ETC5513: Collaborative and Reproducible Practices

Tutorial 4

Author

Michael Lydeamore

Published

16 April 2025

🎯 Objectives

  • Create repositories and syncrhonize them between your local and remote repos
  • Create a Quarto report with a tabell, figures and sections that are labelled and referenced
  • Create branches in local and remote repositories
  • Deal with merge conflicts

Creating a new project

Let’s practice creating a new project from scratch. We will start by making the remote repository in GitHub.

  1. Go to https://github.com and log in.

  2. Click the + icon in the top-right corner → choose “New repository”.

  3. Fill out the form:

    • Repository name: e.g., my-new-project
    • (Optional) Add a short description
    • Choose Public (or Private if preferred)
    • ✅ Check “Add a README file”

  4. Click the “Create repository” button at the bottom.

Your repository is now created and ready to use!

Now, we need to clone the repository.

💻 Step 2: Clone the Repository Using the Terminal

  1. On your new repository page, click the green “Code” button.

  2. Choose the SSH tab (⚠️ not HTTPS) and copy the URL.
    It will look like this:

    git@github.com:your-username/my-new-project.git

  3. Open your terminal.

  4. Navigate to the folder where you want to store your project (e.g., Documents):

    cd ~/Documents

  5. Use the git clone command followed by the URL:

    git clone git@github.com:your-username/my-new-project.git

  6. Move into the project folder:

    cd my-new-project

````markdown ## 🌿 Step 3: Create a Branch, Make Changes, and Push

Now that your repository is cloned, you’re ready to create a branch, make some changes, and push it to GitHub.

Branching

🔀 1. Create a New Branch

In the terminal, make sure you’re inside your project folder:

cd my-new-project
Tip

Remember you can always check where you are by typing

pwd

Create and switch to a new branch (you can name it anything — here we’ll use feature):

git branch feature
git switch feature
Tip

You can also do this in one command with

git switch -c feature

✅ You are now working in a new branch called feature.

✍️ 2. Make a Change to a File

Open the README.md file in RStudio.

Add a new line to the bottom, such as:

This is a change I made on the feature branch.

Save the file.

💾 3. Stage and Commit the Change

Check which files were changed:

git status

Stage the file:

git add README.md

Commit the change:

git commit -m "Added a line to README on feature branch"

✅ Your change is now saved locally in your branch.

🚀 4. Push the Branch to GitHub

Now push your new branch to the remote (GitHub):

git push -u origin feature

✅ You should now see the feature branch appear on GitHub. Go to your repository in the browser and click the “branches” dropdown to check!

Tip

We need the -u flag on the push command to tell git to link together the remote (origin) and our local branch. From now on, we can just use git push and git will remember the link.

🔁 Merge Your Branch Using the Terminal

Now that you’ve made and committed changes on your feature branch, let’s merge those changes into the main branch — all from the terminal.

🔄 1. Switch Back to the main Branch

First, make sure you’re back on the main branch:

git switch main

🔃 2. Pull the Latest Changes from GitHub

Before merging, make sure your local main branch is up to date with the remote:

git pull origin main

🔀 3. Merge the Feature Branch into Main

Now merge your feature branch into main. For example, if your branch is called feature:

git merge feature

✅ This combines the changes from feature into main.

🚀 4. Push the Merged Changes to GitHub

Now push the updated main branch to GitHub:

git push origin main

✅ Your main branch on GitHub now includes the changes from your feature branch!

🧹 5. (Optional) Delete the Feature Branch

You can now delete the feature branch locally:

git branch -d feature

If you also want to delete it on GitHub:

git push origin --delete feature

⚔️ Create and Resolve a Merge Conflict

Now that you know how merging works, let’s deliberately cause a merge conflict and walk through how to fix it.

Merge conflicts happen when two branches change the same part of a file in different ways — Git doesn’t know which version to keep.

🔧 1. Start Fresh in main

Make sure you’re on the main branch:

git switch main

Create a new branch but do not switch to it:

git branch conflict-branch

Open the README.md file and change the first line to:

This line was edited on main.

Save the file, then stage and commit the change:

git add README.md
git commit -m "Edit first line on main"

🌿 2. Create a New Branch and Make a Conflicting Change

Switch to the new branch:

git switch conflict-branch

Open README.md again, but this time change the same first line to:

This line was edited on conflict-branch.

Save it, then stage and commit:

git add README.md
git commit -m "Edit first line on conflict-branch"

🔁 3. Merge the Branch into main

Switch back to main:

git switch main

Try to merge the branch:

git merge conflict-branch

🛑 Uh-oh! You’ll see a merge conflict message. Git can’t automatically merge the file.

🧠 4. Resolve the Conflict

Open README.md. You’ll see something like this:

<<<<<<< HEAD
This line was edited on main.
=======
This line was edited on conflict-branch.
>>>>>>> conflict-branch

This means: - Everything between <<<<<<< HEAD and ======= is from main - Everything after ======= is from conflict-branch

Edit the file to keep only one version — or combine them. For example:

This line includes changes from both branches.

Make sure you delete the conflict markers (<<<<<<< HEAD, ======= and >>>>>>> conflict-branch) as part of your changes.

Save the file.

✅ 5. Finalize the Merge

After resolving the conflict:

  1. Stage the fixed file:
git add README.md
  1. Complete the merge with a commit:
git commit -m "Resolved merge conflict in README.md"
  1. Push the updated main branch to GitHub:
git push origin main

🎉 You’ve resolved a merge conflict like a pro!

Cross-referencing and academic referencing

In this exercise you will learn how to reference figures, tables and sections in your report. We will also learn how to cite external sources.

  1. Open the file week4.qmd and add the following to the end of the document:
```{r}
#| label: fig-penguins
#| fig-cap: "Bill length vs bill depth of three species of penguins from the Palmer Station, Antarctica"

