├── .github └── workflows │ └── publish.yml ├── .gitignore ├── CITATION.cff ├── Introduction-RStudio-Git-GitHub.Rproj ├── LICENSE-CODE.md ├── LICENSE.md ├── README.md ├── SSH.qmd ├── _quarto.yml ├── analysis_start.qmd ├── assets ├── GitHub-remote.png ├── LMU-OSC_favicon.jpg ├── LMU-OSC_logo.jpg ├── add-ssh-key.png ├── commit.png ├── file_list.png ├── first_commit.png ├── first_push_confirm_identity.png ├── git_changed.png ├── git_commit_message.png ├── git_commit_message2.png ├── git_commit_message3.png ├── git_diff.png ├── git_history_tab.png ├── git_history_tab_filter.png ├── git_history_tab_filter_example.png ├── git_more_shell.png ├── git_pane.png ├── git_pane_added.png ├── git_push.png ├── github_git_commands.png ├── my_new_repo_name.png ├── new_repo.png ├── new_repo_name.png ├── project_files.png ├── project_screen1.png ├── project_screen2.png ├── project_screen3.png ├── readme_commit.png ├── ssh-key.png └── staged_readme.png ├── commit.qmd ├── custom.scss ├── github.qmd ├── github_sync.qmd ├── index.qmd ├── installing_git.qmd ├── installing_software.qmd ├── making_change.qmd ├── matomo_analytics.html ├── next_steps.qmd ├── rstudio_project.qmd ├── styles.css ├── updates.qmd ├── version_control.qmd └── viewing_history.qmd /.github/workflows/publish.yml: -------------------------------------------------------------------------------- 1 | on: 2 | workflow_dispatch: 3 | push: 4 | branches: main 5 | 6 | name: Quarto Publish 7 | 8 | jobs: 9 | build-deploy: 10 | runs-on: ubuntu-latest 11 | permissions: 12 | contents: write 13 | steps: 14 | - name: Check out repository 15 | uses: actions/checkout@v4 16 | 17 | - name: Set up Quarto 18 | uses: quarto-dev/quarto-actions/setup@v2 19 | 20 | - name: Install R 21 | uses: r-lib/actions/setup-r@v2 22 | with: 23 | r-version: '4.4.0' 24 | 25 | # - name: Install R Dependencies 26 | # uses: r-lib/actions/setup-renv@v2 27 | # with: 28 | # cache-version: 1 29 | 30 | - name: Render and Publish 31 | uses: quarto-dev/quarto-actions/publish@v2 32 | with: 33 | target: gh-pages 34 | env: 35 | GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 36 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # History files 2 | .Rhistory 3 | .Rapp.history 4 | 5 | # Session Data files 6 | .RData 7 | .RDataTmp 8 | 9 | # User-specific files 10 | .Ruserdata 11 | 12 | # Example code in package build process 13 | *-Ex.R 14 | 15 | # Output files from R CMD build 16 | /*.tar.gz 17 | 18 | # Output files from R CMD check 19 | /*.Rcheck/ 20 | 21 | # RStudio files 22 | .Rproj.user/ 23 | 24 | # produced vignettes 25 | vignettes/*.html 26 | vignettes/*.pdf 27 | 28 | # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 29 | .httr-oauth 30 | 31 | # knitr and R markdown default cache directories 32 | *_cache/ 33 | /cache/ 34 | 35 | # Temporary files created by R markdown 36 | *.utf8.md 37 | *.knit.md 38 | 39 | # R Environment Variables 40 | .Renviron 41 | 42 | # pkgdown site 43 | docs/ 44 | 45 | # translation temp files 46 | po/*~ 47 | 48 | # RStudio Connect folder 49 | rsconnect/ 50 | 51 | # Quarto 52 | /.quarto/ 53 | 54 | # Future-proofing: ignore commonly included files that should not be tracked 55 | # Inspired by usethis::git_vaccinate() options 56 | .DS_Store 57 | .Rproj.user 58 | .httr-oauth 59 | .quarto 60 | _site/ 61 | -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- 1 | cff-version: 1.2.0 2 | message: "If you use this software, please cite it as below." 3 | authors: 4 | - family-names: "Croucher" 5 | given-names: "Mike"" 6 | affiliation: "Community Developer Advocate, MathWorks" 7 | title: "Introduction to version Control with git and GitHub within RStudio" 8 | version: 1.0.0 9 | doi: 10 | date-released: 2016-09-03 11 | repository-code: "https://github.com/lmu-osc/Introduction-RStudio-Git-GitHub" 12 | url: "https://github.com/lmu-osc/Introduction-RStudio-Git-GitHub" 13 | -------------------------------------------------------------------------------- /Introduction-RStudio-Git-GitHub.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: knitr 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | -------------------------------------------------------------------------------- /LICENSE-CODE.md: -------------------------------------------------------------------------------- 1 | # Creative Commons Zero v1.0 Universal 2 | 3 | CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE LEGAL SERVICES. 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For the avoidance of doubt, this paragraph does not form part of the public licenses. 170 | > 171 | > Creative Commons may be contacted at creativecommons.org. -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Introduction to version control with Git and GitHub within RStudio 2 | 3 | ## About this work 4 | 5 | This work was originally created by [Mike Croucher](https://github.com/mikecroucher) from [RSE-Sheffield](https://github.com/RSE-Sheffield) under a [Creative Commons Attribution Share Alike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/legalcode). The [original repository](https://doi.org/10.5281/zenodo.61435) was created for a workshop organised by Malika Ihle at the International Society for Behavioural Ecology conference in 2016. It was subsequently adapted by Malika for [Reproducible Research Oxford](https://ox.ukrn.org/). It is now maintained by [Malika Ihle](https://www.osc.uni-muenchen.de/about_us/coordinator/index.html) for the [LMU Open Science Center](https://www.osc.uni-muenchen.de/index.html). The overview image is from [Dumitru Uzun](https://duzun.me/tips/git). You are free to use this work in your own projects. 