class: center, middle, inverse, title-slide # Collaboration, version control & learning to commit ## R-thritis Group ### David Selby ### 12<sup>th</sup> March 2021 ---  --- class: center <img src="http://www.phdcomics.com/comics/archive/phd101212s.gif" width="60%" /> --- ## Motivation .small[— why git & GitHub?] > "Version control is the **only reasonable way** to keep track of changes in code, manuscripts, presentations, and data analysis projects... > > "GitHub **lowers the barriers to collaboration**." > > .right[[Karl Broman](https://kbroman.org/github_tutorial/pages/why.html)] --- ### Local version control - Keep many local copies of files in a folder - e.g. [RCS](https://en.wikipedia.org/wiki/Revision_Control_System "Revision Control System"), Windows File History ### Centralised version control - Check out snapshots of files from single server - e.g. [CVS](https://en.wikipedia.org/wiki/Concurrent_Versions_System "Concurrent Versions System"), Office 365, Dropbox, _Isilon_ ### Distributed version control - Mirror the entire repository, including full history - e.g. Git, Mercurial --- ## Local _vs._ centralised VCS .pull-left[  ] .pull-right[  ] .footnote[Source: [_Pro Git_ (2014)](https://git-scm.com/book/en/v2)] --- ## Centralised _vs._ distributed VCS .pull-left[  ] .pull-right[  ] .footnote[Source: [_Pro Git_ (2014)](https://git-scm.com/book/en/v2)] --- class: fullpage ## Git and GitHub **Git ≠ GitHub** <small>(just as R ≠ RStudio)</small>. GitHub is a _hosting provider_ for your files, via Git software. Others are available: - [Bitbucket](https://bitbucket.org/) - [Gitlab](https://about.gitlab.com/) - [AWS CodeCommit](https://aws.amazon.com/codecommit/) - [Google Cloud Source Repositories](https://cloud.google.com/source-repositories/) GitHub provides extra features on top of Git: - [issue tracking](https://guides.github.com/features/issues/), documentation, wikis - [GitHub Pages](https://pages.github.com/) - [GitHub Actions](https://github.com/features/actions) --- class: inverse, fullpage ## Git command line operations - `git init` / `clone` - start a new repository (or copy an existing one) - `git add` / `rm` - add/remove a file to version control - `git diff` / `status` - see what's changed - `git commit` - save changes to history - `git branch` / `merge` - start new branch / merge one into another - `git push` - upload changes to the remote repository - `git pull` - download changes from remote repository --- class: fullpage, inverse ## GitHub operations 1. Create or **fork** a repository 2. **Add** files 3. **Commit** changes 4. Compare **diff** versions 5. Make and accept **pull requests**. ## RStudio operations 1. **Init**/**Clone** a repository as an RStudio Project 2. **Pull** changes from remote 3. **Add** files locally 4. **Commit** changes 5. **Push** to remote --- class: center, inverse # .big[Demonstration] --- ## Further reading 1. [**Practical Worksheet**](https://personalpages.manchester.ac.uk/staff/david.selby/rthritis/2021-03-12-git/) 1. [Version control for scientific research](https://blogs.biomedcentral.com/bmcblog/2013/02/28/version-control-for-scientific-research/) .small[(Hrynaszkiewicz, 2013)] 1. [Version control with RStudio](https://support.rstudio.com/hc/en-us/articles/200532077-Version-Control-with-Git-and-SVN) .small[(Stephens, 2021)] 1. [Happy Git and GitHub for the useR](https://happygitwithr.com/) .small[(Bryan _et al._, 2016)] 1. [Minimal git/github tutorial guide](https://kbroman.org/github_tutorial/) .small[(Broman, 2013)] --- ## Next **Rthritis** meeting .secondary[.BIG[Statistical modelling with Stan]] Friday 26.sup[th] March @ 11:00 Belay Birlie Yimer .footnote[Contact <david.selby@manchester.ac.uk> to suggest topics/speakers]