Improve colors of graph adjacency matrix
Simply setting the bg or background attribute of buttons and text entry widgets does not seem to affect the displayed background color in the graph adjaceny matrix. I think it would look better if the vertex's color extended across a complete row. The initial implementation only shows the colors along the (static) diagonal:
One way to do this would be to make a custom widget from a Label or Frame class that has bindings to handle clicks and maybe keyboard input.
For the weighted graph, the adjacency matrix cells are editable text entry areas. Those are showing the background color, although they are surrounded by frame of the default background.

This appears to be a problem specific to macOS. Here's how the adjacency matrix appears for Graph.py on Windows:
There appears to be Python library that fixes this issue:
https://pypi.org/project/tkmacosx/