_install() {
# convenience symlink since the package is lowercase but the default
produced binary is uppercase
dosym ${MY_PN} /usr/bin/${PN}
dolib.a lib/lib${MY_PN}.a
- doheader include/*
+ mv include ${PN}
+ doheader -r ${PN}
dodoc doc/*
docinto examples
dodoc input/*
diff --git a/sci-physics/spheno/spheno-3.3.8.ebuild
b/sci-physics/spheno/spheno-4.0.5.ebuild
similarity index 84%
rename from sci-physics/spheno/spheno-3.3.8.ebuild
rename to sci-physics/spheno/spheno-4.0.5.ebuild
index 9a740b89e..7ed53c4c7 100644
--- a/sci-physics/spheno/spheno-3.3.8.ebuild
+++ b/sci-physics/spheno/spheno-4.0.5.ebuild
@@ -3,14 +3,14 @@
EAPI=8
-inherit toolchain-funcs
+inherit fortran-2
MY_PN=SPheno
MY_P=${MY_PN}-${PV}
DESCRIPTION="SPheno stands for S(upersymmetric) Pheno(menology)"
HOMEPAGE="https://spheno.hepforge.org/;
-SRC_URI="https://spheno.hepforge.org/downloads/?f=${MY_P}.tar.gz;
+SRC_URI="https://spheno.hepforge.org/downloads/?f=${MY_P}.tar.gz ->
${P}.tar.gz"
S="${WORKDIR}/${MY_P}"
LICENSE="all-rights-reserved"
@@ -18,16 +18,11 @@ RESTRICT="bindist mirror"
SLOT="0"
KEYWORDS="~amd64"
-DEPEND="virtual/fortran"
-RDEPEND="${DEPEND}"
-
PATCHES=( "${FILESDIR}"/${P}-gfortran.patch )
src_compile() {
# single thread force needed since fortan mods depend on each other
- export MAKEOPTS=-j1
- tc-export FC AR
- emake AR="${AR}" F90="${FC}"
+ emake -j1 F90="${FC}"
}
src_install() {
@@ -35,7 +30,8 @@ src_install() {
# convenience symlink since the package is lowercase but the default
produced binary is uppercase
dosym ${MY_PN} /usr/bin/${PN}
dolib.a lib/lib${MY_PN}.a
- doheader include/*
+ mv include ${PN}
+ doheader -r ${PN}
dodoc doc/*
docinto examples
dodoc input/*
[gentoo-commits] proj/sci:master commit in: sci-physics/hepunits/
commit: 0770aa2dcd1651ec567469c9bdca147ec4b17b6c
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Thu Mar 14 09:40:12 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Thu Mar 14 12:24:32 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0770aa2d
sci-physics/hepunits: add 2.3.3, python3_12
Closes: https://github.com/gentoo/sci/pull/1255
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/hepunits/{hepunits-.ebuild => hepunits-2.3.3.ebuild} | 4 +++-
sci-physics/hepunits/hepunits-.ebuild| 4 +++-
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-physics/hepunits/hepunits-.ebuild
b/sci-physics/hepunits/hepunits-2.3.3.ebuild
similarity index 86%
copy from sci-physics/hepunits/hepunits-.ebuild
copy to sci-physics/hepunits/hepunits-2.3.3.ebuild
index 9816df84b..6e9ada04b 100644
--- a/sci-physics/hepunits/hepunits-.ebuild
+++ b/sci-physics/hepunits/hepunits-2.3.3.ebuild
@@ -1,6 +1,6 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=hatchling
inherit distutils-r1
@@ -21,3 +21,5 @@ RDEPEND="
>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
"
BDEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
diff --git a/sci-physics/hepunits/hepunits-.ebuild
b/sci-physics/hepunits/hepunits-.ebuild
index 9816df84b..6e9ada04b 100644
--- a/sci-physics/hepunits/hepunits-.ebuild
+++ b/sci-physics/hepunits/hepunits-.ebuild
@@ -1,6 +1,6 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=hatchling
inherit distutils-r1
@@ -21,3 +21,5 @@ RDEPEND="
>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
"
BDEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: dev-python/llvmlite/files/, dev-python/umap-learn/, dev-python/tridesclous/, ...
commit: 1a41a5294718de0da9a9e97f14d72440eeb588f8
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Mar 8 16:43:01 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Mar 8 16:43:01 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a41a529
dev-python/{numba*,llvmlite}: treeclean
llvmlite is *still* stuck on llvm:14
Signed-off-by: Andrew Ammerlaan gentoo.org>
.../files/llvmlite-0.39.1-allow-py3.11.patch | 13 ---
.../llvmlite/files/llvmlite-0.39.1-llvm12.patch| 97
dev-python/llvmlite/llvmlite-0.39.1.ebuild | 66 --
dev-python/llvmlite/llvmlite-0.40.1.ebuild | 63 -
dev-python/llvmlite/llvmlite-0.41.0.ebuild | 57
dev-python/llvmlite/metadata.xml | 18
dev-python/numba-dpex/metadata.xml | 12 ---
dev-python/numba-dpex/numba-dpex-0.20.0_rc3.ebuild | 41 -
.../numba/files/numba-0.52.0-skip_tests.patch | 34 ---
.../numba/files/numba-0.56.4-allow-py3.11.patch| 13 ---
dev-python/numba/metadata.xml | 16
dev-python/numba/numba-0.56.4.ebuild | 85 -
dev-python/numba/numba-0.57.1.ebuild | 83 -
dev-python/pynndescent/metadata.xml| 16
dev-python/pynndescent/pynndescent-0.5.6.ebuild| 27 --
dev-python/tridesclous/metadata.xml| 16
dev-python/tridesclous/tridesclous-1.6.4.ebuild| 100
dev-python/tridesclous/tridesclous-1.6.6.ebuild| 101 -
dev-python/umap-learn/metadata.xml | 15 ---
dev-python/umap-learn/umap-learn-0.5.2.ebuild | 25 -
profiles/package.mask | 11 ---
21 files changed, 909 deletions(-)
diff --git a/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch
b/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch
deleted file mode 100644
index d35979ebc..0
--- a/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/setup.py b/setup.py
-index 02b1604..a45c9b8 100644
a/setup.py
-+++ b/setup.py
-@@ -33,7 +33,7 @@ except ImportError:
-
-
- min_python_version = "3.7"
--max_python_version = "3.11" # exclusive
-+max_python_version = "3.12" # exclusive
-
-
- def _guard_py_ver():
diff --git a/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch
b/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch
deleted file mode 100644
index 17eb80e87..0
--- a/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch
+++ /dev/null
@@ -1,97 +0,0 @@
-From 1d928ebcd59b23b5050234a2bf71f9be7f5f6bd1 Mon Sep 17 00:00:00 2001
-From: Richard Barnes
-Date: Wed, 1 Dec 2021 10:29:08 -0700
-Subject: [PATCH] Enable LLVM-12 and LLVM-13
-
- ffi/build.py | 5 ++---
- ffi/targets.cpp| 2 ++
- llvmlite/tests/test_binding.py | 19 ---
- 3 files changed, 20 insertions(+), 6 deletions(-)
-
-Index: llvmlite-0.39.0/ffi/build.py
-===
llvmlite-0.39.0.orig/ffi/build.py
-+++ llvmlite-0.39.0/ffi/build.py
-@@ -163,9 +163,8 @@ def main_posix(kind, library_ext):
- print(msg)
- print(warning + '\n')
- else:
--
--if not out.startswith('11'):
--msg = ("Building llvmlite requires LLVM 11.x.x, got "
-+if not (out.startswith('11') or out.startswith('12') or
out.startswith('13')):
-+msg = ("Building llvmlite requires LLVM 11-13.x.x, got "
-"{!r}. Be sure to set LLVM_CONFIG to the right executable "
-"path.\nRead the documentation at "
-"http://llvmlite.pydata.org/ for more information about "
-Index: llvmlite-0.39.0/ffi/targets.cpp
-===
llvmlite-0.39.0.orig/ffi/targets.cpp
-+++ llvmlite-0.39.0/ffi/targets.cpp
-@@ -204,7 +204,9 @@ LLVMPY_CreateTargetMachine(LLVMTargetRef
- rm = Reloc::DynamicNoPIC;
-
- TargetOptions opt;
-+#if LLVM_VERSION_MAJOR < 12
- opt.PrintMachineCode = PrintMC;
-+#endif
- opt.MCOptions.ABIName = ABIName;
-
- bool jit = JIT;
-Index: llvmlite-0.39.0/llvmlite/tests/test_binding.py
-===
llvmlite-0.39.0.orig/llvmlite/tests/test_binding.py
-+++ llvmlite-0.39.0/llvmlite/tests/test_binding.py
-@@ -18,6 +18,16 @@ from llvmlite.binding import ffi
- from llvmlite.tests import TestCase
-
-
-+def clean_string_whitespace(x: str) -> str:
-+# Remove trailing whitespace from the end of each line
-+x = re.sub(r"\s+$", "", x, flags=re.MULTILINE)
-+# Remove intermediate blank lines
-+x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE)
-+# Remove extraneous whitespace from the
[gentoo-commits] proj/sci:master commit in: dev-python/cadquery/, profiles/, dev-python/cadquery-ocp/, ...
commit: 9659a8b0f5c491a9329ef9c8ac9bc3feeaf630e5
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Mar 8 16:44:35 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Mar 8 16:44:35 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9659a8b0
dev-python/cadquery*: treeclean
Needs bump and port to newer python targets
Work on-going in: https://github.com/gentoo/sci/pull/1211
Possibly re-add later.
