Git Tutorial

This hands-on tutorial will help you get familiar with Git

First steps

Install Git on your computer

Linux
```
$ sudo apt install git
```
MacOS
```
brew install git
```
Windows

Download the latest Git installer at Git for Windows.

Configure your account. This will set the name and email that will appear in your commit.

Use the email that you will use to create GitHub account

$ git config --global user.name "Your Name"
$ git config --global user.email [email protected]

Create your first git repository

$ mkdir bbmri-it-git-tutorial
$ cd bbmri-it-git-tutorial
$ git init
Initialized empty Git repository in /home/user/bbmri-it-git-tutorial

Create a file
```
$ echo . > README.md
```
Check the status
```
$ git status
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
```
git returns some useful information:
- The name of the current branch: main
- The fact that there are no commits yet
- A list of untracked files (i.e., files that are in the current directory but not part of the repository yet)
- Some hints about actions that you can do
Let's follow the hint and add the README.md file to the list of tracked files and check the status
```
$ git add README.md
$ git status
On branch main

No commits yet

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)
        new file:   README.md
```
Something has changed: now git lists the changes that can be committed. The changes are: a new file has been added that was not part of the repository
Let's create our first commit: we commit the addition of the README.md
```
$ git commit -m "Add README.md"
[main (root-commit) 660ae42] Add README.md
1 file changed, 0 insertions(+), 0 deletions(-)
create mode 100644 README.md
```
Git returns some information about the newly created commit, in particular the id of the commit (660ae42) followed by the commit message. Then some information about the files involved in the commit

Tip

In case you didn't give the commit message with -m "My first git commit" git would have opened your default editor to add one.

The default editor can be configured using the command:

$ git config --global core.editor "vim"

NB: The editor must be a valid command on your computer

Let's check again the status of the files
```
$ git status
On branch main
nothing to commit, working tree clean
```
git tells that there are no changes to commit
Now we can see the history of our repository
```
$ git log
commit 660ae424b9c05703a03d2f1b947c93e9ecc39497 (HEAD -> main)
Author: Vittorio Meloni <[email protected]>
Date:   Thu Jun 12 14:16:55 2025 +0200

   Add README.md
```
git returns the list of commits that (surprise) contains only our commit. As before git returns some useful information:
- the commit id, which is the long version of the id. The first part is, of course, the same as the one returned after the commit
- The position of the HEAD of our repository, which is our first commit
- The information of the author of the commit, corresponding to the ones provided configured at the beginning
- The date of the commit
Let's make some changes to the file. Open README.md with your favourite editor and add the line:

This is the repository of <your name> for the BBMRI.it Data Team School

Close the editor and check the status of the changes
```
$ git status
On branch main
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
       modified:   README.md

 no changes added to commit (use "git add" and/or "git commit -a")
```
Since README.md is part of the repository, the list of changes shows there is a modified file now.

Notice also the new hints about the actions that you can perform: git add <file> to stage the file for commit or git restore <file> to restore the file to the HEAD version

Before staging the file for commit we can see the diff of the file against the HEAD

$ git diff
diff --git a/README.md b/README.md
index e69de29..31016e2 100644
--- a/README.md
+++ b/README.md
@@ -0,0 +1 @@
+This is the first repository of Vittorio for the BBMRI.it Data Team School
\ No newline at end of file

For each changed file git shows the changes of the files with respect to the HEAD

Here we can see that the line was added (+)

Let's stage the file for commit, commit the changes and see the status
```
$ git add README.md
$ git status
On branch main
Changes to be committed:
   (use "git restore --staged <file>..." to unstage)
         modified:   README.md
```
We still have the same list of files but the message changed: git tells that the changes are staged and ready to be committed.

Also look at the new hint: git suggests how to unstage the file.

Let's commit the changes and check the log

$ git commit -m "doc: add description of the repository"
[main 172dff9] doc: add description of the repository
1 file changed, 1 insertion(+)

$ git log
commit 172dff9cbf78df528ee88170fb6cd71a56cbc0b0 (HEAD -> main)
Author: Vittorio Meloni <[email protected]>
Date:   Thu Jun 12 15:17:30 2025 +0200

    doc: add description of the repository

commit e91c0112bade625b4425d3d15d18b910da3df4d3
Author: Vittorio Meloni <[email protected]>
Date:   Thu Jun 12 14:16:55 2025 +0200

    Add README.md

git returns the list of commits. We see the first commit and the last one and we can see that the HEAD is changed

Tip

In case, after a commit, we notice some error in the commit message we can use the --amend option to change the last commit message.

