Finding a simple fabfile with a working example of SSH keyfile usage isn't easy for some reason. I wrote a blog post about it (with a matching gist).
Basically, the usage goes something like this:
from fabric.api import *
env.hosts = ['host.name.com']
env.user = 'user'
env.key_filename = '/path/to/keyfile.pem'
def local_uname():
local('uname -a')
def remote_uname():
run('uname -a')
The important part is setting the env.key_filename
environment variable, so that the Paramiko configuration can look for it when connecting.
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