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<!DOCTYPE html>
<html>
<head>
<title>Intro to Git & GitHub</title>
<meta charset="utf-8">
<style>
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<textarea id="source">
## Notes
* Need to update screenshots with directory structure from the end of bash section see
.center[]
* Include .gitignore discussion to show how to hide setup script (did this when teaching on 2023-10-12)
* Ignore big data files, PHI, passwords, etc
* One person had git in a non-standard location that RStudio couldn't find
---
## Notes (cont)
* Windows had a pop up window when doing the first git push, had them pick token instead of the other options
* Windows terminal within RStudio doesn't seem to use bash
* When instructor zooms in on RStudio, you lose the labels next to icons (e.g., Commit, Push, Pull)
* At end, would be good to see how an active research lab uses GitHub to serve up code/data/images for papers
---
## Notes (cont)
* Got through "Modify your R script..." exercise
* then talked through why you'd run git from the command line
* emphasized that 98% of my git use is covered by RStudio
* encouraged to get comfortable using git in RStudio before trying to use git on command line
---
## Notes (cont)
* At the LICENSE part, I showed issue tracker
* Simulated a conversation with PI
* Picked the LICENSE
* Committed changes and closed issue
---
class: center, middle
# Introduction to
.center[]
.center[]
---
class: middle, center
.tiny[.lightgray[“Piled Higher and Deeper” by Jorge Cham]]
---
class: middle, center
.center[ ]
---
class: middle, center
.center[ ]
.center[]
---
class: middle, center
.center[ ]
---
class: middle, center
.center[ ]
---
class: middle, center
---
class: middle, center
.center[ ]
.center[]
--
---
class: middle, center
# One-time configurations
---
class: middle, center
.center[ ]
---
class: middle, center
.center[ ]
---
### User name
Set a name that is identifiable for credit when review version history.
```
$ git config --global user.name "Pat Schloss"
```
--
### User email
Set an email address that will be associated with each history marker.
```
$ git config --global user.email "[email protected]"
```
---
# Line endings
### On macOS and Linux:
```
$ git config --global core.autocrlf input
```
<br>
### On Windows:
```
$ git config --global core.autocrlf true
```
---
### Text editor
```
$ git config --global core.editor "nano -w"
```
--
### Default Branch name
```
$ git config --global init.defaultBranch main
```
--
### Credential storage
```
$ git config --global credential.helper store
```
---
### View the configurations
```
$ git config --list
```
---
## Now to initialize our repository
.center[]
---
## Now to initialize our repository
.center[]
---
## Using git - 98% of what you will do
* Get versions of our files into repository
* Attach a message to our files indicating what happened
.center[]
---
## Untracked files
.center[]
---
## Staging/adding our changes
.center[]
Once files checked, click check icon under "Environment" tab name
---
## Committing our changes
.center[]
Write "Initial commit" in message window
---
## Committing our changes
.center[]
* Click close
* Notice that the staging window is now empty
---
## Create repository in GitHub
- Open the GitHub website and sign in
- Create a new repository with name .red[un-report]
- Do not check the box to add a .red[README] file
- Do not select a .red[.gitignore] file
- Do not select a .red[LICENSE] file
- Click .green[Create repository] button
---
## Connecting GitHub to your computer
.center[]
Make sure that HTTPS is selected and click copy button to the right of the "…or push an existing repository from the command line" section
---
## Connecting GitHub to your computer
.center[]
Enter your GitHub username and wait when asked for your password, we will use a personal access token
---
## Create Personal Access Token
.center[ ]
---
## Create Personal Access Token
.center[ ]
---
## Create Personal Access Token
.center[ ]
---
## Create Personal Access Token
.center[ ]
---
## Create Personal Access Token
.center[ ]
---
## Create Personal Access Token
.center[ ]
---
## Connecting GitHub to your computer
.center[]
* Where asked for your password paste the personal access token
* We shouldn't be asked for password again for 90 (or whatever) days
---
## New file
GitHub suggests adding a README file, let's do it from within RStudio
.center[ ]
Save the file as .blue[README.md]
---
## Let's type some text into the .blue[README.md] file
```
## Notes for UN Report
We plotted life expectancy over time.
