All in One View

Content from Navigating the filesystem

---

Last updated on 2026-10-21 | Edit this page

Overview

Questions

• Why do we use the shell in a Git workshop?
• How do you move around the filesystem in the shell?

Objectives

• explain why the Unix shell is used to work with Git
• apply shell commands to find out where you are in the file system and to move between directories
• apply flags to change the behaviour of a command, e.g. to show hidden files
• apply man or --help to look up the options of a command

Why the shell?

---

In this workshop we will use Git from the Unix shell (also called command line or terminal). There are graphical programs for Git, too, but the shell has some advantages for learning: the commands are the same on Windows, macOS and Linux, you see exactly what Git is doing, and almost every help page and tutorial you will find online uses the command line.

Before we start with Git, we will therefore learn the few shell commands that we need to find our way around: moving between folders and working with files.

Navigating the shell

---

Let’s start by opening the shell (on Windows: Git Bash, on macOS and Linux: Terminal, see Setup). This likely results in seeing a black or white window with a cursor flashing next to a dollar sign. This is our command line, and the $ is the command prompt to show that the system is ready for our input. The appearance of the prompt will vary from system to system, depending on how the set up has been configured. Other common prompts include the % or # signs, but we will use $ in this lesson to represent the prompt generally.

When working in the shell, you are always somewhere in the computer’s file system, in some folder (directory). We will therefore start by finding out where we are by using the pwd command, which you can use whenever you are unsure about where you are. It stands for “print working directory” and the result of the command is printed to your standard output, which is the screen.

Let’s type pwd and press enter to execute the command (Note that the $ sign is used to indicate a command to be typed on the command prompt, but we never type the $ sign itself, just what follows after it.):

BASH

$ pwd

OUTPUT

/Users/riley

The output will be a path to your home directory (in Git Bash on Windows it looks like /c/Users/riley). Let’s check if we recognise it by looking at the contents of the directory. To do that, we use the ls command. This stands for “list” and the result is a print out of all the contents in the directory:

BASH

$ ls

OUTPUT

Applications Documents    Library      Music        Public
Desktop      Downloads    Movies       Pictures

We may want more information than just a list of files and directories. We can get this by specifying various flags (also known as options, parameters, or, most frequently, arguments) to go with our basic commands. Arguments modify the workings of the command by telling the computer what sort of output or manipulation we want.

If we type ls -l and press enter, the computer returns a list of files that contains information similar to what we would find in our Finder (Mac) or Explorer (Windows): the size of the files in bytes, the date it was created or last modified, and the file name.

BASH

$ ls -l

OUTPUT

total 0
drwx------+  6 riley  staff   204 Jul 16 11:50 Desktop
drwx------+  3 riley  staff   102 Jul 16 11:30 Documents
drwx------+  3 riley  staff   102 Jul 16 11:30 Downloads
drwx------@ 46 riley  staff  1564 Jul 16 11:38 Library
drwx------+  3 riley  staff   102 Jul 16 11:30 Movies
drwx------+  3 riley  staff   102 Jul 16 11:30 Music
drwx------+  3 riley  staff   102 Jul 16 11:30 Pictures
drwxr-xr-x+  5 riley  staff   170 Jul 16 11:30 Public

In everyday usage we are more accustomed to units of measurement like kilobytes, megabytes, and gigabytes. Luckily, there’s another flag -h that when used with the -l option, prints unit suffixes: Byte, Kilobyte, Megabyte, Gigabyte, Terabyte and Petabyte in order to reduce the number of digits to three or fewer using base 2 for sizes.

Now ls -h won’t work on its own. When we want to combine two flags, we can just run them together. So, by typing ls -lh and pressing enter we receive an output in a human-readable format (note: the order here doesn’t matter).

BASH

$ ls -lh

OUTPUT

total 0
drwx------+  6 riley  staff   204B Jul 16 11:50 Desktop
drwx------+  3 riley  staff   102B Jul 16 11:30 Documents
drwx------+  3 riley  staff   102B Jul 16 11:30 Downloads
drwx------@ 46 riley  staff   1.5K Jul 16 11:38 Library
drwx------+  3 riley  staff   102B Jul 16 11:30 Movies
drwx------+  3 riley  staff   102B Jul 16 11:30 Music
drwx------+  3 riley  staff   102B Jul 16 11:30 Pictures
drwxr-xr-x+  5 riley  staff   170B Jul 16 11:30 Public

Some files and directories are hidden: their names start with a dot (.), and ls does not show them by default. To see them, we add the -a flag (for “all”):

BASH

$ ls -a

OUTPUT

.             .bash_history  Applications  Documents  Library  Music     Public
..            .gitconfig     Desktop       Downloads  Movies   Pictures

Remember this flag: Git stores all its information in a hidden directory called .git, and ls -a is how we will find it later. The entries . and .. are special: . means “the current directory” and .. means “the directory above”.

We’ve now spent a great deal of time in our home directory. Let’s go somewhere else. We can do that through the cd or Change Directory command: (Note: On Windows and Mac, by default, the case of the file/directory doesn’t matter. On Linux it does.)

BASH

$ cd Desktop

Notice that the command didn’t output anything. This means that it was carried out successfully. Let’s check by using pwd:

BASH

$ pwd

OUTPUT

/Users/riley/Desktop

If something had gone wrong, however, the command would have told you. Let’s test that by trying to move into a non-existent directory:

BASH

$ cd "things to learn about the shell"

OUTPUT

bash: cd: things to learn about the shell: No such file or directory

Notice that we surrounded the name by quotation marks. The arguments given to any shell command are separated by spaces, so a way to let them know that we mean ‘one single thing called “things to learn about the shell”’, not ‘six different things’, is to use (single or double) quotation marks.

Callout

Avoid spaces in file and directory names

Spaces in names are allowed, but they make working in the shell more cumbersome, because you always have to remember the quotation marks. For your project folders and research data, use - or _ instead, for example my-git-repo-riley or 2026-10_survey_data.csv.

We’ve now seen how we can go ‘down’ through our directory structure (as in into more nested directories). If we want to go back, we can type cd ... This moves us ‘up’ one directory, putting us back where we started. If we ever get completely lost, the command cd without any arguments will bring us right back to the home directory, the place where we started.

Callout

Previous Directory

To switch back and forth between two directories use cd -

Challenge

Try exploring

Move around the computer, get used to moving in and out of directories, see how different file types appear in the Unix shell. Be sure to use the pwd and cd commands, and the different flags for the ls command you learned so far.

If you run Windows, also try typing explorer . to open Explorer for the current directory (the single dot means “current directory”). If you’re on a Mac, try open . and for Linux try xdg-open . to open their graphical file manager.

Being able to navigate the file system is very important for using the Unix shell effectively. As we become more comfortable, we can get very quickly to the directory that we want.

Challenge

Getting help

Use the man command to invoke the manual page (documentation) for a shell command. For example, man ls displays all the arguments available to you - which saves you remembering them all! Use the spacebar to navigate the manual pages. Use q at any time to quit.

Note: this command is for Mac and Linux users only. In Git Bash on Windows, type the command name followed by --help instead, e.g. ls --help.

Find out how to list the files in a directory ordered by their last modification date. Can you combine it with the -l argument you learned before?

Answer

BASH

$ man ls

or

BASH

$ ls --help

In the help text, we find the -t flag (“sort by time, newest first”). Combined with -l:

BASH

$ ls -lt

Key Points

• Knowing where you are in your directory structure is key to working with the shell
• pwd shows where you are, ls lists the contents of a directory and cd moves you to another directory
• ls -a also shows hidden files and directories, whose names start with a dot
• man or --help show the options of a command

Content from Working with files and directories

---

Last updated on 2026-10-21 | Edit this page

Overview

Questions

• How can I create, copy, move, and delete files and directories?
• How can I read files?

Objectives

• apply file naming conventions under guidance when creating a project directory
• apply shell commands to create, view, rename, copy and delete files and directories
• apply tab completion, the command history and wildcards to save typing

Working with files and folders

---

As well as navigating directories, we can interact with files on the command line: we can create them, read them, rename them and delete them. In fact, there’s really no limit to what we can do in the shell, but even experienced shell users still switch to graphical user interfaces (GUIs) for many tasks, such as editing formatted text documents, browsing the web or editing images. But if we wanted to make the same change to hundreds of files, say, rename all the images of a scanned book, then we could automate that work by using shell commands.

