All the Birds in the Sky by Charlie Jane Anders

Childhood friends Patricia Delfine, a witch, and Laurence Armstead, a mad scientist, parted ways under mysterious circumstances during middle school. But as adults they both wind up in near-future San Francisco, where Laurence is an engineering genius and Patricia works with a small band of other magicians to secretly repair the world’s ever growing ailments. But something is determined to bring them back together—to either save the world, or end it.