Featuretools/featuretools

the error essentially comes down to the categories being different between the categorical variables you are trying to relate. See this code example

import pandas as pd
from pandas.api.types import is_dtype_equal

s = pd.Series(["a","b","a"], dtype="category")
s2 = pd.Series(["b","b","a"], dtype="category")
s3 = pd.Series(["a","b","c"], dtype="category")

is_dtype_equal(s.dtype, s2.dtype) # this is True
is_dtype_equal(s.dtype, s3.dtype) # this is False

You need update your dataframe before loading it into Featuretool to make sure the Pandas Categoricals have the same values category values. Here's how you do that

# if s is missing categories from s3
new_s = s.astype(s3.dtype)
is_dtype_equal(new_s.dtype, s3.dtype) # this is True

# if both are missing categories from each other
import pandas.api.types as pdtypes
s4 = pd.Series(["b","c"], dtype="category")
categories = set(s.dtype.categories + s4.dtype.categories)
new_s = s.astype("category", categories=categories)
new_s4 = s4.astype("category", categories=categories)
is_dtype_equal(new_s.dtype, new_s4.dtype) # this is True

please also post on SO where I can give a more detailed answer for everyone else