diff --git a/.style/header.tex b/.style/header.tex
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--- a/.style/header.tex
+++ b/.style/header.tex
@@ -4,6 +4,7 @@
\usepackage{listings}
\usepackage{color}
\usepackage{datapie}
+\usepackage{minted} % COMPILE WITH `pdflatex -shell-escape`!
\usepackage{multicol}
\usepackage{upgreek}
\usepackage{siunitx} %pretty measurement unit rendering
diff --git a/scientific_software_management/bib.bib b/scientific_software_management/bib.bib
new file mode 100644
index 0000000000000000000000000000000000000000..7e849df66e429d8b20b69f5e5ef8f5aa055d7266
--- /dev/null
+++ b/scientific_software_management/bib.bib
@@ -0,0 +1,24 @@
+@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}
+}
diff --git a/scientific_software_management/compile.sh b/scientific_software_management/compile.sh
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index 0000000000000000000000000000000000000000..98994fc17209800b73164fdeee7c8179891bca64
--- /dev/null
+++ b/scientific_software_management/compile.sh
@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+pdflatex -shell-escape slides.tex
+bibtex slides
+pdflatex -shell-escape slides.tex
+pdflatex -shell-escape slides.tex
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diff --git a/scientific_software_management/slides.tex b/scientific_software_management/slides.tex
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+++ b/scientific_software_management/slides.tex
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+\input{../.style/header}
+
+\title{Software Management for Open Science}
+\author{Horea Christian}
+\institute{SSC TheAlternative | ETHZ and UZH}
+
+\begin{document}
+ \begin{frame}
+ \titlepage
+ \end{frame}
+ \begin{frame}{These Slides}
+ Type one link, click all others:
+ \begin{itemize}
+ \item Download \textcolor{lg}{\href{http://chymera.eu/pres/ld_packaging-sci/pres.pdf}{\texttt{chymera.eu/pres/ld\_foss/pres.pdf}}}
+ \end{itemize}
+ \end{frame}
+ \section{Requirements}
+ \subsection{... for the Demo Session}
+ \begin{frame}{SSH}
+ Linux and MacOS:
+ \begin{itemize}
+ \item check that you can run
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|ssh userXX@130.60.24.172|
+ \end{itemize}
+ Windows:
+ \begin{itemize}
+ \item Download and launch “Git for Windows†from \textcolor{lg}{\href{https://git-for-windows.github.io}{\texttt{git-for-windows.github.io}}}
+ \item check that you can run
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|ssh userXX@130.60.24.172|
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{GitHub Account}
+ GitHub is a \textbf{social coding platform} providing free accounts:
+ \begin{itemize}
+ \item Register under \textcolor{lg}{\href{https://github.com}{\texttt{github.com}}}
+ \end{itemize}
+ \end{frame}
+ \section{What?}
+ \subsection{What is Packaging?}
+ \begin{frame}{The Package}
+ A package is a software format which is (easily):
+ \begin{itemize}
+ \item distributable (i.e. installable)
+ \item integrated
+ \item testable
+ \item updateable
+ \item uninstallable
+ \item understandable
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Package Management --- best done automatically}
+ \begin{minipage}{0.44\textwidth}
+ Packages interact in complex and nontrivial manners:
+ \begin{itemize}
+ \item architecture requirements
+ \item dependencies (incl. blockers, version-dependent behaviour, static/dynamic linking)
+ \end{itemize}
+ \end{minipage}
+ \begin{minipage}{0.55\textwidth}
+ \begin{figure}
+ \includegraphics[height=0.83\textheight]{img/ng_mi.png}
+ \vspace{-1em}
+ \caption{Minimal neuroscience package dependency stack \cite{Ioanas2017}}
+ \end{figure}
+ \end{minipage}
+ \end{frame}
+ \begin{frame}{Binary Packages}
+ \begin{figure}
+ \centering
+ \includegraphics[width=0.9\textwidth]{img/pm_d.png}
+ \caption{Rudimentary overview of binary package distribution workflow.}
+ \end{figure}
+ \begin{columns}
+ \column{.5\linewidth}
+ Advantages:
+ \begin{itemize}
+ \item Faster installation
+ \item More reproducible installation
+ \end{itemize}
+ \column{.5\linewidth}
+ Disadvantages:
+ \begin{itemize}
+ \item No access to live software
+ \item Man-in-the middle
+ \item Limited support for rolling release
+ \end{itemize}
+ \end{columns}
+ \end{frame}
+ \begin{frame}{Source Packages}
+ \begin{figure}
+ \centering
+ \includegraphics[width=0.9\textwidth]{img/pm_g.png}
+ \caption{Rudimentary overview of source distribution workflow.}
+ \end{figure}
+ \begin{columns}
+ \column{.5\linewidth}
+ Advantages:
+ \begin{itemize}
+ \item Live software is a first-class citizen
+ \item Thin wrapper for upstream
+ \item Acutely version and linking aware
+ \end{itemize}
+ \column{.5\linewidth}
+ Disadvantages:
+ \begin{itemize}
+ \item Slower installation
+ \item More variable installation
+ \end{itemize}
+ \end{columns}
+ \end{frame}
+ \section{Why?}
+ \subsection{Why Package my Software?}
+ \begin{frame}{Recognition}
+ \begin{itemize}
+ \item Establish proof of authorship.
