Adapt the nauty_directg function

edit

Entering digraphs.nauty_directg?? into a SageMath session will show you the source code of the function.

In this case it simply calls an external program directg which is part of nauty.

You can download and edit that program's source code, compile your new version, and call that one instead.

To edit the source code you should start by looking at the file directg.c. Good luck!

You can have a look at:

sage: digraphs?

and read starting from ORDERLY GENERATION section. Indeed, digraphs is also a function that can generate isomorphism classes of digraphs with some property, as long as that property is stable with respect to vertex or edge deletion. Perhaps you could tune a property corresponding to your problem (which is not clear from your description).