Skip to content

Tuesday Overview: Version Control and Collaboration in Research Coding

Goal:
Understand the basics of version control with Git, set up repositories, collaborate using GitHub and GitLab, and integrate version control into your research workflow.

What We Cover

  • Introduction to version control and why it matters for research
  • Setting up Git and configuring your identity
  • Initializing a repository and tracking changes
  • Basic Git commands: git add, git commit, git status, git log
  • Creating and switching branches for collaborative work
  • Merging branches and resolving merge conflicts
  • Using GitHub and ICR GitLab for remote collaboration
  • Integrating Git with VSCode and GitHub Desktop
  • Best practices for team coding and project management
  • Choosing a license in GitLab and GitHub

Key Takeaways

  • Version control helps you track changes, collaborate, and avoid losing work.
  • Git is the most widely used version control system in research and industry.
  • Branching and merging allow for safe experimentation and teamwork.
  • Remote repositories (GitHub, GitLab) enable collaboration and backup.
  • Integrating Git with editors like VSCode streamlines your workflow.

Videos of session

Session Cheat Sheet: Tuesday

Setting Up Git for Your Project

git --version
git config --list
git config --global user.name "Your Name"
git config --global user.email "your.email@icr.ac.uk"
git config --global init.defaultBranch main
git config --list

Basic Git Commands

cd biomarkers_project
code .
git init
git status
git add README.md
git commit -m "Add README for biomarkers project"
git status

Using Git at ICR

Setting up keys for GitLab

ssh-keygen -t ecdsa -C ""

~/.ssh/config 

# Private GitLab instance
Host <your_usernames>.git.icr.ac.uk
  PreferredAuthentications publickey
  IdentityFile ~/.ssh/id_ecdsa

Using the GitLab repository for your project

git init --initial-branch=main
git remote add origin git@git.icr.ac.uk:ralcraft/biomarkers_project.git
git add .
git commit -m "Initial commit"
git push --set-upstream origin main

Working with Branches

git branch experiment
git checkout experiment
echo "# Testing a new analysis" > test.txt
git add test.txt
git commit -m "Add test analysis file"
git checkout main
git merge experiment
# To merge in changes from main
git pull origin main
git merge origin/main
# Resolve conflicts if needed
git push

Collaborating with Others

# Clone a repository (example)
git clone https://git.icr.ac.uk/yourusername/biomarkers_project.git
# Pull latest changes
git pull
# Push your changes
git push

Homework

  • Practice basic Git commands on your project
  • Try creating and merging branches
  • Set up a remote repository and push your changes
  • Review the version control section in The Turing Way handbook

Reflection

  • How does version control help you track changes and collaborate?
  • What challenges did you encounter with branching or merging?
  • How will you use Git in your future research projects?

Complete these tasks before the next session to build confidence with version control and collaboration tools.