Preheat oven to 400 degrees F.
In a medium-sized bowl, whisk together whole wheat flour, baking soda, baking powder, salt, cinnamon, ginger and nutmeg.
In a large bowl, combine pumpkin, molasses, honey, eggs, applesauce, and yogurt.
Add the flour mixture to the pumpkin mixture. Mix until just combined. To avoid tough muffins, do not over mix.
Add toasted almonds, and stir to combine.
Spray two muffin tins (about 20 muffin cups) with nonstick cooking spray. Fill each cups with ¼ cup of the muffin batter.
Bake for 12-14 minutes, or until a toothpick inserted in the center comes out clean.
Cool in the tin on a rack for about 10 minutes. Remove the muffins from the tin and let the muffins cool on the rack.