## Presentation made the 12/11/2019: - Version control with git - Markup languages
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<!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><title>Document Version Control with GIT</title><meta content="yes" name="apple-mobile-web-app-capable"><meta content="black-translucent" name="apple-mobile-web-app-status-bar-style"><meta content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui" name="viewport"><link href="node_modules/reveal.js/css/reveal.css" rel="stylesheet"><link rel="stylesheet" href="node_modules/reveal.js/css/theme/white.css" id="theme"><!--This CSS is generated by the Asciidoctor-Reveal.js converter to further integrate AsciiDoc's existing semantic with Reveal.js--><style type="text/css">.reveal div.right {
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.conum:not([data-value]):empty{display:none}</style><link href="node_modules/reveal.js/lib/css/zenburn.css" rel="stylesheet"><script>var link = document.createElement( 'link' );
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document.getElementsByTagName( 'head' )[0].appendChild( link );</script><!--[if lt IE 9]><script src="node_modules/reveal.js/lib/js/html5shiv.js"></script><![endif]--><link rel="stylesheet" href="custom_css.css"></head><body><div class="reveal"><div class="slides"><section class="title" data-state="title" data-background-image="img/intro.jpg"><h1>Document Version Control with GIT</h1></section><section id="_before_we_start" data-background-image="img/normal.jpg"><h2>Before we start&#8230;&#8203;</h2><div class="imageblock" style=""><img src="img/nocloud.jpg" alt="nocloud"></div></section>
<section><section id="_what_is_version_control" data-background-image="img/normal.jpg"><h2>What is version control?</h2><div class="ulist"><ul><li class="fragment"><p>Version control is a system that records changes to a file or set of files over time so that you can recall specific versions later.</p></li><li class="fragment"><p>Has existed for almost as long as writing has existed (ex. document version)</p></li><li class="fragment"><p>Today, the most capable (as well as complex) revision control systems are those used in software development.</p></li></ul></div></section><section id="_why" data-background-image="img/normal.jpg"><h2>Why?</h2><div class="ulist"><ul><li class="fragment"><p>Revert files back to a previous state</p></li><li class="fragment"><p>"Freeze" important versions of a document</p></li><li class="fragment"><p>Compare changes over time</p></li><li class="fragment"><p>Track progress of a project</p></li><li class="fragment"><p>See who modified something, and when</p></li></ul></div></section><section id="_modern_version_control_systems" data-background-image="img/normal.jpg"><h2>Modern version control systems</h2><div class="ulist"><ul><li class="fragment"><p>Remote backup of files</p></li><li class="fragment"><p>Powerful tool for collaboration</p></li></ul></div></section></section>
<section><section id="_git" data-background-image="img/normal.jpg"><h2>GIT</h2><div class="ulist"><ul><li class="fragment"><p>Developed by Linus Torvalds in 2005</p></li><li class="fragment"><p>The linux Kernel:</p><div class="ulist"><ul><li><p>~63000 files</p></li><li><p>Roughly 15,600 developers from more than 1,400 companies</p></li></ul></div></li></ul></div></section><section id="_characteristics" data-background-image="img/normal.jpg"><h2>Characteristics</h2><div class="ulist"><ul><li class="fragment"><p>Free and open source</p></li><li class="fragment"><p>Distributed</p></li><li class="fragment"><p>Powerful and flexible</p></li><li class="fragment"><p>Learning curve can be steep</p></li></ul></div></section><section data-background-image="img/normal.jpg"><div class="paragraph"><p><span class="image"><img src="img/xkcd_git.png" alt="xkcd git"></span></p></div></section><section id="_how_does_it_work" data-background-image="img/normal.jpg"><h2>How does it work?</h2><div class="imageblock" style=""><img src="img/architecture.png" alt="architecture"></div></section><section id="_installation" data-background-image="img/normal.jpg"><h2>Installation</h2><div class="paragraph"><p><a href="https://git-scm.com/download/win" class="bare">https://git-scm.com/download/win</a></p></div>