+ \item Publicize your innovative workflows, solutions, data structures.
+ \item Create a handle for attribution (including DOI), e.g:
+ \begin{itemize}
+ \item BehavioPy: \textcolor{lg}{\href{http://doi.org/10.5281/zenodo.188169}{\texttt{10.5281/zenodo.188169}}}
+ \item Nipype: \textcolor{lg}{\href{http://doi.org/10.5281/zenodo.50186}{\texttt{10.5281/zenodo.50186}}}
+ \end{itemize}
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Impact}
+ \begin{itemize}
+ \item Reach more potential users.
+ \item Communicate with users to improve your software's usability.
+ \item Retain more users.
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Quality}
+ \begin{itemize}
+ \item Make development more transparent.
+ \item Get \textbf{constructive} feedback.
+ \item Ask for help with concrete reproducible examples.
+ \item Easily manage \textcolor{lg}{\href{https://github.com/gentoo-science/sci/issues}{\texttt{bugs/issues}}} and \textcolor{lg}{\href{https://github.com/gentoo-science/sci/pulls}{\texttt{conributions}}}.
+ \item Implement proper version tracking.
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Sustainability}
+ \begin{itemize}
+ \item Avoid death-by-PhD.
+ \item Ensure long-term availability of your software.
+ \item Give your funding bodies their money's worth.
+ \item Develop a lean start-up.
+ \item Maintain a sustainable and affordable infrastructure for your business/employer.
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Why Not?}
+ \begin{itemize}
+ \item Don't be afraid of your software not being “good/unique enoughâ€!
+ \item Don't be wait until your software is “readyâ€!
+ \item A lot of research software you are already using is not written by “professional†programmers.
+ \end{itemize}
+ \end{frame}
+ \section{How?}
+ \subsection{How Do I Package my Software?}
+ \begin{frame}{Choose an Environment}
+ \begin{columns}
+ \column{.5\linewidth}
+ \begin{figure}
+ \centering
+ \includegraphics[width=0.6\textwidth]{img/gentoo.png}
+ \caption{Gentoo Linux Logo by Gentoo Foundation and Lennart Andre Rolland - CC BY-SA/2.5.}
+ \end{figure}
+ \column{.5\linewidth}
+ \begin{figure}
+ \centering
+ \includegraphics[width=0.6\textwidth]{img/python.png}
+ \caption{Python Logo by Python Software Foundation.}
+ \end{figure}
+ \end{columns}
+ \end{frame}
+ \begin{frame}{Reposit Your Software}
+ \begin{itemize}
+ \item Bitbucket
+ \item GitHub
+ \item GitLab
+ \item ...
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Python Package Distribution}
+ \begin{columns}
+ \column{.4\linewidth}
+ You can package your python software by writing \textbf{one short} file.
+ \begin{itemize}
+ \item Python provides its own package management, e.g. via \textcolor{lg}{\href{https://packaging.python.org/distributing/}{\texttt{setuptools}}}.
+ \item Package metadata saved in \texttt{setup.py}, e.g. \textcolor{lg}{\href{https://github.com/IBT-FMI/SAMRI/blob/master/setup.py}{\texttt{SAMRI/setup.py}}}
+ \end{itemize}
+ \column{.6\linewidth}
+ \begin{figure}
+ \centering
+ \includegraphics[width=0.9\textheight]{img/sp.png}
+ \end{figure}
+ \end{columns}
+ \end{frame}
+ \begin{frame}{Gentoo Packages}
+ \begin{columns}
+ \column{.4\linewidth}
+ You can package your software for Gentoo by writing \textbf{one short} file.