Signed-off-by: Andrew Ammerlaan gentoo.org>
.../cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild | 197 -
dev-python/cadquery-ocp/metadata.xml | 11 --
.../cadquery-pywrap-7.5.3_rc20220113.ebuild| 63 ---
dev-python/cadquery-pywrap/metadata.xml| 12 --
dev-python/cadquery/cadquery-2.2_rc20220506.ebuild | 60 ---
dev-python/cadquery/metadata.xml | 12 --
profiles/package.mask | 7 -
7 files changed, 362 deletions(-)
diff --git a/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild
b/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild
deleted file mode 100644
index 8a97782bd..0
--- a/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild
+++ /dev/null
@@ -1,197 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-
-# OCP uses "python-single-r1" only because VTK uses "python-single-r1".
-inherit check-reqs cmake llvm multiprocessing python-single-r1 toolchain-funcs
-
-MY_PN=OCP
-MY_PV="${PV//_/-}"
-MY_P="${MY_PN}-${MY_PV}"
-OCCT_PV=$(ver_cut 1-3)
-
-DESCRIPTION="Python wrapper for OCCT generated using pywrap"
-HOMEPAGE="https://github.com/CadQuery/OCP;
-SRC_URI="https://github.com/CadQuery/OCP/archive/refs/tags/${MY_PV}.tar.gz ->
${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-# Hard masking due to opencascade slot 0/7.5 having been removed from ::gentoo
in ff9032e688571dde15e9d36cebedf5a247ded1b8
-#KEYWORDS="~amd64 ~x86"
-KEYWORDS=""
-SLOT="0"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# CMake and VTK requirements derive from the "OCP/CMakeLists.txt" file
-# generated by the src_prepare() phase. OCP currently requires opencascade
-# (OCCT) to be built with "-DUSE_GLES2=OFF" and thus "-gles2". See also:
-# https://github.com/CadQuery/OCP/issues/46#issuecomment-808920994
-BDEPEND="
- >=dev-libs/lief-0.11.5[python,${PYTHON_SINGLE_USEDEP}]
- >=dev-util/cmake-3.16
-"
-RDEPEND="
- ${PYTHON_DEPS}
- sci-libs/opencascade:0/7.5[json,tbb,vtk]
- >=sci-libs/vtk-9.0.0[python,${PYTHON_SINGLE_USEDEP}]
-"
-DEPEND="${RDEPEND}
- $(python_gen_cond_dep '
-
>=dev-python/cadquery-pywrap-'${OCCT_PV}'_rc0[${PYTHON_USEDEP}]')
-"
-
-S="${WORKDIR}/${MY_P}"
-
-# The source "OCP/CMakeLists.txt" file is output by "bindgen" in src_prepare().
-CMAKE_IN_SOURCE_BUILD=True
-
-# Ensure the path returned by get_llvm_prefix() contains clang.
-llvm_check_deps() {
- has_version -r "sys-devel/clang:${LLVM_SLOT}"
-}
-
-cadquery-ocp_check_reqs() {
- CHECKREQS_DISK_BUILD=1300M check-reqs_pkg_${EBUILD_PHASE}
-}
-
-pkg_pretend() {
- cadquery-ocp_check_reqs
-}
-
-pkg_setup() {
- cadquery-ocp_check_reqs
- llvm_pkg_setup
- python-single-r1_pkg_setup
-}
-
-# OCP currently requires manual configuration, compilation, and installation
-# loosely inspired by the conda-specific "build-bindings-job.yml" file.
-#
-# Note that the cmake_src_prepare() function called below handles user patches.
-src_prepare() {
- # Most recently installed version of Clang.
- local _CLANG_VERSION="$(CPP=clang clang-fullversion)"
-
- # Most recently installed version (excluding trailing patch) of VTK.
- local _VTK_VERSION="$(best_version -r sci-libs/vtk)"
- _VTK_VERSION="$(ver_cut 1-2 "${_VTK_VERSION##sci-libs/vtk}")"
-
- # Absolute dirname of the most recently installed Clang include
directory,
- # mimicing similar logic in the "dev-python/shiboken2" ebuild. See also:
- # https://bugs.gentoo.org/619490
- local
_CLANG_INCLUDE_DIR="${EPREFIX}/usr/lib/clang/${_CLANG_VERSION}/include"
-
- # Absolute filename of the most recently installed Clang shared library.
- local _CLANG_LIB_FILE="$(get_llvm_prefix)/lib64/libclang.so"
-
- # Absolute dirname of OCCT's include and shared library directories.
- local _OCCT_INCLUDE_DIR="${EPREFIX}/usr/include/opencascade"
- local _OCCT_LIB_DIR="${EPREFIX}/usr/lib64/opencascade"
-
- # Absolute dirname of a temporary directory to store symbol tables for
this
- # OCCT version dumped below by the "dump_symbols.py" script.
