GitHub (and Data Science Tools) 🐱 for Psychologists

.title[
# GitHub (and Data Science Tools) <br> 🐱<br> for Psychologists
]
.subtitle[
## Wake Forest University
]
.author[
### S. Mason Garrison
]

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<span>
<a href="https://DataScience4Psych.github.io/DataScience4Psych/" target="_blank">Data Science for Psychologists</a>
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# Hello world!

<div class="figure" style="text-align: center">
<img src="data:image/png;base64,#d00_slide_files/figure-html/unnamed-chunk-2-1.png" alt="QR code for these slides" width="10%" />
<p class="caption">QR code for these slides</p>
</div>
.footnote[.center[
[DataScience4Psych.github.io/slides/00_ASU/d00_slide](https://datascience4psych.github.io/slides/00_ASU/d00_slide#1) 
]
]

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# What is Git? What is GitHub?

.pull-left[
- **Git:** A FREE distributed Version Control System (VCS). 
  - Effectively, it is a tool for easily tracking changes to your code, collaborating, and sharing. 
  - Track the changes you make  and 
  - can easily revert back to an older version
  - Makes working with others (and yourself) easier 
] 
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.pull-right[ 
<img src="data:image/png;base64,#img/git-logo.png" width="90%" style="display: block; margin: auto;" />
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# What is GitHub?
.pull-left[
- **GitHub:** A web-based platform built that extends Git’s capabilities by providing a web-based interface for collaboration. 
  - It’s widely used for code development, 
  - allowing multiple people to work together 
  - GitHub hosts your repositories (project folders) and 
  - provides tools for managing changes, reviewing code, and collaborating  
- And it’s [FREE for people affiliated with academic institutions!](https://education.github.com/benefits)
]

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.pull-right[ 
<img src="data:image/png;base64,#img/github_logo.png" width="50%" style="display: block; margin: auto;" /><img src="data:image/png;base64,#img/github-mark.png" width="50%" style="display: block; margin: auto;" />
]

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# Why GitHub for Psychologists?

- **Collaboration Made Easy**  
- **Project Management**  
--

- **Transparency and Reproducibility**  
- **Educational Tools**  
- **Streamlined Publishing**  
--

- For psychologists, GitHub offers a platform to enhance research productivity for free ([as long as you're connected to an educational institution](https://education.github.com/benefits))

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# Exploring GitHub's Potential for the Psychology Community

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# GitHub for Project Management

- **Centralized Workspace:** Manage your research projects in a single space, accessible to the whole team.
- **Issue Tracking:** Log tasks, bugs, and feature requests as issues to keep track of project progress.
- **Milestones:** Set important project milestones to track progress towards major goals.
- **Project Boards:** Use Kanban-style boards to visualize workflow, from idea to implementation.

--
- Disclosure: I do not use most of these features consistently...

.footnote[Learn more about GitHub for project management: [GitHub Project Management](https://docs.github.com/en/issues/trying-out-the-new-projects-experience)]

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## Managing Research Projects and Labs

- **Collaboration at Scale:** GitHub enables team members to work together seamlessly, regardless of their location.
- **Transparency and Reproducibility:** By hosting your lab's projects on GitHub, you ensure that your research processes are transparent and your results are reproducible.
- **Example:** My [R Computing Lab](https://github.com/R-Computing-Lab) demonstrates how labs can manage datasets, code, and collaborate on analysis in real(ish)-time.

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<img src="data:image/png;base64,#img/screenshot_r_lab_loggedout.png" width="45%" style="display: block; margin: auto;" />
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<img src="data:image/png;base64,#img/screenshot_r_lab.png" width="45%" style="display: block; margin: auto;" />
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<img src="data:image/png;base64,#img/screenshot_r_lab_loggedout.png" width="90%" style="display: block; margin: auto;" />
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<img src="data:image/png;base64,#img/screenshot_r_lab.png" width="90%" style="display: block; margin: auto;" />
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## Teaching Courses

.pull-left[
- **Interactive Learning:** GitHub provides a platform for sharing up-to-date course materials and notes, making learning more interactive and engaging.
- **Version Control for Syllabi:** Easily update and revise syllabi policies, dates etc. [smasongarrison.github.io/syllabi/](https://smasongarrison.github.io/syllabi/)
- **Examples:** The [Data Science for Psychologists course repository](https://github.com/DataScience4Psych) repository showcases how GitHub can be used to enhance the teaching and learning experience.
]

--
.pull-right[
<img src="data:image/png;base64,#img/syllabus.png" width="80%" style="display: block; margin: auto;" />
<img src="data:image/png;base64,#d00_slide_files/figure-html/unnamed-chunk-10-1.png" width="10%" style="display: block; margin: auto;" />
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### Data Science for Psychologists

