GitDemo/index.Rmd at master · Lemonici/GitDemo · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
---
title: "Git Basics"
output:
  revealjs::revealjs_presentation:
    theme: white
    center: true
    transition: none
    incremental: true
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```

## Git Resources

- Git will feel foreign for a while, but you will get a lot of practice in this class

- A great resource, from which I've heavily borrowed is Jenny Bryan's [Happy Git and GitHub for the useR](https://happygitwithr.com)

- Another good reference is the [GitHub Git Cheat Sheet](https://education.github.com/git-cheat-sheet-education.pdf)

## Git: The What and the Why
- Git is a version control system that manages as set of files as a repository, or a *repo*.

- For the long version of why, see [Excuse me, do you have a moment to talk about version control?](https://peerj.com/preprints/3159/)

- For today, just know:
    - Programming expertise, and skills like this, are essential in Data Science
    - Version control will save back up files, in case of computer problems
    - It is an efficient way to handle collaboration
    - Creating R packages is easy with R Studio and Github
    - Github pages allows you to create and host websites

## Demo Overview:

Here are 6 basic steps to set up Github to interface with R Studio.

1. Github account
2. Upgrade R and R Studio
3. Git installation and initialization
4. Git GUI??
5. Git - to - Github with R Studio
6. Basic Git Commands


## Github Account

- If you have not already registered for a github account, do so now. Visit [github.com](https://www.github.com) to set up your account.

- Note a `github` account can serve as a statistics / data science repository for future employers. Choose an appropriate and searchable id.

- If you have an account, go ahead and log in. We will use this soon.

## R and R Studio Updates

- R is currently on version 4.0.2, if your version is much older than this (3.X.X), you will want to update it [here](https://cloud.r-project.org).

- Updating R can be a bit painful, but keeping current is good practice.

- R Studio is constantly adding improvements and updates, including a git interface.

- To stay current, consider downloading the [Preview version](https://www.rstudio.com/products/rstudio/download/preview/) and updating at the start of every semester.

## Git installation and Git initialization

- If you are lucky, git is already installed on your computer.

- To check you have git, open the terminal or command line, and type `git --version`. In newer versions of R Studio there is a command line tab.

- If `git --version` does not return an error, then you are in luck. Otherwise, git needs to be be [installed](https://happygitwithr.com/install-git.html).

- If you have not already done so we need to initialize git with the following commands in the terminal:
```
git config --global user.name 'First Last'
git config --global user.email 'who@montana.edu'
```
Note the email should correspond to the one you used to sign up for github.

## Git GUI?

- If you are leery of using the command line, now that R Studio has some point and click options.

- Otherwise, two options are options are:
    - [gitkraken](https://www.gitkraken.com) and
    - [github desktop](https://desktop.github.com)


## Git - to - Github with R Studio: 1

- Our goal is to work locally, in R Studio, and *push* updates to Github.

- First, go to your github page and create a new repo. To do this,
    - Repository name: git_demo
    - Description: “practice with git”
    - Select Public
    - YES Initialize this repository with a README.
    - Click: create repository.

- Next, we will clone this repo and create an R Studio project associated with it.

## Git - to - Github with R Studio: 2 (part 1)

- Now we want to create a local git repo associated with the one hosted on github.

- First we need to set up version control in R Studio [(more details here)](https://support.rstudio.com/hc/en-us/articles/200532077-Version-Control-with-Git-and-SVN)
    1. Tools ... Global Options .. Git/SVN
    2. Click enable version controll interface for R Studio projects

## Git - to - Github with R Studio: 2 (part 2)

- Then we will create this git repo as an R project, by cloning the one on github.
    1. File ... New Project ... Version Control ... Git
    2. Repository URL: This can be obtained from the clone button in github.
    3. Project directory name: this will be the name of the folder containing the repo
    4. Create project as subdirectory of: this is location for the file, you may want to think about a structured file system on your local computer.


## Git - to - Github with R Studio: 3 (part 1)

We now have created a local git repo.

1. Click on the terminal window and type `git status`, you will see our current work is up to date.

2. Now click on README.md in the file pane and add a new line that says, "modified in R Studio" and save this file.

## Git - to - Github with R Studio: 3 (part 2)

3. Open the Git tab in the top right and we will see that README.md has been updated.
    1. Click on staged (this is essentially the same as typing git add README.md in the terminal)
    2. Click on commit, this will open up a new window. A commit basically amounts to saving a version of all of the current status of all of the files in the repo.
    3. Type a message, such as "changes from R Studio" and click commit
    4. Click on push, and enter github username and password, if necessary. Note: you may want to simplify the push-pull actions by saving github account information [details](https://happygitwithr.com/push-pull-github.html#am-i-really-going-to-type-github-username-and-password-on-each-push)

## Git - to - Github with R Studio: 4

- Now return to your github page. If you refresh, you should seee a new commit that contains the additional info we added in R studio.

- Go ahead and modify the README.md in github to add a line stating modified in github.

- Commit the update along with a message. We will now see that there have been three commits.

- The final step is to call a `pull` command from R Studio to bring those updates to your local repo.

- It is always good practice to `pull` before a `push`, especially as you start to collaborate with others.

## Basic Git Commands (part 1)

We will just cover a few basic commands for now, but the [github cheetsheet](https://education.github.com/git-cheat-sheet-education.pdf) is a good reference:

- `add`: this adds or stages a file to be committed. It can also be used to track new files. Create an .Rmd file and save it within this directory as sample.Rmd . The file will not immediately show up in the Git window, we need to start tracking it. In the terminal type `git add sample.Rmd`. Note: sometimes this does not seem to work the first time and you might want to try gitKraken or some other option.

- `status`: shows the current state of the git repo. Type `git status`

## Basic Git Commands (part 2)

- `commit`: saves the version of all files in the repo. Only updated files that have been staged are saved in this version. In the terminal type `git commit -m 'added sample.Rmd file for tracking`.

- `pull`: will retrieve and merge from the remote (github in this case). Type `git pull`.

- `push`: sends updates that have been committed to the remote. Type `git push`. Now inspect your repo on github.

## For Next Time

>- Homework 1 (and all future assignments) will require using Github.

>- Homework assignments will be submitted using Github Classroom.