- local _OCCT_DUMP_SYMBOLS_ROOT_DIR="${T}/dump_symbols"
- local _OCCT_DUMP_SYMBOLS_DIR="${_OCCT_DUMP_SYMBOLS_ROOT_DIR}/lib_linux"
-
- # Absolute dirname of VTK's include directory,
- local _VTK_INCLUDE_DIR="${EPREFIX}/usr/include/vtk-${_VTK_VERSION}"
-
- #
[gentoo-commits] proj/sci:master commit in: dev-python/numpy/, dev-python/numpy/files/
commit: f492b712e25ed39d4495625460de60c1a04b
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Mar 8 16:41:11 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Mar 8 16:41:11 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f492
dev-python/numpy: drop duplicate
Signed-off-by: Andrew Ammerlaan gentoo.org>
.../files/numpy-1.22.0-no-hardcode-blasv2.patch| 50 --
dev-python/numpy/metadata.xml | 24 ---
dev-python/numpy/numpy-1.23.5.ebuild | 184 -
3 files changed, 258 deletions(-)
diff --git a/dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch
b/dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch
deleted file mode 100644
index d87a16a4b..0
--- a/dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-Originally added in:
https://gitweb.gentoo.org/repo/gentoo.git/commit/dev-python/numpy/files?id=e5ce90a04e79f6413604e96e4803cb95ada7c859
-https://bugs.gentoo.org/567938
a/numpy/distutils/system_info.py
-+++ b/numpy/distutils/system_info.py
-@@ -505,33 +505,7 @@ def get_info(name, notfound_action=0):
- 'blas_armpl': blas_armpl_info,
- 'lapack_armpl': lapack_armpl_info,
- 'fftw3_armpl': fftw3_armpl_info,
-- 'atlas': atlas_info, # use lapack_opt or blas_opt instead
-- 'atlas_threads': atlas_threads_info,# ditto
-- 'atlas_blas': atlas_blas_info,
-- 'atlas_blas_threads': atlas_blas_threads_info,
-- 'lapack_atlas': lapack_atlas_info, # use lapack_opt instead
-- 'lapack_atlas_threads': lapack_atlas_threads_info, # ditto
-- 'atlas_3_10': atlas_3_10_info, # use lapack_opt or blas_opt instead
-- 'atlas_3_10_threads': atlas_3_10_threads_info,#
ditto
-- 'atlas_3_10_blas': atlas_3_10_blas_info,
-- 'atlas_3_10_blas_threads': atlas_3_10_blas_threads_info,
-- 'lapack_atlas_3_10': lapack_atlas_3_10_info, # use lapack_opt
instead
-- 'lapack_atlas_3_10_threads': lapack_atlas_3_10_threads_info, #
ditto
-- 'flame': flame_info, # use lapack_opt instead
-- 'mkl': mkl_info,
-- # openblas which may or may not have embedded lapack
-- 'openblas': openblas_info, # use blas_opt instead
-- # openblas with embedded lapack
-- 'openblas_lapack': openblas_lapack_info, # use blas_opt instead
-- 'openblas_clapack': openblas_clapack_info, # use blas_opt instead
-- 'blis': blis_info, # use blas_opt instead
-- 'lapack_mkl': lapack_mkl_info, # use lapack_opt instead
-- 'blas_mkl': blas_mkl_info, # use blas_opt instead
- 'accelerate': accelerate_info, # use blas_opt instead
-- 'openblas64_': openblas64__info,
-- 'openblas64__lapack': openblas64__lapack_info,
-- 'openblas_ilp64': openblas_ilp64_info,
-- 'openblas_ilp64_lapack': openblas_ilp64_lapack_info,
- 'x11': x11_info,
- 'fft_opt': fft_opt_info,
- 'fftw': fftw_info,
-@@ -951,10 +925,7 @@ class system_info:
- return [b for b in [a.strip() for a in libs.split(',')] if b]
-
- def get_libraries(self, key='libraries'):
--if hasattr(self, '_lib_names'):
--return self.get_libs(key, default=self._lib_names)
--else:
--return self.get_libs(key, '')
-+ return self.get_libs(key, '')
-
- def library_extensions(self):
- c = customized_ccompiler()
diff --git a/dev-python/numpy/metadata.xml b/dev-python/numpy/metadata.xml
deleted file mode 100644
index 26b229a9c..0
--- a/dev-python/numpy/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-
-https://www.gentoo.org/dtd/metadata.dtd;>
-
-
-s...@gentoo.org
-Gentoo Science Project
-
-
-pyt...@gentoo.org
-Python
-
-
- NumPy is a general-purpose array-processing Python package designed to
- efficiently manipulate large multi-dimensional arrays of arbitrary
- records without sacrificing too much speed for small multi-dimensional
- arrays. There are also basic facilities for discrete fourier transform,
- basic linear algebra and random number generation.
- It is the successor of Numeric and numarray.
-
-
-numpy/numpy
-numpy
-
-
diff --git a/dev-python/numpy/numpy-1.23.5.ebuild
b/dev-python/numpy/numpy-1.23.5.ebuild
deleted file mode 100644
index 5a9224e54..0
--- a/dev-python/numpy/numpy-1.23.5.ebuild
+++ /dev/null
@@ -1,184 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-PYTHON_REQ_USE="threads(+)"
-FORTRAN_NEEDED=lapack
-inherit distutils-r1 flag-o-matic fortran-2 pypi toolchain-funcs
-
-DOC_PV=${PV}
-# For when docs aren't ready yet,
[gentoo-commits] proj/sci:master commit in: profiles/, dev-python/pytorch-lightning/
commit: a6dbed04be114775959f5c09e3230a148e9605f8
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Mar 8 16:42:02 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Mar 8 16:42:02 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6dbed04
dev-python/pytorch-lightning: treeclean
Signed-off-by: Andrew Ammerlaan gentoo.org>
dev-python/pytorch-lightning/metadata.xml | 12 -
.../pytorch-lightning-1.8.6.ebuild | 31 --
profiles/package.mask | 4 ---
3 files changed, 47 deletions(-)
diff --git a/dev-python/pytorch-lightning/metadata.xml
b/dev-python/pytorch-lightning/metadata.xml
deleted file mode 100644
index df24db4ac..0
--- a/dev-python/pytorch-lightning/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- s...@gentoo.org
- Science Project
-
-
- Lightning-AI/lightning
- pytorch-lightning
-
-
diff --git a/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
b/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
deleted file mode 100644
index a775be3bf..0
--- a/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-DISTUTILS_USE_PEP517=setuptools
-DISTUTILS_SINGLE_IMPL=1
-PYPI_NO_NORMALIZE=1
-inherit distutils-r1 pypi
-
-DESCRIPTION="Lightweight PyTorch wrapper for ML researchers"
-HOMEPAGE="https://github.com/Lightning-AI/lightning;
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}]
- $(python_gen_cond_dep '
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/fsspec[${PYTHON_USEDEP}]
- sci-visualization/tensorboard[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- dev-python/ratelimit[${PYTHON_USEDEP}]
- ')
-"
diff --git a/profiles/package.mask b/profiles/package.mask
index adc653878..527c834e4 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,10 +30,6 @@
#--- END OF EXAMPLES ---
-# Andrew Ammerlaan (27-02-2024)
-# Depends on removed sci-visualization/tensorboard
-dev-python/pytorch-lightning
-
# Andrew Ammerlaan (29 Dec 2023)
# Depends on removed llvm:14, at the time of writing no llvm:15
# update available.
[gentoo-commits] proj/sci:master commit in: dev-python/schema/
commit: 8dada7f9fe93d4e46879d6855e3c97f9d8f6dcfe
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Mar 8 16:36:04 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Mar 8 16:36:04 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8dada7f9
dev-python/schema: moved to ::gentoo
Signed-off-by: Andrew Ammerlaan gentoo.org>
dev-python/schema/metadata.xml| 13 -
dev-python/schema/schema-0.7.4.ebuild | 26 --
2 files changed, 39 deletions(-)
diff --git a/dev-python/schema/metadata.xml b/dev-python/schema/metadata.xml
deleted file mode 100644
index 440ea4da1..0
--- a/dev-python/schema/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- s...@gentoo.org
- Gentoo Science Project
-
-
-
- schema
- keleshev/schema
-
-
diff --git a/dev-python/schema/schema-0.7.4.ebuild
b/dev-python/schema/schema-0.7.4.ebuild
deleted file mode 100644
index faa082e58..0
--- a/dev-python/schema/schema-0.7.4.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 pypy3 )
-inherit distutils-r1 pypi
-
-DESCRIPTION="Schema validation just got Pythonic"
-HOMEPAGE="https://pypi.org/project/schema/;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-BDEPEND="test? ( dev-python/mock[${PYTHON_USEDEP}] )"
-
-distutils_enable_tests pytest
-
-src_prepare() {
- distutils-r1_src_prepare
-
- # Prevent schema from unconditionally requiring the last-rited
contextlib2,
- # which schema actually conditionally requires only under EOL Python
2.x.
