If you want to eliminate rows that have negligible entries, i'd use np.allclose.
zero_row_indices = [i for i in r.shape[0] if np.allclose(r[i,:],0)]
nonzero_row_indices =[i for i in r.shape[0] if not np.allclose(r[i,:],0)]
r_new = r[nonzero_row_indices,:]