6 | 7 | ## Before the session 8 | Please watch this 10 min introductory [videorecording](https://osf.io/dcqt9/). 9 | 10 | ## Overview of the exercice 11 | In this session, you are going to start using the version control system Git from within RStudio to keep your local workflow tidy while having access to all previous versions of your files. You will then backup your workflow online on a remote GitHub server, which will allow you to access your work from any computer, and sharing it with your collaborators or publically. Specifically, you will 12 | * install and configure Git (as well as R and RStudio if needed), and create a GitHub account 13 | * create a local RStudio project under version control 14 | * make changes and **commit** them to your local repository (i.e. save your changes locally in your version control system) 15 | * connect your local repository to your GitHub account by creating a remote GitHub repository and setting it as the 'origin' of your local repository from the command line (this is the procedure you will have to follow to 'upgrade' your former RStudio projects that were not under version control and backed-up on GitHub; but in the future, I recommend you first create a GitHub repository (your remote origin) and then **clone** it locally (i.e. copy it to your computer while maintaining a connection to your remote (GitHub) version). This procedure, easily done from RStudio, will be covered in the [second workshop](https://lmu-osc.github.io/Collaborative-RStudio-GitHub/)) 16 | * **push** your local changes to your remote repository (i.e. synchronise your changes to your GitHub version) 17 | 18 | Once this workflow is set up, you can easily work with several computers or with collaborators: if you have changes in your GitHub version (if you or a collaborator pushed changes from another computer or if you made changes online, directly on GitHub), you can **pull** them into your local version (i.e fetch changes and merge them locally, to keep your copy up-to-date). 19 | 20 |
21 | 22 |
23 | 24 | ## Step-by-step tutorial 25 | The material is self-paced and includes a worked-example. It is necessary that you work through the sections in order. 26 | 27 | * [Installing R and RStudio](./installing_software.qmd) 28 | * [Installing and configuring Git](./installing_git.qmd) - Set up your own machine 29 | * [Getting an account on GitHub](./github.qmd) - Sign up for GitHub 30 | * [Securing your connection to GitHub](./SSH.qmd) - Create a secure SSH key to identify yourself on GitHub 31 | * [Creating an RStudio project](./rstudio_project.qmd) - Creating an example, version controlled project 32 | * [Starting our analysis project](./analysis_start.qmd) - A simple script to get us started 33 | * [Getting our project under version control](./version_control.qmd) - First step into a larger world 34 | * [Making some changes](./making_change.qmd) - Making our script more useful 35 | * [Committing our change](./commit.qmd) - How to commit a change 36 | * [Viewing history](./viewing_history.qmd) - How to view the history of your project or of a single file 37 | * [Connecting our local repository to GitHub](./github_sync.qmd) - Backup! Making our code available to the world. 38 | * [Subsequent updates](./updates.qmd) - Now we are set up, the workflow is easy. 39 | * [Things we haven't told you](./next_steps.qmd) - Steps to further learning 40 | -------------------------------------------------------------------------------- /SSH.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Secure the connection between your computer and GitHub" 3 | format: html 4 | --- 5 | 6 | When working with a GitHub repository, you'll often need to identify yourself to GitHub using your username and password. There are several ways to secure this connection further. Establishing a secure connection is mandatory since August 2021. 7 | 8 | Today we will use **SSH Keys** to secure your identification to GitHub as this is a common way to secure connections, which you may encounter again in other contexts in the future. 9 | 10 | SSH keys come in pairs, a public key that gets shared with services like GitHub, and a private key that is stored only on your computer. If the keys match, you're granted access. 11 | 12 | The procedure below only need to be executed once per GitHub account and for each computer you will use to connect to GitHub. 13 | 14 | ## Checking for existing SSH key pair 15 | The first step in using SSH authorization with GitHub is to generate your own key pair. 16 | However, you might already have an SSH key pair on your machine. You can check to see if one exists by moving to your `.ssh` directory and listing the contents. 17 | 18 | On windows, open **Git Bash** (start menu -> Git Bash). On MacOS, open 19 | the **Terminal** app. On Linux, open your distribution's (or any 20 | other) terminal emulator. Enter the following commands one after the 21 | other (hitting ENTER after each command). 22 | 23 | ```bash 24 | ls ~/.ssh 25 | ``` 26 | 27 | The `ls` command lists the content of a directory, here `~/.ssh`. Check the directory listing to see if you already have a public SSH key. By default, the filenames of the public keys are one of the following: 28 | 29 | ```bash 30 | id_rsa.pub 31 | id_ecdsa.pub 32 | id_ed25519.pub 33 | ``` 34 | 35 | If you do have one, you can skip the section that generate a SSH key pair, and go to the section 'Adding a new SSH key to your GitHub account'. 