- sed -i -e '/\binstall_requires=/d' setup.py || die
-}
[gentoo-commits] proj/sci:master commit in: app-arch/libdeflate/
commit: 0dd79437900279db51502a489ce30d51301d06d8
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Mar 8 16:32:30 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Mar 8 16:34:57 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0dd79437
app-arch/libdeflate: moved to ::gentoo
Signed-off-by: Andrew Ammerlaan gentoo.org>
app-arch/libdeflate/libdeflate-1.11.ebuild | 28
app-arch/libdeflate/libdeflate-1.6.ebuild | 21 -
app-arch/libdeflate/libdeflate-1.7.ebuild | 28
app-arch/libdeflate/libdeflate-1.8.ebuild | 28
app-arch/libdeflate/libdeflate-1.9.ebuild | 28
app-arch/libdeflate/libdeflate-.ebuild | 28
app-arch/libdeflate/metadata.xml | 19 ---
7 files changed, 180 deletions(-)
diff --git a/app-arch/libdeflate/libdeflate-1.11.ebuild
b/app-arch/libdeflate/libdeflate-1.11.ebuild
deleted file mode 100644
index 9e7344b22..0
--- a/app-arch/libdeflate/libdeflate-1.11.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 2019-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
-HOMEPAGE="https://github.com/ebiggers/libdeflate;
-
-if [[ ${PV} == * ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/ebiggers/libdeflate;
-else
- SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz
-> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="static-libs test"
-RESTRICT="!test? ( test )"
-
-src_install() {
- emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install
- if ! use static-libs; then
- find "${ED}" -name '*.a' -delete || die
- fi
- dodoc NEWS.md README.md
-}
diff --git a/app-arch/libdeflate/libdeflate-1.6.ebuild
b/app-arch/libdeflate/libdeflate-1.6.ebuild
deleted file mode 100644
index 666506943..0
--- a/app-arch/libdeflate/libdeflate-1.6.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 2019-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
-HOMEPAGE="https://github.com/ebiggers/libdeflate;
-SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz ->
${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-src_install() {
- if ! use static-libs; then
- find "${ED}" -name '*.a' -delete || die
- fi
- emake install DESTDIR="${ED}" PREFIX=/usr LIBDIR=/usr/"$(get_libdir)"
- dodoc NEWS README.md
-}
diff --git a/app-arch/libdeflate/libdeflate-1.7.ebuild
b/app-arch/libdeflate/libdeflate-1.7.ebuild
deleted file mode 100644
index bfafcfecd..0
--- a/app-arch/libdeflate/libdeflate-1.7.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 2019-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
-HOMEPAGE="https://github.com/ebiggers/libdeflate;
-
-if [[ ${PV} == * ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/ebiggers/libdeflate;
-else
- SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz
-> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="static-libs test"
-RESTRICT="!test? ( test )"
-
-src_install() {
- emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install
- if ! use static-libs; then
- find "${ED}" -name '*.a' -delete || die
- fi
- dodoc NEWS README.md
-}
diff --git a/app-arch/libdeflate/libdeflate-1.8.ebuild
b/app-arch/libdeflate/libdeflate-1.8.ebuild
deleted file mode 100644
index bfafcfecd..0
--- a/app-arch/libdeflate/libdeflate-1.8.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 2019-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
-HOMEPAGE="https://github.com/ebiggers/libdeflate;
-
-if [[ ${PV} == * ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/ebiggers/libdeflate;
-else
- SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz
-> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="static-libs test"
-RESTRICT="!test? ( test )"
-
-src_install() {
- emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install
- if ! use static-libs; then
- find "${ED}" -name '*.a' -delete || die
- fi
- dodoc NEWS README.md
-}
diff --git a/app-arch/libdeflate/libdeflate-1.9.ebuild
[gentoo-commits] proj/sci:master commit in: dev-libs/oneDNN/
commit: 0791f711debf39eceb002891a40a91b33553044f
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Mar 8 16:33:29 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Mar 8 16:34:58 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0791f711
dev-libs/oneDNN: moved to ::gentoo
Signed-off-by: Andrew Ammerlaan gentoo.org>
dev-libs/oneDNN/metadata.xml| 11 ---
dev-libs/oneDNN/oneDNN-2.7.2.ebuild | 60 -
dev-libs/oneDNN/oneDNN-3.0.1.ebuild | 60 -
dev-libs/oneDNN/oneDNN-3.2.1.ebuild | 60 -
4 files changed, 191 deletions(-)
diff --git a/dev-libs/oneDNN/metadata.xml b/dev-libs/oneDNN/metadata.xml
deleted file mode 100644
index 0d6dc84a7..0
--- a/dev-libs/oneDNN/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- s...@gentoo.org
- Gentoo Science Project
-
-
- oneapi-src/oneDNN
-
-
diff --git a/dev-libs/oneDNN/oneDNN-2.7.2.ebuild
b/dev-libs/oneDNN/oneDNN-2.7.2.ebuild
deleted file mode 100644
index 1c66ec72c..0
--- a/dev-libs/oneDNN/oneDNN-2.7.2.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DOCS_BUILDER="doxygen"
-DOCS_DIR="${WORKDIR}/${P}_build"
-# There is additional sphinx documentation but we are missing dependency
doxyrest.
-inherit cmake docs
-
-DESCRIPTION="oneAPI Deep Neural Network Library"
-HOMEPAGE="https://github.com/oneapi-src/oneDNN;
-SRC_URI="https://github.com/oneapi-src/oneDNN/archive/refs/tags/v${PV}.tar.gz
-> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-IUSE="test"
-# TODO: get the tests up and running
-#RESTRICT="!test? ( test )"
-RESTRICT="test"
-
-BDEPEND="sys-devel/DPC++"
-
-DEPEND="
- dev-cpp/tbb:=
- dev-libs/level-zero:=
- virtual/opencl
-"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
- # DPC++ compiler required for full functionality
- export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
- export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
-
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DDNNL_CPU_RUNTIME=DPCPP
- -DDNNL_GPU_RUNTIME=DPCPP
- -DDNNL_BUILD_TESTS="$(usex test)"
- )
- cmake_src_configure
-}
-
-src_compile() {
- cmake_src_compile
- docs_compile
-}
-
-src_install() {
- cmake_src_install
- # Correct docdir
- mv "${ED}/usr/share/doc/dnnl/"* "${ED}/usr/share/doc/${PF}" || die
- rm -r "${ED}/usr/share/doc/dnnl" || die
-}
diff --git a/dev-libs/oneDNN/oneDNN-3.0.1.ebuild
b/dev-libs/oneDNN/oneDNN-3.0.1.ebuild
deleted file mode 100644
index 1c66ec72c..0
--- a/dev-libs/oneDNN/oneDNN-3.0.1.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DOCS_BUILDER="doxygen"
-DOCS_DIR="${WORKDIR}/${P}_build"
-# There is additional sphinx documentation but we are missing dependency
doxyrest.
-inherit cmake docs
-
-DESCRIPTION="oneAPI Deep Neural Network Library"
-HOMEPAGE="https://github.com/oneapi-src/oneDNN;
-SRC_URI="https://github.com/oneapi-src/oneDNN/archive/refs/tags/v${PV}.tar.gz
-> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-IUSE="test"
-# TODO: get the tests up and running
-#RESTRICT="!test? ( test )"
-RESTRICT="test"
-
-BDEPEND="sys-devel/DPC++"
-
-DEPEND="
- dev-cpp/tbb:=
- dev-libs/level-zero:=
- virtual/opencl
-"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
- # DPC++ compiler required for full functionality
- export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
- export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
-
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DDNNL_CPU_RUNTIME=DPCPP
- -DDNNL_GPU_RUNTIME=DPCPP
- -DDNNL_BUILD_TESTS="$(usex test)"
- )
- cmake_src_configure
-}
-
-src_compile() {
- cmake_src_compile
- docs_compile
-}
-
-src_install() {
- cmake_src_install
- # Correct docdir
- mv "${ED}/usr/share/doc/dnnl/"* "${ED}/usr/share/doc/${PF}" || die
- rm -r "${ED}/usr/share/doc/dnnl" || die
-}
diff --git a/dev-libs/oneDNN/oneDNN-3.2.1.ebuild
b/dev-libs/oneDNN/oneDNN-3.2.1.ebuild
deleted file mode 100644
index 1c66ec72c..0
--- a/dev-libs/oneDNN/oneDNN-3.2.1.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DOCS_BUILDER="doxygen"
-DOCS_DIR="${WORKDIR}/${P}_build"
-# There is additional sphinx documentation but we are missing dependency
doxyrest.