Creating a project directory

Let’s create a directory for the project we will work on for the rest of this workshop. First, we move to the Desktop, so that we can easily find the directory in the graphical file manager, too:

BASH

$ cd
$ cd Desktop
$ pwd

OUTPUT

/Users/riley/Desktop

Callout

Where is my Desktop?

On some Windows computers, the Desktop is inside a OneDrive folder, for example OneDrive/Desktop. If cd Desktop doesn’t work, ask your instructor for help.

Here, we create a new directory with the mkdir command (meaning ‘make directories’). We call it my-git-repo- followed by our first name in lower case letters, for example my-git-repo-riley. Please use your own name instead of <name> in the commands of this lesson:

BASH

$ mkdir my-git-repo-<name>
$ ls

OUTPUT

my-git-repo-riley

Callout

Why add your name?

Later in the workshop, this directory will become a repository on Codeberg, next to the repositories of all other participants, and you will work with the repository of a partner. If everybody’s repository had the same name, it would be easy to mix them up. With your name in it, it’s always clear whose repository you are looking at.

Now let’s move into the new directory. But wait! There’s a trick to make things a bit quicker. Instead of typing the whole name, type cd my and then press the Tab key. We notice that the shell completes the line to cd my-git-repo-riley/. Press Enter to run the command.

BASH

$ cd my-git-repo-<name>
$ pwd

OUTPUT

/Users/riley/Desktop/my-git-repo-riley

Callout

Tab for Auto-complete

Pressing tab at any time within the shell will prompt it to attempt to auto-complete the line based on the files or sub-directories in the current directory. Where two or more files have the same characters, the auto-complete will only fill up to the first point of difference, after which we can add more characters, and try using tab again. We would encourage using this method throughout today to see how it behaves (as it saves loads of time and effort!).

Creating and reading files

Our directory is still empty. Every project should have a README.md file that explains what the project is about, so let’s create one. To create a new, empty file, we can use the touch command:

BASH

$ touch README.md
$ ls

OUTPUT

README.md

The .md extension signifies that we have chosen to use the Markdown format, a lightweight markup language with plain text formatting syntax. We will see more of Markdown later.

To write something into a file, we would usually use a text editor, which we will meet in the Git episodes. For a quick start, we can also use the echo command, which prints a text, together with >, which sends the output of a command into a file instead of to the screen:

BASH

$ echo "# My Git repository" > README.md

The hash character # at the beginning of the line makes it a heading in Markdown.

Caution

> overwrites files

If the file after > already exists, its content is replaced without warning. Use >> instead to add a line at the end of a file.

To look at the content of the file, we use the cat command:

BASH

$ cat README.md

OUTPUT

# My Git repository

Callout

Re-using commands

On a blank command prompt, press the up arrow key and notice that the previous command you typed appears before your cursor. We can continue pressing the up arrow to cycle through your previous commands. The down arrow cycles back toward your most recent command. This is another important labour-saving function and something we’ll use a lot.

Challenge

Adding a line

Use the up arrow key to get back the echo command, and change it so that it adds the line “This is where I practise Git.” to README.md. Then check the content of the file.

Answer

BASH

$ echo "This is where I practise Git." >> README.md
$ cat README.md

OUTPUT

# My Git repository
This is where I practise Git.

cat prints the whole file to the screen. For long files, this is not very practical, so there are a few more commands to view files. Try them with README.md:

• head README.md shows the first ten lines of a file (head -n 1 README.md only the first line),
• tail README.md shows the last ten lines (tail -n 1 README.md only the last line),
• less README.md shows the file one screen at a time: use the spacebar to go to the next screen and q to quit.

Remember how to quit less with q: Git uses less to show long output, for example the history of a project with git log.

Moving, copying and deleting files

Instead of moving a file, you might want to copy a file (make a duplicate), for instance to make a backup before modifying a file. The cp command takes two arguments: the old name and the new name.

BASH

$ cp README.md README-backup.md
$ ls

OUTPUT

README-backup.md  README.md

We may also want to change a file name to something more descriptive. We can move it to a new name by using the mv or move command, giving it the old name as the first argument and the new name as the second argument:

BASH

$ mv README-backup.md old-readme.md
$ ls

OUTPUT

README.md  old-readme.md

This is equivalent to the ‘rename file’ function.

Challenge

Moving a file into a directory

If the last argument you give to the mv command is a directory, not a file, the file given in the first argument will be moved to that directory. Create a directory called backup and use the mv command to move the file old-readme.md into it. Check the result with ls and ls backup.

Answer

BASH

$ mkdir backup
$ mv old-readme.md backup
$ ls backup

OUTPUT

old-readme.md

This would also work:

BASH

$ mv old-readme.md backup/old-readme.md

If we had lots of files, it would be tedious to type all the filenames. Luckily the shell supports wildcards! The ? matches exactly one character and * matches zero or more characters. For example, ls backup/*.md lists all files in the backup directory whose names end in .md.

Callout

More on wildcards

Wildcards are a feature of the shell and will therefore work with any command. The shell will expand wildcards to a list of files and/or directories before the command is executed, and the command will never see the wildcards. As an exception, if a wildcard expression does not match any file, Bash will pass the expression as a parameter to the command as it is. For example typing ls *.pdf results in an error message that there is no file called *.pdf.

Finally, onto deleting. The command to delete a file is rm, or remove. Adding the -r flag, we can delete directories with all their content.

Unlike deleting from within our graphical user interface, there is no warning, no recycling bin from which you can get the files back and no other undo options! For that reason, please be very careful with rm and extremely careful with rm -r.

Let’s clean up and delete the backup, so that only our README.md is left before we start with Git:

BASH

$ rm -r backup
$ ls

OUTPUT

README.md

Callout

Version control as a safety net

Git cannot protect you from rm either, but it can help a lot: if a file is part of a Git repository and its changes are committed, you can get the last committed version back even after deleting it. This is one of many reasons to use version control, as we will see next.

Key Points

• mkdir creates a directory and touch creates an empty file
• echo "text" > file writes text into a file, >> adds it at the end
• cat, head, tail and less show the content of files
• mv moves or renames, cp copies and rm deletes files – there is no undo for rm
• Tab completion, the up arrow key and wildcards (*, ?) save a lot of typing

Content from What is Git/Codeberg?

---

Last updated on 2026-10-21 | Edit this page

Overview

Questions

• What is Git?
• What is Codeberg?

Objectives

• explain the relevance and benefits of version control
• explain Git as an example of distributed versioning software and how it differs from a hosting platform like Codeberg

What is Version Control?

---

Version control is a name used for software which can help you record changes you make to the files in a directory on your computer. Version control software and tools (such as Git and Subversion/SVN) are often associated with software development, and increasingly, they are being used to collaborate in research and academic environments. Version control systems work best with plain text files such as documents or computer code, but modern version control systems can be used to track changes in most types of file.

At its most basic level, version control software helps us register and track sets of changes made to files on our computer. We can then reason about and share those changes with others. As we build up sets of changes over time, we begin to see some benefits.

Benefits of using version control?

• Collaboration - Version control allows us to define formalized ways we can work together and share writing and code. For example merging together sets of changes from different parties enables co-creation of documents and software across distributed teams.
• Versioning - Having a robust and rigorous log of changes to a file, without renaming files (v1, v2, final_copy)
• Rolling Back - Version control allows us to quickly undo a set of changes. This can be useful when new writing or new additions to code introduce problems.
• Understanding - Version control can help you understand how the code or writing came to be, who wrote or contributed particular parts, and who you might ask to help understand it better.
• Backup - While not meant to be a backup solution, using version control systems mean that your code and writing can be stored on multiple other computers.

There are many more reasons to use version control, and we’ll explore some of them for research data management, but first let’s learn a bit about a popular version control tool called Git.

What are Git and Codeberg?

---

We often hear the terms Git and Codeberg (or GitHub, GitLab, …) used interchangeably but they are different things.