(e.g., git commit --amend -m "correct message")

NB: only the last commit can be amended

Branching

In this section we will start to use branches so we can diverge from the main line without messing with it and restarting

First of all we can check the list of branches in our repository
```
$ git branch
* main
```
Currently, we only have the main branch.
Let's create a new branch named develop and check again the list of branches
```
$ git branch develop
$ git branch
develop
* main
```
Now the list contains the new develop branch, but we are still in the main branch as indicated by the * before the name.

Tip

When your repository contains several branches, it may be really (really!) helpful to always have a glimpse of the current branch

In bash, you can set the PS1 variable in your .bashrc file to include the current git branch in your command prompt

An example is:

PS1='$(__git_ps1 " (%s)")\ $ '

that results in

(main) $

We can now move to develop branch:

(main) $ git switch develop
Switched to branch 'develop'

(develop) $ git branch
* develop
main

Let's start to add some new content to our project by creating a new python script and commiting it

(develop) $ mkdir src/
(develop) $ echo . > src/script.py
(develop) $ git add src/script.py
(develop) $ git commit -m "feat: add the hello world script"
[develop f3de86b] feat: add the hello world script
1 file changed, 0 insertions(+), 0 deletions(-)
create mode 100644 src/script.py

Tip

Git doesn't allow the addition of a new empty directory (i.e., we couldn't directly add the src directory, it would have resulted in no effect). There may be situations when we want to have an empty directory. In this cases we can add a .keepme file into the directory to keep it

Let's check the updated history

(develop) $ git log
commit f3de86bc2769edefa18f728649b43b6fff3ecb83 (HEAD -> develop)
Author: Vittorio Meloni <[email protected]>
Date:   Thu Jun 12 17:20:22 2025 +0200

    feat: add the hello world script

commit 172dff9cbf78df528ee88170fb6cd71a56cbc0b0 (main)
Author: Vittorio Meloni <[email protected]>
Date:   Thu Jun 12 15:17:30 2025 +0200

    doc: add description of the repository

commit e91c0112bade625b4425d3d15d18b910da3df4d3
Author: Vittorio Meloni <[email protected]>
Date:   Thu Jun 12 14:16:55 2025 +0200

    Add README.me

Now the log shows that the HEAD is in the develop branch where we have one commit while the main is one commit behind

We can start editing our script

Add the following function to your python script
```
print("Hello world!")
```
And now perform the commit as you know at this point! :)
```
(develop) $ git add src/script.py
(develop) $ git commit -m "feat: say hello to world"
```
NB You may have noticed that we have started using conventional commits. This is really encouraged!

Let's change our files to say hello to lot of people

def say_hello(recipient):
   print(f"Hello {recipient}")

say_hello("biobankers!")
say_hello("BBMRI IT!")
say_hello("")

And stage the file for changes

(develop) $ git add src/script.py
On branch develop
Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
        modified:   src/script.py

Wait! In the last line we said hello to no one. We don't want to create a commit with this error. Let's unstage the file

(develop) $ git restore --staged src/script.py
(develop) $ git status
On branch develop
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
        modified:   src/script.py

no changes added to commit (use "git add" and/or "git commit -a")

We unstaged the file so we don't have anything to commit.

NB: Notice that unstaging the file doesn't remove the changes to it. To discard the changes we should git restore the file after unstaging it

After removing the line, commit the changes

(develop) $ git add src/script.py
(develop) $ git commit -m "feat: add say_hello function to say hello to lot of people"

We have made quiet some changes now. Let's check the log and see the history them

commit 5ce1ad6f1809bf1069a2754a555eca86f8540a65 (HEAD -> develop)
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 10:20:44 2025 +0200

    feat: add say_hello function to say hello to lot of people

commit b86eb31793155a5539646d7475c193610308e95b
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 10:01:40 2025 +0200

    feat: say hello to world

commit 757baec96c0dc6b802a2a785e3f2521c774df82d
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 09:52:06 2025 +0200

    feat: add the hello world script

commit 504e6942e04d808c2004d46ad6034c6b6873f0b3 (main)
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 09:50:56 2025 +0200

    doc: add description of the repository

commit c8dc3aa36b62dc47c961bc5b7a866656144e8694
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 09:48:51 2025 +0200

