Version Control:

# Version Control:
## A Practical Introduction to Git and Github
### <p>Joseph V. Casillas</p>
### <p>From Proposal to Publication:</br> Pathways to Open Science | 07-14-2021</p>

---

# Hi! 👋🏼

.Large[

|                                     |                                         |
| ----------------------------------: | :-------------------------------------- |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M476 3.2L12.5 270.6c-18.1 10.4-15.8 35.6 2.2 43.2L121 358.4l287.3-253.2c5.5-4.9 13.3 2.6 8.6 8.3L176 407v80.5c0 23.6 28.5 32.9 42.5 15.8L282 426l124.6 52.2c14.2 6 30.4-2.9 33-18.2l72-432C515 7.8 493.3-6.8 476 3.2z"/></svg> | joseph.casillas@rutgers.edu |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"/></svg>     | [@jvcasill](https://twitter.com/jvcasill) |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"/></svg>        | https://github.com/jvcasillas/github_workshop |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"/></svg>        | https://www.jvcasillas.com/github_workshop/index.html |

]

---
exclude: true
class: center, middle
background-color: #fd9426

---
exclude: true
class: center, middle
background-color: #fd9426

---
class: middle

# What are we going to do today?

.Large[

1. What is version control and why do I care?

2. Get familiar with Git/Github

]

???

get familiar with git/github
understand conceptually what it is, what it does, what it is for
learn how it can be a tool for our research (safety measures, promote open science)
open doors for collaboration

---

class: middle
background-image: url("./assets/img/final_doc.png")
background-size: 525px
background-position: 100% 50%

# What is version control?

???

Version control is a system that records changes to a file or set of files over time so that you can recall specific versions later

---
background-image: url("./assets/img/data_science1.png")
background-size: contain

---
background-image: url("./assets/img/data_science3.png")
background-size: contain

---
background-image: url("./assets/img/datascience_workflow.png")
background-size: contain

---
background-image: url("./assets/img/datascience_workflow2.png"), url(./assets/img/workflow_10.png)
background-size: 600px, 700px
background-position: 15% 90%, 95% 40%

---
class: title-slide-section-grey, middle
background-image: url("./assets/img/final_doc.png")
background-size: 525px
background-position: 100% 50%

# .white[So what is version control?]

# **Recording changes to a file<br>or set of files over time so<br>that you can recall specific<br>versions later**

---
background-image: url(./assets/img/vc1_github_01.png)
background-size: contain
count: false

---
background-image: url(./assets/img/vc1_github_02.png)
background-size: contain
count: false

---
background-image: url(./assets/img/vc1_github_03.png)
background-size: contain
count: false

---
background-image: url(./assets/img/vc1_github_04.png)
background-size: contain
count: false

---
background-image: url(https://octodex.github.com/images/hula_loop_octodex03.gif)
background-size: 300px
background-position: 90% 10%

# Version control

### How do we do it for reproducible research?

- Git

- Github

- Gitlab

- Bitbucket

]

---

class: title-slide-section-red, middle
background-image: url(https://media.giphy.com/media/3o7aTwT5vjBVfsYEj6/giphy.gif)
background-size: 500px
background-position: 90% 50%

# What you'll need...

---

<br>

## .black[What you'll need]

.Large[
- .RUred[Git]
- .RUgrey[GitHub account]
- .RUgrey[Github Desktop]
]
]

## **Git**

.Large[

- Installation and setup: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git

- Troubleshooting: https://happygitwithr.com/install-git.html

- You should have this already 🙏

]
]

---

<br>

## .black[What you'll need]

.Large[
- .RUgrey[Git]
- .RUred[GitHub account]
- .RUgrey[Github Desktop]
]
]

## **GitHub**

.Large[

- It's free

- Use an academic email if you have one (more perks)

- Give consideration to your username
  - avoid spaces, uncommon characters
  - shorter is better than longer
  - usually your real name (or related to it)

- You should have this already 🙏

]
]

---

<br>

## .black[What you'll need]

.Large[
- .RUgrey[Git]
- .RUgrey[GitHub account]
- .RUred[Github Desktop]
]
]

