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git for Scientific Software Development
Jack Atkinson 
Principal Research Software Engineer
ICCS - University of Cambridge
2026-07-16
Precursors
Slides and Materials
To access links or follow on your own device these slides can be found at:
jatkinson1000.github.io/git-for-science
All materials are available at:
Licensing
Except where otherwise noted, these presentation materials are licensed under the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) License.
Learning Objectives
- Recap the basic git commands
- Understand key components of git repositories to aid in collaboration
- Link git version control to online tools of GitHub/GitLab
- Learn how to use git and GitHub/GitLab to better manage development and collaboration
- branches
- issues
- merge/pull requests
- code review
git Geography
Locations
- Local
- Workspace
- Staging area or index
- Local repo
- Stash
- Remote
- Remote repo
Tip
These (and more) can be explored in Andrew Peterson’s Interactive git cheat sheet
The basic commands
git clone <repo> [<dir>]- Clone a repository into a new directory
git status- Check the state of the local workspace
git add <filepath>- Update the index with any changes
git commitgit commit -m <message>- Commit changes in the index to (local) record
git push <remote> <branch>- Send your locally committed changes to the remote repo
git pull <remote> <branch>- Get changes from the remote repo locally
README
- A file in the main directory of your repository.
- The entry point for new users.
- Helps to ensure your code:
- is accessible
- is used properly
- has longevity
- Today encouraged to be written in Markdown as
README.md.
README - examples
README - good examples
- pyTCR - Tropical cyclone rainfall modelling
- FTorch - coupling PyTorch to Fortran
- pyrealm - plant modelling
- Fortitude - a Fortran linter
- Station Bathymetry - notebook-based repo for data analysis
- The ‘Best-README-template’
Adding a License - GitLab
1) From the main repo select the “+” dropdown menu and “New file”.
2) In the filename type “LICENSE” and GitLab will detect and offer you a dropdown to choose a LICENSE template.
3) Once you have chosen you can “Commit Changes” to add the file. It will appear as a LICENSE file at the top of the repository and will be detected by GitLab in the right hand side metadata.
Adding a License - GitHub
From the main repo select “Add file” and “+ Create new file”.
In the filename type “LICENSE” and GitHub will detect and offer you the option to choose a LICENSE template.
Adding a License - GitHub
Select your desired license and follow the instructions to apply it to your repository. Once complete it will appear as a LICENSE file at the top of the repository and will be detected by GitHub in the right hand side metadata.
Issues
Both GitHub and GitLab have methods for tracking issues.
These are useful for organising work.
- managing separate tasks
- logging problems/tasks as they arise
- tracking and scheduling development
Note
Issues are part of GitHub/GitLab, NOT the git repository.
They will not be kept if you move the project elsewhere and do not appear on your local system.
GitHub
GitLab
Aside - Commit Messages
