I have just set up a virtual machine using Vagrant and Puphpet. I know I have MySQL because I can mysql
in the command line. I just did a basic install.
I put the information on puphpet.com - maybe you missed it
You can connect using the SSH tab (username/password are 'vagrant') in Sequel Pro. The database input fields have to match the settings in the config.yaml.
If you cannot connect using vagrant/vagrant ssh into the vm type passwd and enter vagrant twice. You've now set the password for the vagrant user to vagrant. This does not affect the ssh functionality in vagrant, because vagrant uses ssh-keys.