36 | 37 | **If you don't have an existing public and private key pair (which is to be expected!), or if you receive an error that ~/.ssh doesn't exist, that this file location doesn't exist, or that you can't access this folder, go ahead and generate a new SSH key pair!** 38 | 39 | ## Generating an SSH key pair 40 | 41 | In the command line, type the following by replacing your_email@email.com with your own email address. Pay attention to spaces and capital letter! 42 | 43 | ```bash 44 | # MAKE SURE TO REPLACE "your_email@email.com" WITH YOUR EMAIL ADDRESS 45 | ssh-keygen -t ed25519 -C "your_email@email.com" 46 | ``` 47 | 48 | This creates a new SSH key pair, using the provided email as a label. 49 | 50 | When you're prompted to "Enter a file in which to save the key," press ENTER. This accepts the default file location. 51 | This is the promt that will appear: 52 | 53 | ```bash 54 | Generating public/private ed25519 key pair. 55 | Enter file in which to save the key (/Users/username/.ssh/id_ed25519): 56 | ``` 57 | 58 | You will then be asked to provide a passphrase. Protecting your keys with a password is optional but highly recommended. Note: when you type passwords in the command line, nothing is displayed, not even \***. 59 | This is the promt that will appear: 60 | 61 | ```bash 62 | Enter passphrase (empty for no passphrase): 63 | Enter same passphrase again: 64 | ``` 65 | 66 | When the key generation is complete, you should see the following confirmation: 67 | 68 | ```bash 69 | Your identification has been saved in /Users/username/.ssh/id_ed25519. 70 | Your public key has been saved in /Users/username/.ssh/id_ed25519.pub. 71 | The key fingerprint is: 72 | SHA256:6nr/zo0g7Bz7WMRwy34maBhQy1UZyX47gT+egRdlIhs your_email@email.com 73 | The key's randomart image is: 74 | +--[ED25519 256]--+ 75 | | .o++ | 76 | | o oF . o | 77 | | . o+ =.+. | 78 | | . + += . | 79 | | . +S++ | 80 | | . ..oB= | 81 | | . ++*=. | 82 | | o.==* o | 83 | | .o.o+** . | 84 | +----[SHA256]-----+ 85 | ``` 86 | 87 | 88 | ## Adding a new SSH key to your GitHub account 89 | 90 | We now need to tell GitHub about your public key. Display the contents of your new public key file with `cat`. 91 | **Be careful**: do not copy the content of your *private* key, but your *public* key. Your public key ends with `.pub`. 92 | Please type the command below exactly as it is, in its entirety: 93 | 94 | ```bash 95 | # Run this code 96 | cat ~/.ssh/id_ed25519.pub 97 | ``` 98 | 99 | The output should look something like this: 100 | 101 | ``` 102 | # The output looks like this. The characters after ssh-ed25519 will be different for you, however. 103 | ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIFEKiimOpcayfHhlbjmnIBAUX74FY/o20k9yFA16XOLm your_email@email.com 104 | ``` 105 | 106 | Copy the contents of the output to your clipboard. 107 | 108 | Login to github.com and bring up your account settings by clicking on your profile photo (top right) and selecting **Settings**. Click on **SSH and GPG keys** (left sidebar), and then click on the green button 'New SSH key' or '**Add SSH key**'. 109 | 110 | ![](./assets/ssh-key.png) 111 | 112 | In the "Title" field, add a descriptive label for the new key, e.g. something that would identify the device you just connected. For example, if you're using a personal laptop, you might call this key "Personal MacBook Air". Finally, paste the contents of your clipboard into the Key text box and hit the green 'Add key' button to save. Enter your GitHub password if prompted. 113 | 114 | ![](./assets/add-ssh-key.png) 115 | 116 | 117 | 118 | ## Adding your key to the ssh-agent 119 | 120 | To manage your keys, it is best to use a piece of software called `ssh-agent`. 121 | 122 | Depending on your system, the following might not be necessary. On 123 | most GNU/Linux distributions, your key will be automatically added to 124 | the `ssh-agent` after the first time you enter it. If you keep getting 125 | asked for your key each time you want to clone or push to a GitHub 126 | repository, you can follow the following instructions. 127 | 128 | In the command line, start the ssh-agent with this command: 129 | 130 | ```bash 131 | eval "$(ssh-agent -s)" 132 | ``` 133 | 134 | which should display an output similar to something like this: 135 | 136 | ``` 137 | Agent pid 59566 138 | ``` 139 | 140 | Then, add your key to the ssh-agent by typing the entirety of this command: 141 | 142 | ```bash 143 | ssh-add ~/.ssh/id_ed25519 144 | ``` 145 | 146 | ## Testing Your Connection to GitHub 147 | 148 | (These instructions are a slightly abbreviated version of the page here: https://docs.github.com/en/authentication/connecting-to-github-with-ssh/testing-your-ssh-connection) 149 | 150 | Finally, we can "ask" GitHub at the command line if our connection is acceptable with the following code: 151 | 152 | ```bash 153 | ssh -T git@github.com 154 | # Attempts to ssh to GitHub 155 | ``` 156 | 157 | You will likely be asked about "fingerprinting" to which you can type `yes`, fingerprinting is okay, and press Enter. You should then receive a message like this: 158 | 159 | ``` 160 | > Hi USERNAME! You've successfully authenticated, but GitHub does not 161 | > provide shell access. 