## **GitHub Desktop**

.Large[
- This will make interacting with Git much easier

- You can download the app here: https://desktop.github.com

- You should have this already 🙏

]
]

---

class: middle
background-image: url(https://raw.githubusercontent.com/jvcasillas/media/master/teaching/img/think.png)
background-size: 400px
background-position: 90% 50%

# What is Git?

---
background-image: url(https://git-scm.com/images/logos/downloads/Git-Icon-1788C.png)
background-size: 250px
background-position: 95% 50%

# Git

### What is it?

<br>

.Large[
- Open source version control system
]

.Large[
- Keeps track of changes you make to files
]

.Large[
- Conceptually similar to dropbox/box/google drive/<br>one drive/etc., "but for nerds"
]

---
background-image: url(https://git-scm.com/images/logos/downloads/Git-Icon-1788C.png)
background-size: 250px
background-position: 95% 50%

# Git

### How does it work?

- Git keeps track of incremental changes in project files

- We can think of it like taking snapshots of a repository (project) 📷

- We access Git via **the command line**

]
]

background-image: url(https://raw.githubusercontent.com/jvcasillas/media/master/teaching/gifs/scared.gif)
background-size: 325px
background-position: 95% 50%

---
background-color: black
background-image: url(https://www.redhat.com/sysadmin/sites/default/files/styles/full/public/2020-12/linux-command-line-ls-output.jpg?itok=3mL5X-30)
background-size: contain

---

class: middle
background-image: url(https://raw.githubusercontent.com/jvcasillas/media/master/teaching/gifs/confused.gif)
background-size: 600px
background-position: 93% 50%

# What is Github?

---
background-image: url(./assets/img/octocat_rainbow.png)
background-position: 93% 50%
background-size: 300px

# Github

### What is it?

<br>

.Large[

- An online interface to Git

- A place to store repositories (projects)

- Owned by microsoft 😞

]

---
class: title-slide-section-red, center, middle

# Walk-through

???

profile, repos, public, private
not to late to catch up

---
class: middle
background-color: black

# **Git**

.Large[
.white[a version control system that let's you manage and keep track of your source code history via repositories]

]
]

# **Github**

.Large[
.white[a cloud based hosting service that lets you manage Git repositories]

]
]

---
background-color: black
background-image: url(./assets/img/github101.png)
background-size: 700px

<!--
Exercise I

create repo (projects)
create text file
commit changes

(key ideas: repo, commit)
(tips: think carefully about names)
-->

---

class: title-slide-section-red
background-image: url(https://octodex.github.com/images/daftpunktocat-thomas.gif), url(https://github.githubassets.com/images/modules/logos_page/GitHub-Logo.png)
background-size: contain, 400px
background-position: 100% 50%, 20% 85%

# Exercise I

---
background-image: url(./assets/img/new_repo_icon.png), url(./assets/img/new_repo_menu.png)
background-size: 300px, 300px
background-position: 95% 15%, 95% 75%

# Exercise I

## Your first repo

### 1. Create new repository

- Option b) Click on the profile icon in the<br>upper right hand corner, from the<br>dropdown menu select **Your repositories**,<br>click the **New** icon
]

---
count: false
background-image: url(./assets/img/name_repo.png)
background-size: 600px
background-position: 95% 50%

# Exercise I

## Your first repo

### 2. Name your repo **my-repo** and<br>check the box for **Add a README file**

---
count: false
background-image: url(./assets/img/create_repo.png)
background-size: 700px
background-position: 60% 85%

# Exercise I

## Your first repo

### 3. Click **Create repository**

---
count: false
background-image: url(https://raw.githubusercontent.com/jvcasillas/media/master/teaching/gifs/rock_clap.gif)
background-size: contain

---
count: false
background-image: url(./assets/img/readme.png)
background-size: 600px
background-position: 50% 85%

# Exercise I

## Your first repo

### 4. Click **README.md**

---
count: false
background-image: url(./assets/img/pencil_icon.png)
background-size: 500px
background-position: 50% 55%

# Exercise I

## Your first repo

### 5. Click the pencil icon and edit the file by adding some text

---
count: false
background-image: url(./assets/img/commit_icon.png)
background-size: 400px
background-position: 50% 75%

