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diff --git a/scientific_software_management/reset_system.sh b/scientific_software_management/reset_system.sh
new file mode 100644
index 0000000000000000000000000000000000000000..23d558c8689708553599eb40638a49ad217b9c43
--- /dev/null
+++ b/scientific_software_management/reset_system.sh
@@ -0,0 +1,9 @@
+# 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
diff --git a/scientific_software_management/slides.pdf b/scientific_software_management/slides.pdf
index 32ac1abe92f234fe55d2963e7ace65d527912ef7..e8d008952d02214780eac5a4420e121d97fd9137 100644
Binary files a/scientific_software_management/slides.pdf and b/scientific_software_management/slides.pdf differ
diff --git a/scientific_software_management/slides.tex b/scientific_software_management/slides.tex
index 6aeb01bef9d62b737ef8b29e33b8de48864d96bf..928bda83d84ce6dc32b271d414a2df830ffe4eb3 100644
--- a/scientific_software_management/slides.tex
+++ b/scientific_software_management/slides.tex
@@ -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}