Removed layers, simplified architectures

[DomInvivo]

• Removal of unused GNNs
• Creation of ResidualConnection classes to avoid having multiple architectures. Then removed the architectures that relied on these residual connections
• Added some documentation and unit-tests
• Refactor PNA to have inheritance and avoid duplicated code
• Removed duplicated MLPs functions
• Changed the DGN networks to support both an input and output FeedForward network

This pull-request has a lot of progress in the refactoring of the code, but there is still a lot to do.
The examples will no longer run after the merging, but I want to avoid pull-requests too large, so I think we can still go forward with the PR and do the remaining changes in another PR.

[hadim]

Thanks Dom for this first cleanup. I haven't run the code as it is mainly a cleaning and refactoring PR.

I am often picky and opinionated when reviewing so feel free to disagree or comment more on my reviews.

The platform also switched to black as a Python code formatted. There is a GA setup to check each commit has formatted code (see https://github.com/invivoai/goli/blob/master/.github/workflows/lint.yml#L31). black is pretty standard and you should be able to configure it on your favourite IDE.