<div class="paragraph"><p>Package managers are heavily recommended!</p></div></section><section id="_creating_a_remote_repository" data-background-image="img/normal.jpg"><h2>Creating a remote repository</h2><div class="ulist"><ul><li class="fragment"><p>register at the remote git server</p><div class="ulist"><ul><li><p><a href="https://git.webhosting.rug.nl/" class="bare">https://git.webhosting.rug.nl/</a></p></li></ul></div></li><li class="fragment"><p>create repository</p></li><li class="fragment"><p>add participants <em>ssh public keys</em></p></li><li class="fragment"><p>clone the repository in your machine</p></li></ul></div></section><section id="_readme_and_gitignore" data-background-image="img/normal.jpg"><h2>README and .gitignore</h2><div class="paragraph"><p>Every repository should have these 2 files:</p></div>
<div class="ulist"><ul><li><p><strong>README</strong>: project description and useful information</p></li><li><p><strong>.gitignore</strong>: special file indicating GIT which files are <strong>not</strong> to be tracked</p></li></ul></div></section><section id="_workflow" data-background-image="img/normal.jpg"><h2>workflow</h2><div class="imageblock" style=""><img src="img/git_workflow.jpg" alt="git workflow"></div></section><section id="_copying_remote_repository_clone" data-background-image="img/normal.jpg"><h2>copying remote repository: clone</h2><div class="ulist"><ul><li><p><strong>git clone <em>repository</em></strong></p></li><li><p>Clones the remote repository into the local one</p></li></ul></div></section><section id="_staging_changes_local" data-background-image="img/normal.jpg"><h2>staging changes (local)</h2><div class="ulist"><ul><li class="fragment"><p><strong>git add <em>files</em></strong></p></li><li class="fragment"><p>Adds the changes into the local staging area</p></li></ul></div></section><section id="_saving_changes_commit_local" data-background-image="img/normal.jpg"><h2>Saving changes: commit (local)</h2><div class="ulist"><ul><li class="fragment"><p><strong>git commit "message"</strong></p></li><li class="fragment"><p>Saves the changes in the staging area into the repository</p></li><li class="fragment"><p>Creates a "snapshot" of the current state of one or more files</p></li><li class="fragment"><p>A message describing the changes must be provided</p></li></ul></div></section><section id="_history_and_revert_local" data-background-image="img/normal.jpg"><h2>history and revert (local)</h2><div class="ulist"><ul><li class="fragment"><p><strong>git log <em>files</em></strong></p></li><li class="fragment"><p>returns a history of the file modifications</p></li><li class="fragment"><p><strong>git revert <em>commit</em></strong></p></li><li class="fragment"><p>removes one or more commits from the local files, changes must be committed after</p></li></ul></div></section><section id="_upload_to_remote_repository_push" data-background-image="img/normal.jpg"><h2>upload to remote repository: push</h2><div class="ulist"><ul><li class="fragment"><p><strong>git push</strong></p></li><li class="fragment"><p>Uploads the state of the local repository to the remote one</p></li></ul></div></section><section id="_download_from_remote_repository_pull" data-background-image="img/normal.jpg"><h2>Download from remote repository: pull</h2><div class="ulist"><ul><li class="fragment"><p><strong>git pull</strong></p></li><li class="fragment"><p>Fetch and merges the documents in the remote repository into the local one</p></li><li class="fragment"><p>Merging files can generate conflicts, git will ask us to fix them and commit the changes</p></li></ul></div></section><section id="_branching" data-background-image="img/normal.jpg"><h2>Branching</h2><div class="imageblock" style=""><img src="img/version-control-flow.png" alt="version control flow"></div></section><section id="_other_advanced_stuff" data-background-image="img/normal.jpg"><h2>other (advanced) stuff</h2><div class="ulist"><ul><li><p>tags</p></li><li><p>partial reverts</p></li><li><p>change history</p></li><li><p>&#8230;&#8203;</p></li></ul></div></section></section>
<section><section id="_docs_as_code" data-background-image="img/normal.jpg"><h2>Docs as code</h2><div class="ulist"><ul><li class="fragment"><p>Software is a small part of the documents a project must handle</p></li><li class="fragment"><p>Still, version control and remote collaboration are needed for all the documents</p></li><li class="fragment"><p>In the last years there is a big push of treating documents the same way as programming files</p><div class="ulist"><ul><li><p><a href="https://www.writethedocs.org/guide/docs-as-code/" class="bare">https://www.writethedocs.org/guide/docs-as-code/</a></p></li></ul></div></li></ul></div></section><section id="_advantages" data-background-image="img/normal.jpg"><h2>Advantages</h2><div class="ulist"><ul><li class="fragment"><p>Working in plain text files (rather than binary file formats like Word)</p></li><li class="fragment"><p>Collaborating using version control such as git and GitHub</p></li><li class="fragment"><p>Storing docs in the same