-inherit cmake docs
-
-DESCRIPTION="oneAPI Deep
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: a28423309bc3562113676a5009af778a18447267
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 21:10:29 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 21:10:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a2842330
sci-biology/fsl: updated C++ version
Signed-off-by: Horea Christian chymera.eu>
sci-biology/fsl/fsl-6.0.4.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild
index cd91cf192..6e5d6e779 100644
--- a/sci-biology/fsl/fsl-6.0.4.ebuild
+++ b/sci-biology/fsl/fsl-6.0.4.ebuild
@@ -151,8 +151,8 @@ src_compile() {
# define the default build system to match upstream official standard
# -> individual projects may overwrite the '-std=' flag
- export ANSI_CFLAGS="-std=c99"
- export ANSI_CXXFLAGS="-std=c++98"
+ export ANSI_CFLAGS="-std=c11"
+ export ANSI_CXXFLAGS="-std=c++11"
export USERLDFLAGS="${LDFLAGS}"
export USERCFLAGS="${CFLAGS}"
[gentoo-commits] proj/sci:master commit in: dev-python/ripser/
commit: 8cc0b06c161939b5d472b4d66eb94ea6bba14ac7
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 02:10:18 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 02:10:18 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8cc0b06c
dev-python/ripser: unkeyword 0.6.4 for ~x86
Signed-off-by: Horea Christian chymera.eu>
dev-python/ripser/ripser-0.6.4.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/dev-python/ripser/ripser-0.6.4.ebuild
b/dev-python/ripser/ripser-0.6.4.ebuild
index e0ea6f24b..21d6b6ccd 100644
--- a/dev-python/ripser/ripser-0.6.4.ebuild
+++ b/dev-python/ripser/ripser-0.6.4.ebuild
@@ -13,7 +13,7 @@ HOMEPAGE="https://ripser.scikit-tda.org/;
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
RDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
[gentoo-commits] proj/sci:master commit in: sci-biology/behaviopy/
commit: 13b5f620d3c2bb529a52a878dec2d91f9f3a732d
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 02:03:56 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 02:03:56 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=13b5f620
sci-biology/behaviopy: treeclean
Signed-off-by: Horea Christian chymera.eu>
sci-biology/behaviopy/behaviopy-0.2.ebuild | 42 --
sci-biology/behaviopy/metadata.xml | 26 --
2 files changed, 68 deletions(-)
diff --git a/sci-biology/behaviopy/behaviopy-0.2.ebuild
b/sci-biology/behaviopy/behaviopy-0.2.ebuild
deleted file mode 100644
index dc875e7a5..0
--- a/sci-biology/behaviopy/behaviopy-0.2.ebuild
+++ /dev/null
@@ -1,42 +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
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="https://github.com/TheChymera/behaviopy;
-SRC_URI="https://github.com/TheChymera/behaviopy/archive/${PV}.tar.gz ->
${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="evaluation"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/seaborn[${PYTHON_USEDEP}]
- dev-python/statsmodels[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
-"
-
-python_prepare_all() {
- if ! use evaluation; then
- rm behaviopy/evaluation.py || die
- fi
- distutils-r1_python_prepare_all
-}
-
-python_test() {
- cd behaviopy/examples || die
- echo "backend : Agg" > matplotlibrc || die
- for i in *py; do
- echo "Executing $i"
- ${EPYTHON} $i || die
- done
-}
diff --git a/sci-biology/behaviopy/metadata.xml
b/sci-biology/behaviopy/metadata.xml
deleted file mode 100644
index a33886a68..0
--- a/sci-biology/behaviopy/metadata.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- gen...@chymera.eu
- Horea Christian
-
-
- s...@gentoo.org
- Gentoo Science Project
-
-
- BehavioPy is a Python toolkit providing evaluation (e.g. event
- tracking) and plotting functions for behavioural data. Manual
event
- tracking is done via a simple and configurable PsychoPy-based
- interface. Plotting functions are designed to work with
preformatted
- data in CSV format (e.g. as exported by pandas), and use
Seaborn and
- custom BehavioPy styles for maximum beautification.
-
-
- TheChymera/behaviopy
-
-
- Installs evaluation submodule.
-
-
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools/
commit: 17688a432b33d4ce2ecb5fe1cbc25e7e36efe288
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 02:05:41 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 02:05:41 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=17688a43
sci-biology/deeptools: dropped ~x86, added PEP517
Signed-off-by: Horea Christian chymera.eu>
sci-biology/deeptools/deeptools-3.5.0.ebuild | 5 +++--
sci-biology/deeptools/deeptools-3.5.1.ebuild | 5 +++--
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild
b/sci-biology/deeptools/deeptools-3.5.0.ebuild
index a76bf6690..7c2eaa739 100644
--- a/sci-biology/deeptools/deeptools-3.5.0.ebuild
+++ b/sci-biology/deeptools/deeptools-3.5.0.ebuild
@@ -3,7 +3,8 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
@@ -13,7 +14,7 @@
SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
# TODO: fix this
RESTRICT="test"
diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild
b/sci-biology/deeptools/deeptools-3.5.1.ebuild
index a76bf6690..7c2eaa739 100644
--- a/sci-biology/deeptools/deeptools-3.5.1.ebuild
+++ b/sci-biology/deeptools/deeptools-3.5.1.ebuild
@@ -3,7 +3,8 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
@@ -13,7 +14,7 @@
SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
# TODO: fix this
RESTRICT="test"
[gentoo-commits] proj/sci:master commit in: dev-python/python-igraph/
commit: 4b964b67decfbc018fd145a28ffb37296b7b573a
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 02:01:43 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 02:01:43 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4b964b67
dev-python/python-igraph: unkeyword 0.10.4 for ~x86
Signed-off-by: Horea Christian chymera.eu>
dev-python/python-igraph/python-igraph-0.10.4.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/dev-python/python-igraph/python-igraph-0.10.4.ebuild
b/dev-python/python-igraph/python-igraph-0.10.4.ebuild
index 5ef24cedf..3ee6e1eb4 100644
--- a/dev-python/python-igraph/python-igraph-0.10.4.ebuild
+++ b/dev-python/python-igraph/python-igraph-0.10.4.ebuild
@@ -14,7 +14,7 @@ S="${WORKDIR}/igraph-${PV}"
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
RDEPEND="
>=dev-libs/igraph-$(ver_cut 1-2)
[gentoo-commits] proj/sci:master commit in: dev-python/persim/
commit: 5da1ece965b466bed18247c3ad817756a7c7db9e
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 02:01:02 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 02:01:02 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5da1ece9
dev-python/persim: unkeyword 0.3.1 for ~x86
Signed-off-by: Horea Christian chymera.eu>
dev-python/persim/persim-0.3.1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/dev-python/persim/persim-0.3.1.ebuild
b/dev-python/persim/persim-0.3.1.ebuild
index 78b86d6ea..994dca206 100644
--- a/dev-python/persim/persim-0.3.1.ebuild
+++ b/dev-python/persim/persim-0.3.1.ebuild
@@ -13,7 +13,7 @@ HOMEPAGE="https://persim.scikit-tda.org/;
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
RDEPEND="
dev-python/hopcroftkarp[${PYTHON_USEDEP}]
[gentoo-commits] proj/sci:master commit in: dev-python/kmapper/
commit: e9b71ec05b7d2c6970f7ab6bcc9cf58a778dbfcb
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 02:00:10 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 02:00:10 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e9b71ec0
dev-python/kmapper: unkeyword 2.0.1-r1 for ~x86
Signed-off-by: Horea Christian chymera.eu>
dev-python/kmapper/kmapper-2.0.1-r1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/dev-python/kmapper/kmapper-2.0.1-r1.ebuild
b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild
index c8bdf2b00..22f35fbda 100644
--- a/dev-python/kmapper/kmapper-2.0.1-r1.ebuild
+++ b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild
@@ -15,7 +15,7 @@ S="${WORKDIR}"/kepler-mapper-${PV}
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
RDEPEND="${PYTHON_DEPS}
dev-python/jinja[${PYTHON_USEDEP}]
[gentoo-commits] proj/sci:master commit in: dev-python/panel/
commit: 6957b6dbc342e421ef445b7e78905a1cc697f20b
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 01:58:01 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 01:58:01 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6957b6db
dev-python/panel: revbump for missing dep, PEP517, and PYTHON_COMPAT
Signed-off-by: Horea Christian chymera.eu>
dev-python/panel/{panel-0.14.2.ebuild => panel-0.14.2-r1.ebuild} | 6 --
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/dev-python/panel/panel-0.14.2.ebuild