    Add README.md

We notice that there are 5 changes now in develop now, but main is still at commit 504e694

Let's visualize the repository to clarify the current situation. (we are using gitg here)

We decided that we have enough changes and we want to merge them into the main branch. First let's go back to main

(develop) $ git switch main
(main) $ git log
commit 504e6942e04d808c2004d46ad6034c6b6873f0b3 (HEAD -> main)
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 09:50:56 2025 +0200

    doc: add description of the repository

commit c8dc3aa36b62dc47c961bc5b7a866656144e8694
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 09:48:51 2025 +0200

    Add README.md

Now the HEAD is in main and the list of commits only contains the previous commits

And now we can merge the changes

(main) $ git merge develop
Updating 504e694..5ce1ad6
Fast-forward
src/script.py | 5 +++++
1 file changed, 5 insertions(+)
create mode 100644 src/script.py

Git recap the changes performed in develop.

As usual let's see the log

(main) $ git log
commit 5ce1ad6f1809bf1069a2754a555eca86f8540a65 (HEAD -> main, develop)
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 10:20:44 2025 +0200

    feat: add say_hello function to say hello to lot of people

commit b86eb31793155a5539646d7475c193610308e95b
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 10:01:40 2025 +0200

    feat: say hello to world

commit 757baec96c0dc6b802a2a785e3f2521c774df82d
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 09:52:06 2025 +0200

    feat: add the hello world script

commit 504e6942e04d808c2004d46ad6034c6b6873f0b3
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 09:50:56 2025 +0200

    doc: add description of the repository

commit c8dc3aa36b62dc47c961bc5b7a866656144e8694
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 09:48:51 2025 +0200

    Add README.md

Git shows here that now develop and main converged on the same commit

It's time to raise the bar and create some conflicts!

First, we create two more branches from develop that we call featA and featB

(main) $ git switch develop
(develop) $ git branch featA
(develop) $ git switch -c featB

Notice that we used git switch -c featB that is a shorcut for git branch featB; git switch featB

We are in featB branch now

Let's edit the script adding a sentence to tell people what we're doing.

def say_hello(recipient):
   print(f"Hello {recipient}. I'm learning Git!")

say_hello("biobankers!")
say_hello("BBMRI IT!")

And as usual we commit our changes.

(featB) $ git add src/script
(featB) $ git commit -m "feat: tell people what I'm doing"
(featB) $ git log
commit 9891aadff70fbed845e5a85c17271d8d7badf3fa (HEAD -> featB)
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 11:34:58 2025 +0200

   feat: tell people what I'm doing

commit 5ce1ad6f1809bf1069a2754a555eca86f8540a65 (main, featA, develop)
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 10:20:44 2025 +0200

    feat: add say_hello function to say hello to lot of people

...

We added a new commit in featB. Nothing different for now

Let's leave featB and move to featA

(featB) $ git switch featA

Edit again the script.

def say_hello(recipient):
   print(f"Hello {recipient}. I'm learning GIT!")
   print(f"It's awesome")

say_hello("biobankers!")
say_hello("BBMRI IT!")

And commit the changes

(featA) $ git add src/script.py
(featA) $ git commit -m "feat: tell people what I am doing and how awesome it is"
(featA) $ git log 
commit a586eb0fc9e3e72b5e9e963e212346711a2ac2e3 (HEAD -> featA)
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 11:51:28 2025 +0200

    feat: tell people what I am doing and how awesome it is

commit 5ce1ad6f1809bf1069a2754a555eca86f8540a65 (main, develop)
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 10:20:44 2025 +0200

    feat: add say_hello function to say hello to lot of people

...

We decided that both feature branches have done enough work and we want to merge them in develop.

First we switch to develop branch
```
(featA) $ git switch develop
```
Let's visualize the situation now

We see that both branches diverged from the same point and both have made one change.

