code: def _update_Pxy(self):
          
          scipy.copyto(self.Pxy_no_omega, self.Phi_x.transpose(),
                  where=CODON_SINGLEMUT)
          self.Pxy_no_omega[0][CODON_TRANSITION] *= self.kappa
          self.Pxy = self.Pxy_no_omega.copy()
          self.Pxy[0][CODON_NONSYN] *= self.omega
          _fill_diagonals(self.Pxy, self._diag_indices)
docs: Update `Pxy` using current `omega`, `kappa`, and `Phi_x`.