# Exercise I

## Your first repo

### 6. Scroll to the bottom and click **Commit changes**

---

# Exercise I - Review

1. Create new repository
  - Option a) Click the **New** icon anywhere 
  - Option b) Click on the profile icon in the upper right hand corner, from the dropdown menu select **Your repositories**, click the **New** icon
2. Name your repo **my-repo** and<br>check the box for **Add a README file** 
3. Click **Create repository**
4. Click **README.md**
5. Click the pencil icon and edit the file by adding some text
6. Scroll to the bottom and click **Commit changes**

]

---
background-image: url(https://octodex.github.com/images/puddle_jumper_octodex.jpg)
background-size: 300px
background-position: 94% 10%

# Exercise I - Review

### Key ideas

- **Repositories** are projects

- We **commit** changes to the repository

- **README** files have special status on Github

]

### Tips

- Remember to think carefully about names

- Avoid spaces and uncommon characters (if possible)

]

---
exclude: true
count: false
class: center, middle
background-color: #fd9426

<!--
Exercise II
clone repo to our machine
commit changes
push changes

(key ideas: clone, commit, push)
(tips: think carefully about where projects live)
git clone REPO
-->

---
background-image: url(./assets/img/clones.png)
background-size: contain

# Exercise II

---
background-image: url(./assets/img/ex2_clone1.png)
background-size: contain

---
count: false
background-image: url(./assets/img/ex2_clone2.png)
background-size: contain

---
count: false
background-image: url(./assets/img/ex2_clone3.png)
background-size: contain

---
count: false
background-image: url(./assets/img/ex2_clone4.png)
background-size: contain

---
count: false
background-image: url(./assets/img/ex2_clone5.png)
background-size: contain

---
class: title-slide-section-red, middle, center

# Walk-through

---
background-image: url(https://octodex.github.com/images/snowoctocat.png)
background-size: 250px
background-position: 93% 10%

# Exercise II

### Cloning

1. Clone **my-repo** repo on to your computer  
(Github desktop: File > Clone repository)

2. Edit the README.md file using a text editor<br>and put some text in the body

3. Save everything, commit the changes to origin with<br>an informative message

4. Push changes from your local (cloned) repo to origin (the cloud)

5. Check github to see if it worked

]

---

# Exercise II - Review

### Key ideas

- We **clone** repositories from **origin** to our computers (**local** copies)

- We work like normal and **commit** changes

- When we finish we **push** changes from our local copy to origin

- The changes are then visible on Github

### Tips

- Always think carefully about where projects live

- Practice this procedure (clone > edit > commit > push) with dummy repos to get the hang of it

- Don't be afraid to burn the house down

---
exclude: true
class: center, middle
background-color: #fd9426

---
class: middle

# What this means...

---
count: false
background-image: url(./assets/img/vc1_github_05.png)
background-size: contain

---
count: false
background-image: url(./assets/img/vc1_github_06.png)
background-size: contain

---
count: false
background-image: url(./assets/img/vc1_github_07.png)
background-size: contain

---
count: false
background-image: url(./assets/img/vc1_github_08.png)
background-size: contain

---
count: false
background-image: url(./assets/img/vc1_github_09.png)
background-size: contain

---
count: false
background-image: url(./assets/img/vc1_github_10.png)
background-size: contain

---
exclude: true
count: false
class: center, middle
background-color: #fd9426

<!--

fork repo from github
clone to local machine
make changes
commit changes
push changes
submit PR

(key ideas: fork, clone, commit, push)

-->

---
class: bottom
background-color: black
background-image: url(https://octodex.github.com/images/grim-repo.jpg)
background-size: contain

# Exercise III

---
background-image: url(https://octodex.github.com/images/steroidtocat.png)
background-size: 300px
background-position: 90% 10%

# Exercise III

### Collaborating with forks

1. **Fork** the github_practice repo

2. Clone repo to your computer

3. Open the README.md file

3. Edit README.md

4. Commit changes

5. Push changes to origin (your copy on Github)

6. Submit a **pull request**

]

---
background-image: url(./assets/img/vc1_github_15.png)
background-size: contain