Git is one of the most widely used version control systems in the world. It is a free, open source tool that can be downloaded to your local machine and used for logging all changes made to a group of designated computer files (referred to as a “git repository” or “repo” for short) over time. It can be used to control file versions locally by you alone on your computer, but is perhaps most powerful when employed to coordinate simultaneous work on a group of files shared among distributed groups of people.

Rather than emailing documents with tracked changes and some comments and renaming different versions of files (example.txt, exampleV2.txt, exampleV3.txt) to differentiate them, we can use Git to save (or in Git parlance, “commit”) all that information with the document itself. This makes it easy to get an overview of all changes made to a file over time by looking at a log of all the changes that have been made. And all earlier versions of each file still remain in their original form: they are not overwritten, should we ever wish to “roll back” to them.

Git was originally developed to help software developers work collaboratively on software projects, but it can be and is used for managing revisions to any file type on a computer system, including text documents and spreadsheets. Once installed, interaction with Git is done through the Command Prompt in Windows, or the Terminal on Mac/Linux. Since Word documents contain special formatting, Git unfortunately cannot version control those, nor can it version control PDFs, though both file types can be stored in Git repositories.

Callout

Distributed version control

Git is a distributed version control system: every copy of a repository – on your laptop, on a colleague’s computer or on Codeberg – contains the complete history of the project. You can work and commit offline and synchronise with the other copies later. No copy is technically special; it is only by agreement that a team treats one of them, for example the repository on Codeberg, as the shared, central one.

How can Git help with research data management?

• It documents how your data, scripts and documentation changed over time, and who changed what and why
• It lets you go back to earlier versions without keeping multiple copies of files (data_final_v2_corrected.csv)
• It makes your work reproducible: you can refer to the exact version of a script or document that produced a result

Codeberg on the other hand is a website for hosting and sharing Git repositories remotely. It offers a web interface for browsing files and their history, and adds features for working together, such as issues, pull requests, wikis and websites. Codeberg is run by Codeberg e.V., a non-profit association based in Berlin, Germany. It is funded by donations, built on the free software Forgejo and dedicated to hosting free and open content: open source software, but also documentation, teaching materials like this lesson, and research projects.

There are many other Git hosting services that offer similar features, such as GitHub, GitLab (often run by universities and research institutions as their own instance) and Bitbucket. Because they all build on Git, almost everything you learn in this lesson applies to them as well: only the buttons in the web interface look a little different.

Callout

Why Codeberg?

We use Codeberg in this lesson because it is a non-profit, community-run platform hosted in the EU, it is built entirely on free software, and it does not track its users or use their content for commercial purposes. For research and teaching materials that are meant to be shared openly, this makes it a good fit.

Codeberg is intended for free and open content. Please check the Terms of Use before you use it for your own projects.

How can Codeberg help with research data management?

• A place to share code, documentation and small datasets, and to collaborate on them with colleagues inside and outside your institution
• A place to discover and reuse (“fork”) openly licensed projects, for example analysis scripts or metadata schemas
• Issues and pull requests document discussions and decisions together with the project
• A simple way to publish a project website with Codeberg Pages

Uses in Research Data Management

---

Consider these common scenarios:

Scenario 1: A research group cleaning a shared dataset

A doctoral researcher has exported survey data as a CSV file for cleaning. Several people in the group work on the data and the scripts that process it, so they need to make sure that edits don’t get lost or overwrite each other. They also need to be able to undo changes, keep the raw data unchanged, and explain later in a publication how the data was processed.

The group can use Git to record every change to the cleaning scripts and the documentation, together with a message explaining why it was made. By hosting the project on Codeberg, they can review each other’s changes before they are merged, and discuss problems they find in the data in issues. Months later, the history still shows who changed what, when and why.

Scenario 2: Reusing another group’s workflow

A data steward wants to help a research group set up a data processing workflow. She finds a project on Codeberg in which another institute has published scripts, a README and a metadata template for exactly this type of data under an open licence.

Instead of starting from scratch, she can fork the project, adapt it to the new group’s needs, and keep track of all changes. If she fixes a bug along the way, she can suggest the fix to the original project with a pull request, so that everybody benefits.

Scenario 3: Documenting and publishing a data project

A project team wants to describe their dataset, its variables and the conditions for reuse on a small website, and keep this documentation up to date while the project continues.

They keep the documentation as text files in a Git repository and publish them with Codeberg Pages. Every change to the documentation is versioned, so readers can see what changed, and the team can link to the exact version that belonged to a data publication.

Key Points

• Version control helps track changes to files and projects
• Git and Git hosting platforms like Codeberg are not the same

Content from Getting started with Git

---

Last updated on 2026-10-21 | Edit this page

Overview

Questions

• What are repositories and how are they created?
• What do add and commit mean?
• How do I check the status of my repository?

Objectives

• apply Git to turn a directory into a repository
• apply the two steps add and commit to record changes to files
• apply git status to check the state of a repository
• apply a README file as a method of documenting a project

Setting up Git

When we use Git on a new computer for the first time, we need to configure a few things. The basic elements of a configuration for Git are:

• your name and email address,
• what your preferred text editor is,
• the name of your default branch (branches are an important component of Git that we will cover later).

To start we will check in on our current Git configuration. Open your shell terminal window and type:

BASH

$ git config --list

On MacOS, without any configuration your output might look like this:

OUTPUT

credential.helper=osxkeychain
init.defaultbranch=main

If you followed our instructions for installing Git for Windows, your output might look like this:

OUTPUT

diff.astextplain.textconv=astextplain
filter.lfs.clean=git-lfs clean -- %f
filter.lfs.smudge=git-lfs smudge -- %f
filter.lfs.process=git-lfs filter-process
filter.lfs.required=true
http.sslbackend=schannel
core.autocrlf=true
core.fscache=true
core.symlinks=true
core.editor=nano.exe
pull.rebase=false
credential.helper=manager
credential.https://dev.azure.com.usehttppath=true
init.defaultbranch=master

If you are using Linux or WSL 2 on Windows, you might not see any output at all.

If you have different output, then you may have your Git configured already. If you have not configured Git, we will do that together now. First, we will tell Git our user name and email.

Please note: Use the same email address in your Git configuration in the shell as you entered into Codeberg when you created your Codeberg account. Later in the lesson we will be using Codeberg, and it uses the email address to link your commits to your account. Keep in mind that the email address in your commits will be publicly visible once you share them. If you are concerned about privacy, you can use the private noreply address that Codeberg shows in your account settings under “Account” instead.

Type these two commands into your shell, replacing Your Name and the email address with your own:

BASH

$ git config --global user.name "Your Name"
$ git config --global user.email "yourname@domain.name"

If you enter the commands correctly, the shell will merely return a command prompt and no messages. To check your work, ask Git what your configuration is using the same command as above:

BASH

git config --list

OUTPUT

user.name=Your Name
user.email=yourname@domain.name

Let’s also set our default text editor. A text editor is necessary with some of your Git work, and the default from Git is Vim, which is a text editor that is hard to learn at first. Therefore, we recommend setting a simpler text editor in your Git configuration for this lesson.

Callout

Text editors

There are a lot of text editors to choose from, and a lot of people are enthusiastic about their preferences.

Nano is a good choice because it works on Mac, Windows, and Linux; it runs directly in your shell; and has on-screen reminders of how to use it. If you followed our instructions for installing Git for Windows, it should already be your default editor.

Vi and Vim also run directly in the shell and have many powerful features, but are less beginner-friendly.

If you will be using Git or the Shell with a group of people for a project or for work, asking for recommendations or preferences can help you pick an editor to get started with. If you already have your favorite, then you can set it as your default editor with Git.

Any text editor can be made default by adding the correct file path and command line options (see the Git documentation). However, the simplest core.editor value is "nano -w", which will run the Nano text editor directly in your shell. To select it, type the following into your shell:

BASH

$ git config --global core.editor "nano -w"

Lastly, we need to make sure the name of our default branch is set to main, as that is what Codeberg and most other Git hosting platforms use. To do this, type the following into your shell:

BASH

$ git config --global init.defaultBranch main

Callout

You may already have seen a setting for init.defaultbranch when you looked at your configuration earlier, overriding Git’s internal default. If your system configuration sets the default branch to main, you don’t necessarily have to set it again yourself, but doing so protects you from any system-level changes.