162 | ``` 163 | 164 | That's it! 165 | 166 | Going forward, you can use the SSH clone URL when copying a repo to your local machine (we will cover this in the second tutorial). You are completely done with the setting up part, which you will need to repeat only if you change computer. 167 | Let the fun begin! 168 | 169 | *** 170 | 171 | -------------------------------------------------------------------------------- /_quarto.yml: -------------------------------------------------------------------------------- 1 | project: 2 | type: website 3 | 4 | 5 | website: 6 | title: "" 7 | page-footer: 8 | center: "Copyright, 2024 Open Science Center at LMU Munich" 9 | border: false 10 | search: 11 | location: sidebar 12 | repo-url: https://github.com/lmu-osc/Introduction-RStudio-Git-GitHub 13 | repo-actions: [edit, issue] 14 | page-navigation: true 15 | favicon: assets/LMU-OSC_favicon.jpg 16 | margin-header: | 17 | ![](/assets/LMU-OSC_logo.jpg){width="175"} 18 | navbar: 19 | left: 20 | - href: index.qmd 21 | 22 | 23 | sidebar: 24 | style: docked 25 | contents: 26 | - text: "Home" 27 | href: index.qmd 28 | - section: "Tutorial" 29 | contents: 30 | - href: installing_software.qmd 31 | text: "Installing R and RStudio" 32 | - href: installing_git.qmd 33 | text: "Installing and configuring Git" 34 | - href: github.qmd 35 | text: "Getting an account on GitHub" 36 | - href: SSH.qmd 37 | text: "Securing your connection to GitHub" 38 | - href: rstudio_project.qmd 39 | text: "Creating an RStudio project" 40 | - href: analysis_start.qmd 41 | text: "Starting our analysis project" 42 | - href: version_control.qmd 43 | text: "Getting our project under version control" 44 | - href: making_change.qmd 45 | text: "Making some changes" 46 | - href: commit.qmd 47 | text: "Committing our change" 48 | - href: viewing_history.qmd 49 | text: "Viewing history" 50 | - href: github_sync.qmd 51 | text: "Connecting our local repository to GitHub" 52 | - href: updates.qmd 53 | text: "Subsequent updates" 54 | - href: next_steps.qmd 55 | text: "Things we haven’t told you" 56 | 57 | 58 | format: 59 | html: 60 | theme: 61 | - cosmo 62 | - custom.scss 63 | css: styles.css 64 | toc: true 65 | include-in-header: 66 | - file: matomo_analytics.html 67 | 68 | 69 | 70 | -------------------------------------------------------------------------------- /analysis_start.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Starting our analysis project" 3 | format: html 4 | --- 5 | 6 | 7 | The purpose of this tutorial is to teach you version control. In order to do this, however, we'll need to make up a simple project that needs controlling! 8 | 9 | Our initial project will be extremely simple -- a very small data file and a script that loads and plots it. Later, we'll add code to fit a nonlinear curve to it. 10 | 11 | Download this data to your project folder: [Example data](https://raw.githubusercontent.com/RSE-Sheffield/Code_cafe/master/example_data.csv) (right click to open in a new window and use your Web browser's save as functionality (likely another right click on the page)). You may need to manually add the file extension ".csv"). 12 | 13 | Create a new R script in RStudio. **File** -> **New File** -> **R script** 14 | 15 | Enter the following commands into your new R script 16 | 17 | ```r 18 | mydata = read.csv("example_data.csv") 19 | plot(mydata$xdata,mydata$ydata) 20 | ``` 21 | 22 | Save the R script as `myscript.R`. When you run it, it should load and plot the data. 23 | 24 | Your directory should now contain 4 files: 25 | 26 | ![](./assets/file_list.png) 27 | 28 | *** 29 | 30 | -------------------------------------------------------------------------------- /assets/GitHub-remote.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmu-osc/Introduction-RStudio-Git-GitHub/daade7c25ff2a369bb325fabf657ca8773f8edda/assets/GitHub-remote.png -------------------------------------------------------------------------------- /assets/LMU-OSC_favicon.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmu-osc/Introduction-RStudio-Git-GitHub/daade7c25ff2a369bb325fabf657ca8773f8edda/assets/LMU-OSC_favicon.jpg -------------------------------------------------------------------------------- /assets/LMU-OSC_logo.jpg: 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change" 3 | format: html 4 | --- 5 | 6 | 7 | **All files need to be saved before being 'committable'**. 8 | 9 | Now, click on the **git** tab in RStudio. You'll notice that there are two files listed -- our script, which has been modified, and our script too, which was added. Click on the staged box to stage the change to the first script. 10 | 11 | ![](./assets/git_changed.png) 12 | 13 | Now click on **Diff** to give a summary of what's changed. Lines that have been added are green. Lines that have been removed are red. From git's point of view, a modification to a line is actually two operations: the removal of the original line followed by the creation of the new line. 14 | 15 | ![](./assets/git_diff.png) 16 | 17 | Add a commit message and click on commit 18 | 19 | ![](./assets/git_commit_message2.png) 20 | 21 | Now stage the second script, and commit it with a new message. 