This is may be by design, but I found it unexpected (see below). If it is by design, it would help to add "shallow" to the doctring.

In [220]: g = ct.rss()

In [221]: g.D[0,0]
Out[221]: -1.8274167505512213

In [222]: g2 = g.copy()

In [223]: g2.D[0,0] = 1

In [224]: g.D[0,0]
Out[224]: 1.0

One way to deep copy is to use control.ss; continuing from above:

In [225]: g3 = ct.ss(g)

In [226]: g3.D[0,0] = 5

In [227]: g.D[0,0]
Out[227]: 1.0