Hi, this is a solution for users who had the same issue as me.
Today I tried to connect my repository from JupyterLab to my GitHub and I had some troubles with it.
I used jupyter-git for several days and it seemed to work fine (for example, commit worked as it should), but then I decided to connect to my GitHub. I generated SSH keys from the docs:

https://docs.github.com/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent?platform=linux

Then I ran ssh -vT [email protected] and I successfully authenticated. After that, I was able to push commits from the terminal. But when I opened another terminal window and tried to push, or tried to do "Git -> Push to remote" in JupyterLab, I got the message:

[email protected]:Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists."

I didn't find any solution on the Internet that could work for me, so, this is the solution that worked for me.

Step 1:

In the jupyterlab terminal:

ssh -T [email protected] -v
ssh-add -l
env | grep -E '^SSH_'
git remote -v

If ssh-add -l shows “The agent has no identities” or if env is empty for SSH_ — this is our case.

Step 2:

Add these lines to the end of ~/.bashrc:

if [ -z "$SSH_AUTH_SOCK" ]; then
    eval "$(ssh-agent -s)" >/dev/null
    ssh-add ~/.ssh/id_ed25519 2>/dev/null
fi

Now, every time you open a terminal (and when starting JupyterLab), the agent will launch and load the key automatically.

Step 3:

# Add the key to the persistent agent
ssh-add ~/.ssh/id_ed25519

# Check
ssh-add -l
ssh -T [email protected]

Step 4 (if required):

Open/create ~/.ssh/config and paste:

Host github.com
  HostName github.com
  User git
  IdentityFile ~/.ssh/id_ed25519
  IdentitiesOnly yes

Close the file.
Enter the following commands in terminal:

chmod 700 ~/.ssh
chmod 600 ~/.ssh/*
ssh-keyscan github.com >> ~/.ssh/known_hosts

Restart the JupyterLab server.

I'm newbie, but hope this helps you if you are facing the same problem.