diff --git a/scientific_software_management/get_samri_data.sh b/scientific_software_management/get_samri_data.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ca2d64584837c1b6ccdf4adcb3af5d9e5d929835
--- /dev/null
+++ b/scientific_software_management/get_samri_data.sh
@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+wget https://raw.githubusercontent.com/IBT-FMI/SAMRI/master/setup.py -O samri/setup.py
diff --git a/scientific_software_management/img/fork.png b/scientific_software_management/img/fork.png
new file mode 100644
index 0000000000000000000000000000000000000000..12bcd26d8f71db5c637504e669221e5be086e859
Binary files /dev/null and b/scientific_software_management/img/fork.png differ
diff --git a/scientific_software_management/img/git.png b/scientific_software_management/img/git.png
new file mode 100644
index 0000000000000000000000000000000000000000..18c5b29d788326339b39df657ad2c9134de2ac45
Binary files /dev/null and b/scientific_software_management/img/git.png differ
diff --git a/scientific_software_management/img/pr.png b/scientific_software_management/img/pr.png
new file mode 100644
index 0000000000000000000000000000000000000000..029e4b4a4ea58f31d8e26ddff450f69a0a392a4a
Binary files /dev/null and b/scientific_software_management/img/pr.png differ
diff --git a/scientific_software_management/samri/setup.py b/scientific_software_management/samri/setup.py
new file mode 100644
index 0000000000000000000000000000000000000000..e0613913351492c3a07e6633c8579c975149bbed
--- /dev/null
+++ b/scientific_software_management/samri/setup.py
@@ -0,0 +1,23 @@
+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']
+ },
+ )
diff --git a/scientific_software_management/slides.tex b/scientific_software_management/slides.tex
index 7edc8a73529b65d53806e4fba1665c23b9c8a214..c74acd1328ec2de391b3a752446a3a7cf82f1e67 100644
--- a/scientific_software_management/slides.tex
+++ b/scientific_software_management/slides.tex
@@ -11,49 +11,80 @@
\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}}}
+ \item Download \textcolor{lg}{\href{https://thealternative.ch/ssm/slides.tex}{\texttt{thealternative.ch/ssm/slides.tex}}}
\end{itemize}
\end{frame}
\section{Requirements}
- \subsection{... for the Demo Session}
+ \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|
+ \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
- \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|ssh userXX@130.60.24.172|
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|ssh YOURUSER@130.60.24.66|
\end{itemize}
\end{frame}
- \begin{frame}{GitHub Account}
+ \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
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|nano file|
+ \item Save via: \keys{Ctrl + c}
+ \item Exit via: \keys{Ctrl + x}
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Git and Social Coding}
+ Git needs to know who you are.
+ \begin{itemize}
+ \item On the server, run:
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git config --global user.name "Your Name"|
+ \vspace{-3.1em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git config --global user.email yourname@example.com|
+ \end{itemize}
+
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 Use a password which you can remember.
\end{itemize}
\end{frame}
\section{What?}
- \subsection{What is Packaging?}
+ \subsection{What is software management?}
\begin{frame}{The Package}
+ \begin{center}
+ \textcolor{ldorange}{\Large Better organization for your research!}
+ \end{center}
+ \vspace{1.5em}
+
A package is a software format which is (easily):
+ \begin{multicols}{2}
\begin{itemize}
- \item distributable (i.e. installable)
+ \item distributable
\item integrated
\item testable
\item updateable
\item uninstallable
\item understandable
\end{itemize}
+ \end{multicols}
\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)
+ \item version-dependent behaviour
+ \item optional features
+ \item incompatibilities
+ \item static/dynamic linking
\end{itemize}
\end{minipage}
\begin{minipage}{0.55\textwidth}
@@ -68,14 +99,14 @@
\begin{figure}
\centering
\includegraphics[width=0.9\textwidth]{img/pm_d.png}
- \caption{Rudimentary overview of binary package distribution workflow.}
+ \caption{Rudimentary overview of binary package distribution.}
\end{figure}
\begin{columns}
\column{.5\linewidth}
Advantages:
\begin{itemize}
\item Faster installation
- \item More reproducible installation
+ \item Less variable installation
\end{itemize}
\column{.5\linewidth}
Disadvantages:
@@ -86,11 +117,11 @@
\end{itemize}
\end{columns}
\end{frame}
- \begin{frame}{Source Packages}
+ \begin{frame}{Source-Based Packages}
\begin{figure}
\centering
\includegraphics[width=0.9\textwidth]{img/pm_g.png}
- \caption{Rudimentary overview of source distribution workflow.}
+ \caption{Rudimentary overview of source-based package distribution.}
\end{figure}
\begin{columns}
\column{.5\linewidth}
@@ -109,16 +140,14 @@
\end{columns}
\end{frame}
\section{Why?}
- \subsection{Why Package my Software?}
- \begin{frame}{Recognition}
+ \subsection{Why does open science require package management?}
+ \begin{frame}{Quality}
\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}
+ \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}{Impact}
@@ -128,34 +157,37 @@
\item Retain more users.