b/dev-python/panel/panel-0.14.2-r1.ebuild
similarity index 92%
rename from dev-python/panel/panel-0.14.2.ebuild
rename to dev-python/panel/panel-0.14.2-r1.ebuild
index bf4df1861..4674f8161 100644
--- a/dev-python/panel/panel-0.14.2.ebuild
+++ b/dev-python/panel/panel-0.14.2-r1.ebuild
@@ -3,9 +3,10 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
# Panel imports from "distutils" at runtime.
-DISTUTILS_USE_SETUPTOOLS=rdepend
+#DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1 pypi
DESCRIPTION="High-level app and dashboarding solution for Python"
@@ -20,6 +21,7 @@ KEYWORDS="~amd64 ~x86"
DEPEND="
>=dev-python/param-1.10.0[${PYTHON_USEDEP}]
>=dev-python/pyct-0.4.4[${PYTHON_USEDEP}]
+ dev-python/bleach[${PYTHON_USEDEP}]
"
RDEPEND="${DEPEND}
dev-python/markdown[${PYTHON_USEDEP}]
[gentoo-commits] proj/sci:master commit in: dev-python/bokeh/
commit: 50a05ce19aefe2890f26918b5900d757c669e66b
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 01:44:52 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 01:44:52 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=50a05ce1
dev-python/bokeh: enable py3.11, py3.12
Signed-off-by: Horea Christian chymera.eu>
dev-python/bokeh/bokeh-2.4.2.ebuild | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/dev-python/bokeh/bokeh-2.4.2.ebuild
b/dev-python/bokeh/bokeh-2.4.2.ebuild
index 0a0c64b4b..7347e5110 100644
--- a/dev-python/bokeh/bokeh-2.4.2.ebuild
+++ b/dev-python/bokeh/bokeh-2.4.2.ebuild
@@ -3,9 +3,8 @@
EAPI=8
-PYTHON_COMPAT=( python3_10 )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-DISTUTILS_IN_SOURCE_BUILD=1
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 optfeature pypi
DESCRIPTION="Statistical and interactive HTML plots for Python"
[gentoo-commits] proj/sci:master commit in: dev-python/holoviews/
commit: f0a6b43352bd5ec0fe2a8087bbe51c4d0f880bca
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 01:59:14 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 01:59:14 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f0a6b433
dev-python/holoviews: unkeyword 1.15.3 for ~x86
Signed-off-by: Horea Christian chymera.eu>
dev-python/holoviews/holoviews-1.15.3.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/dev-python/holoviews/holoviews-1.15.3.ebuild
b/dev-python/holoviews/holoviews-1.15.3.ebuild
index 783d9b1cb..154b7195d 100644
--- a/dev-python/holoviews/holoviews-1.15.3.ebuild
+++ b/dev-python/holoviews/holoviews-1.15.3.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
# HoloViews imports from "distutils" at runtime.
DISTUTILS_USE_SETUPTOOLS=rdepend
@@ -15,7 +15,7 @@ HOMEPAGE="https://holoviews.org;
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
# Reported upstream:
# https://github.com/holoviz/holoviews/issues/5592
RESTRICT="test"
[gentoo-commits] proj/sci:master commit in: sci-libs/spyking-circus/
commit: 86470a713355810e48fc85922f5f40b3f9b2b489
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 01:16:57 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 01:16:57 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=86470a71
sci-libs/spyking-circus: unkeyword 1.1.0 for ~x86
Signed-off-by: Horea Christian chymera.eu>
sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
index 976a8535b..9b9233020 100644
--- a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
+++ b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
@@ -13,7 +13,7 @@
SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz -
LICENSE="CeCILL-2"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
# Wants to run mpirun (and fails)
RESTRICT="test"
@@ -27,7 +27,7 @@ RDEPEND="
>=dev-python/mpi4py-3.0.0[${PYTHON_USEDEP}]
>=dev-python/numpy-1.17.4[${PYTHON_USEDEP}]
>=dev-python/psutil-5.6.7[${PYTHON_USEDEP}]
- >=dev-python/statsmodels-0.10.1[${PYTHON_USEDEP}]
+ dev-python/statsmodels[${PYTHON_USEDEP}]
>=dev-python/tqdm-4.40.0[${PYTHON_USEDEP}]
>=dev-python/scipy-1.3.1[${PYTHON_USEDEP}]
"
[gentoo-commits] proj/sci:master commit in: sci-biology/afni/, sci-biology/afni/files/
commit: fa3769352840642eb37e6125ee2fa69fef802cd4
Author: Horea Christian chymera eu>
AuthorDate: Wed Feb 28 23:30:07 2024 +
Commit: Horea Christian gmail com>
CommitDate: Wed Feb 28 23:30:07 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=fa376935
sci-biology/afni: drop 20.1.16, 20.3.03, 22.0.21
Signed-off-by: Horea Christian chymera.eu>
sci-biology/afni/afni-20.1.16.ebuild | 73 ---
sci-biology/afni/afni-20.3.03.ebuild | 73 ---
sci-biology/afni/afni-22.0.21.ebuild | 75
sci-biology/afni/files/afni-20.1.16-python.patch | 11
4 files changed, 232 deletions(-)
diff --git a/sci-biology/afni/afni-20.1.16.ebuild
b/sci-biology/afni/afni-20.1.16.ebuild
deleted file mode 100644
index e3e16f834..0
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying
functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/;
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sys-devel/llvm:*
- media-libs/libjpeg-turbo:0
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXpm
- x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-#
http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
- app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
- eapply "${FILESDIR}/${P}-python.patch" || die
- find -type f -exec sed -i -e "s/-lXp //g" {} +
- cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy
Makefile"
- # Unbundle imcat
- sed -e "s/ imcat / /g" \
- -i Makefile.INCLUDE || die "Could not edit includes files."
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC)
\$(CFLAGS)~" \
- -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC)
\$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR= $(tc-getAR)~" \
- -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
- -i Makefile || die "Could not edit Makefile"
- # they provide somewhat problematic makefiles :(
- sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
- -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
- # upstream checks if $CC is EXACTLY gcc, else sets variables
for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e
"s~/usr/~${EPREFIX}/usr/~g;" -i
- default
-}
-
-src_compile() {
- emake -j1 all plugins suma_exec
-}
-
-src_install() {
- emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
- for CONFLICT in ${BIN_CONFLICTS[@]}; do
- rm "${ED}/usr/bin/${CONFLICT}"
- done
-}
diff --git a/sci-biology/afni/afni-20.3.03.ebuild
b/sci-biology/afni/afni-20.3.03.ebuild
deleted file mode 100644
index 1d9043ebb..0
--- a/sci-biology/afni/afni-20.3.03.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying
functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/;
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sys-devel/llvm:*
- media-libs/libjpeg-turbo:0
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXpm
- x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-#
http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
- app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
- eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die
-
[gentoo-commits] proj/sci:master commit in: sci-biology/afni/, sci-biology/afni/files/
commit: 19c71d97b19391b8797187494008509914db24ed
Author: Horea Christian chymera eu>
AuthorDate: Wed Feb 28 22:43:04 2024 +
Commit: Horea Christian gmail com>
CommitDate: Wed Feb 28 22:43:04 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=19c71d97
sci-biology/afni: add 24.0.04, 24.0.08
Signed-off-by: Horea Christian chymera.eu>
sci-biology/afni/afni-24.0.04.ebuild | 111
sci-biology/afni/afni-24.0.08.ebuild | 115 +
sci-biology/afni/files/afni-24.0.04-whirlgif.patch | 39 +++
sci-biology/afni/metadata.xml | 3 +
4 files changed, 268 insertions(+)
diff --git a/sci-biology/afni/afni-24.0.04.ebuild
b/sci-biology/afni/afni-24.0.04.ebuild
new file mode 100644
index 0..c00ef846f
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.04.ebuild
@@ -0,0 +1,111 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="http://stnava.github.io/ANTs/;
+SRC_URI="
+ https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz ->
${P}.gh.tar.gz
+
https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz ->
nifti-${NIFTI_HASH}.tar.gz
+
https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz ->
gifti-${GIFTI_HASH}.tar.gz
+ "
+
+SLOT="0"
+LICENSE="GPL-3+"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-libs/glib:2
+ dev-libs/libf2c
+ dev-libs/expat
+ dev-build/ninja
+ media-libs/freeglut
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-libs/gsl
+ sci-libs/gts
+ sys-devel/llvm:*
+ sys-libs/libomp
+ dev-libs/libpthread-stubs
+ virtual/jpeg-compat:62
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXmu
+ x11-libs/libXpm
+ x11-libs/libXt
+ x11-libs/motif[-static-libs]
+ "
+DEPEND="
+ ${RDEPEND}
+ app-shells/tcsh
+ "
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+src_prepare() {
+ tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+ tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+ cmake_src_prepare
+ default
+ }
+
+src_configure() {
+ if use !whirlgif; then
+ eapply "${FILESDIR}/${P}-whirlgif.patch"
+ fi
+ export CFLAGS="-pthread ${CFLAGS}"
+ export GIT_REPO_VERSION=3.0.1.1
+ local mycmakeargs=(
+ -DLIBDIR=/usr/$(get_libdir)
