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This looks like an error in .normalize_coordinates(). That function is
assuming that after you clear denominators, then the coefficients are in
the maximal order. This is clearly false. That function needs to be
fixed, please open an issue on github so we can track it and get it fixed.
As a workaround, you can scale phi so that all the coefficients are in
the maximal order (this does not change the canonical height calculation).