repositories as the programming code itself</p></li><li class="fragment"><p>Versioning docs through git tags/releases (rather than duplicating all the files to archive each release)</p></li><li class="fragment"><p>Generate other formats or websites without modifying the document</p></li></ul></div></section><section id="_just_a_little_problem" data-background-image="img/normal.jpg"><h2>Just a little problem&#8230;&#8203;</h2><div class="ulist"><ul><li class="fragment"><p>The most common document formats: word, pdf&#8230;&#8203; are binary files</p></li><li class="fragment"><p>git (text based) doesn&#8217;t work with them</p></li></ul></div></section><section id="_solutions" data-background-image="img/normal.jpg"><h2>Solutions?</h2><div class="ulist"><ul><li class="fragment"><p>Markup languages:</p></li><li class="fragment"><p>Markup languages are ways of annotating an electronic document.</p></li><li class="fragment"><p>Usually markup will either specify how something should be displayed or what something means.</p><div class="ulist"><ul><li><p>html, xml, latex&#8230;&#8203;</p></li></ul></div></li></ul></div></section><section id="_markup_languages" data-background-image="img/normal.jpg"><h2>Markup languages</h2><div class="ulist"><ul><li class="fragment"><p>Documents are written in plain text, then a program convert them into the final document</p></li><li class="fragment"><p>The same document can be used to generate files in other formats: latex, word, pdf or even slides</p></li><li class="fragment"><p>Formating is done by the computer, output is always consistent</p></li><li class="fragment"><p>Fast and light</p></li><li class="fragment"><p>Can be used in version control systems</p></li></ul></div></section><section id="_markup_languages_advanced_features" data-background-image="img/normal.jpg"><h2>Markup languages: Advanced features</h2><div class="ulist"><ul><li class="fragment"><p>Automatic generation of documents</p></li><li class="fragment"><p>Inline comments (not rendered in the final document)</p></li><li class="fragment"><p>Split one the document into several. Ex: main document, chapters and bibliography</p></li><li class="fragment"><p>Code executed and plots rendered <em>in</em> the document</p></li></ul></div></section><section id="_latex" data-background-image="img/normal.jpg"><h2>Latex</h2><div class="ulist"><ul><li class="fragment"><p>Extensively used for technical papers</p></li><li class="fragment"><p>Beautiful generated documents</p></li><li class="fragment"><p>Very powerful&#8230;&#8203;</p></li><li class="fragment"><p>&#8230;&#8203;and very heavy</p></li><li class="fragment"><p>Setup and document customization are complex</p></li></ul></div></section><section id="_latex_example" data-background-image="img/normal.jpg"><h2>Latex: example</h2><pre class="highlight listingblock"><code>\documentclass{article}
\usepackage{graphicx}
\begin{document}
\title{Introduction to \LaTeX{}}
\author{Author's Name}
\maketitle
\begin{abstract}
The abstract text goes here.
\end{abstract}
\section{Introduction}
Here is the text of your introduction.
\begin{equation}
\label{simple_equation}
\alpha = \sqrt{ \beta }
\end{equation}
\subsection{Subsection Heading Here}
Write your subsection text here.
\begin{figure}
\centering
\includegraphics[width=3.0in]{myfigure}
\caption{Simulation Results}
\label{simulationfigure}
\end{figure}
\section{Conclusion}
Write your conclusion here.
\end{document}</code></pre></section><section id="_latex_example_ii" data-background-image="img/normal.jpg"><h2>Latex: example II</h2><pre class="highlight listingblock"><code>\documentclass[12pt]{article}
\usepackage{lingmacros}
\usepackage{tree-dvips}
\begin{document}
\section*{Notes for My Paper}
Don't forget to include examples of topicalization.
They look like this:
{\small
\enumsentence{Topicalization from sentential subject:\\
\shortex{7}{a John$_i$ [a &amp; kltukl &amp; [el &amp;
{\bf l-}oltoir &amp; er &amp; ngii$_i$ &amp; a Mary]]}
{ &amp; {\bf R-}clear &amp; {\sc comp} &amp;
{\bf IR}.{\sc 3s}-love &amp; P &amp; him &amp; }
{John, (it's) clear that Mary loves (him).}}
}
\subsection*{How to handle topicalization}
I'll just assume a tree structure like (\ex{1}).
{\small
\enumsentence{Structure of A$'$ Projections:\\ [2ex]
\begin{tabular}[t]{cccc}
&amp; \node{i}{CP}\\ [2ex]
\node{ii}{Spec} &amp; &amp;\node{iii}{C$'$}\\ [2ex]
&amp;\node{iv}{C} &amp; &amp; \node{v}{SAgrP}
\end{tabular}
\nodeconnect{i}{ii}
\nodeconnect{i}{iii}
\nodeconnect{iii}{iv}
\nodeconnect{iii}{v}
}
}
\subsection*{Mood}
Mood changes when there is a topic, as well as when
there is WH-movement. \emph{Irrealis} is the mood when
there is a non-subject topic or WH-phrase in Comp.
