calyx_depth.py: divest from odgi's Python bindings

[anshumanmohan]

The algorithm calls parse_data.py, which in turn calls odgi's Python bindings, to learn the input graph's dimensions. Instead, use mygfa.preprocess:

pollen/mygfa/mygfa/preprocess.py

Lines 64 to 69 in de4f8db

	def get_maxes(graph: mygfa.Graph) -> Tuple[int, int, int]:
	"""Return the maximum number of nodes, steps, and paths in the graph."""
	max_nodes = len(graph.segments)
	max_steps = max([len(steps) for steps in node_steps(graph).values()])
	max_paths = len(graph.paths)
	return max_nodes, max_steps, max_paths

This will free us from odgi's Python bindings.

This work has been broken down as such:

• Stop using odgi's Python bindings in calyx_depth.py #116
• Divesting from odgi's Python bindings: testing #147
• Divesting from odgi's Python bindings: documentation #148

For context, see tracking issue #105

[sampsyo]

Yay; this would be very satisfying!!