Let's start merging from featB

(develop) $ git merge featB
Updating 5ce1ad6..9891aad
Fast-forward
src/script.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)

Great! It works.

Time to merge featA

(develop) $ git merge --no-ff featA
Auto-merging src/script.py
CONFLICT (content): Merge conflict in src/script.py
Automatic merge failed; fix conflicts and then commit the result.
(develop|MERGING) $

Doh! Git tell us there is a conflict. We need to fix it before continuing.

NB: the changes to PS1 gives us also some information about the status. In this case it tells us that we have a MERGE in progress

Let's open the file and check what's going on
```
def say_hello(recipient):
<<<<<<< HEAD
   print(f"Hello {recipient}. I'm learning Git!")
=======
   print(f"Hello {recipient}. I'm learning GIT!")
   print(f"It's awesome")
>>>>>>> featA

say_hello("biobankers!")
say_hello("BBMRI IT!")
```
Git shows us the conflict!

The code between <<<<<<< HEAD and ======= is the current develop, where we already merged featB

The code between ======= and >>>>>>> featA is the one we want to merge.

The problem here is that we modified the same line differently. In featB we wrote "Git" in featA we wrote "GIT", all uppercase.

Git couldn't decide which line was correct so it gives us the responsibility to resolve the conflict

We decide to keep "Git!" from featB and the rest from featA
```
def say_hello(recipient):
   print(f"Hello {recipient}. I'm learning Git!")
   print(f"It's awesome")

say_hello("biobankers!")
say_hello("BBMRI IT!")
```

Now we need to tell Git that the conflicts are fixed. As usual git status comes in handy

(develop|MERGING) $ git status
On branch develop
You have unmerged paths.
  (fix conflicts and run "git commit")
  (use "git merge --abort" to abort the merge)

Unmerged paths:
  (use "git add <file>..." to mark resolution)
        both modified:   src/script.py

no changes added to commit (use "git add" and/or "git commit -a")

Git suggests what to do to tell it that we solved the conflicts. Let's do this.

(develop|MERGING) $ git add src/script.py
(develop|MERGING) $ git status
On branch develop
All conflicts fixed but you are still merging.
  (use "git commit" to conclude merge)

Changes to be committed:
        modified:   src/script.py

Hang in there! We're almost done

We just need to commit the fixing as git status suggests

(develop|MERGING) $ git commit -m "feat: merge featA"
[develop cfb3f54] feat: merge featA
(develop) $

NB: Git doesn't take responsiblity of the content of the conflicting files. It's up to you. In other words, if you don't change the conflicting files and perfom git add without removing the conflict, git accept it. No worries, though you can always perform another commit to solve the situation

Let's check the history now

(develop) $ git log 
commit cfb3f5409d653a62a650a3ffa2311c8f693368c1 (HEAD -> develop)
Merge: 9891aad a586eb0
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 12:26:24 2025 +0200

    feat: merge featA

commit a586eb0fc9e3e72b5e9e963e212346711a2ac2e3 (featA)
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 11:51:28 2025 +0200

    feat: tell people what I am doing and how awesome it is

commit 9891aadff70fbed845e5a85c17271d8d7badf3fa (featB)
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 11:34:58 2025 +0200

    feat: tell people what I'm doing

commit 5ce1ad6f1809bf1069a2754a555eca86f8540a65 (main)
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 10:20:44 2025 +0200

    feat: add say_hello function to say hello to lot of people

Now we have in develop the commits from the two feature branches plus a "merge" commit.

Visually, we can see that all the two branches have converged to develop

Since the works on featA and featB are done and everything is merged in develop we can remove the branches.

(develop) $ git branch -D featA featB
Deleted branch featA (was a586eb0).
Deleted branch featB (was 9891aad)

Working with remote repositories

It's time to work with remote branches to keep our files on a server and to collaborate on projects

We will use repository on GitHub so, if you don't have one, create an account and a repository (steps 1 and 2). You can name your repository as you want. For the tutorial we will use the name bbmri-it-data-training

Clone your newly created repository locally and enter the directory
```
$ git clone https://github.com/<your_username>/bbmri-it-training
Cloning into 'bbmri-it-training'...
$ cd bbmri-it-training
(main) $
```
We have created a complete copy of the remote repository in our local machine

By defult, git refers to the remote repository as the origin. We can check the name and the url of the remote repository with the command git remote -v

(main) $ git remote -v
origin  [email protected]:<your_username>/bbmri-it-training.git (fetch)
origin  [email protected]:<your_username>/bbmri-it-training.git (push)

Let's create a README.md, write a simple documentation and commit it.

