So, this note is a bit strange because I set up the repo and keys before renaming it and giving it to "mila-iqia". This makes these setup instructions useful in general, but somewhat useless on the computers where my repo is currently checked out.
# add entry to config, with "clockwork" being the github repo
cat >> ~/.ssh/config
Host github-clockwork
Hostname github.com
IdentityFile ~/.ssh/github_keys/clockwork-id_rsa
# in case it didn't exist beforehand, give it the right permissions
chmod 644 ~/.ssh/config
ssh-keygen -f ~/.ssh/github_keys/clockwork-id_rsa -t ecdsa -b 521
# make sure permissions are right
chmod -R 644 ~/.ssh/github_keys/*id_rsa.pub
chmod -R 600 ~/.ssh/github_keys/*id_rsa
# checkout the code locally
git clone git@github-clockwork:mila-iqia/clockwork.git
# updating the remote after moving to mila-iqia
git remote set-url origin git@github-slurm_monitoring_and_reporting:mila-iqia/clockwork.git