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Commit aa72bd2a authored by Horea Christian's avatar Horea Christian
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PRESENTED: 2019-11-11 Linux Days Zurich

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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/slides.tex
View file @ aa72bd2a
......@@ -19,14 +19,14 @@
\begin{frame}{SSH}
Linux and MacOS:
\begin{itemize}
\item check that you can run
\item Check that you can run:
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|ssh YOURUSER@130.60.24.66|
\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
\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:
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|ssh YOURUSER@130.60.24.66|
\end{itemize}
......@@ -34,7 +34,7 @@
\begin{frame}{Command Line Text Editor}
Usable via SSH and ubiquitous. There are many alternatives, but here we use \textcolor{lg}{\texttt{nano}}:
\begin{itemize}
\item Open file
\item Open file:
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|nano file|
\item Save via: \keys{Ctrl + c}
......@@ -53,7 +53,7 @@
GitHub is a \textbf{social coding platform} providing free accounts:
\begin{itemize}
\item Register under \textcolor{lg}{\href{https://github.com}{\texttt{github.com}}}
\item Register under \textcolor{lg}{\href{https://github.com}{\texttt{github.com}}}.
\item Use a password which you can remember.
\end{itemize}
\end{frame}
......@@ -68,12 +68,12 @@
A package is a software format which is (easily):
\begin{multicols}{2}
\begin{itemize}
\item distributable
\item integrated
\item testable
\item updateable
\item uninstallable
\item understandable
\item Distributable
\item Integrated
\item Testable
\item Updateable
\item Uninstallable
\item Understandable
\end{itemize}
\end{multicols}
\end{frame}
......@@ -81,10 +81,10 @@
\begin{minipage}{0.44\textwidth}
Packages interact in complex and nontrivial manners:
\begin{itemize}
\item version-dependent behaviour
\item optional features
\item incompatibilities
\item static/dynamic linking
\item Version-dependent behaviour
\item Optional features
\item Incompatibilities
\item Static/dynamic linking
\end{itemize}
\end{minipage}
\begin{minipage}{0.55\textwidth}
......@@ -209,7 +209,7 @@
You can package your python software by writing \textbf{one short} file.
\begin{itemize}
\item Python provides its own limited 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}}}
\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{.45\linewidth}
\inputminted[bgcolor=tlg,fontsize=\Tiny,tabsize=4]{python}{samri/setup.py}
......@@ -220,8 +220,8 @@
\column{.55\linewidth}
A Gentoo package is \textbf{one short} file.
\begin{itemize}
\item regardless of the programming language
\item can automatically interpret information contained in the package, e.g. in \textcolor{lg}{\texttt{setup.py}}
\item Regardless of the programming language
\item Can automatically interpret information contained in the package, e.g. in \textcolor{lg}{\texttt{setup.py}}
\end{itemize}
\column{.47\linewidth}
\vspace{-3em}
......@@ -249,21 +249,21 @@
\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
\item Check available package names, versions, and details.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|eix nibabel|
\item see package dependencies
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|eix -v nibabel|
\item See package dependencies.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|equery g nibabel|
\item see what packages depend on a said package
\item See what packages depend on a said package.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|equery d nibabel|
\item see files installed by package
\item See files installed by package.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|equery f nibabel|
\item try to install a new package
\item Try to install a new package.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|emerge -p nibabel|
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|emerge -p psychopy|
\end{itemize}
\end{frame}
\begin{frame}{Reproduce a Scientific Article}
......@@ -271,17 +271,17 @@
\begin{itemize}
\item Get the source code for brand-new articles:
\begin{itemize}
\item Work-in-progress (reexecution time \SI{\approx 3}{\second})
\item Work-in-progress (reexecution time \SI{\approx 2}{\minute})
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git clone https://gitlab.com/Chymera/nvcz.git |
\item Preprint (reexecution time \SI{\approx 2}{\minute})
\item Preprint (reexecution time \SI{\approx 11}{\minute})
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git clone https://bitbucket.org/TheChymera/irsabi.git |
\end{itemize}
\item Switch to article directory
\item Switch to article directory.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|cd nvcz|
\item Attempt to reexecute
\item Attempt to reexecute.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|./compile.sh|
%\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git chechout 28b5d2d1|
......@@ -323,12 +323,12 @@
\begin{frame}{Transparency means less work for you!}
You could write the following files from scratch, but you can also reuse analogous files from existing packages.