.pull-left[
<img src="data:image/png;base64,#img/screenshot_coursebook.png" width="85%" style="display: block; margin: auto;" />
<img src="data:image/png;base64,#d00_slide_files/figure-html/unnamed-chunk-12-1.png" width="10%" style="display: block; margin: auto;" />
.footnote[.center[
[DataScience4Psych.github.io/DataScience4Psych/](https://DataScience4Psych.github.io/DataScience4Psych/) 
]
]]
.pull-right[
<img src="data:image/png;base64,#img/screenshot_courserepo.png" width="85%" style="display: block; margin: auto;" />
]

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## Publishing Academic Papers

- **Streamlined Publication Process:** GitHub supports the publishing process with version control and collaboration, making the development and review of manuscripts more efficient.
- **Open Collaboration:** Encourages open and collaborative peer review and feedback from the global community.
- **Example:** The Journal of Open Source Software (JOSS) uses GitHub to manage submissions, reviews, and publication processes.  https://joss.theoj.org/papers/10.21105/joss.06203

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<img src="data:image/png;base64,#img/screenshot_joss.png" width="50%" style="display: block; margin: auto;" />
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<img src="data:image/png;base64,#img/screenshot_joss_review.png" width="50%" style="display: block; margin: auto;" />
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<img src="data:image/png;base64,#img/screenshot_joss.png" width="90%" style="display: block; margin: auto;" />
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<img src="data:image/png;base64,#img/screenshot_joss_review.png" width="90%" style="display: block; margin: auto;" />
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## Website Hosting with GitHub

- **Showcase Your Work:** GitHub Pages allows researchers and academics to host their professional portfolios, CVs, and even project pages for free.
- **Example:** Visit [S. Mason Garrison's CV](https://smasongarrison.github.io/CV-Tex/SMasonGarrisonCV.pdf) hosted on GitHub for an example of how you can use GitHub Pages to host your academic CV.

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<img src="data:image/png;base64,#img/screenshot_cv_host.png" width="100%" style="display: block; margin: auto;" />
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<img src="data:image/png;base64,#img/screenshot_cv_commits.png" width="100%" style="display: block; margin: auto;" />
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# Intriguing, right?

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## Terminology Cheat Sheet

- **Repositories (Repo)**: Store your projects in repositories, including all files, revisions, and documentation.
- **Commits**: Save changes to your project, creating a transparent history of your work and decisions.
- **Push**: Send your committed changes to a remote repository on GitHub.com.
- **Pull**: Fetch changes from a remote repository and merge them into your local repository.
--

- **Pull Requests**: Propose changes to a project and discuss those changes with project collaborators before merging them.
- **Branches**: Work on different versions of a repository at the same time, allowing for parallel development.
- **Issues**: Track ideas, enhancements, tasks, or bugs for your projects. Organize with labels, assignees, and milestones.

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# Git and GitHub

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## Version control

- We introduced GitHub as a platform for collaboration
- But it's much more than that...
- It's actually designed for version control

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## Versioning

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## Versioning (with human readable messages)

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## Why do we need version control?

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# Git and GitHub tips

- Git is a version control system -- like “Track Changes” features from Microsoft Word on steroids. GitHub is the home for your Git-based projects on the internet -- like DropBox but much, much better).

--
- There are millions of git commands -- ok, that's an exaggeration, but there are a lot of them -- and very few people know them all. 99% of the time you will use git to add, commit, push, and pull.

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- We will be doing Git things and interfacing with GitHub through RStudio/GitHub Desktop, but if you google for help you might come across methods for doing these things in the command line -- skip that and move on to the next resource unless you feel comfortable trying it out.

--
- There is a great resource for working with git and R: [happygitwithr.com](http://happygitwithr.com/). Some of the content in there is beyond the scope of this talk, but it's a good place to look for help.

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## Let's take a tour - Git and GitHub

- Connect an R project to Github repository
- Working with a local and remote repository
- Making a change locally, committing, and pushing
- Making a change on GitHub and pulling

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## Create a GitHub account

.small[
.instructions[
Go to [github.com](https://github.com/), and create an account (unless you already have one)... This is going to be the first step of the activity, so you can get ahead and do it now.
]
]

Tips for selecting a username:<sup>✦</sup>

.small[
- Incorporate your actual name.
- Reuse username from other contexts, e.g., Twitter or Slack.
- Pick a username you'll be comfortable revealing to your future boss.
- Shorter is better than longer.
- Be as unique as possible in as few characters as possible.
- Make it timeless. Don't highlight your current university, employer, etc.
- Avoid words laden with special meaning in programming, like `NA`.
]

--
.small[ 
<sup>✦</sup> Source: [Happy git with R](http://happygitwithr.com/github-acct.html#username-advice) by Jenny Bryan
]

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## Practical Demonstration

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## Part 1: Setting Up Your GitHub Repository

1. **Sign Up on GitHub**
   - Visit [GitHub.com](https://github.com/) and create a new account.
   
