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Commit e31ebba0 authored by Alexander Schoch's avatar Alexander Schoch
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Merge branch 'master' of gitlab.ethz.ch:thealternative/courses 

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parents a9f88eac b7cd1042
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.gitignore 0 → 100644
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# LaTeX traces
*.log
*.toc
*.aux
*.out
*-blx.bib
*run.xml
*.fdb_latexmk
*.fls
*.synctex.gz
*.snm
*.nav
# Bibtex traces
*.bak
*.blg
*.bbl
# PythonTeX traces and binaries
pythontex-*/
*.pytxcode
# Gedit
*~
.style/header.tex
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\documentclass[aspectratio=169]{beamer} \documentclass[aspectratio=169]{beamer}
\usepackage[T1]{fontenc} %pipes don't display properly without this \usepackage[T1]{fontenc} % the pipe character doesn't display properly without this
\usepackage[utf8]{inputenc} \usepackage[utf8]{inputenc}
\usepackage{listings} \usepackage{listings}
\usepackage{color} \usepackage{color}
\usepackage{datapie} \usepackage{datapie}
\usepackage{minted} % COMPILE WITH `pdflatex -shell-escape`!
\usepackage{multicol} \usepackage{multicol}
\usepackage{upgreek} \usepackage{upgreek}
\usepackage{siunitx} %pretty measurement unit rendering \usepackage{siunitx} % pretty measurement unit rendering
\usepackage{hyperref} %enable hyperlink for urls \usepackage{hyperref} % enable hyperlink for URLs
\usepackage{lmodern} \usepackage{lmodern}
\usepackage{setspace} \usepackage{setspace}
\usepackage[os=win]{menukeys} % by default keys are given for MacOS
\usefonttheme[onlymath]{serif} \usefonttheme[onlymath]{serif}
\setcounter{MaxMatrixCols}{20} \setcounter{MaxMatrixCols}{20}
...@@ -26,9 +28,9 @@ ...@@ -26,9 +28,9 @@
%Define generic colors %Define generic colors
\definecolor{slg}{gray}{0.25} \definecolor{slg}{gray}{0.25}
\definecolor{lg}{gray}{0.55} \definecolor{lg}{gray}{0.53}
\definecolor{vlg}{gray}{0.73} \definecolor{vlg}{gray}{0.73}
\definecolor{tlg}{gray}{0.9} \definecolor{tlg}{gray}{0.91}
%Define data colors %Define data colors
\definecolor{mygreen}{rgb}{0,0.6,0} \definecolor{mygreen}{rgb}{0,0.6,0}
......
git_gitlab_course/boilerplate-single.html 0 → 100644
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git_gitlab_course/outline.txt 0 → 100644
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git /gitlab tutorial planned for UZH zentrale informatik
target group:
bachelor informatik
master/phd students
both mostly want to use git with code or latex
targets:
version control (backup, recover old state, make changes visible)
publish (how, which license)
contribute (work together on same project)
structure:
presentation and then practical examples for each topic
for each topic add link/resource to more advanced explanations
motivation 10'/5':
demonstrate how git can recover files and make visible who changed what
explain service provider benefits (backup, collaboration)
ask what interest of participants are to focus advanced topics
git intro 5'/15':
install git
create first local repository
do first commit
show it worked with git status / git log
remote intro 10'/30':
create repository online
do steps of git global config on welcome screen
do steps of create new repository on welcome screen
edit Readme to learn about markdown
do add license on gitlab webpage
git GUI client 5'/15':
install github desktop
open repo & do commit
sync with push/pull
view changes of previous commits
advanced topics sorted by preference (each around 20'):
create branch & merge request
create issue & mention it in commit
fork & merge back into origin
add different remotes
use SSH key
resources considered:
compicampus course gives a good overview, but not suitable structured
git-scm.com has many advanced resources
git boot on git-scm.com has many advanced resources
cheatsheet github
"git for ages 4 and up" (well made youtube tutorial)
personal experience
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git_gitlab_course/remark-latest.min.js 0 → 100644
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git_gitlab_course/template.html 0 → 100644
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<html>
<body>
<h1>Hallo Welt</h1>
<h2>Hallo Welt</h2>
</body>
</html>
\ No newline at end of file
scientific_software_management/bib.bib 0 → 100644
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@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}
}
scientific_software_management/compile.sh 0 → 100755
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#!/usr/bin/env bash
pdflatex -shell-escape slides.tex
bibtex slides
pdflatex -shell-escape slides.tex
pdflatex -shell-escape slides.tex
scientific_software_management/get_samri_data.sh 0 → 100755
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#!/usr/bin/env bash
wget https://raw.githubusercontent.com/IBT-FMI/SAMRI/master/setup.py -O samri/setup.py
scientific_software_management/reset_system.sh 0 → 100644
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# 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
scientific_software_management/samri/metadata.xml 0 → 100644
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<?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>
scientific_software_management/samri/samri-0.4.ebuild 0 → 100644
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# 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}"
scientific_software_management/samri/setup.py 0 → 100644
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from setuptools import setup, find_packages
packages = find_packages(exclude=('samri.tests*', 'samri.*.tests*'))
setup(
name="SAMRI",
version="9999",
description = "Small animal magnetic resonance imaging via Python.",
author = "Horea Christian",
author_email = "chr@chymera.eu",
url = "https://github.com/IBT-FMI/SAMRI",
keywords = ["fMRI", "pipelines", "data analysis", "bruker"],
classifiers = [],
install_requires = [],
provides = ["samri"],
packages = packages,
include_package_data=True,
extras_require = {
},
entry_points = {'console_scripts' : \
['SAMRI = samri.cli:main']
},
)
scientific_software_management/slides.tex 0 → 100644
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