Assigning physical boundary ids with multi-part polygons is broken

[Stephan Kramer]

When assigning physical boundary ids with shapes that consist of multiple parts (i.e. shapes with holes in them), boundary ids are not assigned correctly. This is caused by the corresponding shapefile not being read in correctly in the ShapeData object in input_output_for_id.py. The multiple parts of the shape, i.e. the different sub-polygons that describe the different boundaries of a single shape, are separated and treated as entirely different polygons in the ShapeData.points array together with polygons belonging to other shapes in that same shapefile. In define_boundary_id.py it is then assumed (incorrectly) that ShapeData.records(), which is an array with a record for each *shape*, is of the same length as the points array (which is now an array of all the separated polygons).

Work-around: make sure that the shapefile you specify for physical boundary contains no shapes with holes.