\begin{itemize}
\item Copy a metadata file from a Python package
\item Copy a metadata file from a Python package.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|cp /usr/portage/sci-libs/nibabel/metadata.xml .|
\item Copy an ebuild file from a Python package
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|cp /usr/portage/dev-python/astropy/metadata.xml .|
\item Copy an ebuild file from a Python package.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|cp /usr/portage/sci-libs/nibabel/*2.5.1.ebuild samri-0.4.ebuild|
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|cp /usr/portage/dev-python/astropy/*2.0.1.ebuild samri-0.4.ebuild|
\end{itemize}
\end{frame}
\begin{frame}{Write a Package Atom --- The Metadata File}
......@@ -352,10 +352,10 @@
\end{frame}
\begin{frame}{Write a Package Atom --- Finishing Touches}
\begin{itemize}
\item Not all packages are perfect. Append the following to the ebuild.
\item Not all packages are perfect. Append the following to the ebuild:
\vspace{-0.6em}
\inputminted[bgcolor=tlg,fontsize=\scriptsize,tabsize=4,firstline=49,lastline=49]{bash}{samri/samri-0.4.ebuild}
\item Check your work.
\item Check your work. Minor formatting differences (e.g. indents) are not critical.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|wget https://thealternative.ch/ssm/samri/samri-0.4.ebuild -P ~|
\vspace{-3.1em}
......@@ -368,7 +368,10 @@
\end{frame}
\begin{frame}{Social Coding --- Upload Your Package for Reuse}
\begin{itemize}
\item Quality Control.
\item Download the data and make git aware of your files.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|ebuild samri-0.4.ebuild manifest && git add .|
\item Run a quality check.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|repoman full|
\item Record and publish your work in version control.
......@@ -383,13 +386,13 @@
\end{frame}
\begin{frame}{Use Your Work}
\begin{itemize}
\item Package index update (done by the superuser).
\item Update the package index (as superuser).
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|eix-sync|
\item Try out the install command yourself.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|emerge -pv samri|
\item Install (done by the superuser).
\item Install (as superuser).
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|emerge -v samri|
\end{itemize}
......@@ -401,7 +404,7 @@
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|cd ~/nvcz|
\item Compile.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|./compile|
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|./compile.sh|
\item Log out from SSH: \keys{Ctrl + d}
\item Get the document locally.
\vspace{-0.6em}
......@@ -418,15 +421,42 @@
\item Automatically adjust the t-statistic threshold for the entire document.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}:grep -rlI 3\.5 | xargs sed -i -e "s/3.5/3.0/g":
\item Visualize what you have changed.
\item Clean up trace files and visualize what you have changed.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git diff|
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|./cleanup.sh && git diff|
\item Compile, log out.
\item Get the document locally.
\vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|scp YOURUSER@130.60.24.66:nvcz/article.pdf newarticle.pdf|
\end{itemize}
\end{frame}
\begin{frame}{Results}
You have:
\begin{itemize}
\item Packaged a new piece of scientific software, now automatically installable:
\begin{itemize}
\item By anybody else
\item By you on any machine
\end{itemize}
\item Updated data analysis visualizations in a reproducible article.
\begin{itemize}
\item It's that easy to contribute to well-organized research!
\end{itemize}
\end{itemize}
\vspace{-.5em}
\begin{columns}
\column{.5\linewidth}
\begin{figure}
\centering
\includegraphics[width=0.52\textwidth]{img/fig_old.png}
\end{figure}
\column{.5\linewidth}
\begin{figure}
\centering
\includegraphics[width=0.52\textwidth]{img/fig_new.png}
\end{figure}
\end{columns}
\end{frame}
\section{Meta}
......
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