Remove `dot` dependency

[mgxd]

trafficstars

Summary

Nipype still uses pydot for graph rendering:

https://github.com/nipy/nipype/blob/bf48f7722f057a1eb2005390eb0a7ebcd35ee8bf/nipype/pipeline/engine/utils.py#L1381

This has lead to problems (https://github.com/nipreps/fmriprep/issues/2870) and is on its way out in networkx (https://github.com/networkx/networkx/issues/5723), and might just easily be replaced with nx.nx_agraph.write_dot

[effigies]

Actually this line:

https://github.com/nipy/nipype/blob/bf48f7722f057a1eb2005390eb0a7ebcd35ee8bf/nipype/pipeline/engine/utils.py#L1373

At the very least nipype should set a timeout and allow a TimeoutError to be raised.