Creating a repository

A Git repository is a data structure used to track changes to a set of project files over time. Repositories are stored within the same directory as these project files, in a hidden directory called .git. We can create a new git repository either by using Codeberg’s web interface, or via the command line. Let’s use the command line to create a git repository for the experiments that we’re going to do today.

We will use the directory my-git-repo-<name> on the Desktop that we created in the shell episodes. Let’s make sure we are in it:

BASH

$ cd ~/Desktop/my-git-repo-<name>
$ pwd

OUTPUT

/Users/riley/Desktop/my-git-repo-riley

The ~ is a shortcut for your home directory, so this command works no matter where you are at the moment.

Using Git

One of the main barriers to getting started with Git is understanding the terminology necessary to executing commands. Although some of the language used in Git aligns with common-use words in English, other terms are not so clear. The best way to learn Git terminology - which consists of a number of verbs such as add, commit and push (preceded by the word ‘git’) - is to use it, which is what we will be doing during this lesson. We will explain these commands as we proceed from setting up a new version-controlled project to publishing our own website.

On a command line interface, Git commands are written as git verb options, where verb is what we actually want to do and options is additional optional information which may be needed for the verb. So let’s get started with our setup.

We will now create an empty git repository to track changes to our project. To do this we will use the git init command, which is short for initialise.

BASH

$ git init

OUTPUT

Initialized empty Git repository in /Users/riley/Desktop/my-git-repo-riley/.git/

The my-git-repo-<name> directory is now a git repository.

If we run the ls command now, we only see our README.md; however, adding the -a flag for all files via ls -a will show all hidden files, which in this case includes the new hidden directory .git. Flags can be thought of as command line options that can be added to shell commands.

Note that whenever we use git via the command line, we need to preface each command (or verb) with git, so that the computer knows we are trying to get git to do something, rather than some other program.

Displaying the current project’s status

We can run the git status command to display the current state of a project. Let’s do that now.

BASH

$ git status

OUTPUT

On branch main

No commits yet

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	README.md

nothing added to commit but untracked files present (use "git add" to track)

The output tells us that we are on the main branch and that there are no commits yet.

Callout

Branches and commits

Commits in Git are like snapshots of our project. They are ordered into sequences, or “branches”, with each commit pointing back to the one before it in the branch. Git keeps track of the last commit in each branch with a special label; in this lesson we mostly use one branch with the label “main”.

Two steps: Adding and committing

We will now save our first project file, the README.md we created in the shell episodes, in the repository. This is a two-step process. First, we add any files for which we want to save the changes to a staging area, then we commit those changes to the repository. This two-stage process gives us fine-grained control over what should and should not be included in a particular commit.

The status above is telling us that git has noticed a file in our directory that we are not yet tracking (an untracked file). With colourised output, the filename will appear in red. To change this, and to tell Git we want to track any changes we make to README.md, we use git add.

BASH

$ git add README.md

This adds our Markdown file to the staging area (the area where git checks for file changes). To confirm this we want to use git status again.

BASH

$ git status

OUTPUT

On branch main

No commits yet

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)

    new file:   README.md

If we are using colourised output, we will see that the filename has changed colour (from red to green). Git also tells us that there is a new file to be committed but, before we do that, let’s add some more text to the file.

We will open the file README.md with a text editor. If you set Nano as your core.editor value, this would be a good time to try it out:

BASH

nano -w README.md

If you don’t want to try Nano, use whatever text editor you feel comfortable with (e.g. Notepad on Windows or TextEdit on macOS) to open the file.

When you have the file open, you see the two lines we wrote with echo. Add a third line, for example Created in a Git and Codeberg workshop.. Then save the file and close the text editor.

Now, let’s check if Git has spotted the changes:

BASH

$ git status

OUTPUT

On branch main

No commits yet

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)

	new file:   README.md

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	modified:   README.md

This lets us know that git has indeed spotted the changes to our file, but that it hasn’t yet staged them, so let’s add the new version of the file to the staging area.

BASH

$ git add README.md

Now we are ready to commit our first changes. Commit is similar to ‘saving’ a file to Git. However, compared to saving, a commit provides a lot more information about the changes we have made, and this information will remain visible to us later.

BASH

$ git commit -m 'Add README.md'

OUTPUT

[main (root-commit) e9e8fd3] Add README.md
 1 file changed, 3 insertions(+)
 create mode 100644 README.md

We can see that one file has changed and that we made three insertions, which were the three lines of our README.md. We can also see the commit message ‘Add README.md’, which we added by using the -m flag after git commit. The commit message is used to record a short, descriptive, and specific summary of what we did to help us remember later on without having to look at the actual changes. If we just run git commit without the -m option, Git will launch Nano (or whatever other editor we configured as core.editor) so that we can write a longer message.

Having made a commit, we now have a permanent record of what was changed, and git has also recorded some additional metadata: who made the commit (you!) and when the commit was made (timestamp). You are building a mini-history of your process of working with the files in this directory.

Callout

More on the Staging Area

If you think of Git as taking snapshots of changes over the life of a project, git add specifies what will go in a snapshot (putting things in the staging area), and git commit then actually takes the snapshot, and makes a permanent record of it (as a commit). If you don’t have anything staged when you type git commit, Git will prompt you to use git commit -a or git commit --all, which is kind of like gathering everyone to take a group photo! However, it’s almost always better to explicitly add things to the staging area, because you might commit changes you forgot you made. (Going back to the group photo simile, you might get an extra with incomplete makeup walking on the stage for the picture because you used -a!) Try to stage things manually, or you might find yourself searching for “git undo commit” more than you would like!

At the moment, our changes are only recorded locally, on our computer. If we wanted to work collaboratively with someone else they would have no way of seeing what we’ve done. We will fix that in the next episode by using Codeberg to share our work.

Key Points

• When you initialize a Git repository in a directory, Git starts tracking the changes you make inside that directory.
• This tracking creates a history of the way the files have changed over time.
• Git uses a two-step process to record changes to your files. Changes to files must first be added to the staging area, then committed to the Git repository.

Content from Sharing your work

---

Last updated on 2026-10-21 | Edit this page

Overview

Questions

• How can I use Git and Codeberg to share my work?
• How do I link a local Git repository to Codeberg?
• How do I move changes between a local Git repository and a Codeberg repository?
• How can I see the differences between my current file and my most recent commit?

Objectives

• apply Codeberg to create a remote repository
• apply SSH keys to authenticate securely with Codeberg
• apply push and pull to exchange changes between a local and a remote repository
• apply git diff and git log to inspect changes and the history of a repository
• explain best practices such as meaningful commit messages and the role of licences for reuse

The power of sharing

---

The real power of Git lies in being able to share your work with others and in being able to work collaboratively. The best way to do this is to use a remote hosting platform. For this lesson, we are using Codeberg. Let’s log in there now.

Create a repository on Codeberg

---

Once we have logged in to Codeberg, we can create a new repository by clicking the + icon in the upper-right corner of any page then selecting New repository. Let’s do this now.

• Click “New repository”

Clicking “New repository” will take you to a creation page with different options. For this workshop, we are not using most of the options available.

• Name your repository like your local directory: my-git-repo-<name>, for example my-git-repo-riley.
• Leave the repository public (do not tick “Make repository private”), so that your partner can see it later in the lesson.

Codeberg will offer to initialize the repository with a README, a license or a .gitignore file. Do not do any of that for now – we want you to start with a completely empty repository on Codeberg.

• Click the “Create repository” button.

Callout

Choosing a license

When you are ready to use Codeberg to host your own work, you should review the different license options. Choosing a license is an important part of openly sharing your creative and research work online. For help in wading through the many types of open source licenses, please visit https://choosealicense.com/.

Connecting your local repository to the Codeberg repository

---

The next page that Codeberg displays contains some information to help you connect your repository on Codeberg with your local repository (on your own computer). To make this connection, we want to tell our local repository that Codeberg is the remote repository. In order to do that we need the information that Codeberg displays in the “Quick guide” on this page.

