Once you completed all tasks inside a project you can mark it done by clicking on mark done icon.
Marking a project done in the project overlay
In the project overlay a "mark project done" button will appear at the top right once all tasks are checked off.
Troubleshooting - I can't mark a project done
If a project still has open tasks you will see the button but it can't be clicked. If you don't see any open tasks, switch to the backburner to see if there are any backburner tasks still in that project.