---
background-image: url(./assets/img/vc1_github_16.png)
background-size: contain

---
background-image: url(./assets/img/vc1_github_17.png)
background-size: contain

---
background-image: url(https://octodex.github.com/images/socialite.jpg)
background-size: contain

---
class: title-slide-section-red, middle, center

# Walk-through

---
background-image: url(https://octodex.github.com/images/steroidtocat.png)
background-size: 300px
background-position: 90% 10%

# Exercise III

### Collaborating with forks

1. **Fork** the github_practice repo

2. Clone repo to your computer

3. Open the README.md file

3. Edit README.md

4. Commit changes

5. Push changes to origin (your copy on Github)

6. Submit a **pull request**

]

---
background-image: url(https://octodex.github.com/images/steroidtocat.png)
background-size: 300px
background-position: 90% 10%

# Exercise III - Review

### Key ideas

- We can **fork** other peoples repos

- We can then *clone* our **forked** copy and make changes

- Edit > commit > push

- We can send our modifications to the original repo via **pull requests**

### Tips

- Learn from other people by forking their projects 👍

- It is extremely fulfilling to contribute to other people's projects 😄

- If you get stuck/make a mistake you can always burn the house down 🔥

---
exclude: true
class: center, middle
background-color: #fd9426

---
background-image: url(https://octodex.github.com/images/labtocat.png)
background-size: 300px
background-position: 90% 10%

# Git/Github

### Metaphors and terminology

**there are more**
]

---
background-image: url(https://raw.githubusercontent.com/jvcasillas/media/master/general/gifs/throw_into_pool.gif)
background-size: 500px

---
class: middle
background-image: url(https://octodex.github.com/images/femalecodertocat.png)
background-size: 300px
background-position: 90% 50%

# Next steps...

- Merge conflicts

- The command line
]

---
count: false
class: title-slide-final
background-image: url(https://github.com/jvcasillas/ru_xaringan/raw/master/img/logo/ru_shield.png), url(https://octodex.github.com/images/spidertocat.png)
background-size: 70px, 250px
background-position: 15% 15%, 95% 0%

<br>

# Thank you!

.Large[

|                                     |                                         |
| ----------------------------------: | :-------------------------------------- |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M476 3.2L12.5 270.6c-18.1 10.4-15.8 35.6 2.2 43.2L121 358.4l287.3-253.2c5.5-4.9 13.3 2.6 8.6 8.3L176 407v80.5c0 23.6 28.5 32.9 42.5 15.8L282 426l124.6 52.2c14.2 6 30.4-2.9 33-18.2l72-432C515 7.8 493.3-6.8 476 3.2z"/></svg> | .lightgrey[joseph.casillas@rutgers.edu] |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"/></svg>     | .lightgrey[@jvcasill]                   |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"/></svg>        | .lightgrey[https://github.com/jvcasillas/github_workshop] |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"/></svg>        | .lightgrey[https://www.jvcasillas.com/github_workshop/index.html] |

]

---
count: false
class: title-slide-section-grey, middle, center

# More about projects

---
count: false
class: middle, center

# Workflows and projects

### What does your workflow currently look like?

### What do you organize for?

### How do you do it?

### Where do your files live?

---
count: false
# RStudio projects

### If your projects include R scripts, RMarkdown documents, HTML slides, etc., you should be using RStudio projects

--
count: false

- What are they?

--
count: false

.content-box-blue[
`.rproj` files create an independent RStudio environment that limits the scope of your R session to the project in question.
]

--
count: false

- Why use them?

--
count: false

- They simplify organizing projects
  - They integrate well with github
  - They promote a project-oriented workflow

---
count: false
class: title-slide-section-grey, middle, center

# What's in a project anyway?

---
count: false

# Directory structure

### Student

--
count: false

background-image: url(./assets/img/student_project.png)
background-size: 700px
background-position: 95% 50%

---
count: false
background-color: black
background-image: url(./assets/img/student_project.png)
background-size: contain

---
count: false

# Directory structure

### Researcher

count: false
background-image: url(./assets/img/researcher_project.png)
background-size: 700px
background-position: 95% 50%

---
count: false
background-color: black
background-image: url(./assets/img/researcher_project.png)
background-size: contain

---
count: false
# Directory structure

### A note on READMEs

- Every folder/directory should have a README.md file that explains...
  - the purpose of the folder
  - the contents of the folder
  - any keys/glossaries necessary to understand the contents of the folder
  - timestamps
  - etc.