We will use the Secure Shell (SSH) protocol for this lesson, so please make sure that “SSH” is selected next to the address box and that the address starts with git@codeberg.org:. It will look something like this:

Callout

HTTPS vs. SSH

We use SSH here because, while it requires some additional configuration, it is a security protocol widely used by many applications. The steps below describe SSH at a minimum level for Codeberg.

In the previous episode we created a local repository on our own computer. Now we have also created a remote repository on Codeberg. But at this point, the two are completely isolated from each other. We want to link them together to synchronize them and share our project with the world.

To connect the repository on our own computer (local) to the repository we just created on Codeberg, we will use the commands provided by Codeberg under the heading “Pushing an existing repository from the command line”.

Let’s use these instructions now. Move back to your shell application and enter the first command:

BASH

$ git remote add origin git@codeberg.org:yourname/my-git-repo-<name>.git 

Make sure to use the URL of your actual repository: the only differences should be your username instead of yourname and your name instead of <name>.

Let’s breakdown the elements of the command. All commands related to Git in the shell start by invoking the Git language by typing git at the start. remote add is the command in the Git language we use to configure a remote repository, e.g., another Git repository that contains the same content as our local repository, but that is not on our computer. origin is the nickname we’re telling our local machine to use to for the following long web address. After we enter this command, we can use origin to refer to this specific repository on Codeberg instead of the URL.

We can check that it is set up correctly with the command:

BASH

$ git remote -v

OUTPUT

origin  git@codeberg.org:<your_codeberg_username>/my-git-repo-<name>.git (fetch)
origin  git@codeberg.org:<your_codeberg_username>/my-git-repo-<name>.git (push)

SSH Background and Setup

---

We still need to do a little more setup before we can actually connect to this remote repository. We need to set up a way for our local computer to authenticate with Codeberg so that Codeberg recognizes our computer as belonging to the same person who owns the Codeberg repository.

We will use SSH as our authentication method. SSH stands for Secure SHell protocol. SSH is a cryptographic network protocol that allows secure communication between computers using an otherwise insecure network.

SSH uses what is called a key pair – two keys that work together to validate access. One key is used publicly (the public key) and the other key is kept private (the private key).

You can think of the public key as a padlock, and only you have the key (the private key) to open it. You use the public key where you want a secure method of communication, such as your Codeberg account. You give this padlock, or public key, to Codeberg and say “lock the communications to my account with this so that only computers that have my private key can unlock communications and send Git commands as my Codeberg account.”

What we will do now is the minimum required to set up the SSH keys and add the public key to a Codeberg account. I’m not going to lie, this is a bit tedious and confusing. But you have to do it to get to the fun part, so hang in there.

The first thing we are going to do is check if this has already been done on the computer you’re on.

Callout

Keeping your keys secure

You shouldn’t really forget about your SSH keys, since they keep your account secure. It’s good practice to audit your secure shell keys every so often. Especially if you are using multiple computers to access your account.

We will run the list command (ls) to check what key pairs already exist on your computer. In our command we use the ~ as the shorthand for “my home directory.”

BASH

ls -al ~/.ssh

Your output is going to look a little different depending on whether or not SSH has ever been set up on the computer you are using.

If you have not set up SSH, your output might look like this:

OUTPUT

ls: cannot access '/c/Users/YourName/.ssh': No such file or directory

If SSH has been set up on the computer you’re using, the public and private key pairs will be listed. The file names are either id_ed25519/id_ed25519.pub or id_rsa/id_rsa.pub depending on how the key pairs were set up.

If you do not have SSH set up, let’s set it up now. Use this command to create key pairs:

BASH

$ ssh-keygen -t ed25519 -C "yourname@domain.name"

OUTPUT

Generating public/private ed25519 key pair.
Enter file in which to save the key (/c/Users/YourName/.ssh/id_ed25519):

We want to use the default file, so just press Enter.

OUTPUT

Created directory '/c/Users/YourName/.ssh'.
Enter passphrase (empty for no passphrase):

Your computer is now asking you for a passphrase to protect this SSH key pair. We recommend that you use a passphrase and that you make a note of it. There is no “reset my password” option for this setup. If you forget your passphrase, you have to delete your existing key pair and do this setup again. It’s not a big deal, but easier if you don’t have to repeat it.

OUTPUT

Enter same passphrase again:

After entering the same passphrase a second time, you will receive the confirmation

OUTPUT

Your identification has been saved in /c/Users/YourName/.ssh/id_ed25519
Your public key has been saved in /c/Users/YourName/.ssh/id_ed25519.pub
The key fingerprint is:
SHA256:SMSPIStNyA00KPxuYu94KpZgRAYjgt9g4BA4kFy3g1o yourname@domain.name
The key's randomart image is:
+--[ED25519 256]--+
|^B== o.          |
|%*=.*.+          |
|+=.E =.+         |
| .=.+.o..        |
|....  . S        |
|.+ o             |
|+ =              |
|.o.o             |
|oo+.             |
+----[SHA256]-----+

The “identification” is actually the private key. You should never share it. The public key is appropriately named. The “key fingerprint” is a shorter version of a public key.

Now that we have generated the SSH keys, we will find the SSH files when we check.

BASH

ls -al ~/.ssh

OUTPUT

drwxr-xr-x 1 YourName 197121   0 Jul 16 14:48 ./
drwxr-xr-x 1 YourName 197121   0 Jul 16 14:48 ../
-rw-r--r-- 1 YourName 197121 419 Jul 16 14:48 id_ed25519
-rw-r--r-- 1 YourName 197121 106 Jul 16 14:48 id_ed25519.pub

Now we need to give our public key (the padlock) over to Codeberg.

First, we need to copy the public key. Be sure to include the .pub at the end, otherwise you’re looking at the private key.

BASH

cat ~/.ssh/id_ed25519.pub

OUTPUT

ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIDmRA3d51X0uu9wXek559gfn6UFNF69yZjChyBIU2qKI yourname@domain.name

Copy that entire line of output, and we will paste the copied text into Codeberg in the next step.

Now, going to codeberg.org, click on your profile icon in the top right corner to get the drop-down menu. Click “Settings,” then on the settings page, click “SSH / GPG keys” in the menu on the left side. In the “Manage SSH keys” section, click the “Add key” button. Now, you can add a key name (a person might use the name “My 2026 work laptop,” just a little description to remind themselves which computer this public key connects to). Paste your SSH key into the “Content” field, and click “Add key” to complete the setup.

Now that we’ve set that up, let’s check our authentication from the command line.

BASH

$ ssh -T git@codeberg.org

The first time you connect, SSH will ask whether you trust the host codeberg.org. You can compare the fingerprint shown with the ones published in the Codeberg documentation, then type yes and press Enter.

OUTPUT

Hi there, YourName! You've successfully authenticated with the key named My 2026 work laptop, but Forgejo does not provide shell access.
If this is unexpected, please log in with password and setup Forgejo under another user.

Pushing changes

---

Now we have established a connection between the two repositories, but we still haven’t synchronized their content, so the remote repository is still empty. To fix that, we will have to “push” our local changes to the Codeberg repository. We do this using the git push command:

BASH

$ git push -u origin main

OUTPUT

Enumerating objects: 3, done.
Counting objects: 100% (3/3), done.
Writing objects: 100% (3/3), 226 bytes | 226.00 KiB/s, done.
Total 3 (delta 0), reused 0 (delta 0), pack-reused 0
To codeberg.org:<your_codeberg_username>/my-git-repo-<name>.git
 * [new branch]      main -> main
branch 'main' set up to track 'origin/main'.

The nickname of our remote repository is “origin” and the default local branch name is “main”. The -u flag tells git to remember the parameters, so that next time we can simply run git push and Git will know what to do.

Pushing our local changes to the Codeberg repository is sometimes referred to as “pushing changes upstream to Codeberg”. The word upstream here comes from the git flag we used earlier in the command git push -u origin main. The flag -u refers to --set-upstream, so when we say pushing changes upstream, it refers to the remote repository.

If you set a passphrase for your SSH key, you will be prompted to enter it to complete the command.

When we do a git push, we will see Git ‘pushing’ changes upstream to Codeberg. Because our file is very small, this won’t take long but if we had made a lot of changes or were adding a very large repository, we might have to wait a little longer. We can check where we’re at with git status.