22 | 23 | ![](./assets/git_commit_message3.png) 24 | 25 | 26 | *** 27 | 28 | -------------------------------------------------------------------------------- /custom.scss: -------------------------------------------------------------------------------- 1 | /*-- scss:defaults --*/ 2 | // Base document colors 3 | $navbar-bg: #009933; 4 | $link-color: #006426; 5 | $sidebar-hl: #006426; 6 | -------------------------------------------------------------------------------- /github.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Create an account on GitHub" 3 | format: html 4 | --- 5 | 6 | 7 | Although git can be used on its own, most people choose to use it in conjunction with an online repository service. The most popular of these, by far, is GitHub. 8 | 9 | It has become so standard that some organisations will ask to see your GitHub profile as part of job applications! 10 | 11 | * Create a free account on GitHub. 12 | * https://github.com/join 13 | 14 | You do not need to select any additional products proposed upon creation of the account. 15 | 16 | *** 17 | 18 | -------------------------------------------------------------------------------- /github_sync.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: " Connecting our local repository to GitHub" 3 | format: html 4 | --- 5 | 6 | Our project is fully version controlled so we have access to a detailed history of every change we've ever made to it. This is a great first step but all of this only exists on our own computers at the moment. 7 | 8 | It's time to upload our project to GitHub! 9 | 10 | Putting your code on GitHub confers a number of benefits: 11 | 12 | * Everything is backed up for you. 13 | * Your project is made available to others. This is a vital part of modern scientific dissemination. 14 | * GitHub has a range of project management and collaboration tools that work on a per-project basis. 15 | * Your GitHub profile can be used as part of your online-identity. 16 | 17 | **Creating a new repository on GitHub** 18 | 19 | * Log into GitHub and go to your profile page. On the **repositories** tab, click **New** 20 | 21 | 22 | 23 | At the **Create a new repository** screen, give your repo a name and click **Create Repository**. 24 | In this case only, when you didn't start by creating a repo on GitHub but want to push from an exisiting local repository for the first time like we are doing now and like you would to upgrade your old projects, do NOT select 'create a README file' but directly 'Create repository'. 25 | 26 | ![](./assets/new_repo_name.png) 27 | 28 | The **Quick Setup** screen gives sets of git commands that can be used in various circumstances. 29 | First, make sure you select the SSH tab (the url shown in the blue box should start with git@github.com). 30 | 31 | 32 | 33 | We are then interested in **…or push an existing repository from the command line**. Copy these commands to the clipboard using the copy button on GitHub. 34 | 35 | ![](./assets/github_git_commands.png) 36 | 37 | In RStudio, navigate to the **git** tab and click on **More -> New terminal** 38 | 39 | ![](./assets/git_more_shell.png) 40 | 41 |
42 | 43 | Paste the git commands into the Shell and press Enter to execute them. 44 | Given this is your first push, you may be asked again to authenticate your identity by entering the password of your SSH key 45 | 46 | ![](./assets/first_push_confirm_identity.png) 47 | 48 | 49 | and/or prompted with such sentence in the terminal: 50 | 51 | ```bash 52 | Are you sure you want to continue connecting (yes/no/[fingerprint])? 53 | ``` 54 | to which you should answer `yes` 55 | 56 |
57 | 58 | > **Warning for Windows OS with RStudio > 2022.12.0** 59 | > If you get an error saying you do not have a SSH key in the appropriate location, this is due to a known bug in the RStudio / Git bash interaction which we expect to be eventually resolved with updates. A temporary solution is to open the Windows Power Shell instead of Git Bash as terminal within RStudio: for this, go to RStudio -> Tools -> Global Options -> Terminal -> New terminals open with -> choose Windows Power Shell -> Click Apply -> close the panel -> Complete the steps above (i.e. paste or type the commands presented by your new GitHub repo) -> change back the default terminal within RStudio to Git Bash. 60 | 61 |
62 | 63 | Finally, confirm that the project has been uploaded to your GitHub profile (you may need to refresh your GitHub page). 64 | 65 | *** 66 | 67 | -------------------------------------------------------------------------------- /index.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Introduction to version Control with git and GitHub within RStudio" 3 | format: html 4 | --- 5 | 6 | ## About this work 7 | 8 | This work was originally created by [Mike Croucher](https://github.com/mikecroucher) from [RSE-Sheffield](https://github.com/RSE-Sheffield) under a [Creative Commons Attribution Share Alike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/legalcode). It was subsequently adapted by [Malika Ihle](https://www.osc.uni-muenchen.de/about_us/coordinator/index.html) during her time at [Reproducible Research Oxford](https://ox.ukrn.org/) and alter the the [LMU Open Science Center](https://www.osc.uni-muenchen.de/index.html). The overview image is from [Dumitru Uzun](https://duzun.me/tips/git). You are free to use this work in your own projects. 9 | 10 | ## Before the session 11 | Please watch this 10 min introductory [videorecording](https://osf.io/dcqt9/). 