2. **Create Your First Repository**
   - Click the "+" icon in the top right corner and select "New repository".
   - Name your repository and optionally add a description.

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## Part 2: Local Setup and Version Control

- Option A: Using RStudio (for R users)
- Option B: Using GitHub Desktop (for a GUI approach)

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## Option A: Using RStudio
- 3 **Install Git**
   - Download and install Git from [git-scm.com](https://git-scm.com/).
- 4 **Configure Git with RStudio**
   - In RStudio, go to Tools > Global Options > Git/SVN and make sure Git is recognized.
- 5 **Clone a Repository**
   - Use the "New Project" wizard in RStudio to clone your repository for local work.

.footnote[**Resources to Learn More**
   - [GitHub Guides](https://guides.github.com/)
   - [Happy Git and GitHub for the useR](http://happygitwithr.com/)
]

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## Option B: Using RStudio

- 3 **Install and Set Up GitHub Desktop**
   - Download and install GitHub Desktop from [desktop.github.com](https://desktop.github.com/).
   - Open GitHub Desktop and sign in with your GitHub account.
- 4 **Configure GitHub**  
   - Configure your GitHub and email account under GitHub Desktop’s Preferences to ensure your commits are properly attributed to you.
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- 5  **Clone the Repository Using GitHub Desktop**
   - In GitHub Desktop, go to `File` > `Clone Repository`.
   - Select the repository you created on GitHub from the list and choose a local path where you want to store the project files.
   - Click `Clone` to create a local copy of your repository.
  
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# Part 3: Make Changes and Committing with GitHub
  
- 6 **Make Changes Locally**: 
   - Add or modify files in your local project folder.
- 7 **Commit Your Changes**: 
   - Summarize your changes in a commit message and commit them. 
   - In RStudio, use the Git tab. 
   - In GitHub Desktop, use the Changes tab.
  
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- 7A **RStudio (Git tab)**
   - Open RStudio and click on the Git tab in the top right panel.
   - Check the box next to the files you want to commit, add a commit message in the top left panel, and click `Commit`.
- 7B **GitHub Desktop (Changes tab)**
   - Open GitHub Desktop; you should see the changes listed.
   - Select the files you want to commit, add a commit message in the bottom left panel describing your changes, and click `Commit to main` (assuming you are working on the main branch).

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# Part 4: Keeping in Sync

- 8 **Push to GitHub**: Upload your changes to GitHub. Use the "Push" button in RStudio or GitHub Desktop.
--

- 8A **RStudio (Git tab)**
   - With your changes committed, click the `Push` button in RStudio to upload your changes to the remote repository on GitHub.
- 8B **GitHub Desktop (Changes tab)**
   - With your changes committed, click the `Push origin` button in GitHub Desktop to upload your changes to the remote repository on GitHub.
--

- 9 **View your changes** 
   - Your changes are now reflected on GitHub, and you can view them by navigating to your repository on the GitHub website.  
- 10 **Pull from GitHub**: If changes are made on GitHub directly (by you or collaborators), you can update your local repository by clicking the `Pull` button in RStudio or GitHub Desktop.
   - Start experimenting with small projects to get comfortable with the workflow. Happy coding!

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## Additional Resources

- [GitHub Guides](https://guides.github.com/)
- [Happy Git and GitHub for the useR](http://happygitwithr.com/)
- GitHub Desktop Documentation: For detailed guides and troubleshooting, visit [docs.github.com/en/desktop](https://docs.github.com/en/desktop).
- Interactive Tutorials: GitHub offers interactive tutorials to understand the workflow better; find them at [lab.github.com](https://lab.github.com/).

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# Conclusion and Q&A

- Today, we explored how GitHub can revolutionize research and collaboration in psychology.
- We've seen its potential from managing labs to hosting websites.
- Remember, the journey of a thousand miles begins with a single step. Start small and explore!

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## Any Questions?

Feel free to ask any questions now, or reach out to me after the talk via email _garrissm@wfu.edu_ or on github _github.com/smasongarrison_.

.footnote[.center[
[DataScience4Psych.github.io/DataScience4Psych/](https://DataScience4Psych.github.io/DataScience4Psych/) 
]
]