Better mesh surface checks

[meganrm]

Use Case

We need to make sure ingredients don't overlap with surfaces defined by a mesh

Solution

This is some code we removed that may be a good check to do but is currently redundant with other surface checks

        # the compartment the ingr belongs to
        # current_ingr_compartment = self.get_compartment(self.env)
        # for compartment in self.env.compartments:
        #     if current_ingr_compartment.name == compartment.name:
        #         continue
        #     distances, ingr_indexes = compartment.OGsrfPtsBht.query(packing_location)

        #     # NOTE: this could be optimized by walking down the sphere tree representation
        #     # of the instead of going right to the bottom
        #     if distances < self.encapsulating_radius + compartment.encapsulating_radius:
        #         # pos_of_attempting_ingr = self.get_new_pos(
        #         #     self, packing_location, rotation, self.positions[total_levels - 1]
        #         # )
        #         distances, ingr_indexes = compartment.OGsrfPtsBht.query(
        #             [packing_location]
        #         )

        #         radii = [self.radius]
        #         overlap_distance = distances - numpy.array(radii)
        #         overlap_indexes = numpy.nonzero(overlap_distance < 0.0)[0]
        #         if len(overlap_indexes) != 0:
        #             return True

Alternatives

Please describe any alternatives you've considered, even if you've dismissed them