vc_slides.Rmd

---
title: "Version control for reproducible science"
author: "Brad Duthie"
date: "4 December 2019"
output:
  beamer_presentation: default
header-includes:
- \usepackage{hyperref}
colorlinks: true
linkcolor: blue
urlcolor: blue
---


## What version control software does

\begin{itemize}
\setlength\itemsep{1em}
\item Software that records changes you make to files over time
\begin{itemize}
\item Manage different {\it versions} of files
\item Recover old files, keep track of file changes
\item Collaborate with others on shared files
\end{itemize}
\end{itemize} \pause

\vspace{6 mm}
\hrule
\vspace{6 mm}

\begin{itemize}
\setlength\itemsep{1em}
\item {\bf Put more intuitively}, version control takes a snapshot in time (called a '{\bf commit}') of all the files in one of your folders (called '{\bf repositories}')
\begin{itemize}
\item Visualise changes to your files over time
\item Look at the differences between file versions
\item Record who changed files, and what they changed
\end{itemize}
\end{itemize}

## Version control makes science easier


\begin{itemize}
\setlength\itemsep{1em}
\item Organise files and avoid having to 'save as' multiple versions 
\begin{itemize}
\item analysis\_1.R
\item analysis\_2.R
\item analysis\_FINAL.R
\item analysis\_FINAL\_no\_really\_this\_time.R
\end{itemize} \pause
\item Have a clear history of what you have done, when, and why (through commit comments)
\item Never worry about losing your data, analysis, or writing when integrating with \href{http://github.com}{GitHub}
\end{itemize}


## Version control can help open science

\begin{columns}
\begin{column}{0.35\textwidth}  
    \begin{center}
    \begin{itemize}
     \item[] \includegraphics[width=70px]{images/github_logo.png} \vspace{5 mm}
     \item[] \includegraphics[width=70px]{images/gitlab.png} \vspace{5 mm}
     \end{itemize}
     \end{center}
\end{column}
\begin{column}{0.65\textwidth}
\begin{itemize}
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\item Transparent record of data collection, analysis, and writing
\item Record publicly available on \href{http://github.com}{GitHub}, \href{http://bitbucket.org}{Bitbucket}, or \href{http://gitlab.com}{GitLab}
\item GitHub repository can be copied, reproduced, and discussed
\item \href{https://git-scm.com/}{git} and GitHub can track individual contributions to a project
\end{itemize}
\end{column}
\end{columns}

## Most researchers use git (and GitHub)

\begin{columns}
\begin{column}{0.35\textwidth}  
    \begin{center}
    \begin{itemize}
     \item[] \includegraphics[width=70px]{images/git.png}
     \end{itemize}
     \end{center}
\end{column}
\begin{column}{0.65\textwidth}
\begin{itemize}
\setlength\itemsep{1em}
\item Free and open-source
\item Separate from \href{http://github.com}{GitHub} \pause
\item Works across platforms
\begin{itemize}
\item Windows
\item Linux
\item Mac
\end{itemize}
\item Invented by \href{https://en.wikipedia.org/wiki/Linus_Torvalds}{Linus Torvalds}
\end{itemize}
\end{column}
\end{columns}


## Objectives: using version control

\textbf{By the end of today you will be able to use git with \href{http://github.com}{GitHub} and \href{http://gitkraken.com}{GitKraken} to manage your projects with version control.} \pause

\begin{itemize}
\setlength\itemsep{1em}
\item Understand key concepts of version control
\item Perform basic tasks in GitHub and GitKraken
\begin{itemize}
\item Staging and committing files
\item Pushing to and pulling from GitHub
\item Branching, merging, \& resolving merge conflicts
\end{itemize}
\end{itemize} \pause

\textbf{Discuss, share, and get additional help by \href{https://github.com/StirlingCodingClub/version_control/issues}{raising an issue} in the \href{https://github.com/StirlingCodingClub/version_control}{version\_control repository} on the \href{https://github.com/StirlingCodingClub}{Stirling Coding Club} GitHub organisation.}

## Why focus on using GitKraken?


\begin{columns}
\begin{column}{0.45\textwidth}  
    \begin{center}
    \begin{itemize}
         \item[] \includegraphics[width=100px]{images/gitkraken.png}
     \end{itemize}
     \end{center}
\end{column}
\begin{column}{0.55\textwidth}
\begin{itemize}
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\item Free to download and use
\item Easy GitHub integration
\item Graphical user interface
\item Visualisation of repository
\end{itemize}
\end{column}
\end{columns}

\vspace{8mm}
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\vspace{2mm}

\textbf{\href{https://stirlingcodingclub.github.io/version_control/vc_notes.html}{Accompanying notes to these slides} are available in the \href{https://github.com/StirlingCodingClub/version_control}{version\_control} repository, and include instructions for using the command line interface, and for editing directly in GitHub.}