In a medium mixing bowl, mix the whole-wheat flour, baking powder, baking soda, cinnamon, and ginger. In a separate larger bowl, mix the canned pumpkin, yogurt, honey, vegetable oil, and vanilla. Gradually add the dry ingredients to the wet ingredients and mix on medium-low speed with a hand mixer. Put the cupcake liners in the cupcake tin and fill the liners about 3/4 of the way, being careful not to overfill. Bake until a toothpick inserted into a pupcake comes out clean, about 18 to 20 minutes. Remove the pupcakes from the pan and cool on cooling rack, about 20 minutes.
For the icing, mix all ingredients until well combined. Ice the pupcakes when completely cooled.
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