12 | 13 | ## Overview of the exercice 14 | In this session, you are going to start using the version control system Git from within RStudio to keep your local workflow tidy while having access to all previous versions of your files. You will then backup your workflow online on a remote GitHub server, which will allow you to access your work from any computer, and sharing it with your collaborators or publically. Specifically, you will 15 | 16 | * install and configure Git (as well as R and RStudio if needed), and create a GitHub account 17 | * create a local RStudio project under version control 18 | * make changes and **commit** them to your local repository (i.e. save your changes locally in your version control system) 19 | * connect your local repository to your GitHub account by creating a remote GitHub repository and setting it as the 'origin' of your local repository from the command line. This is the procedure you will have to follow to 'upgrade' your former RStudio projects that were not under version control and backed-up on GitHub; but in the future, I recommend you first create a GitHub repository (your remote origin) and then **clone** it locally (i.e. copy it to your computer while maintaining a connection to your remote (GitHub) version). This procedure, easily done from RStudio, will be covered in the [second workshop](https://lmu-osc.github.io/Collaborative-RStudio-GitHub/) 20 | * **push** your local changes to your remote repository (i.e. synchronise your changes to your GitHub version) 21 | 22 | Once this workflow is set up, you can easily work with several computers or with collaborators: if you have changes in your GitHub version (if you or a collaborator pushed changes from another computer or if you made changes online, directly on GitHub), you can **pull** them into your local version (i.e fetch changes and merge them locally, to keep your copy up-to-date). 23 | 24 |
25 | 26 |
27 | 28 | ## Step-by-step tutorial 29 | The material is self-paced and includes a worked-example. It is necessary that you work through the sections in order. 30 | 31 | * [Installing R and RStudio](./installing_software.qmd) 32 | * [Installing and configuring Git](./installing_git.qmd) - Set up your own machine 33 | * [Getting an account on GitHub](./github.qmd) - Sign up for GitHub 34 | * [Securing your connection to GitHub](./SSH.qmd) - Create a secure SSH key to identify yourself on GitHub 35 | * [Creating an RStudio project](./rstudio_project.qmd) - Creating an example, version controlled project 36 | * [Starting our analysis project](./analysis_start.qmd) - A simple script to get us started 37 | * [Getting our project under version control](./version_control.qmd) - First step into a larger world 38 | * [Making some changes](./making_change.qmd) - Making our script more useful 39 | * [Committing our change](./commit.qmd) - How to commit a change 40 | * [Viewing history](./viewing_history.qmd) - How to view the history of your project or of a single file 41 | * [Connecting our local repository to GitHub](./github_sync.qmd) - Backup! Making our code available to the world. 42 | * [Subsequent updates](./updates.qmd) - Now we are set up, the workflow is easy. 43 | * [Things we haven't told you](./next_steps.qmd) - Steps to further learning 44 | -------------------------------------------------------------------------------- /installing_git.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Installing and configuring Git" 3 | format: html 4 | --- 5 | 6 | RStudio version control functionality is provided by another software called **git** 7 | 8 | 9 | **Install git** 10 | 11 | Git is one of the most popular version control systems in the world. It is free and open source. 12 | 13 | * Windows & OS X: http://git-scm.com/downloads 14 | * Windows: download the .exe file, run it and accept all the default settings (unless you know what you are doing) and keep clicking 'next' 15 | * OS X: at the link above, select the first option that suggests to install git through installing homebrew, by pasting a line of command provided in their instructions in your terminal, and accept the prompts appearing in your terminal. 16 | * Debian/Ubuntu: `sudo apt-get install git-core` 17 | * Fedora/RedHat: `sudo yum install git-core` 18 | 19 | **Configure git** 20 | 21 | After installing git, you need to tell it who you are. 22 | 23 | By default, git is used through a _command line interface_. We'll use 24 | git in this way now in order to perform its initial and minimal 25 | configuration. In the remaining of this tutorial, you'll learn how to 26 | use git through Rstudio instead of a command line interface. 27 | 28 | On windows, open **Git Bash** (start menu -> Git Bash). On MacOS, open 29 | the **Terminal** app. On Linux, open your distribution's (or any 30 | other) terminal emulator. Enter the following commands EXACTLY (spaces and quotation marks included) one after the 31 | other (hitting ENTER after each command). On successful completion, you should see no output from these commands. 32 | 33 | Make sure to replace `you@youremail.com` and `Your Name` by your email 34 | address and your name. 35 | 36 | ```bash 37 | git config --global user.email "you@youremail.com" 38 | git config --global user.name "Your Name" 39 | ``` 40 | 41 | 42 | *** 43 | 44 | -------------------------------------------------------------------------------- /installing_software.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Installing R and RStudio" 3 | format: html 4 | --- 5 | 6 | 7 | Many users of R use it from within another free piece of software called **RStudio.