Scientific software management draft

.style/header.tex

@@ -4,6 +4,7 @@
 \usepackage{listings}
 \usepackage{color}
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+\usepackage{minted} % COMPILE WITH `pdflatex -shell-escape`!
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scientific_software_management/bib.bib

+@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

+#!/usr/bin/env bash
+
+pdflatex -shell-escape slides.tex
+bibtex slides
+pdflatex -shell-escape slides.tex
+pdflatex -shell-escape slides.tex

scientific_software_management/slides.tex

+\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 enough”!
+					\item Don't be wait until your software is “ready”!
+					\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}