Bring a large pot of salted water to a boil, and cook your pasta al dente. Reserve 1 cup of pasta water, drain and set aside.
In the same pot, heat the butter on medium heat and saute the diced onion until soft, for about 5-7 minutes.
Add in the garlic and cook until fragrant, for about 1 minute. Next add in the tomato paste, pumpkin, and spices and stir together.
Whisk the tapioca flour into the milk, and pour it into the pot with the pasta water. Whisk together until smooth and add in the parmesan. Let it cook down for 3-4 minutes on medium/low heat.
Add in the spinach and pasta, and let it simmer until the sauce thickens.
Serve fresh with shaved parmesan and crushed pecans.