Setting Up Your Course Workspace in VS Code

What is the course workspace?

The course workspace is where you keep everything you write and build this term. It is a VS Code folder, copied from a GitHub template, that holds your journals, literature notes, project files, and reusable templates, all version-controlled with Git. Everything is plain Markdown and plain files, so you own your work and can read it anywhere.

There is no separate notes app and no plugins to configure. You organize your work with folders and write in Markdown, the same tools you use for the rest of the course.

Step 1: Install VS Code, R, and Git

If you have not already, follow the Install VS Code guide. You also need R and Git, covered in Install R and Getting Started with GitHub.

Step 2: Create your copy from the template

  1. Go to the v2v-workspace repository.
  2. Click Use this template, then Create a new repository.
  3. Name it something like mc451-workspace. Private is fine.
  4. Click Create repository.

You now have your own copy of the workspace on GitHub.

Step 3: Clone it into VS Code

  1. Copy your new repository’s URL (the green Code button).
  2. In VS Code, open the Command Palette: Ctrl+Shift+P (Windows) or Cmd+Shift+P (Mac).
  3. Type Git: Clone and press Enter.
  4. Paste your repository URL.
  5. Choose a folder you will remember, for example Documents/MC451/.
  6. When VS Code asks, click Open to open the cloned workspace.

Step 5: Read the README

Open README.md in the file explorer (left sidebar). It explains the folder structure and how to start a journal entry.

The workspace is pre-organized:

  • 00_inbox captures ideas quickly.
  • 01_journal holds your weekly reflections (committed to GitHub).
  • 02_literature holds reading notes and Zotero annotations.
  • 03_project holds your active research work.
  • 04_resources holds images, PDFs, and attachments.
  • **_templates** holds reusable templates.

Follow this structure to stay organized.

Step 6: Start a journal entry from the template

  1. In the file explorer, open _templates/journal-entry.md.
  2. Right-click it and choose Copy, then right-click the 01_Journal/ folder and choose Paste.
  3. Rename the copy for the week, for example week-02-curiosity-and-trust.md.
  4. Fill in the prompts and write your reflection.
TipKeep files findable

Name files in lower case with hyphens instead of spaces (week-02-curiosity.md, not Week 2 Notes.md). Consistent names sort cleanly and never break links.

Step 7: Basic Markdown syntax

Notes use Markdown. The essentials:

Syntax Result
# Heading 1 Large heading
## Heading 2 Medium heading
**Bold text** Bold text
*Italic text* Italic text
- List item Bullet list
1. Numbered item Numbered list
[Link text](https://example.com) Hyperlink
> Quote Block quote
`code` Inline code

VS Code shows a live preview with Ctrl/Cmd+Shift+V.

Step 8: Commit and push your work

At the end of each week, save your work to GitHub. You can use VS Code’s Source Control panel (the branch icon in the left bar): stage your changes, write a short message, and click Commit, then Sync Changes. Or use the terminal:

git add .
git commit -m "Week 2 journal and literature notes"
git push

This gives you a backup, a history of your work, and a way for Dr. Leith to see your entries. It also builds the version-control habit you use in the White Paper.

Troubleshooting

The extension prompt never appeared

Open the Extensions view (Ctrl/Cmd+Shift+X), type @recommended, and install the listed extensions.

I cannot push to GitHub

Confirm you are signed in to GitHub in VS Code (the Accounts icon, bottom-left) and that you cloned your copy of the repository, not the original template.

VS Code opened the wrong folder

Use File > Open Folder and select the workspace folder you cloned, not a parent folder above it.

Next steps

  1. Install VS Code, R, and Git.
  2. Create your copy from the template and clone it.
  3. Install the recommended extensions.
  4. Read README.md.
  5. Start your first journal entry from the template.
  6. Begin Phase I: The Journalist.

Resources

Stuck? Come to office hours.