** 8 | RStudio is a powerful and productive user interface for R. It’s free and open source, and works great on Windows, Mac, and Linux. 9 | 10 | **Install R** 11 | 12 | Install R first. Downloads are available at https://cran.rstudio.com/ 13 | 14 | * Direct link for Windows https://cran.r-project.org/bin/windows/base/ 15 | * Direct link for MacOS X https://cran.r-project.org/bin/macosx/ 16 | * Direct link for Linux https://cran.r-project.org/bin/linux/ 17 | 18 | **Install RStudio** 19 | 20 | Next, install RStudio. 21 | 22 | * Downloads are available at https://www.rstudio.com/products/rstudio/download/ 23 | 24 | 25 | 26 | *** 27 | 28 | -------------------------------------------------------------------------------- /making_change.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Making some changes" 3 | format: html 4 | --- 5 | 6 | The next version of our project will do 3 changes. 7 | 8 | 1. Add the following code to the end of your R script. 9 | 10 | ```r 11 | # some guesses for the parameters. 12 | p1 = 1 13 | p2 = 0.2 14 | 15 | # do the fit 16 | fit = nls(ydata ~ p1*cos(p2*xdata) + p2*sin(p1*xdata), data = mydata, start = list(p1=p1,p2=p2)) 17 | 18 | #Plot the fitted line 19 | new = data.frame(xdata = seq(min(mydata$xdata),max(mydata$xdata),len=200)) 20 | lines(new$xdata,predict(fit,newdata=new)) 21 | 22 | ``` 23 | 24 | 2. change the command that plots our data in this file. Change the lines 25 | 26 | ```r 27 | plot(mydata$xdata,mydata$ydata) 28 | ``` 29 | 30 | to 31 | 32 | ```r 33 | plot(mydata$xdata,mydata$ydata,col='red') 34 | ``` 35 | 36 | We do this so we can illustrate how git handles modifications of existing lines as well as simply adding extra lines of code. 37 | 38 | Make sure the code runs before proceeding further and save the script. 39 | 40 | 3. Finally, we will **create another R file** (File -> New File -> R script). 41 | 42 | Enter the command: 43 | 44 | ```r 45 | #Simulate some data 46 | plot(rnorm(100,0,1)) 47 | ``` 48 | And save the file as `myscript_too` 49 | 50 | 51 | *** 52 | 53 | -------------------------------------------------------------------------------- /matomo_analytics.html: -------------------------------------------------------------------------------- 1 | 2 | 15 | -------------------------------------------------------------------------------- /next_steps.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Things we haven't told you" 3 | format: html 4 | --- 5 | 6 | 7 | You've come a long way! You've installed and configured all the software you need and have learned the basics required to put your code under version control and make it openly available to the world. 8 | 9 | As you've seen, the standard git workflow is fairly straightforward and adds very little overhead to your workflow once you're set up. 10 | 11 | Git and GitHub are extremely powerful systems and there is a lot more you can learn if you wish. Here are some pointers:- 12 | 13 | * Learn command line git by following this tutorial from Software Carpentry - http://swcarpentry.github.io/git-novice/ 14 | * Make your analysis citable and more discoverable by using Zenodo to assign it a Digital Object Identifier - https://zenodo.org/features 15 | 16 | **Testing and version control** 17 | 18 | By employing testing, you can ensure that your code behaves the way you expect. 19 | 20 | * Unit testing in R, the bare minimum - http://www.johnmyleswhite.com/notebook/2010/08/17/unit-testing-in-r-the-bare-minimum/ 21 | * Continuous Integration. Every time you push a change to GitHub, your tests are automatically run. - https://docs.travis-ci.com/user/languages/r 22 | 23 | **Dealing with dependencies** 24 | 25 | Your code works on your machine but not on someone else's because they are using a different version of R and have different versions of packages installed. How might we fix this? 26 | 27 | * https://lmu-osc.github.io/introduction-to-renv/ - renv enhances your project directory by storing your package dependencies inside it. 28 | 29 | *** 30 | ::: {style="text-align: right"} 31 | [Go to the second tutorial!](https://lmu-osc.github.io/Collaborative-RStudio-GitHub/){.btn .btn-success .btn role="button"} 32 | ::: 33 | 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /rstudio_project.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Creating an RStudio project" 3 | format: html 4 | --- 5 | 6 | 7 | A project is a folder that contains everything concerning your analysis and may include code, data and documentation. It is a complete research object that can be used to describe and reproduce your research. 8 | 9 | Create a new project in RStudio as follows: 10 | 11 | **File** -> **New Project** -> **New Directory** 12 | 13 | 14 | 15 | In the **Project Type** screen, click on **Empty Project** or **New project** 16 | 17 | 18 | 19 | In the **Create New Project** screen, give your project a name (e.g.'my_first_test_repo') and ensure that **create a git repository** is checked. Click on **Create Project**. 20 | 21 | 22 | 23 | RStudio will create a new folder containing an empty project and set R's working directory to within it. 24 | 25 | 26 | Two files are created in the otherwise empty project: 27 | 28 | ![](./assets/project_files.png) 29 | 30 | * **.gitignore** - Specifies files that should be ignored by the version control system (e.g. sensible data files that should not be made public, or documentation that you don't need version controlled). 