```
--
Check out the change in the git staging window
.center[ ]
---
## Stage, add and commit the change
.center[ ]
---
## Let's add a line to README.md
```
We plotted life expectancy over time.
Each point represents a country
```
--
Notice the change in the git staging window
.center[ ]
---
## Commit the new changes
.center[ ]
Notice the "diff" at the bottom of the window indicating what has changed
---
## Exercise
Follow the previous examples to...
- Add a third line to the README.md
```
We plotted life expectancy over time.
Each point represents a country.
Continents are grouped by color.
```
- Stage and commit the above change
- What happens if you click "View file @ XYZ1234" in the "Changes" view of an
earlier commit? When would you want to use this?
---
## Exercise
Which of the following commit messages would be most appropriate for the last commit?
1. “Changes”
1. “Added line ‘Continents are grouped by color.’ to notes.txt”
1. “Describe grouping”
---
class: middle, center
.center[]
<br>
.lightgray[Source: https://xkcd.com/1296/]
---
## Show the commit logs
.center[]
---
## Let's edit our README.md file further
.center[]
---
## Let's check out the diff before committing
.center[]
---
## Let's stage and commit from the diff window
.center[]
---
## How to get this up to GitHub?
.green[Push]. Click the upward pointing arrow.
.center[]
---
## GitHub changes
.center[]
---
## GitHub commit history
.center[]
---
## GitHub diffs
.center[]
---
## Let's create a file on GitHub
.center[]
---
## Let's create a file on GitHub
.center[]
---
## Let's create a file on GitHub
.center[]
---
## Let's create a file on GitHub
.center[]
---
## Let's create a file on GitHub
.center[]
---
## Let's commit changes on GitHub
.center[]
---
## New file already on GitHub
.center[]
---
## How do we get our file back to our local computer?
.center[]
---
## How do we get our file back to our local computer? .red[Pull]
.center[]
---
## Exercise
* Modify your R script to include the following after the ggplot code chunk:
```
ggsave("figures/gdpPercap_lifeExp.png")
```
* Rerun the ggplot code chunk along with the following ggsave line
* Update your REAMDE.md file
* Stage the changes and new file, commit those changes, and push to GitHub
---
## Exercise
* Create a new Git repository on your computer called workshop
* Write three lines about what you have learned about R and bash a file called README.md, commit your changes
* Modify one line, add a fourth line
* Display the differences between its updated state and its original state
* Push it to GitHub
---
## Why run git from the terminal?
* RStudio and other git-based tools with a graphical user interface (GUI) have
gotten really good over the past few years, especially for most of our needs
--
* But they aren't as powerful as running the commands from the command line
--
* Believe it or not, typing can be a lot faster than pointing and clicking!
--
* If you need help doing something, Google likely point you to
solutions using the command line
--
* You don't always have access to a GUI (e.g., HPC)
---
## git from the terminal
How do we look at the staging area?
```
$ git status
```
--
Modify README.md to include your name and the date
```
$ git status
```
--
See the change as git sees it
```
$ git diff
```
---
## git from the terminal
To stage the change (can add more than one file)
```
$ git add README.md
$ git status
```
--
To commit the change
```
$ git commit -m "Added my name and date"
$ git status
```
---
## git from the terminal
To push the changes
```
$ git push
$ git status
```
--
To pull any changes (there aren't any)
```
$ git pull
```
Why might you want to pull from GitHub before committing any changes on your
local computer?
---
## Exercise
* Change the ColorBrewer palette to `Dark2`
* Rerun the code and be sure to save the output with `ggsave`
* Use `git status` to look at the staging area
* Use `git diff` to look at what has changed
* Stage, commit, and push your changes
---
## Collaboration
.center[]
---
## Collaboration
.center[]
---
## Collaboration
.center[]
---
## From here...
* Option 1: Fork repository / Create project from repository / Push / File pull request
* Option 2: Clone repository to new project / Push to main user's repository
* Option 3: Create feature branch / Clone repository to new project / Work on new feature branch / Push to main user's repository / Merge branches
Cover how to handle merge conflicts?
<!-- ------------------------------------------ -->
</textarea>
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