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Commit e31ebba0 authored by Alexander Schoch's avatar Alexander Schoch
Browse files

Merge branch 'master' of gitlab.ethz.ch:thealternative/courses

merge
parents a9f88eac b7cd1042
<html>
<body>
<h1>Hallo Welt</h1>
<h2>Hallo Welt</h2>
</body>
</html>
\ No newline at end of file
@conference{repsep,
author = {Horea-Ioan Ioanas and Markus Rudin},
title = {Reproducible Self-Publishing for {P}ython-Based Research},
year = 2018,
month = aug,
publisher = {EuroSciPy},
url = {https://figshare.com/articles/Reproducible_Self-Publishing_for_Python-Based_Research/7247339},
doi = {10.6084/m9.figshare.7247339.v1},
}
@article{Ioanas2017,
author = {Horea-Ioan Ioanas and Bechara Saab and Markus Rudin},
title = {Gentoo Linux for Neuroscience - a replicable, flexible, scalable, rolling-release environment that provides direct access to development software},
volume = {3},
number = {},
year = {2017},
doi = {10.3897/rio.3.e12095},
publisher = {Pensoft Publishers},
abstract = {},
issn = {},
pages = {e12095},
URL = {https://doi.org/10.3897/rio.3.e12095},
eprint = {https://doi.org/10.3897/rio.3.e12095},
journal = {Research Ideas and Outcomes}
}
#!/usr/bin/env bash
pdflatex -shell-escape slides.tex
bibtex slides
pdflatex -shell-escape slides.tex
pdflatex -shell-escape slides.tex
#!/usr/bin/env bash
wget https://raw.githubusercontent.com/IBT-FMI/SAMRI/master/setup.py -O samri/setup.py
# reset the system
rm -rf /var/db/repos/chymeric/
emerge -C samri
eix-sync
# reset the overlay repo
cd overlay/location/with/Chymera/account
git reset --hard commitwhichwasbeforethepull
git push -f origin master
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>chr@chymera.eu</email>
<name>Horea Christian</name>
</maintainer>
<longdescription lang="en">
SAMRI (Small Animal Magnetic Resonance Imaging) — pronounced "Sam-rye" — provides
fMRI preprocessing, metadata parsing, and data analysis functions and workflows.
SAMRI integrates functionalities from a number of other packages to create
higher-level tools. The resulting interfaces aim to maximize reproducibility,
simplify batch processing, and minimize the number of function calls required to
generate figures and statistical summaries from the raw data.
</longdescription>
<upstream>
<remote-id type="github">IBT-FMI/SAMRI</remote-id>
</upstream>
</pkgmetadata>
# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
PYTHON_COMPAT=( python{3_5,3_6} )
inherit distutils-r1
DESCRIPTION="Small Animal Magnetic Resonance Imaging"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
IUSE="test"
KEYWORDS="~amd64 ~x86"
DEPEND="
test? (
dev-python/pytest[${PYTHON_USEDEP}]
sci-biology/samri_bidsdata
sci-biology/samri_bindata
)
"
RDEPEND="
dev-python/argh[${PYTHON_USEDEP}]
dev-python/joblib[${PYTHON_USEDEP}]
>=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}]
>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/seaborn[${PYTHON_USEDEP}]
dev-python/statsmodels[${PYTHON_USEDEP}]
media-gfx/blender
>=sci-biology/fsl-5.0.9
sci-biology/bru2nii
sci-biology/mouse-brain-atlases
sci-libs/nibabel[${PYTHON_USEDEP}]
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-0.14.0_pre20170830[${PYTHON_USEDEP}]
<=sci-libs/pybids-0.6.5[${PYTHON_USEDEP}]
sci-libs/scikits_image[${PYTHON_USEDEP}]
sci-libs/scipy[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
"
S="${WORKDIR}/SAMRI-${PV}"
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