(main) $ git add README.md
(main) $ git commit -m "doc: initialize documentation"

We have created a new commit in our local repository. The remote origin repository is not updated though. To send our commits to the remote repository we use the push command

(main) $ git push origin main
Enumerating objects: 3, done.
Counting objects: 100% (3/3), done.
Writing objects: 100% (3/3), 268 bytes | 268.00 KiB/s, done.
Total 3 (delta 0), reused 0 (delta 0), pack-reused 0 (from 0)
To github.com:<your_username>/bbmri-it-training.git
* [new branch]      main -> main

Let's see the current log

(main) $ git log
commit ba78648d9b538267cad8335c67f7ef028281f077 (HEAD -> main, origin/main)
Author: Vittorio Meloni <[email protected]>
Date:   Fri Jun 13 14:57:00 2025 +0200

    doc: initialize documentation

Git log shows that main and the origin/main (the version of main in the remote) are aligned

Let's create the script as previously, commit and push

(main) $ git add src/script.py
(main) $ git commit -m "feat: add script"
(main) $ git push origin main

The next step is to fetch remotely created branches.

Go to your repository page on Github and create the develop branch following the official tutorial

Now launch the command to fetch branches
```
(main) $ git fetch
From github.com:<your_username>/bbmri-it-training
* [new branch]      develop    -> origin/develop
```
It created a copy of the remote branch called origin/develop that will get the changes from the remote repository each time we will fetch them.

To start working on develop we need to move to the local branch
```
(main) $ git switch develop
branch 'develop' set up to track 'origin/develop'.
Switched to a new branch 'develop'
```
Notice the info branch 'develop' set up to track 'origin/develop'.

Git is telling us that the branch develop is linked to the branch origin/develop

Let's start adding some changes. We can edit the src/script.py, commit the changes and check the status

def say_hello(recipient):
   print(f"Hello remote {recipient}. I'm learning Git!")
   print(f"It's awesome")

say_hello("biobankers!")
say_hello("BBMRI IT!")

(develop) $ git add src/script.py
(develop) $ git commit -m "feat: add remote to greetings"
(develop) $ git status
On branch develop
Your branch is ahead of 'origin/develop' by 1 commit.
   (use "git push" to publish your local commits)

nothing to commit, working tree clean

Notice that the status gives us hints about the status of the local copy of develop with respect to the origin

Now you can push to origin/develop

(develop) $ git push origin develop

Next step is getting changes from remote branch to our local version repository.

Go to your repository page on GitHub and go to develop

Navigate to the src/script.py file.

Click on the edit icon

write some changes and commit them

Tip

On GitHub you can open an online Visual Studio Code editor of your repository by pressing . (dot) on your keyboard.

Our local copy is now behind the remote. We need to fetch the changes that will be applied to origin/develop

(develop) $ git fetch origin develop
remote: Enumerating objects: 7, done.
remote: Counting objects: 100% (7/7), done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 4 (delta 0), reused 0 (delta 0), pack-reused 0 (from 0)
Unpacking objects: 100% (4/4), 1.09 KiB | 1.09 MiB/s, done.
From github.com:<your_username>/bbmri-it-training
 * branch            develop    -> FETCH_HEAD
   f461f60..7adb0e6  develop    -> origin/develop

And finally, apply them with merge

(develop) $ git merge origin/develop
Updating f461f60..7adb0e6
 Fast-forward
 src/script.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

Tip

git provides a shortcut for fetch + merge which is git pull We could obtain the same result with git pull origin develop

Name		Name	Last commit message	Last commit date
Latest commit History 18 Commits
README.md		README.md
all_merged.png		all_merged.png
before_conflict.png		before_conflict.png
commit_changes.png		commit_changes.png
develop_and_main_merged.png		develop_and_main_merged.png
edit_this_file.png		edit_this_file.png
git_branching.png		git_branching.png
switch_to_develop.png		switch_to_develop.png

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