From c43d1bcc885b057b5d2150135f814bb848a027c4 Mon Sep 17 00:00:00 2001 From: Brianna Yao Date: Fri, 4 Dec 2020 21:23:01 -0500 Subject: [PATCH 1/3] sci-biology/rat-brain-atlases: New package ahead of Gentoo Science --- sci-biology/rat-brain-atlases/Manifest | 1 + sci-biology/rat-brain-atlases/metadata.xml | 16 ++++++++++++ .../rat-brain-atlases-0.1.ebuild | 25 +++++++++++++++++++ 3 files changed, 42 insertions(+) create mode 100644 sci-biology/rat-brain-atlases/Manifest create mode 100644 sci-biology/rat-brain-atlases/metadata.xml create mode 100644 sci-biology/rat-brain-atlases/rat-brain-atlases-0.1.ebuild diff --git a/sci-biology/rat-brain-atlases/Manifest b/sci-biology/rat-brain-atlases/Manifest new file mode 100644 index 0000000..7128c17 --- /dev/null +++ b/sci-biology/rat-brain-atlases/Manifest @@ -0,0 +1 @@ +DIST rat-brain-atlases-0.1.tar.xz 4784449120 SHA256 8bf10b2737ebacf2658b09a97a76455775e1b86aedaa2bef3fd538e960fc5310 SHA512 0fbd4991bbf8767029ca0aac456b48926b6e02f6d1a35ba462502ec41242ed9bc1c1827ad28e32518d024c84d71baca54148f38420980a4da2193de92e29aaf0 WHIRLPOOL cdba1192810adf1d34c93f0084fc99abc83a6ee9a0b5cf641da3b108759af4ffafeefa49e25e5635be4d54630813b7cf1ed7c4ade0fc347c2416ac572db8d734 diff --git a/sci-biology/rat-brain-atlases/metadata.xml b/sci-biology/rat-brain-atlases/metadata.xml new file mode 100644 index 0000000..89c34d5 --- /dev/null +++ b/sci-biology/rat-brain-atlases/metadata.xml @@ -0,0 +1,16 @@ + + + + + horea.christ@gmail.com + Horea Christian + + + sci@gentoo.org + Gentoo Science Project + + + Digital rat brain atlases in NIfTI format for use in magnetic + resonance rat brain imaging. + + diff --git a/sci-biology/rat-brain-atlases/rat-brain-atlases-0.1.ebuild b/sci-biology/rat-brain-atlases/rat-brain-atlases-0.1.ebuild new file mode 100644 index 0000000..c8c189f --- /dev/null +++ b/sci-biology/rat-brain-atlases/rat-brain-atlases-0.1.ebuild @@ -0,0 +1,25 @@ +# Copyright 2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +DESCRIPTION="A collection of rat brain atlases in NIfTI format" +HOMEPAGE="https://github.com/IBT-FMI/rat-brain-atlases" +SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz" + +LICENSE="fairuse" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +pkg_pretend() { + CHECKREQS_DISK_BUILD="42G" + check-reqs_pkg_pretend +} + +# We disable this phase to not check requirements twice. +pkg_setup() { :; } + +src_install() { + insinto "/usr/share/${PN}" + doins * +} From 9012867b6c3082ef1598c8f2b3c2333c52b38e35 Mon Sep 17 00:00:00 2001 From: Jimmy2027 Date: Mon, 7 Dec 2020 09:51:38 +0100 Subject: [PATCH 2/3] added torchio ebuild --- sci-libs/torchio/Manifest | 1 + sci-libs/torchio/metadata.xml | 20 ++++++++++++++ sci-libs/torchio/torchio-0.17.42.ebuild | 36 +++++++++++++++++++++++++ 3 files changed, 57 insertions(+) create mode 100644 sci-libs/torchio/Manifest create mode 100644 sci-libs/torchio/metadata.xml create mode 100644 sci-libs/torchio/torchio-0.17.42.ebuild diff --git a/sci-libs/torchio/Manifest b/sci-libs/torchio/Manifest new file mode 100644 index 0000000..14bbf75 --- /dev/null +++ b/sci-libs/torchio/Manifest @@ -0,0 +1 @@ +DIST torchio-0.17.42.tar.gz 23194366 SHA256 afc1a26c61cdaabd34bc44992a0afa72c2130a1d8aa509bdbe7326c4e6546caa SHA512 c6a2696a2b76d3699eb47f77ce490f0aff4aea93bf4d6e64a2bf96801d098f9e898a7f6dd657581aadb3f7edb46f40c1676a31c2c6ded14a38f9457536c07d1e WHIRLPOOL 47733cc96b417a0b2c401a6b98600955a8ff003edc42e50cf328151631a74decac3a3a8dfcdc30be3d6a687b9240a5b9fe8d8e18c8f4a1b3c743918d0627f6b7 