library(palmerpenguins)

ggplot(penguins, aes(x=bill_length_mm, y=bill_depth_mm, colour=species)) +
  geom_point()
```

  1. Add a sentence below this chunk that says: @fig-penguins shows that the three species of penguins have clusters of bill depths and bill lengths that largely do not overlap

  2. Render the document. You should see a hyperlink to Figure 1, that links back to your original figure.

Home extension: Academic referencing

With Quarto, we no longer need to type out references manually. With the help of some external software, our external references can be automatically generated.

Tip

If you get stuck on this section, check out the video on Moodle.

  1. Download Zotero: https://www.zotero.org/ and register for a free account.
  2. Install the Better BibTeX for Zotero extension: https://retorque.re/zotero-better-bibtex/installation/
  3. Install the relevant Connector for your web browser: https://www.zotero.org/download/connectors
  4. We will add the reference by it’s Digial Object Identifier or DOI. The DOI for palmerpenguins is 10.5281/zenodo.3960218. Press the small “Add item by identifier” button in Zotero, and paste in the DOI:

  1. In Zotero, right click the newly added item, go to “Better BibTex” -> “copy BibTeX to clipboard”

  1. Inside your project, create a new file called references.bib. Paste the BibTeX you just copied in there. It should look something like this:
@misc{horstAllisonhorstPalmerpenguinsV0102020,
  title = {Allisonhorst/Palmerpenguins: V0.1.0},
  shorttitle = {Allisonhorst/Palmerpenguins},
  author = {Horst, Allison M and Hill, Alison Presmanes and Gorman, Kristen B},
  year = {2020},
  month = jul,
  doi = {10.5281/ZENODO.3960218},
  urldate = {2025-03-24},
  abstract = {CRAN release of palmerpenguins v0.1.0 R package by Horst, Hill and Gorman (July 2020).},
  copyright = {Open Access},
  howpublished = {Zenodo}
}
  1. In week4.qmd, add the following to the YAML:
bibliography: references.bib

  1. In the sentence we wrote describing Figure 1, add the following to the end of the sentence: @horstAllisonhorstPalmerpenguinsV0102020.

  2. Re-render the document. You should have a reference to the package where you typed @horstAllisonhorstPalmerpenguinsV0102020, and you should see a references section at the end of the document.