\emph{Realis} is the mood when there is a subject topic
or WH-phrase.
\end{document}</code></pre></section><section id="_latex_alternative_lyx" data-background-image="img/normal.jpg"><h2>Latex alternative: Lyx</h2><div class="ulist"><ul><li class="fragment"><p>WYSIWYG latex editor</p></li><li class="fragment"><p>Documents are generated in .lyx, a subset of latex</p></li><li class="fragment"><p>Can be used together with version control</p></li><li class="fragment"><p>Provides, by default, templates for many of the biggest scientific journals</p></li></ul></div></section><section id="_lyx_example" data-background-image="img/normal.jpg"><h2>Lyx: example</h2><div class="imageblock" style=""><img src="img/nvbqz.png" alt="nvbqz"></div></section><section id="_lyx_example_ii" data-background-image="img/normal.jpg"><h2>Lyx: example II</h2><div class="imageblock" style=""><img src="img/lyxlilipond.png" alt="lyxlilipond"></div></section><section id="_lightweight_markup_languages" data-background-image="img/normal.jpg"><h2>Lightweight Markup languages</h2><div class="ulist"><ul><li class="fragment"><p>Also called Plain Text Markup or humane markup language</p></li><li class="fragment"><p>Provide a way of formating the document, while still being readable</p></li><li class="fragment"><p>Widely used on websites and code documentation</p></li></ul></div></section><section id="_lml_current_options" data-background-image="img/normal.jpg"><h2>LML: current options</h2><div class="ulist"><ul><li><p>Markdown</p></li><li><p>reStructuredText (rst)</p></li><li><p>Asciidoc</p></li></ul></div></section><section id="_markdown" data-background-image="img/normal.jpg"><h2>Markdown</h2><div class="ulist"><ul><li class="fragment"><p>Created for minimal formating of web text</p></li><li class="fragment"><p>used <strong><em>everywhere</em></strong>: web, jupyter notebooks, r-markdown&#8230;&#8203;</p></li><li class="fragment"><p>There is no standard, currently exist many flavours of it (github, commonmark, pandoc)</p></li><li class="fragment"><p>Originally not intended for documents, very limited</p></li><li class="fragment"><p>Different flavors and tools try to overcome this limitation</p><div class="ulist"><ul><li><p>(+ pandoc)</p></li></ul></div></li></ul></div></section><section id="_markdown_example" data-background-image="img/normal.jpg"><h2>Markdown: example</h2><div class="imageblock" style=""><img src="img/quicktourexample_small.png" alt="quicktourexample small"></div></section><section id="_asciidoc" data-background-image="img/normal.jpg"><h2>Asciidoc</h2><div class="ulist"><ul><li class="fragment"><p>Developed for book creation.</p></li><li class="fragment"><p>Limited number of users</p></li><li class="fragment"><p>Standardized and extensible, great documentation</p></li><li class="fragment"><p>Lack of resources makes that bugs or request take time to be fixed</p></li></ul></div></section><section id="_restructuredtext" data-background-image="img/normal.jpg"><h2>reStructuredText</h2><div class="ulist"><ul><li class="fragment"><p>Originally intended for python documentation</p></li><li class="fragment"><p>medium sized but very tech-savvy community</p></li><li class="fragment"><p>Syntax is a little different than the other two</p></li><li class="fragment"><p>Very powerful and extensible</p></li></ul></div></section><section id="_which_one_to_use" data-background-image="img/normal.jpg"><h2>Which one to use?</h2><div class="ulist"><ul><li><p>Notetaking:</p><div class="ulist"><ul><li><p>Markdown</p></li><li><p>Asciidoc</p></li><li><p>reStructuredText</p></li></ul></div></li><li><p>Anything more serious:</p><div class="ulist"><ul><li><p>reStructuredText</p></li><li><p>Latex/Lyx</p></li></ul></div></li></ul></div></section></section>
<section id="_resources" data-background-image="img/normal.jpg"><h2>Resources</h2><div class="paragraph"><p><a href="https://chocolatey.org" class="bare">https://chocolatey.org</a></p></div>
<pre class="highlight listingblock"><code>choco install git vscode pandoc</code></pre></section>
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