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Preheat the oven to 350F and line a 24-count mini muffin tin with paper liners, or spray the cavities well with non-stick spray.
In a large bowl, sift together both flours, the baking powder, baking soda, salt, pumpkin pie spice and cinnamon. Set aside.
In a medium sized mixing bowl, whisk together the oil with the egg and maple syrup. Add the pumpkin puree, almond milk and vanilla extract and whisk well. Pour the wet ingredients into the dry, and stir just until there are no remaining streaks of flour. Add in the mini chocolate chips, stirring gently with a wooden spoon to incorporate.
Using a small cookie scoop or spoon, fill the muffin cavities 3/4 cup full and bake for 10-11 minutes. Check after 10 minutes, and using a toothpick, insert into the center of the muffin and if there is batter remaining on the toothpick, bake the muffins for another minute or two. If it comes out clean, the muffins are done! Remove the muffins to a wire rack to cool completely.