+ -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+ -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+ -DCOMP_COREBINARIES=ON
+ -DUSE_SYSTEM_NIFTI=OFF
+ -DUSE_SYSTEM_GIFTI=OFF
+ -DUSE_SYSTEM_XMHTML=OFF
+ -DUSE_SYSTEM_GTS=ON
+
-DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+
-DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+ -DCOMP_GUI=ON
+ -DCOMP_PLUGINS=ON
+ -DUSE_OMP=ON
+ -DCOMP_PYTHON=OFF
+ -DUSE_SYSTEM_F2C=ON
+ )
+ tc-export CC
+ cmake_src_configure
+}
+
+src_compile() {
+ cmake_src_compile
+ pushd src/python_scripts
+ distutils-r1_src_compile
+ popd
+}
+
+src_install() {
+ cmake_src_install
+ pushd src/python_scripts
+ distutils-r1_src_install
+ popd
+ cd "${D}"
+ rm usr/bin/mpeg_encode
+}
diff --git a/sci-biology/afni/afni-24.0.08.ebuild
b/sci-biology/afni/afni-24.0.08.ebuild
new file mode 100644
index 0..75ff5b6b6
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.08.ebuild
@@ -0,0 +1,115 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="http://stnava.github.io/ANTs/;
+SRC_URI="
+
[gentoo-commits] proj/sci:master commit in: dev-python/nptyping/
commit: 564661cd321e2a05582ea2d02ed2f27d740260b1 Author: Alexander Puck Neuwirth neuwirth-informatik de> AuthorDate: Tue Feb 27 20:10:18 2024 + Commit: Alexander Puck Neuwirth neuwirth-informatik de> CommitDate: Wed Feb 28 09:41:41 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=564661cd dev-python/nptyping: update maintainers Closes: https://bugs.gentoo.org/922385 Closes: https://github.com/gentoo/sci/pull/1252 Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de> dev-python/nptyping/metadata.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/dev-python/nptyping/metadata.xml b/dev-python/nptyping/metadata.xml index 8cbc6e175..45345f0dc 100644 --- a/dev-python/nptyping/metadata.xml +++ b/dev-python/nptyping/metadata.xml @@ -9,6 +9,7 @@ gen...@chymera.eu Horea Christian + nptyping ramonhagenaars/nptyping
[gentoo-commits] proj/sci:master commit in: sci-libs/mpfun90/
commit: 6207d8fa844029e500e904fa9060392dc0882238
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Feb 27 14:27:03 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Feb 27 16:11:48 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6207d8fa
sci-libs/mpfun90: new package, add 2023.02.26
Closes: https://github.com/gentoo/sci/pull/1250
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-libs/mpfun90/metadata.xml | 18 ++
sci-libs/mpfun90/mpfun90-2023.02.26.ebuild | 29 +
2 files changed, 47 insertions(+)
diff --git a/sci-libs/mpfun90/metadata.xml b/sci-libs/mpfun90/metadata.xml
new file mode 100644
index 0..e3eb0d9c1
--- /dev/null
+++ b/sci-libs/mpfun90/metadata.xml
@@ -0,0 +1,18 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ sci-phys...@gentoo.org
+ Gentoo Physics Project
+
+
+ This package permits one to perform floating-point computations (real
and complex) to arbitrarily high numeric precision
+
+
+ APN-Pucky/mpfun90
+
+
diff --git a/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild
b/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild
new file mode 100644
index 0..4f885fa2c
--- /dev/null
+++ b/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs fortran-2
+
+DESCRIPTION="High-Precision Software"
+HOMEPAGE="
+ https://www.davidhbailey.com/dhbsoftware/
+ https://github.com/APN-Pucky/mpfun90
+"
+MY_PV=$(ver_rs 1- '-')
+SRC_URI="https://github.com/APN-Pucky/mpfun90/archive/refs/tags/${MY_PV}.tar.gz;
+S="${WORKDIR}/mpfun90-${MY_PV}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+src_compile() {
+ emake -j1 dynamic
+}
+
+src_install() {
+ doheader *.mod
+ dolib.so libmpfun90.so
+ dolib.a libmpfun90.a
+}
[gentoo-commits] proj/sci:master commit in: sci-physics/collier/, sci-physics/collier/files/
commit: cc8a759de134ec89f2272ec173bc96c53e98594b
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Feb 27 14:17:47 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Feb 27 16:10:07 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=cc8a759d
sci-physics/collier: new package, add 1.2.8
Closes: https://github.com/gentoo/sci/pull/1249
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/collier/collier-1.2.8.ebuild | 36
sci-physics/collier/files/collier-1.2.7-mod.patch | 40 +++
sci-physics/collier/metadata.xml | 22 +
3 files changed, 98 insertions(+)
diff --git a/sci-physics/collier/collier-1.2.8.ebuild
b/sci-physics/collier/collier-1.2.8.ebuild
new file mode 100644
index 0..b50f9a279
--- /dev/null
+++ b/sci-physics/collier/collier-1.2.8.ebuild
@@ -0,0 +1,36 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+
+inherit fortran-2 cmake
+
+MY_P=COLLIER-${PV}
+
+DESCRIPTION="A Complex One-Loop LIbrary with Extended Regularizations"
+HOMEPAGE="https://collier.hepforge.org/index.html;
+SRC_URI="https://collier.hepforge.org/downloads/?f=${P}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="static-libs"
+BDEPEND="
+ virtual/fortran
+"
+PATCHES=(
+"${FILESDIR}/${PN}-1.2.7-mod.patch"
+)
+
+src_configure() {
+ local mycmakeargs=(
+ -Dstatic=$(usex static-libs ON OFF)
+ -DLIB_INSTALL_DIR="${EPREFIX}"/usr/$(get_libdir)
+
-DSYSCONFIG_INSTALL_DIR="${EPREFIX}"/usr/$(get_libdir)/cmake/collier
+ )
+ cmake_src_configure
+}
diff --git a/sci-physics/collier/files/collier-1.2.7-mod.patch
b/sci-physics/collier/files/collier-1.2.7-mod.patch
new file mode 100644
index 0..030900b5c
--- /dev/null
+++ b/sci-physics/collier/files/collier-1.2.7-mod.patch
@@ -0,0 +1,40 @@
+--- a/CMakeLists.txt 2023-05-08 17:21:39.559979698 +0200
b/CMakeLists.txt 2023-05-08 17:43:20.599147534 +0200
+@@ -282,7 +282,36 @@
+ message("Collier install include prefix: ${INCLUDE_INSTALL_DIR}")
+ message("Collier install library prefix: ${LIB_INSTALL_DIR}")
+
+-set(COLLIER_HEADERS "${CMAKE_Fortran_MODULE_DIRECTORY}/collier.mod")
++set(COLLIER_HEADERS "${CMAKE_Fortran_MODULE_DIRECTORY}/collier.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/cache.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/buildtensors.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/coli_aux2.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/coli_stat.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_aux.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_coefs.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_global.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_init.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_tensors.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/combinatorics.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_2pt.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_3pt.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_4pt.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_5pt.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_6pt.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_global.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_statistics.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/globalc.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/globald.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/inittensors.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/master.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductionab.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductionc.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductiond.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductionefg.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductiontn.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/tensorreduction.mod"
++)
+ set_target_properties(collier PROPERTIES PUBLIC_HEADER "${COLLIER_HEADERS}")
+
+ include(PackageConfigInstall)
diff --git a/sci-physics/collier/metadata.xml b/sci-physics/collier/metadata.xml
new file mode 100644
index 0..f863d8237
--- /dev/null
+++ b/sci-physics/collier/metadata.xml
@@ -0,0 +1,22 @@
+
+https://www.gentoo.org/dtd/metadata.dtd;>
+
+
+alexan...@neuwirth-informatik.de
+Alexander Puck Neuwirth
+
+
+sci-phys...@gentoo.org
+Gentoo Physics Project
+
+
+ A package for evaluation of scalar and tensor one-loop integrals
+ based on the FF package by G.J. van Oldenborgh.
+ It features an easy Fortran, C++, and Mathematica interface
+ to the scalar one-loop functions of FF and in addition provides
+ the 2-, 3-, and 4-point tensor coefficient functions.
+
[gentoo-commits] proj/sci:master commit in: dev-python/archspec/
commit: d339bf57b4986531b167e379c24097d613408faa
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Feb 27 13:55:11 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Feb 27 16:08:48 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d339bf57
dev-python/archspec: add 0.2.2
Co-authored-by: Andrew Nowa Ammerlaan gentoo.org>
Closes: https://github.com/gentoo/sci/pull/1244
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
dev-python/archspec/archspec-0.2.2.ebuild | 13 +
1 file changed, 13 insertions(+)
diff --git a/dev-python/archspec/archspec-0.2.2.ebuild
b/dev-python/archspec/archspec-0.2.2.ebuild
new file mode 100644
index 0..a7287fc72
--- /dev/null
+++ b/dev-python/archspec/archspec-0.2.2.ebuild
@@ -0,0 +1,13 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=poetry
+inherit distutils-r1 pypi
+
+DESCRIPTION="Labels for various aspects of a system architecture like CPU,
etc."