]

]

---
count: false
class: title-slide-section-grey, middle, center

# Say my name

---
count: false

# Naming conventions

### Why?

- You probably don't spend much time thinking about how you name files and documents

- You should

- The idea is to follow a few simple guidelines that will make facilitate 
organizing your projects and make the file structure easily searchable

---
count: false

# Naming conventions

### How?

- Use descriptive names 
  - .red[Bad]: `Experiment`
  - .blue[Good]: `qualifying_paper_1`

- no capitals, no spaces (use `_` or `-`)
  - .red[Bad]: `Experiment for syntax class`
  - .blue[Good]: `semantic_predictability_exp_1`

- no non-standard characters
  - .red[Bad]: `Analysis of ð for ICPhS 2019`
  - .blue[Good]: `spirantization_icphs_2019`

]

- Numbers: use 2 places minimum, year-month-day
  - .red[Bad]: `Analysis 1`
  - .blue[Better]: `01_analysis`
  - .green[Best]: `2019-02-20_data_download`

]

count: false
background-image: url(./assets/img/numbers.png)
background-size: 400px
background-position: 90% 90%

---
count: false
class: title-slide-section-grey, middle, center

# Github integration

---
count: false
background-color: black
background-image: url(./assets/img/github01.png)
background-size: contain

---
count: false
background-color: black
background-image: url(./assets/img/github02.png)
background-size: contain

---
count: false
class: title-slide-section-grey, center, middle

# Tips and tricks

---
count: false

# Tips and tricks

### Nested projects

- You can have RStudio projects inside of larger projects
- Only the larger project is a repo
- Ex.  
  - Project: `dissertation` (← repo)
  - Nested project: `production_semantic_processing_las`
  - Nested project: `prod_perc_bilabials_jphon`

--
count: false

### Alfred

- Productivity app 
- Only on Mac (I think), free
- Works like Spotlight search, but customizable
- Set to search for `.rproj` files
- Allows you to quickly open and close RStudio projects

---

# Advanced

---
count: false

# Review

<p></p>

- Standard way: 
  - Create repo 
  - Clone local copy
  - Make changes
  - Commit/push changes to remote
]

---
count: false
background-image: url(./assets/img/vc3_github_01.pdf)
background-size: contain

---
count: false
background-image: url(./assets/img/vc3_github_02.pdf)
background-size: contain

---
count: false
background-image: url(./assets/img/vc3_github_09.pdf)
background-size: contain

---
count: false
background-image: url(./assets/img/vc3_github_10.pdf)
background-size: contain

---
count: false
background-image: url(./assets/img/vc3_github_11.pdf)
background-size: contain

---
count: false

# Review

<p></p>

.lightgrey[
- Standard way: 
    - Create repo 
    - Clone local copy 
    - Make changes 
    - Commit/push changes to remote
]

<p></p>

- When collaborating: 
    - Fork repo
    - Clone local copy
    - Make changes
    - Commit/push changes to remote
    - Submit pull request to origin
]

---
count: false
background-image: url(./assets/img/vc3_github_03.pdf)
background-size: contain

---
count: false
background-image: url(./assets/img/vc3_github_04.pdf)
background-size: contain

---
count: false
background-image: url(./assets/img/vc3_github_05.pdf)
background-size: contain

---
count: false
background-image: url(./assets/img/vc3_github_06.pdf)
background-size: contain

---
count: false
class: bottom, center
background-image: url(https://octodex.github.com/images/socialite.jpg)

# Useful workflow when collaborating with many people

---
count: false
background-image: url(./assets/img/vc3_github_07.pdf)
background-size: contain

---
count: false
background-color: #EDEDED
background-image: url(./assets/img/vc3_github_08.pdf)
background-size: contain

