Continuous integration doesn't mean all development happens in master. A policy that works well for me is that anything that will require more than 2 minor commits to accomplish should happen in a feature branch. If tests pass in the branch (and you probably want to insert code review/sign-off at this stage as well), merge to master. If tests pass in master, deploy.

From what I can tell, this just makes it easy to run tests in branches. My team uses something similar that kicks off a build whenever someone comments "build it" in a GitHub pull request, and posts the results to the pull request discussion.