01-intro-git.qmd

# Intro to Git

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, fig.align = "center")
```

## Background info

- Git was written to allow developers work on the source code of the Linux kernel (text files)
  - One kernel release they got in a terrible mess
  - This provoked Linus Torvalds into action
  - For an excellent insight into his thinking watch this talk he gave at Google [here](https://youtu.be/4XpnKHJAok8)  
  - (Especially if used at the command line) Git can be intimidating to use and we can get Git errors (which like LaTeX and R errors can be quite cryptic)  
    ```{r}
    #| out-width: "50%"
    #| fig-cap: "Image: <a href='https://xkcd.com/1597/>'> xkcd.com/1597</a>"
    #| fig-alt: "XKCD comic 1597 showing how to use Git"
    knitr::include_graphics("https://imgs.xkcd.com/comics/git.png")
    ```  
- A Git repository is a folder/directory on your computer which has been Git initialised 
  - Using either the command line  
    ```
    git init mynewfolder
    ```  
  - Or GitHub Desktop  
    ```{r, out.width = "50%"}
    knitr::include_graphics("img/ghd-new-repo.png")
    ```
  - Repos on GitHub are already Git initialised 
    - When you clone them down to your computer they work in GitHub Desktop
- Git is commonly referred to as version control software
- Git is better described as a *content addressable filesystem* which translates to *Git tracks the contents of the files in your repo*
  - Git creates a little database of the contents of your files - snapshots (commits) are taken when you tell it to
  - Git looks for changes in your files when you save them, so when you have unsaved changes in a file/s Git shows no changes until you save  
    ```{r}
    knitr::include_graphics("img/no-local-changes.png")
    ```  
  - Git takes snapshots of your files - when you tell it to - *commits* - I saved my file from above, enter a commit message and click "Commit to master"
    ```{r}
    knitr::include_graphics("img/stashed-changes.png")
    ```  
  - Commits are identified by the 40-character checksum SHA-1 hash of the contents of your files at that time  
    ```{r}
    knitr::include_graphics("img/git-commit-hash-1.png")
    ```  
    
    ```{r}
    knitr::include_graphics("img/git-commit-hash-2.png")
    ```  
    
    ```{r}
    knitr::include_graphics("img/git-commit-hash-3.png")
    ```  
  - Git knows the state of your files at every commit
    - You can easily restore your files to a previous state
  - For Git the state of your files only changes when their contents change
    - If you reopen a file, make no changes, then close it, Git will show no changes in your repo
    - If you add an empty folder/directory to your repo Git will show no changes in your repo
    - This differs to OneDrive/SharePoint/Google Drive which are file synchronisation systems
  - I recommend not to place your Git repos in a location that is sync'd by either OneDrive or Google Drive

## The `.git` folder

- When you initialise a directory the `.git` folder is created
- This contains all of the files Git uses to track the contents of your files
- Here is the `.git` folder of a repo on my computer (I have selected to View hidden files in Windows Explorer)  
  ```{r, out.width = "50%"}
  knitr::include_graphics("img/windows-explorer-repo.png")
  ```  
- GitHub (and Git servers in general) store repositories as bare repositories. This means that they only contain the `.git` directory which is on your local machine. Hence perhaps a little confusingly when you view your repository on GitHub you cannot see the `.git` directory listed in the repo contents (as you see in a File Explorer on your local machine).
  ```{r}
  knitr::include_graphics("img/repo-github-view.png")
  ```  
- Here are its contents - don't edit these manually  
  ```{r, out.width = "50%"}
  knitr::include_graphics("img/dot-git-folder-contents.png")
  ```  
- Explanation of these is (from [here](https://www.tutorialspoint.com/what-is-git-folder-and-why-is-it-hidden))  
  ```{r}
  knitr::include_graphics("img/dot-git-folder-explanation.png")
  ```  

## Common Git commands

- I recommend you use GitHub Desktop instead of these commands
- These commands are what GitHub Desktop is using behind the scenes
- Git is the name of the program, `git` is the name of the executable available at your command line  
  ```bash
  git init 
  git add <filename>
  git status
  git commit -m "Your commit message"
  git commit --amend -m "Your amended commit message"
  git push 
  git pull 
  git clone
  git branch
  git checkout
  git merge
  git fetch 
  ```