BASH

$ git status

OUTPUT

On branch main
Your branch is up-to-date with 'origin/main'.
nothing to commit, working tree clean

This output lets us know where we are working (the main branch). We can also see that we have no changes to commit and everything is in order.

We can use the git diff command to see changes we have made before making a commit. Open README.md with any text editor and enter some text on a new line, for instance “A new line” or something else. We will then use git diff to see the changes we made:

BASH

$ git diff

OUTPUT

diff --git a/README.md b/README.md
index aed0629..989787e 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,4 @@
 # My Git repository
 This is where I practise Git.
 Created in a Git and Codeberg workshop.
+A new line

The command produces lots of information and it can be a bit overwhelming at first, but let’s go through some key information here:

1. The first line tells us that Git is producing output similar to the Unix diff command, comparing the old and new versions of the file.
2. The second line tells exactly which versions of the file Git is comparing; aed0629 and 989787e are unique computer-generated identifiers for those versions.
3. The third and fourth lines once again show the name of the file being changed.
4. The remaining lines are the most interesting; they show us the actual differences and the lines on which they occur. In particular, the + markers in the first column show where we have added lines.

We can now commit these changes:

BASH

$ git add README.md
$ git commit -m 'Add another line'

If we are very forgetful and have already forgotten what we changed, git log allows us to look at what we have been doing with our git repository (in reverse chronological order, with the very latest changes first).

BASH

$ git log

OUTPUT

commit 8e2eb9920eaa0bf18a4adfa12474ad58b765fd06
Author: Your Name <your_email>
Date:   Mon Jun 5 12:41:45 2017 +0100

    Add another line

commit e9e8fd3f12b64fc3cbe8533e321ef2cdb1f4ed39
Author: Your Name <your_email>
Date:   Fri Jun 2 18:15:43 2017 +0100

    Add README.md

This shows us the two commits we have made and shows the messages we wrote. It is important to try to use meaningful commit messages when we make changes. This is especially important when we are working with other people who might not be able to guess as easily what our short cryptic messages might mean. Note that it is best practice to always write commit messages in the imperative (e.g. ‘Add README.md’, rather than ‘Adding README.md’).

Pushing changes (again)

---

Now, let’s have a look at the repository on Codeberg again (that is, https://codeberg.org/some-researcher/my-git-repo-<name> with some-researcher replaced with your username). We see that the README.md file is there, but there is only one commit:

Codeberg shows the content of README.md below the list of files: it contains our three lines, but not the new line we just added.

This is because we haven’t yet pushed our local changes to the remote repository. This might seem like a mistake in design but it is often useful to make a lot of commits for small changes so you are able to make careful revisions later and you don’t necessarily want to push all these changes one by one.

Another benefit of this design is that you can make commits without being connected to internet.

But let’s push our changes now, using the git push command:

BASH

$ git push

OUTPUT

Enumerating objects: 5, done.
Counting objects: 100% (5/5), done.
Writing objects: 100% (3/3), 272 bytes | 272.00 KiB/s, done.
Total 3 (delta 0), reused 0 (delta 0), pack-reused 0
To codeberg.org:<your_codeberg_username>/my-git-repo-<name>.git
   e9e8fd3..8e2eb99  main -> main

And let’s check on Codeberg that we now have 2 commits there.

Challenge

Challenge: Two different push commands

The first time we pushed our changes, we used a longer command:

BASH

$ git push -u origin main

The second time, we used a shorter command:

BASH

$ git push

Why didn’t we use the same command both times?

Show me the solution

Branches can be configured with an “upstream” branch (a branch on a remote repository), which is used automatically for push and pull operations.

The main branch’s upstream wasn’t set when we created it. The -u (or --set-upstream) flag tells git push which remote branch to use; it also sets the remote branch as the local branch’s upstream. Once we’ve set it, we don’t need to specify the remote branch in future push and pull operations. This saves on typing and means we won’t push to or pull from the wrong remote branch.

Pulling changes

---

When working with others, or when we’re making our own changes from different machines, we need a way of pulling those remote changes back into our local copy. For now, we can see how this works by making a change on the Codeberg website and then ‘pulling’ that change back to our computer.

Let’s go to our repository on Codeberg and make a change. Click on README.md in the list of files and then on the pencil icon (“Edit file”). Add a line, for example a sentence about what you would like to use Git for. Scroll to the bottom, make sure “Commit directly to the main branch” is selected and click “Commit changes” (the default commit message will be “Update README.md”, which is fine for our purposes).

Callout

The README file

It is good practice to add a README file to each project to give a brief overview of what the project is about. If you put your README file in your repository’s root directory, Codeberg will recognize and automatically surface your README to repository visitors

Our local repository is now out of sync with our remote repository, so let’s fix that by pulling the remote changes into our local repository using the git pull command.

BASH

$ git pull

OUTPUT

remote: Enumerating objects: 4, done.
remote: Counting objects: 100% (4/4), done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 3 (delta 0), reused 0 (delta 0), pack-reused 0
Unpacking objects: 100% (3/3), done.
From codeberg.org:<your_codeberg_username>/my-git-repo-<name>
   8e2eb99..0f5a7b0  main     -> origin/main
Updating 8e2eb99..0f5a7b0
Fast-forward
 README.md | 1 +
 1 file changed, 1 insertion(+)

The above output shows that we have fast-forwarded our local repository to include the change to README.md. We can confirm this with the shell command we already know:

BASH

$ cat README.md

When we begin collaborating on more complex projects, we may have to consider more aspects of git functionality, but this should be a good start. In the extended version of this workshop, we look more closely at collaborating with others on Codeberg using issues and pull requests.

Key Points

• remote repositories on Codeberg help you collaborate and share your work
• push is a Git verb for sending changes from the local repository to a remote repository
• pull is a Git verb for bringing changes from a remote repository to the local repository
• diff is a Git verb for viewing the difference between an edited file and the file’s most recent commit

Content from Review

---

Last updated on 2026-10-21 | Edit this page

Overview

Questions

• How can I cement my understanding of Git’s functions?

Objectives

• explain Git commands in everyday language
• explain the functions of Git by drawing or sketching them

Let’s review

---

It is likely that some things won’t have stuck from the last hour. To try to reinforce how things work we can work in groups to develop diagrams to illustrate Git functions and language. This should make carrying out more complicated aspects of Git clearer in our heads.

Challenge

How would you explain it?

In groups:

• make a list of commands and concepts we’ve discussed in the first hour
• try to come up with synonyms or explanations for what the commands are doing
• try to ‘draw’ what different commands mean
• come up with your own analogies and diagrams to explain how Git works.

Tips for visualising git

Here are some tips for illustrating the commands and concepts we’ve used with Git:

• try to express Git commands in a ‘non-Git’ way
• try to visualise what commits are doing to your repository
• sketch out how information flows from one repository to another.

Be as creative and artistic as you like!

If you want to practise more, feel free to keep making changes to your file and committing those changes. If you want to explore more git commands, search for some more online or visit the lesson resources.

Key Points

• the language of Git can be confusing and intimidating
• rephrasing commands and drawing concepts can clarify Git’s workflow

Content from Managing a project with issues

---

Last updated on 2026-10-21 | Edit this page

Overview

Questions

• How can I use Codeberg to plan and track the work in a project?
• How can I report a problem or make a suggestion for someone else’s project?

Objectives

• apply issues to report problems and suggest tasks in someone else’s repository
• apply labels, assignees, milestones and project boards to plan and track the tasks in a project
• apply references to commits, issues and people in comments
• explain how the history of issues makes a project transparent and traceable

Callout

Extended workshop

This episode and the next one are part of the extended (lunch-to-lunch) version of this workshop. They build on the my-git-repo-<name> repositories that you created and pushed to Codeberg in the previous episodes.

For the exercises, find a partner and exchange your Codeberg usernames and the names of your repositories.

What are issues?

---

So far we have used Codeberg to store and share files. But a project is more than its files: there are tasks to do, problems to fix, questions to answer and decisions to document. Codeberg has a feature for this called issues.

An issue is like a ticket or a to-do item that belongs to a repository. It has a title, a description, and a discussion below it, and it is either open (still to be done) or closed (done or no longer relevant). By default, anybody with a Codeberg account can open an issue in a public repository. This makes sense: people can report problems and ask questions, even if they are not allowed to change anything themselves.

