Input file documentation for transport package

TODO: some front matter describing YAML format and explaining how to read below.

geometry:                                                                                   # Geometry specification:
  vertices: [list of list of float,, or <class 'numpy.ndarray'> or <class 'torch.Tensor'>]  # Caretsian vertex coordinates (n_vertices x 2).
  edges: [list of list of int,, or <class 'numpy.ndarray'> or <class 'torch.Tensor'>]       # Indices of vertices in edges (n_edges x 4).
  quads: [list of list of int,, or <class 'numpy.ndarray'> or <class 'torch.Tensor'>]       # Indices of edges in each quad (n_quads x 4).
material:                                                                                   # Material specification:
  fname: [string]                                                                           # File name to load materials data from.
  rotation: ((1, 0, 0), (0, 1, 0, (0, 0, 1)))                                               # 3 x 3 rotation matrix from material to simulation frame.
checkpoint: null                                                                            # Checkpoint file to read at start-up.
checkpoint-out: null                                                                        # Checkpoint file to write.

Component classes: