Happier version control with Git and GitHub

# Happier version control with Git and GitHub
## (and Rstudio)
### Byron C. Jaeger
### Wake Forest School of Medicine
### 2021-09-28 (updated: 2021-09-28)

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# .larger[HELLO]

My name is Byron

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# .larger[DISCLAIMERS]

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# I am recycling materials

- Alice Bartlett: [Git for humans, 2016](https://speakerdeck.com/alicebartlett/git-for-humans) (slides)

- Jenny Bryan:

+ [Rstudio::conf 2017](https://www.rstudio.com/resources/rstudioconf-2017/happy-git-and-gihub-for-the-user-tutorial/) (full tutorial with demos)
    
    + [Excuse me, do you have a moment to talk about version control?](https://peerj.com/preprints/3159v2/) (article)
    
    + [useR! 2019](https://www.youtube.com/watch?v=ZCeBnQBQ1h8) (quick tutorial with demo; see 10:44 - 14:35)
    
    + [Happy Git with R, 2021](https://happygitwithr.com/) (full textbook)
    
<br>

Why? Because these materials are _fantastic_. Don't re-invent the wheel.

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# I know the basics of git, and that is about it!

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# .larger[Tell me<br>about you]

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# .larger[GIT]

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# Happy Git with R by Jenny Bryan

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# .larger[What is Git]

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# Git is a .blue[version control system]

- It is an application that runs on your computer, just like Microsoft Word or Google Chrome.

- Its original purpose was to help groups of developers work collaboratively on big software projects.

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# .larger[What does<br/>Git do]

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# Git manages the evolution of a set of files (.blue[repository])

Imagine “Track Changes” from Microsoft Word on a whole directory instead of just one file.

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# .larger[Who made Git?]

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# .larger[Git for<br/>data science]

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# Git (with the help of GitHub) has been repurposed for activities other than software development, such as

# [writing books](https://github.com/hadley/r4ds)

# [managing personal websites](https://github.com/rbind/apreshill)

# [writing scientific articles](https://github.com/bcjaeger/ACC-AHA-BP-guideline-groups)

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# .larger[Git for<br/>beginners]

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# .larger[is<br>unfriendly]

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# .larger[JARGON]

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# Wait, should I even use this?

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# .larger[Yes<br>I'll give you 5 reasons why]

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# .larger[Git lets you tell the story of your project]

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# Git takes snapshots of all the files in a folder

# This folder is called a .blue[repository] or .blue[repo]

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# When you want to take a snapshot of a file or files, you create a .blue[commit].

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# When you .blue[commit] a file or set of files,<br>Git will save some information automatically.

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# 1. Who

# 2. When

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# You can add more information about the changes you made with a .blue[commit message].

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.largish[_Character vectors may be automatically converted to factors by some data import functions. Our data management directly changes character values in the vectors (creating `NA` factor values), so we are delaying conversion to factors until the modeling phase._]

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# Wait, `NA` factor values?

(Even though it's a Git presentation, you should know this about R)

```r
chr <- c("A", "B", "C")

f <- factor(chr)

f[2] <- "D"

f
```

```
## [1] A    <NA> C   
## Levels: A B C
```

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# .blue[Repository] - your project folder

# .blue[Commit] - save a snapshot

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# .larger[Git lets you time travel]

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# Once you've saved some snapshots of your repository, git lets you travel through them

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# Git stores the whole history of your project

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# Each of these commits has an identifier called a .blue[hash]

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# Getting the files from a commit in the past is known as doing a .blue[check out]

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# I can tell Git what commit I want to check out using the commit hash.

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# I can tell Git what commit I want to check out using the commit hash.

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# My other commits still exist, but when I look in my repo, it's like they never happened

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# .blue[hash] - a computer generated id

# .blue[check out] - time travel to a specific commit

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# .larger[Git lets you experiment]

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# So far, everything has been linear and neat.

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# This isn't really how projects develop.

# Sometimes you want to experiment.

# Sometimes your experiments don't work.

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# In Git, you can create easily discardable experiments with .blue[branches]

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# A .blue[branch] is a moveable label attached to a single commit

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# The default branch name in git is .blue[master (or main)]

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# You can add your own branches too

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# A user will often do a lot of work on a branch

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# Branches are useful for trying things out.

# They are easy to throw away if you don't like the changes.

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# Once projects are up and running, most development is done in branches.

# The main branch is the 'live' version.

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# When you are happy with the changes you made in a branch, you need a way to get those changes back into the main branch.

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# To get changes from one branch into another, you .blue[merge] them.

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# So, this commit combines all the commits from both branches.

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# .blue[branch] - a moveable label that points to a commit

# .blue[merge] - the combination of commits from two or more branches

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# .larger[Git helps you back up your work]

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# Everyone knows you should back up your work regularly.

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# Ideally, to somewhere that is not the same place as your computer.

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# Safer

# Access from different places

# Shared

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# In Git this place is called a .blue[remote]

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# To get some work from a repository stored in a remote for the first time, the first thing you do is .blue[clone] the repository.

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# Now everyone<br>has the repo on<br>their computer

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# Ligong can send<br>his changes to<br>the remote

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# this is known<br>as a .blue[push]

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# Now Shakia's<br>repo is behind<br>the remote.

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# To get these<br>changes, Shakia<br>can .blue[pull] them

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# .blue[clone] - copy a repository from a remote location to your local computer.

# .blue[push] - send your local commit(s) to your remote

# .blue[pull] - copy the most recent version of the remote to your local computer (merge conflicts can happen).

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# .larger[Git helps you collaborate]

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# When you clone a repository, you attempt to push and pull commits to the remote

# What could go wrong?

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# Instead of cloning someone else's repo, you can .blue[fork] the repo.

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# When you .blue[fork] a repo, you create a copy of it on your GitHub account. (this is not a clone)

# Now you have a remote you can clone and commit changes to.

# This positions you to request that the repo owner to merge a branch of your forked repo into their main branch, i.e., a .blue[pull request].

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# .larger[Git is a lot. Where should<br>I start?]

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# Go to [https://github.com/](https://github.com/) and click "Sign up"

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# .larger[Make a pull request]

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# Go to [my GitHub](https://github.com/bcjaeger)

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# Click 'Repositories' near the top of the page

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# Search 'seminar-git' (maybe already at top)

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# Click on the 'seminar-git' repository

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# Click on index.Rmd (don't click index.html)

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# Click the pencil to .blue[fork] the repo

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# If you see this, you are in the right place!

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# If you don't have that screen, don't worry. Clicking the pencil has forked the repo and created a new branch. Check your profile page.

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# Scroll down to about here.

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# Add your own adjectives or exclamations

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# Document, then click propose changes

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# Review, then click 'create pull request'

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# .larger[Yes!]

# You completed your first pull request!

# .rainbow-text[Great work!]

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# .larger[Make a repo on GitHub]

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# click 'Repositories' on your profile page

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# click 'new'

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# Name your repo

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# Give it a description

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# Make it public or private

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# Initialize with a README file

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# Click 'Create  repository'

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# You did it!

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# Jargon

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# .larger[Git and Rstudio]

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# .larger[Demo]

# Create a project that uses Git and GitHub
# Create a project from GitHub (fork and clone)
# Initiate pull requests!

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# .larger[Create]

# `create_project()`
# `use_git()`
# `use_github()`

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# .larger[Fork & clone]

# `create_from_github()`
# `pr_init()`
# `pr_finish()`

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# .larger[Thank you!]