Heat oil in a large, heavy-bottomed pot over medium heat. Add onion, garlic and jalapeño and season with salt and pepper. Cook, stirring occasionally, until onion is softened and translucent, 5 to 8 minutes. Add spices and stir to coat. Cook a minute or two to toast the spices, then add chipotles and tomatoes. Season with salt and pepper and cook, stirring occasionally, until the tomatoes start to caramelize a bit on the bottom of the pot, concentrating their flavor.