31 | * **my_first_test_repo.Rproj** - Configuration information for the RStudio project 32 | 33 | There is no need to worry about the contents of either of these for the purposes of this tutorial. 34 | 35 | *** 36 | 37 | -------------------------------------------------------------------------------- /styles.css: -------------------------------------------------------------------------------- 1 | /* css styles */ 2 | 3 | .nav-page .nav-page-text { 4 | font-size: 15pt; 5 | } 6 | -------------------------------------------------------------------------------- /updates.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Subsequent updates" 3 | format: html 4 | --- 5 | 6 | 7 | Once a local repository has been associated with GitHub, it's not necessary to use the command line for subsequent uploads. We'll demonstrate this now by adding a **README.md** file to our project. 8 | 9 | On GitHub, the README.md file is special since it is rendered by GitHub and is used by many people as an introduction to the project. 10 | 11 | In RStudio, click on **File->New File->Text File**. Add the following text to the file and save it as **Readme.md**. 12 | 13 | ```bash 14 | # My Example Repo 15 | 16 | This repo is used to demonstrate GitHub to users of R and R Studio. 17 | ``` 18 | 19 | In the **git** tab of RStudio, the **Readme.md** file should be the only file you see. Stage it as shown below and click **commit**. 20 | 21 | ![](./assets/staged_readme.png) 22 | 23 | Supply a commit message and click commit. 24 | 25 | ![](./assets/readme_commit.png) 26 | 27 | Finally, click **push** to upload to GitHub. 28 | 29 | ![](./assets/git_push.png) 30 | 31 | You can see that the standard workflow loop is very quick and simple 32 | 33 | * Make your change 34 | * Stage your change 35 | * Commit 36 | * Push to GitHub 37 | 38 | *** 39 | 40 | -------------------------------------------------------------------------------- /version_control.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Getting our project under version control" 3 | format: html 4 | --- 5 | 6 | 7 | We now have the first version of our analysis so let's get it under version control. By default, the git version control pane is in the top right hand corner of RStudio. Find it and click on the **git** tab. 8 | 9 | ![](./assets/git_pane.png) 10 | 11 | If you hover the mouse pointer over the yellow ? marks in GitHub, you'll see a tooltip telling us that the file is **untracked**. This means that git is not tracking versions of this file. 12 | 13 | Tick **staged** for each file. In some future cases, you may want to stage only one or a few file to create a coherent commit (unit of change). 14 | 15 | ![](./assets/git_pane_added.png) 16 | 17 | All of our files are now **staged**, ready for the first **commit**. Click on the **commit** button 18 | 19 | ![](./assets/commit.png) 20 | 21 | Details of the commit will appear in the next panel. You need to specify a **commit message** -- something descriptive about the changes you've made. Since this is our first commit, we'll follow tradition and call it **First Commit** 22 | 23 | Once you've typed a commit message, click on **Commit** and you're done. 24 | 25 | ![](./assets/first_commit.png) 26 | 27 | The following messages from git will show. 28 | 29 | 30 | 31 | Click on **Close** and you are done. 32 | 33 | *** 34 | 35 | -------------------------------------------------------------------------------- /viewing_history.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Viewing history" 3 | format: html 4 | --- 5 | 6 | 7 | In this **Diff** pop up window, which you found in the **git** tab of RStudio, you can also press the **History** button to review the history of your project or files. 8 | 9 | 10 | ![](./assets/git_history_tab.png) 11 | 12 | 13 | By default, the history search feature will show all files added, changed, or deleted for each commit. This can be extremely useful for finding bugs or looking back to how your project looked a few months ago. However, it is often more practical to review the changes made to a single file over time; this enables, for example, clear tracking of the evolution of data cleaning and analysis steps in your project. 14 | 15 | 16 | To the right of the **History** button, there should now be a drop-down box titled `(all commits)`. Press this box to see the other options, which should be titled "Filter by File" and "Filter by Directory." Select the **"Filter by File"** option. 17 | 18 | 19 | ![](./assets/git_history_tab_filter.png) 20 | 21 | 22 | A file-section window should appear on your screen; select the file you would like to review, e.g. `myscript.R`. 23 | 24 | You will then get only the specific commits in which the selected file was included (i.e. when it was added, deleted, or edited). Click on any of the commit messages to view that specific commit, and scroll further down the screen to view changes made to the file during that commit. 25 | 26 | 27 | ![](./assets/git_history_tab_filter_example.png) 28 | 29 | 30 | It's not possible to revert back to a previous commit using the RStudio interface. For that, you need to learn some command-line git which is beyond the scope of this session. 31 | 32 | 33 | *** 34 | 35 | --------------------------------------------------------------------------------