In research data management, issues are useful for example to

• collect tasks for a data publication (“Add README with variable descriptions”, “Choose a license”),
• report problems with a dataset (“Column age contains negative values in survey_2026.csv”),
• document decisions and the discussion that led to them, so that they can be found again later.

Caution

Issues in public repositories are public

Everybody can read the issues of a public repository, and closed issues stay visible. Never put personal data, passwords or other confidential information into an issue.

Create an issue

---

Your partner’s repository has a README, but it doesn’t say who works on the project. You would like to suggest adding a list of contributors – and you would like to help with it and be on that list yourself. Since it’s your partner’s project, you don’t change it directly, but open an issue in their repository to make your suggestion.

We navigate to the repository of our partner, https://codeberg.org/some-researcher/my-git-repo-<partner> (with some-researcher replaced by our partner’s username and <partner> by their name). We click the tab “Issues” and then the button “New issue”.

We give the issue a short, descriptive title, for example “Add a list of contributors”, and a description:

MARKDOWN

The people who contribute to this project should be mentioned in its documentation.
Their names could be listed in one of the following locations:

- a section in `README.md`
- a separate `CONTRIBUTORS.md` file

The description is written in Markdown, just like our README.md. Click on “Preview” above the text field to see how it will look.

Callout

Markdown code spans and blocks

Markdown provides syntax for formatting text in a monospaced font. This is usually used for file names, commands and code.

For a monospaced snippet within a normal paragraph, enclose the snippet in single backticks, for example

MARKDOWN

The filename `README.md` will be set in a monospaced font.

For a whole block of monospaced text, for example some lines of code or the output of a command, start and end the block with a line consisting of three backticks:

MARKDOWN

```
$ git status
On branch main
nothing to commit, working tree clean
```

On the right side of the form you may see fields for labels, milestones, projects and assignees. As we are not a collaborator in our partner’s repository, we can’t set most of them – that’s the job of the repository owner, which we’ll come to in a moment.

We click “Create issue”. This takes us to the new issue’s page. At the top we see its title, followed by its number, #1.

Callout

Issue numbers

On Codeberg, issues and pull requests share the same numbering in a repository. Our issue is the first one in our partner’s repository, so it gets the number #1; the next issue or pull request will be #2. We can refer to any issue or pull request with its number, as we will see.

Comment on an issue and reference a commit

---

We want to add a concrete suggestion where the list could be linked: in the README, which our partner created in their first commit. So we write a comment that refers to this commit.

When we mention a commit by its identifier, Codeberg automatically turns it into a link to that commit. To find the identifier, we open our partner’s repository in a second browser tab and click on “Commits”. The commit “Add README.md” is at the bottom of the list, with a short sequence of numbers and letters on the right: the beginning of the commit’s identifier, also called its hash or SHA. Next to it is a button to copy the full identifier.

Back on the issue page, we write a comment like this, pasting the identifier of the commit:

MARKDOWN

The README was added in commit e9e8fd3f12b64fc3cbe8533e321ef2cdb1f4ed39 – it could link to the list of contributors.
I'm happy to help with this and would like to be on the list, too.

and click “Comment”. Our comment appears below the description, and Codeberg shows a shortened version of the identifier as a link.

Callout

Mentioning people, issues and commits

Codeberg recognises some special references in issues, comments and pull requests:

• @username mentions a person, who will be notified,
• #1 links to issue or pull request number 1 in the same repository,
• a commit identifier links to that commit.

Triage: labels, assignees and milestones

---

In the meantime, our partner has opened an issue in our repository, too. Now we switch roles: as the owner of our repository, we are responsible for sorting incoming issues. This is often called triage.

We go to our own my-git-repo-<name> repository, click the tab “Issues” and open the issue from our partner.

Labels

Labels are coloured tags that help to group and filter issues, for example by type (“bug”, “question”, “documentation”) or by status (“in progress”, “needs discussion”).

Our repository doesn’t have any labels yet, so we create some first. On the “Issues” tab we click on “Labels”. Codeberg offers to load a predefined set of labels: select the “Default” set and confirm. This creates commonly used labels such as bug, enhancement and question.

To add our own label, we click “New label”, call it documentation, choose a colour and click “Create label”.

Back on the issue, we click on “Labels” in the sidebar on the right and select documentation.

Assignees

The “Assignees” field shows who is responsible for working on an issue. Only people with write access to the repository can be assigned, so we assign ourselves: click on “Assignees” in the sidebar and select your own username.

Milestones

A milestone groups issues that should be done by a certain point, for example “README complete” or, in a data project, “Data publication v1.0”. On the “Issues” tab, click “Milestones”, then “New milestone”. Give it a title and, optionally, a due date and click “Create milestone”. Then add the issue to the milestone in the sidebar of the issue. On the “Milestones” page you can now see how many of the milestone’s issues are already closed.

Project boards

---

When a project has many issues, it helps to see at a glance what is waiting, what is being worked on and what is done. Codeberg offers project boards for this, also known as Kanban boards.

We click the tab “Projects” in our repository and then “New project”.

Callout

No “Projects” tab?

If you don’t see a “Projects” tab, it may be switched off for your repository. You can enable it in the repository “Settings” under “Units” (or “Advanced settings”, depending on the Codeberg version).

We give the project a title, for example “My Git repository”, and choose the template “Basic kanban”. This creates a board with columns such as “To Do”, “In Progress” and “Done”. We click “Create project”.

To put an issue on the board, we open the issue and select our project under “Projects” in the sidebar. Back on the board, the issue appears as a card in the first column. We can now drag the card from one column to another, for example to “In Progress” once we start working on it.

Note that the board is only an overview: moving a card to “Done” does not close the issue. Closing an issue is something we do on the issue itself.

Task lists

---

Some issues contain several small steps. Markdown task lists turn these into checkboxes:

MARKDOWN

- [ ] Create `CONTRIBUTORS.md`
- [ ] Link it from `README.md`

Codeberg shows the checkboxes in the issue, and in the list of issues you can see how many of them are already ticked.

Close an issue

---

Below the comment field of every issue there is a button “Close”. If you write something in the comment field first, you can add a final comment when you close the issue. Closed issues no longer appear in the list of open issues, but they are not deleted: you can still find them with the search or the “Closed” filter on the “Issues” tab. This makes issues a searchable record of what was done in a project and why.

Don’t close your partner’s issue yet! In the next episode, we will close it automatically with a pull request that solves it.

Challenge

Challenge: Issues in your own work

Think about a project you are currently working on (for example a dataset, a publication or a website).

1. Write down three things that could be an issue in this project.
2. Which labels would be useful to organise them?
3. Would a milestone make sense? What would it be called?

If you like, create a new repository on Codeberg for this project and add the issues there. Remember not to include confidential information if the repository is public.

Challenge

Challenge: Explore the history of an issue

Open the issue that your partner created in your repository and scroll down.

What does Codeberg record in the history of the issue, apart from the comments? Why could this be useful?

Show me the solution

Besides comments, Codeberg records events such as adding or removing labels, assigning people, adding the issue to a milestone or project, and closing or reopening the issue – each with the person who did it and when. This makes it easy to follow who did what at which point in time, which is helpful in teams and for documenting a project.

Key Points

• Issues are used to report problems, ask questions and plan tasks in a repository
• Anybody with a Codeberg account can open issues in a public repository
• Labels, assignees and milestones help to organise issues
• Project boards give an overview of the state of issues
• Commits, issues (#1) and people (@username) can be referenced in issues and comments
• Closed issues remain as a searchable record of the project

Content from Contributing with pull requests

---

Last updated on 2026-10-21 | Edit this page

Overview

Questions

• How can I suggest changes to a project on Codeberg?
• How can changes be reviewed before they become part of a project?

Objectives

• apply a fork, a branch and a pull request to contribute changes to another person’s repository
• apply closing keywords to link a pull request to an issue
• analyse proposed changes collaboratively in a pull request review
• explain basic concepts of access control using the example of repository permissions

Pull requests and merge requests

---

In the previous episode, we used an issue to suggest a change to our partner’s repository. In this episode, we make the change ourselves and propose it to our partner with a pull request, link the pull request to the issue, and go through a review before the changes are merged. We do all of this in the Codeberg web interface.