\end{itemize}
\end{frame}
- \begin{frame}{Quality}
+ \begin{frame}{Recognition}
\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.
+ \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}{Sustainability}
+ A sustainable project \textbf{cannot} depend on environments remaining unchanged.
\begin{itemize}
+ \item Ensure long-term viability of your software.
\item Avoid death-by-PhD.
- \item Ensure long-term availability of your software.
- \item Give your funding bodies their money's worth.
+ \item Give your funders their money's worth.
\item Develop a lean start-up.
- \item Maintain a sustainable and affordable infrastructure for your business/employer.
+ \item Maintain a reliable and affordable infrastructure for your work.
\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 Don't 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}
+ \subsection{How do I package my software?}
+ \begin{frame}{Choose Appropriate Technologies}
\begin{columns}
\column{.5\linewidth}
\begin{figure}
@@ -171,56 +203,67 @@
\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}
+ \column{.55\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 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}}}
\end{itemize}
- \column{.6\linewidth}
- \begin{figure}
- \centering
- \includegraphics[width=0.9\textheight]{img/sp.png}
- \end{figure}
+ \column{.45\linewidth}
+ \inputminted[bgcolor=tlg,fontsize=\Tiny,tabsize=4]{python}{samri/setup.py}
\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.
+ \column{.55\linewidth}
+ A Gentoo package is \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}}}
+ \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{.6\linewidth}
- \begin{figure}
- \centering
- \includegraphics[width=0.7\textheight]{img/eb.png}
- \end{figure}
+ \column{.47\linewidth}
+ \vspace{-3em}
+ \inputminted[bgcolor=tlg,fontsize=\Tiny,tabsize=4,firstline=1,lastline=36]{bash}{samri/samri-0.4.ebuild}
+ \vspace{-3.2em}
+ \inputminted[bgcolor=tlg,fontsize=\Tiny,tabsize=4,firstline=47,lastline=49]{bash}{samri/samri-0.4.ebuild}
\end{columns}
\end{frame}
+ \begin{frame}{Reposit Your Software}
+ \begin{figure}
+ \centering
+ \includegraphics[width=0.4\textwidth]{img/git.png}
+ \caption{Git Logo by Jason Long (\href{https://creativecommons.org/licenses/by/3.0/}{CC-BY-3.0})}
+ \end{figure}
+ You can self-host, but hosting also available via social coding platforms:
+ \begin{multicols}{3}
+ \begin{itemize}
+ \item GitLab
+ \item GitHub
+ \item Bitbucket
+ \end{itemize}
+ \end{multicols}
+ \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|
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|eix nibabel|
\item see package dependencies
- \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|equery g samri|
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|equery g nibabel|
\item see what packages depend on a said package
- \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|equery d nipype|
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|equery d nibabel|
+ \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
- \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|emerge -p =nilearn-0.1.4.1|
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|emerge -p nibabel|
\end{itemize}
\end{frame}
\begin{frame}{Reproduce a Scientific Article}
@@ -229,22 +272,26 @@
\item Get the source code for brand-new articles:
\begin{itemize}
\item Work-in-progress (reexecution time \SI{\approx 3}{\second})
- \vspace{-0.5em}
+ \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})
- \vspace{-0.5em}
- \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git clone git clone https://bitbucket.org/TheChymera/irsabi.git |
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git clone https://bitbucket.org/TheChymera/irsabi.git |
\end{itemize}
\item Switch to article directory
- \vspace{-0.5em}
+ \vspace{-0.6em}
\mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|cd nvcz|
\item Attempt to reexecute
- \vspace{-0.5em}
+ \vspace{-0.6em}
\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.}
+ \begin{center}
+ \textcolor{ldorange}{\Large But you can solve the issue yourself!}
+ \end{center}
+ \vspace{2em}
Write a new package atom for the package manager.
\begin{itemize}
\item Gentoo Linux makes this wholly autonomous.
@@ -255,28 +302,130 @@
\end{itemize}
\end{itemize}
\end{frame}
- \begin{frame}{Write an ebuild}
+ \begin{frame}{Write a Package Atom --- The Overlay}
\begin{itemize}
- \Item Fork an overlay on GitHub.
- \textcolor{lg}{\href{https://github.com/TheChymera/overlay}{\texttt{github.com/TheChymera/overlay}}}
+ \item Fork an overlay on GitHub, e.g. from \textcolor{lg}{\href{https://github.com/TheChymera/overlay}{\texttt{github.com/TheChymera/overlay}}}
+ \begin{figure}
+ \vspace{-0.1em}
+ \includegraphics[width=0.94\textwidth]{img/fork.png}
+ \end{figure}
\item Go back to your home directory.