+HOMEPAGE="https://archspec.readthedocs.io/en/latest/index.html;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
[gentoo-commits] proj/sci:master commit in: dev-python/uhi/
commit: 5edb5364f5454e45df68b8fca3b621352e7905e8
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Feb 27 14:03:00 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Feb 27 16:07:10 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5edb5364
dev-python/uhi: new package, add 0.4.0
Closes: https://github.com/gentoo/sci/pull/1245
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
dev-python/uhi/metadata.xml | 19 +++
dev-python/uhi/uhi-0.4.0.ebuild | 27 +++
2 files changed, 46 insertions(+)
diff --git a/dev-python/uhi/metadata.xml b/dev-python/uhi/metadata.xml
new file mode 100644
index 0..c1ee047a1
--- /dev/null
+++ b/dev-python/uhi/metadata.xml
@@ -0,0 +1,19 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ This is a package meant primarily for documenting histogram indexing
and the PlottableHistogram Protocol and any future cross-library standards. It
also contains the code for the PlottableHistogram Protocol, to be used in type
checking libraries wanting to conform to the protocol. Eventually, it might
gain a set of tools for testing conformance to UHI indexing, as well. It is not
usually a runtime dependency, but only a type checking, testing, and/or docs
dependency in support of other libraries (such as boost-histogram 0.13+, hist
2.1+, mplhep 0.2.15+, uproot 4+, and histoprint 2+). There are a few useful
runtime usable components (listed below). It requires Python 3.6+. See what's
new.
+
+
+ uhi
+ scikit-hep/uhi
+
+
diff --git a/dev-python/uhi/uhi-0.4.0.ebuild b/dev-python/uhi/uhi-0.4.0.ebuild
new file mode 100644
index 0..89db57b1c
--- /dev/null
+++ b/dev-python/uhi/uhi-0.4.0.ebuild
@@ -0,0 +1,27 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=hatchling
+SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+inherit distutils-r1 pypi
+
+DESCRIPTION="Universal Histogram Interface"
+HOMEPAGE="https://github.com/scikit-hep/uhi;
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+ test? (
+ dev-python/pytest[${PYTHON_USEDEP}]
+ dev-python/boost-histogram[${PYTHON_USEDEP}]
+ )
+"
+BDEPEND="
+ ${RDEPEND}
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: sci-physics/apfelxx/
commit: fded3a905e1414233d7d90fe95ad7e2affdc1bdb
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Feb 27 14:08:07 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Feb 27 15:30:41 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=fded3a90
sci-physics/apfelxx: new package, add 4.8.0
Closes: https://github.com/gentoo/sci/pull/1247
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
sci-physics/apfelxx/apfelxx-4.8.0.ebuild | 39
sci-physics/apfelxx/metadata.xml | 18 +++
2 files changed, 57 insertions(+)
diff --git a/sci-physics/apfelxx/apfelxx-4.8.0.ebuild
b/sci-physics/apfelxx/apfelxx-4.8.0.ebuild
new file mode 100644
index 0..d31224fa3
--- /dev/null
+++ b/sci-physics/apfelxx/apfelxx-4.8.0.ebuild
@@ -0,0 +1,39 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit cmake python-single-r1
+
+DESCRIPTION="Object oriented rewriting of the APFEL evolution code"
+HOMEPAGE="https://github.com/vbertone/apfelxx;
+SRC_URI="https://github.com/vbertone/apfelxx/archive/${PV}.tar.gz ->
${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+RDEPEND="${PYTHON_DEPS}"
+
+src_prepare() {
+ default
+ cmake_src_prepare
+ sed -i "/prefix./s/\/lib/\/$(get_libdir)/g" CMakeLists.txt || die
+ sed -i "s#DESTINATION lib#DESTINATION $(get_libdir)#g" CMakeLists.txt
|| die
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DCMAKE_INSTALL_PREFIX="${EPREFIX}"/usr
+ )
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+ python_optimize
+}
diff --git a/sci-physics/apfelxx/metadata.xml b/sci-physics/apfelxx/metadata.xml
new file mode 100644
index 0..27c6de8e1
--- /dev/null
+++ b/sci-physics/apfelxx/metadata.xml
@@ -0,0 +1,18 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ alexan...@neuwirth-informatik.de
+ Alexander Puck Neuwirth
+
+
+ sci-phys...@gentoo.org
+ Gentoo Physics Project
+
+
+ APFEL++ is a C++ rewriting of the Fortran 77 evolution code APFEL.
However, APFEL++ is based on a completely new code design and guarantees a
better performance along with a more optimal memory management. The new modular
structure allows for better maintainability and easier extensibility. This
makes APFEL++ suitable for a wide range of tasks: from the solution of the
DGLAP evolution equations to the computation of deep-inelastic-scattering (DIS)
and single-inclusive-annihilation cross sections. Also more complex
computations, such as differential semi-inclusive DIS and Drell-Yan cross
sections, are easily implementable in APFEL++.
+
+
+ vbertone/apfelxx
+
+
[gentoo-commits] proj/sci:master commit in: profiles/desc/, sci-physics/lhapdf-sets/
commit: d21400c2bb5b7d9f213047df109b7d40fde8e8a8
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Feb 27 14:14:36 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Feb 27 15:29:14 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d21400c2
sci-physics/lhapdf-sets: Add more PDFs
Closes: https://github.com/gentoo/sci/pull/1248
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
profiles/desc/lhapdf_sets.desc | 4 +++-
sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild | 6 +-
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/profiles/desc/lhapdf_sets.desc b/profiles/desc/lhapdf_sets.desc
index 7270fbee7..66da0763c 100644
--- a/profiles/desc/lhapdf_sets.desc
+++ b/profiles/desc/lhapdf_sets.desc
@@ -14,4 +14,6 @@ nnpdf23_nlo_as_0119_qed_mc - NNPDF23_nlo_as_0119_qed_mc
LHAPDF grid
nnpdf23_nnlo_as_0119_qed_mc - NNPDF23_nnlo_as_0119_qed_mc LHAPDF grid
cteq66 - CTEQ66 LHAPDF grid
cteq6l1 - CTEQ6L1 LHAPDF grid
-mrst2004qed - MRST2004qed LHAPDF grid
\ No newline at end of file
+mrst2004qed - MRST2004qed LHAPDF grid
+nnpdf23_nlo_as_0118 - nnpdf23_nlo_as_0118 grid
+nnpdf31_nnlo_as_0118 - nnpdf31_nnlo_as_0118 grid
\ No newline at end of file
diff --git a/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
index edd3639d2..784d94f97 100644
--- a/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
+++ b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
@@ -17,6 +17,8 @@ IUSE_LHAPDF_SETS="
lhapdf_sets_cteq66
lhapdf_sets_cteq6l1
lhapdf_sets_mrst2004qed
+ lhapdf_sets_nnpdf23_nlo_as_0118
+ lhapdf_sets_nnpdf31_nnlo_as_0118
"
COMMON_URI="https://lhapdfsets.web.cern.ch/lhapdfsets/current;
@@ -36,7 +38,9 @@ SRC_URI="
lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc? (
${COMMON_URI}/NNPDF23_nnlo_as_0119_qed_mc.tar.gz )
lhapdf_sets_cteq66? ( ${COMMON_URI}/cteq66.tar.gz
)
lhapdf_sets_cteq6l1? ( ${COMMON_URI}/cteq6l1.tar.gz
)
- lhapdf_sets_mrst2004qed? (
${HEPFORGE_URI}/MRST2004qed.tar.gz )
+ lhapdf_sets_mrst2004qed? (
${HEPFORGE_URI}/MRST2004qed.tar.gz )
+ lhapdf_sets_nnpdf23_nlo_as_0118? (
${COMMON_URI}/NNPDF23_nlo_as_0118.tar.gz )
+ lhapdf_sets_nnpdf31_nnlo_as_0118?(
${COMMON_URI}/NNPDF31_nnlo_as_0118.tar.gz)
"
MY_PV=$(ver_cut 1-3)