A pull request asks the owner of a repository to pull changes from another branch (often in a fork) into their repository. Other platforms use different names for the same thing: on GitLab, it is called a merge request.

Our goal is to solve the issue “Add a list of contributors” that we opened in our partner’s repository in the previous episode: we will add a file CONTRIBUTORS.md that lists the contributors of the project. At the same time, our partner does the same in our repository, so we will be both author and reviewer of a pull request.

Fork the repository

---

We don’t have write access to our partner’s repository: we can read it, but we can’t change it. So we work in our own copy of it on Codeberg, called a fork. The name comes from a “fork in the road”: once we make changes to our copy, the history of the project splits into two directions. With a pull request, we then ask our partner to pull our changes from the fork into their repository. They can review the changes and decide whether to accept them.

Go to https://codeberg.org/some-researcher/my-git-repo-<partner>, with some-researcher replaced by your partner’s username and <partner> by their name, and click “Fork” in the upper right part of the screen. Keep the name of the repository: as it contains your partner’s name, it doesn’t clash with your own repository. Click “Fork repository” to confirm.

Codeberg takes us to our fork: https://codeberg.org/<your_codeberg_username>/my-git-repo-<partner>. Below the repository name it says “forked from some-researcher/my-git-repo-”.

Add a file on a new branch

---

It is good practice to make every contribution on its own branch, named after what it does. That way, main stays clean, and you can work on several contributions at the same time. Codeberg can create the branch for us when we save our change.

In our fork, we click “Add file” above the list of files and select “New file”. We name the file CONTRIBUTORS.md and enter something like:

MARKDOWN

# Contributors

The following people have contributed to this project:

- Some Researcher (owner)
- Conner Learner

with the names replaced by your partner’s name and your own.

Callout

All-caps file names

It is customary to give files with information about a project a name in capital letters, so that they stand out in the list of files. Examples are README, LICENSE, CONTRIBUTING (how to contribute) or CITATION (how to cite the project), often with a file extension such as .md or .cff.

Below the editor, we enter the commit message “Add CONTRIBUTORS.md”. Instead of committing directly to main, we select “Create a new branch for this commit and start a pull request”, name the branch add-contributors and click “Commit changes”.

Callout

Branching and merging

Branches get their name because you can create a new one (say, “patch”) that splits off from an existing one like “main”, allowing different sets of changes to be made in parallel. Later on, Git can take the changes from “patch” and merge them into the “main” branch. This is exactly what will happen with our branch add-contributors when the pull request is merged.

Open the pull request

---

Codeberg now takes us to the page for a new pull request. At the top, it shows which branches will be compared: the target (often called base) on the left, the source on the right. Check that the pull request goes

• into the main branch of your partner’s repository (some-researcher/my-git-repo-<partner>),
• from the add-contributors branch of your fork (<your_codeberg_username>/my-git-repo-<partner>),

and change the selection if necessary.

Below, Codeberg shows the commits and the changes that will be part of the pull request. The title is filled in with our commit message. In the description, we explain what we did and link the pull request to the issue we opened in the previous episode. Use the number of your issue in your partner’s repository:

MARKDOWN

This adds a list of contributors to the project.

Closes #1

Callout

Closing issues automatically

If the description of a pull request (or a commit message in it) contains a phrase like Closes #1, Fixes #1 or Resolves #1, Codeberg links the pull request to issue #1 and closes the issue automatically when the pull request is merged. This saves a few clicks and makes sure that closing the issue isn’t forgotten. It also documents why an issue was closed.

We click “Create pull request”. This takes us to the page of the pull request in our partner’s repository. It looks similar to an issue page, with a few extra tabs at the top:

• “Conversation”: the description and all comments,
• “Commits”: the commits that are part of the pull request,
• “Files changed”: the changes, shown as a diff like the output of git diff.

If we go to the issue in our partner’s repository, we can see that Codeberg has added a note there that the pull request references it.

Callout

Pull requests within a team

If you are a collaborator in a repository, you don’t need a fork: you can create a branch directly in the shared repository and open a pull request from that branch into main. Many teams work this way, so that every change is reviewed by a second person before it becomes part of main. In the repository settings under “Branches”, you can even protect main, so that changes can only get there through a pull request.

Review a pull request

---

Now we switch roles. Our partner has opened a pull request in our repository, and it’s our job to review it.

We go to our own my-git-repo-<name> repository, click on the tab “Pull requests” and open the pull request from our partner. Then we click on “Files changed” to see the changes.

When we hover over a line of the changes, a small + button appears next to the line number. Clicking it opens a text field to comment on this particular line. Let’s ask for a small change, for example:

MARKDOWN

Thanks! Could you add a link to your Codeberg profile after your name?

We click “Start review”. We could add more comments on other lines in the same way. When we’re done, we click “Finish review” at the top of the changes, choose “Request changes”, write a short summary and submit the review.

Callout

Reviews

Reviewing changes before they are merged is a common practice in software development (code review), but it is just as useful for documentation, metadata or data files: a second pair of eyes catches mistakes, and the discussion is saved together with the change. Comments on individual lines keep separate topics in separate discussions.

Update a pull request

---

Back in our role as author, we see the review on our pull request in our partner’s repository. To update a pull request, we don’t need to create a new one: we simply add a new commit to the same branch.

In our fork, we use the branch selector above the list of files to switch to the branch add-contributors. We click on CONTRIBUTORS.md and then on the pencil icon (“Edit file”), and change our line, for example:

MARKDOWN

- Conner Learner ([@conner-learner](https://codeberg.org/conner-learner))

As commit message, we enter “Add link to Codeberg profile”. This time, we keep “Commit directly to the add-contributors branch” selected and click “Commit changes”.

If we reload the pull request page, we see the new commit in the conversation. We can answer the review comment, for example with “Done!”, and mark the conversation as resolved.

Merge the pull request

---

Switching roles a last time, we look at the updated pull request in our own repository. If we’re happy with the changes, we can approve them: click “Finish review” in the “Files changed” tab, choose “Approve” and submit.

At the bottom of the “Conversation” tab, Codeberg tells us whether the pull request can be merged without conflicts. We click the merge button (“Create merge commit”) and confirm.

Codeberg now creates a merge commit in our main branch. If we open the linked issue, we see that it has been closed automatically, with a note in its history pointing to the pull request that closed it.

Finally, we update the repository on our own computer, so that it contains the merged changes too. This is the same git pull as in the episode Sharing your work:

BASH

$ cd ~/Desktop/my-git-repo-<name>
$ git pull

OUTPUT

...
Fast-forward
 CONTRIBUTORS.md | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 CONTRIBUTORS.md

Challenge

Challenge: The whole workflow

Draw the complete workflow of this episode on a sheet of paper or a whiteboard, together with your partner. Include your partner’s repository, your fork, the branch add-contributors, the pull request and your own repository on your computer, and show with arrows where the fork, the commits, the pull request, the merge and the final git pull happen.

Challenge

Challenge: When to use what?

You are working on a data project with two colleagues and want to suggest a change. In which of these situations would you use

• a commit directly to main,
• an issue,
• a pull request?

1. You found a typo in the README of a public dataset from another institute.
2. You noticed that some values in a data file look wrong, but you don’t know how to fix them.
3. You want to add a new section to your team’s documentation, and the team has agreed to review all changes.
4. You are the only person working on your own repository and want to save your progress.

Show me the solution

1. A pull request from a fork (or an issue, if you don’t want to make the change yourself): you don’t have write access to the repository.
2. An issue: describe the problem, so that the people who know the data can investigate and fix it.
3. A pull request from a branch in the shared repository, so that your colleagues can review it.
4. A commit directly to main is fine – although a branch and a pull request can still help you to keep track of bigger changes.

Key Points

• A pull request (on GitLab: merge request) suggests changes from one branch to another, often from a fork to the original repository
• Work on a new branch for each contribution
• Closes #<number> in a pull request description closes the issue when the pull request is merged
• Reviewers can comment on individual lines and approve or request changes
• New commits on the branch update the pull request