diff --git a/sci-libs/torchio/metadata.xml b/sci-libs/torchio/metadata.xml new file mode 100644 index 0000000..3c4ca9a --- /dev/null +++ b/sci-libs/torchio/metadata.xml @@ -0,0 +1,20 @@ + + + + + klugh@ethz.ch + Hendrik Klug + + + TorchIO is a Python package containing a set of tools to efficiently read, + preprocess, sample, augment, and write 3D medical images in deep learning + applications written in PyTorch, including intensity and spatial transforms + for data augmentation and preprocessing. Transforms include typical computer + vision operations such as random affine transformations and also + domain-specific ones such as simulation of intensity artifacts due to MRI + magnetic field inhomogeneity or k-space motion artifacts. + + + fepegar/torchio + + diff --git a/sci-libs/torchio/torchio-0.17.42.ebuild b/sci-libs/torchio/torchio-0.17.42.ebuild new file mode 100644 index 0000000..b72e79e --- /dev/null +++ b/sci-libs/torchio/torchio-0.17.42.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{6,7,8} ) +DISTUTILS_SINGLE_IMPL=1 +DISTUTILS_USE_SETUPTOOLS=rdepend + +inherit distutils-r1 + +DESCRIPTION="A set of tools to efficiently read, preprocess, sample, augment, and write 3D medical images in deep learning applications." +HOMEPAGE="https://torchio.readthedocs.io/" +SRC_URI="https://github.com/fepegar/torchio/archive/v${PV}.tar.gz -> ${P}.tar.gz" +KEYWORDS="~amd64 ~x86" +LICENSE="MIT license" +SLOT="0" +IUSE="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" +DEPEND=" + $(python_gen_cond_dep ' + dev-python/click[${PYTHON_USEDEP}] + dev-python/humanize[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/deprecation[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + >=sci-libs/pytorch-1.1[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + ') + sci-libs/simpleitk[${PYTHON_SINGLE_USEDEP}] +" + +RDEPEND="${DEPEND}" + +distutils_enable_tests pytest From 27ef48d0f80bc8dc38be252f224504195a2058bf Mon Sep 17 00:00:00 2001 From: Jimmy2027 Date: Wed, 9 Dec 2020 08:51:59 +0100 Subject: [PATCH 3/3] added norby package --- dev-python/norby/metadata.xml | 14 ++++++++++++++ dev-python/norby/norby-9999.ebuild | 30 ++++++++++++++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 dev-python/norby/metadata.xml create mode 100644 dev-python/norby/norby-9999.ebuild diff --git a/dev-python/norby/metadata.xml b/dev-python/norby/metadata.xml new file mode 100644 index 0000000..aea2d79 --- /dev/null +++ b/dev-python/norby/metadata.xml @@ -0,0 +1,14 @@ + + + + + klugh@ethz.ch + Hendrik Klug + + + Get notified via a telegram bot when your bash command finished. + + + Jimmy2027/NORBY + + diff --git a/dev-python/norby/norby-9999.ebuild b/dev-python/norby/norby-9999.ebuild new file mode 100644 index 0000000..362e266 --- /dev/null +++ b/dev-python/norby/norby-9999.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{7..9} ) + +inherit distutils-r1 +inherit git-r3 + +DESCRIPTION="Get notified via a telegram bot when your bash command finished." +HOMEPAGE="https://github.com/Jimmy2027/NORBY" +#SRC_URI="https://github.com/Jimmy2027/NORBY/archive/${PV}.tar.gz -> ${P}.tar.gz" +EGIT_REPO_URI="https://github.com/Jimmy2027/NORBY.git" +KEYWORDS="~amd64 ~x86" +LICENSE="GNU General Public License v3.0" +SLOT="0" +DEPEND=" + dev-python/requests + " + +RDEPEND="${DEPEND}" + +src_unpack() { + git-r3_src_unpack +} + +python_install_all() { + distutils-r1_python_install_all +}