---
count: false
class: title-slide-section-grey, middle

# **But**...

### ...this isn't the most common method

--
count: false

### ...or the best method

---
count: false
background-color: black
background-image: url(https://i.imgflip.com/2x4s1d.jpg)
background-size: contain

---
count: false
background-color: black
background-image: url(https://user-images.githubusercontent.com/194400/32239744-57300018-be63-11e7-8464-1389b9f8e0ee.png)
background-size: contain

---
count: false
background-image: url(https://cdn2.hubspot.net/hubfs/2249672/Imported_Blog_Media/austin_powers-1.jpg)
background-size: 500px
background-position: 97% 50%

# What gives?

- Most developers use git as version control for software

- The .blue[master branch] is usually left for public releases

- As such it should always work
]]

---
count: false
background-image: url(https://cdn-images-1.medium.com/max/1600/1*ezl84iQSMDnfkOipMVHgDw.png)
background-size: 350px
background-position: 97% 50%

# What's the problem

- You might get complicated merge conflicts
]

.full-width[.content-box-blue[
Person A is working on the same file as Person B, they both make changes 
and Person A tries to submit a pull request to master on a file that is 
different from when (s)he started
]]
]

---
count: false

# What's the solution?

### Branches

- Using branches gives us a way to work on different versions of a repository 
at one time

--
count: false

- By default a new repo has one branch called .large[.blue[master]]

--
count: false

- Master is *the definitive* branch

--
count: false

- We create new branches to experiment, make edits, create new features, etc., 
before committing them to master

--
count: false

- When you create a branch off of master you’re essentially making a copy, or 
snapshot of master at a specific point in time (like making a copy of 
a word file, i.e., `essay_final_version3_for_real.docx`)

--
count: false

- A branch should be used for making 'one logical change', usually to add a 
feature in software development

--
count: false

- If a collaborator makes changes to master while you are working on a branch, 
you can pull in those changes

---
count: false
background-image: url(./assets/img/vc3_github_12.pdf)
background-size: contain

---
count: false
background-image: url(./assets/img/vc3_github_13.pdf)
background-size: contain

---
count: false
background-image: url(./assets/img/vc3_github_14.pdf)
background-size: contain

---
count: false
background-image: url(./assets/img/vc3_github_15.pdf)
background-size: contain

---
count: false
background-image: url(https://guides.github.com/activities/hello-world/branching.png)
background-size: contain

---
count: false
background-image: url(./assets/img/psychopy_network.png)
background-size: contain

---
count: false

# Yeah, but... academic writing is different

.big[
- Using branches in many cases may be overkill, depending on what your working 
on, i.e., slides for class
]

--
count: false

<p></p>

.big[
- But there are concrete examples where it makes sense to use branches...
  - when collaborating with others
  - when working on large projects
  - when making revisions to a manuscript
  - when making changes to your website, cv, conference presentation/poster
  - whenever breaking something small will have a large impact on the project
  - whenever the possibility of "going back" needs to be controlled and 
  easily achieved 
]

---
count: false
background-image: url(./assets/img/diss_ex_1.png)
background-size: 700px

---
count: false
background-image: url(./assets/img/diss_ex_2.png)
background-size: contain

---
count: false
background-image: url(./assets/img/diss_ex_3.png)
background-size: 700px

---
count: false

# Summary - workflows

### Old way

- Working solo: commit/push to master

--
count: false
(.red[medium danger])

--
count: false
- Working as collaborator: commit/push to master

--
count: false
(.red[danger]!)

--
count: false
- Working as outside collaborator: fork, commit/push to remote,  
pull request to master

--
count: false
(.red[low danger])

--
count: false
background-image: url(https://user-images.githubusercontent.com/194400/32239878-ad220b4c-be63-11e7-82f0-49180949fb8e.png)
background-size: 300px
background-position: 97% 50%

### Better way

- Working solo: branch, commit/push, pull request
--
count: false
- Working as collaborator, branch, commit/push, pull request
--
count: false
- Working as outside collaborator: fork, branch, commit/push, pull request

---
count: false
class: middle, inverse
background-image: url(https://user-images.githubusercontent.com/194400/32239666-10da8f34-be63-11e7-928f-c00f552dd2c5.png)
background-size: contain