docs: def initialize(self, calc_reg):
          """
          Initialize the simulation. Organize calculations by dependency.
  
          :param calc_reg: Calculation registry.
          :type calc_reg:
              :class:`~simkit.core.calculation.CalcRegistry`
          """
          self._isinitialized = True
          # TODO: if calculations are edited, loaded, added, etc. then reset
          self.calc_order = topological_sort(calc_reg.dependencies)