- \vspace{-0.5em}
+ \vspace{-0.6em}
\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|
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git clone https://github.com/YourName/overlay.git|
+ \item Make the ebuild directory, and navigate into it.
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|mkdir -p overlay/sci-biology/samri && cd $_|%stopzone
+ \end{itemize}
+ \end{frame}
+ \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
+ \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
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|cp /usr/portage/sci-libs/nibabel/*2.5.1.ebuild samri-0.4.ebuild|
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Write a Package Atom --- The Metadata File}
+ \vspace{-0.9em}
+ \inputminted[bgcolor=tlg,fontsize=\scriptsize,tabsize=4]{xml}{samri/metadata.xml}
+ \end{frame}
+ \begin{frame}{Write a Package Atom --- The Ebuild (header excerpt)}
+ \inputminted[bgcolor=tlg,fontsize=\scriptsize,tabsize=4,firstline=1,lastline=17]{bash}{samri/samri-0.4.ebuild}
+ \end{frame}
+ \begin{frame}{Write a Package Atom --- The Ebuild (dependency excerpts)}
+ \begin{itemize}
+ \item Compile-time dependency example:
+ \vspace{-0.6em}
+ \inputminted[bgcolor=tlg,fontsize=\scriptsize,tabsize=4,firstline=18,lastline=25]{bash}{samri/samri-0.4.ebuild}
+ \item Run-time dependency DIY (fill out, consulting \textcolor{lg}{\href{https://github.com/IBT-FMI/SAMRI}{\texttt{github.com/IBT-FMI/SAMRI}}}):
+ \vspace{-0.6em}
+ \inputminted[bgcolor=tlg,fontsize=\scriptsize,tabsize=4,firstline=26,lastline=29]{bash}{samri/samri-0.4.ebuild}
+ \vspace{-3em}
+ \inputminted[bgcolor=tlg,fontsize=\scriptsize,tabsize=4,firstline=47,lastline=47]{bash}{samri/samri-0.4.ebuild}
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Write a Package Atom --- Finishing Touches}
+ \begin{itemize}
+ \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.
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|wget https://thealternative.ch/ssm/samri/samri-0.4.ebuild -P ~|
+ \vspace{-3.1em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|colordiff ~/samri-0.4.ebuild samri-0.4.ebuild|
+ \vspace{-3.1em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|wget https://thealternative.ch/ssm/samri/metadata.xml -P ~|
+ \vspace{-3.1em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|colordiff ~/metadata.xml metadata.xml|
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Social Coding --- Upload Your Package for Reuse}
+ \begin{itemize}
+ \item Quality Control.
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|repoman full|
+ \item Record and publish your work in version control.
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|git commit -a && git push origin master|
+ \item Include your work in widely used overlay: visit \textcolor{lg}{\href{https://github.com/YourName/overlay}{\texttt{github.com/YourName/overlay}}}.
+ \begin{figure}
+ \vspace{-0.1em}
+ \includegraphics[width=0.94\textwidth]{img/pr.png}
+ \end{figure}
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{Use Your Work}
+ \begin{itemize}
+ \item Package index update (done by the 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).
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|emerge -v samri|
+ \end{itemize}
+ \end{frame}
+ \begin{frame}{The Article Environment is Now Reproducible}
+ \begin{itemize}
+ \item Navigate back to the article directory.
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|cd ~/nvcz|
+ \item Compile.
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|./compile|
+ \item Log out from SSH: \keys{Ctrl + d}
+ \item Get the document locally.
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|scp YOURUSER@130.60.24.66:nvcz/article.pdf .|
\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}
+ \begin{frame}{And the Article is now Automated}
+ \begin{itemize}
+ \item Log back in and navigate to article directory.
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|ssh YOURUSER@130.60.24.66|
+ \vspace{-3.1em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|cd nvcz|
+ \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.
+ \vspace{-0.6em}
+ \mint[bgcolor=tlg,fontsize=\footnotesize]{bash}|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}
@@ -290,19 +439,20 @@
\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\\
+ \item Spread package management in your field\\
\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/}
+ \item \textcolor{lg}{Latest Slides:}\\
+ \texttt{\href{https://thealternative.ch/ssm/slides.tex}{thealternative.ch/ssm/slides.tex}}
+ \item \textcolor{lg}{Source:}\\
+ \texttt{\href{https://gitlab.ethz.ch/thealternative/courses/tree/master/scientific_software_management}{\footnotesize gitlab.ethz.ch/thealternative/courses/tree/master/scientific\_software\_management}}
\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}