See also my post on setting up Python on Windows as well as R.


Install a source code editor. We will use Visual Studio Code in this post.

Windows users

Check if you have Windows Terminal installed. If not, install it from the Microsoft Store.

Launch a Windows Terminal instance. This should start a PowerShell session.

Update the PowerShell execution policy by running the following command:

Set-ExecutionPolicy -Scope CurrentUser -ExecutionPolicy RemoteSigned

Run Get-ExecutionPolicy to check if it is set to RemoteSigned. If not, try setting it again in a terminal with administrative rights.

Check if winget (the Windows package manager) is installed. The following command should bring up details about winget. If not, install it from the Microsoft Store.

winget --help

When using winget for the first time, you will be asked to accept some terms and conditions.

Native Windows

Install Git using winget:

winget install git.git

Install these additional packages if you regularly use GitHub:

winget install github.githubdesktop
winget install github.cli
winget install github.gitlfs

Windows with Windows Subsystem for Linux (WSL) - Ubuntu

Install WSL (you may have to reboot after the installation):

wsl --install

Launch VS Code and install the WSL and Remote - SSH extensions.


Configure Git global user settings:

git config --global "Your Name"
git config --global ""


Authenticate VS Code using HTTPS.

Also authenticate your GitHub account on GitHub Desktop and GitHub CLI if you installed them.

That’s all you need to do to get Git working over HTTPS (easy!). Read further for setting up SSH authentication, which is more complicated.


Use Git Bash for running the following commands if you are using native Windows. If you are using WSL, use the Ubuntu Bash shell instead.

Check for existing SSH keys:

ls -al ~/.ssh

If no keys exist, generate a new key using ED25519 (recommended over RSA):

ssh-keygen -t ed25519 -C "<comment>"

Start the SSH agent as follows (you may also need add these to ~/.bashrc or equivalent if it doesn’t activate automatically):

eval $(ssh-agent)

Copy the SSH public key to your clipboard (saved at ~/.ssh/ and add to GitHub/GitLab. The key can be used for authentication, signing, or both.

If the key will be used for signing as well, configure the following:

git config --global commit.gpgsign true
git config --global gpg.format ssh
git config --global user.signingkey ~/.ssh/

In VS Code, enable commit signing in the settings:

"git.enableCommitSigning": true

Troubleshooting SSH issues

Native Windows

If the above configurations did not work, try using OpenSSH for Windows instead of the SSH that comes with Git.

Set OpenSSH to run automatically. Go to Task Manager > Services > Open Services, find OpenSSH Authentication Agent > Properties > Startup Type > Automatic.

Configure Git to use OpenSSH (in Git Bash):

git config --global core.sshCommand "C:/Windows/System32/OpenSSH/ssh.exe"
eval $(ssh-agent)

To revert to the SSH agent supplied by Git for Windows (in Git Bash):

git config --global core.sshCommand "C:/Program Files/Git/usr/bin/ssh.exe"
eval $(ssh-agent)

Linux and WSL

If there are SSH issues on Ubuntu, try using Keychain.

If there are SSH issues on KDE, see here and here.

VS Code with WSL

Install packages such as Miniconda using the WSL Bash shell (use the Unix shell script to install).

Clone Git repositories using the WSL Bash shell using SSH.

Launch VS Code using the WSL Bash shell by navigating to the Git repository directory and running code ..

Install local VS Code extensions in WSL.

Testing if SSH works

Use the following commands to test whether SSH has been configured properly for GitLab, GitHub, and GitHub Gist:

ssh -T  # GitLab
ssh -T  # GitHub

If connection to these hosts are being tested for the first time, a warning might appear stating that the authenticity of the host can’t be established and if you want to continue connecting. If the fingerprint matches that of GitLab or GitHub, type “yes” and continue.

You should get the following outputs if it’s working:

Welcome to GitLab, @username!

Hi username! You've successfully authenticated, but GitHub does not
provide shell access.

If you don’t get the above, then there may be issues with the connection. To troubleshoot, use the following command to run SSH in verbose mode:

ssh -Tvvv  # GitLab
ssh -Tvvv  # GitHub

Enabling SSH via HTTPS might resolve this problem.

First, test if SSH is working over the HTTPS port (443); you should get the same outputs as above:

ssh -T -p 443  # GitLab
ssh -T -p 443  # GitHub

If it works, create a file called ~/.ssh/config and add the following configurations:

  User git
  Port 443
  PreferredAuthentications publickey
  IdentityFile ~/.ssh/id_ed25519

  User git
  Port 443
  PreferredAuthentications publickey
  IdentityFile ~/.ssh/id_ed25519

  User git
  Port 443
  PreferredAuthentications publickey
  IdentityFile ~/.ssh/id_ed25519

Test again to see if everything is working:

ssh -T  # GitLab
ssh -T  # GitHub
ssh -T  # GitHub Gist

Updating remote URLs for SSH

If the local repository was cloned using HTTPS and you’re using SSH, the remote URL must be updated to use SSH. To check the existing remote:

git remote -v

To change the remote URL to SSH:

git remote set-url origin  # GitLab
git remote set-url origin  # GitHub