From Fedora Project Wiki
Fedora Atomic Host installations use the rpm-ostree deployment method, where packages are assembled on the Fedora release engineering side and delivered as atomic units, rather than the yum/DNF method of client side assembly. Consequently, they do not use the DNF system upgrade mechanism which is used to upgrade between Fedora releases for other Fedora installations. Instead, use the procedure described here.
One OSTree repository per release
It's crucial to note that at the moment, Fedora uses separate OSTree repositories for each major release. This makes switching between versions more painful. For more information, see this ticket.
It's crucial to note that at the moment, Fedora uses separate OSTree repositories for each major release. This makes switching between versions more painful. For more information, see this ticket.
Let's assume you're upgrading from Fedora 40 to 41. First, you'll need to add a remote for the new major version:
ostree remote add fedora-41 --set=gpg-verify=false https://dl.fedoraproject.org/pub/fedora/linux/atomic/41
Then, rebase to it:
rpm-ostree rebase fedora-41:fedora-atomic/f41/x86_64/docker-host
Like any other rpm-ostree update, this is staged for the next reboot, so to finally apply the update:
systemctl reboot
That should be all!