Version Control

1. We have created a repository from a template repository on GitHub.

2. After that, we cloned the repository to our local PC and moved some of our files into the repository.

3. Navigate to your project folder in a terminal.

cd [path/to/project_folder]

4. Verify that your project folder is a git repository by locating the .git folder:

ls -a

Use Git log to check the history of your project:

git log

Alternatively, via GitHub it is also possible to view the history of your project. Let’s see how a mature project looks like in this repository of the happygitwithr book:

git status

Git status shows you the status of your repository. It tells you which files are created, modified, or deleted relative to the last git snapshot (aka commit) of your project.

git diff

Git diff shows you the actual differences between the files that you have changed since the last snapshot.

git --help

This command will show you all the commands that you can use with git.

5. If you have added your files to your git repository on your PC, now add all your files to the staging area:

git add *

5. Commit all the files in the staging area to your repository:

git commit -m "add my files"

You can now push the content of your local repository to the one on github:

git push

Congrats, you have made your first push and your scripts are online!

\___ THANK YOU!

Take a look at your online repository. Who is the author of your commits? If it is not you, you can configure git to use your identity (make sure github knows this email address):

git config --global user.name "Your Name"
git config --global user.email "your@email.com"

1. Add the changed file(s) to the staging area, and commit the changes:

git add src/filename.py anotherfile.txt
git add config/configfile.json
git status
git commit -m "My commit message"
git push

NB: don’t forget your commit message (try what happens if you do!).

Useful git commands:

git log
git log --oneline
git status
git diff
git diff HEAD~3
git --help

The .gitignore file in your template contains files that by definition will not be tracked by git.

For example, if you do not want to track a file .DS_Store (always present on my mac), you enter a line like this in your .gitignore file:

.DS_Store

Similarly, you can ensure all output in a folder will not be tracked:

results/

Or all files with a certain extension:

 *.dat 

NB: There is a .gitkeep file in your template – this does not do the opposite to .gitignore, but is instead used as a placeholder for folders: git does not track empty folders…

1. Continue moving your files into the file template.

2. Add, commit, and push all files you want to track! (Do you want to move a tracked file within a git repository? git mv path/to/file.svg newpath/file.svg and don’t forget to commit!)

3. Are there (temporary) files you do not wish to track? Add them to the .gitignore file. Consider a .gitignore template for your language: examples on this github repo.

4. Continue editing your code, and add/commit/push your changes. Can you do it from your IDE?

5. Experiment with editing and committing on github itself. You can then ‘download’ your code to your local repository using git pull.

6. What happens if you edit the same file online and locally, and try to push/pull?

• Commits should be atomic: comprehensive ‘units’ of changes.

  • DO: edit/add an .svg and add it to your .Rmd presentation in the same commit
  • DON’T: edit for a full day and put this in a single commit (or worse: forget to…)

• Commits should have informative messages so you (and others) can trace your steps

• Track most files; .gitignore those files you don’t.

• Explore new ideas with branches, keep a stable version on main

• A Software Carpentry course on git

• A version control + git tutorial on Atlassian

• A git cheatsheet from Atlassian

• A book with all the ins and outs of git from the git website