+ \begin{itemize}
+ \item Gentoo packages metadata/instruction text files
+ \item The Gentoo package manager understands external package management formats, e.g. as seen in \textcolor{lg}{\href{https://github.com/TheChymera/overlay/blob/master/sci-biology/samri/samri-9999.ebuild}{\texttt{=sci-biology/samri-9999}}}
+ \end{itemize}
+ \column{.6\linewidth}
+ \begin{figure}
+ \centering
+ \includegraphics[width=0.7\textheight]{img/eb.png}
+ \end{figure}
+ \end{columns}
+ \end{frame}
+ \section{Demo}
+ \subsection{Put what you have learned into practice, and start typing...}
+ \begin{frame}{A Few Basic Gentoo Commands}
+ \begin{itemize}
+ \item check available package names, versions, and details
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|eix samri|
+ \item see package dependencies
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|equery g samri|
+ \item see what packages depend on a said package
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|equery d nipype|
+ \item try to install a new package
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|emerge -p =nilearn-0.1.4.1|
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Reproduce a Scientific Article}
+ Novel frameworks, such as RepSeP \cite{repsep} permit articles to be written as software.
+ \begin{itemize}
+ \item Get the source code for brand-new articles:
+ \begin{itemize}
+ \item Work-in-progress (reexecution time \SI{\approx 3}{\second})
+ \vspace{-0.5em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git clone https://gitlab.com/Chymera/nvcz.git |
+ \item Preprint (reexecution time \SI{\approx 2}{\minute})
+ \vspace{-0.5em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git clone git clone https://bitbucket.org/TheChymera/irsabi.git |
+ \end{itemize}
+ \item Switch to article directory
+ \vspace{-0.5em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|cd nvcz|
+ \item Attempt to reexecute
+ \vspace{-0.5em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|./compile.sh|
+ %\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git chechout 28b5d2d1|
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{What happened? Dependency requirements happened.}
+ Write a new package atom for the package manager.
+ \begin{itemize}
+ \item Gentoo Linux makes this wholly autonomous.
+ \item Solve one problem only once:
+ \begin{itemize}
+ \item Installation will be automatic on all your further systems.
+ \item And on everybody else's systems!
+ \end{itemize}
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Write an ebuild}
+ \begin{itemize}
+ \Item Fork an overlay on GitHub.
+ \textcolor{lg}{\href{https://github.com/TheChymera/overlay}{\texttt{github.com/TheChymera/overlay}}}
+ \item Go back to your home directory.
+ \vspace{-0.5em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|cd|
+ \item Clone your fork of the overlay.
+ \vspace{-0.5em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git clone https://github.com/TheChymera/overlay.git|
+ \item Clone your fork of the overlay.
+ \vspace{-0.5em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git clone https://github.com/TheChymera/overlay.git|
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Write Packaged Free and Open Source Scientific Software}
+ \begin{enumerate}
+ \item correct URL in \textcolor{lg}{\href{https://github.com/IBT-FMI/SAMRI/blob/master/setup.py}{\texttt{SAMRI/setup.py}}}
+ \item Add notice of dependency on nilearn in \textcolor{lg}{\href{https://github.com/IBT-FMI/SAMRI/blob/master/README.md}{\texttt{SAMRI/README.md}}}
+ \item Add notice of dependency on nilearn in \textcolor{lg}{\href{https://github.com/TheChymera/overlay/blob/master/sci-biology/samri/samri-9999.ebuild}{\texttt{=sci-biology/samri-9999}}}
+ \item Remove \texttt{dcmstack} import and dependency from the SAMRI source and the Gentoo SAMRI package
+ \end{enumerate}
+ \end{frame}
+
+
+ \section{Meta}
+ \subsection{About this presentation}
+ \begin{frame}{What now?}
+ \begin{itemize}
+ \item Q\&A round\\
+ \textcolor{lg}{in a few seconds}
+ \item Get help packaging your own Free and Open Source Scientific Software\\
+ \textcolor{lg}{in a few minutes}
+ \item Get help with running your own Gentoo Linux data analysis server\\
+ \textcolor{lg}{in a few hours}
+ \item Spread the word\\
+ \textcolor{lg}{tomorrow at work}
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{These Slides}
+ \begin{itemize}
+ \item \textcolor{lg}{Latest Slides:}\\ \url{http://chymera.eu/pres/ld_packaging-sci/pres.pdf}
+ \item \textcolor{lg}{Source:}\\ \url{https://bitbucket.org/TheChymera/ld_packaging-sci/}
+ \end{itemize}
+ %separate sources from info so it looks nicer
+ \begin{itemize}
+ \item \textcolor{lg}{License:} \href{https://creativecommons.org/licenses/by-sa/3.0/}{CC BY-SA 3.0}
+ \item \small\textcolor{lg}{Special Thanks to} Mickey Vaenskae
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{References}
+ \bibliographystyle{abbrv}
+ \bibliography{./bib}
+ \end{frame}
+\end{document}