git-rstudio-practical.qmd

---
email: "[stephen.gregory@cefas.gov.uk](mailto:stephen.gregory@cefas.gov.uk)"
format: 
  revealjs:
    theme: custom.scss
    incremental: false # true
from: markdown+emoji
execute: 
  eval: true
  echo: false
  message: false
  warning: false
  code-fold: true
  code-summary: "expand for full code"
  fig-align: "center"
embed-resources: true
lightbox: true
---

##  {background-image="background-title.png" background-size="100%"}

::: {.absolute top="0%" left="0%" width="1100" style="font-size: 1.75em; color: #1C2442; font-weight: bold;"}
Using [`git`](http://git-scm.com/) in [`RStudio`](https://www.rstudio.com/)
:::

::: {.absolute top="15%" left="0%" width="1100" style="font-size: 1.25em; color: #00AAB4;"}
Stephen, Jennifer, Tiago & David
:::

```{r setup}
#| include: false

# libraries
library(here)

# do a sum
a <- 1 + 1
print(a)

```


## Setup {background-image="background-body.png" background-size="100%"}

:::: {.columns}
::: {.column width="75%"}
* Assume `R`, `RStudio` & `git` installed & working together
  - [If not, see Appendix]{.small-text}
* Create a [`GitHub`](http://github.com/) account
* Create a repository ("repo") on `GitHub`
* `clone` the repo as an `RStudio` project
* Write a `README.md` using markdown
:::

::: {.column width="25%"}
![](rstudio-git-project.png)
:::
::::


## Regular use {background-image="background-body.png" background-size="100%"}


:::: {.columns}
::: {.column}

::: {.small-text}
**Step 1** Click *Pull* on *Git panel*
:::

* Create, edit, modify, e.g., R scripts, then:

::: {.small-text}
**Step 2** Click *Commit* on *Git panel*

**Step 3** Check boxes to *Stage* changes to commit

**Step 4** Write *Commit message* & click *Commit*

**Step 5** Once committed, don't forget to *Push*
:::

* Changes visible on `GitHub` :sweat_smile:

:::

::: {.column}
![](regular-use.png)
:::
::::


## Other options in [`RStudio`](https://www.rstudio.com/)

:::: {.columns}
::: {.column width="40%"}
![Other `git` options in the *Git panel*](rstudio-options.png)

![`RStudio` *Git window*](git-window.png)
:::

::: {.column width="60%"}
::: {.small-text}
* **Diff** opens *Git window* with output of `git diff <file>` of choosen file
* **Commit** opens *Git window* is where we stage and commit changes to files
* **Pull** does a `git pull` (also accessible from *Git window*)
* **Push** does a `git push` (also accessible from *Git window*)
* **History** opens a window with output of `git log`

::: {.callout-important title="Go directly to `bash` and don't pass go"}
By now, you've exhausted `git` options in `RStudio`: use `bash`!
:::

* **More** menu allows access to `git revert` & add files to `.gitignore`
* Create and checkout a *Branch* using buttons on the RHS
:::
:::
::::

<!-- ##  {background-image="close_bg.png" background-size="100%"} -->
<!-- ::: {.absolute top="44%" left="53%" width="150"} -->
<!-- {{< meta email >}} -->
<!-- ::: -->

## Appendix {background-image="background-body.png" background-size="100%"}


## Install [`R`](https://www.r-project.org/) on Windows

:::: {.columns}
::: {.column}
* Visit the [`R`](https://www.r-project.org/) website
* Follow the links to `download R`, incl. select mirror and OS
* Double click installer and follow instructions
* Install required packages with `install.packages()`
:::

::: {.column}
![`R` website](r-website.png)
:::
::::


## Install [`RStudio`](https://posit.co/products/open-source/rstudio/) on Windows

:::: {.columns}
::: {.column}
* Download [`RStudio`](https://posit.co/download/rstudio-desktop/) installer
* Double click installer and follow instructions
:::

::: {.column}
![`RStudio Desktop` download page](rstudio-download.png)
:::
::::


## Install [`git`](http://git-scm.com/) on Windows

:::: {.columns}
::: {.column}
* Download [`git`](http://git-scm.com/), currently v 2.45.2
* Double click installer and follow instructions

::: {.callout-important title="Installation location"}
Note the location where `git` is installed, e.g.

`C:\Users\{...}\AppData\Local\Programs\`
:::

<!-- * At "Choose the default behaviour of `git pull`": select `Rebase` -->
* Set `git` configurations, e.g., `user.name`, `user.email`, etc. 
:::

::: {.column}
![Initial `git` installer screen](git-setup1.png)
:::
::::


## Getting them to work together

:::: {.columns}
::: {.column}
* [`git`](http://git-scm.com/) authentication is OS-specific - see David's slides
* Connect `RStudio` and `git`: Tools > Global Options... > Git/SVN 
:::

::: {.column}
![Connect `RStudio` and `git`](rstudio-git.png)
:::
::::