skgraph.tools.find_surface_nodes is very slow

[ma-sadeghi]

...so slow, that for large-enough networks (>100k nodes), it becomes the bottle-neck for CubicTemplate.

[jgostick]

oh? I thought the bottleneck was in the trim function?

[ma-sadeghi]

I just profiled CubicTemplate and find_surface_nodes seems to be taking up almost ~95% of the total run time for large networks.

[ma-sadeghi]

Here's some concrete timings for reference:

32x32x32

• Total time: 2.5 s
• skgraph.tools.find_surface_nodes: 2.45
• skgraph.generators.cubic_template: 0.05

64x32x32

• Total time: 7.5 s
• skgraph.tools.find_surface_nodes: 7.4
• skgraph.generators.cubic_template: 0.1

As you can see, it gets worse as you go to larger networks.