Update dependencies

[luisfpereira]

This PR updates dependencies.

In particular, it:

• adds torch, torch-sparse, torch-scatter, and torch-geometric

• removes unused dependencies (some of which I believe are dependencies of the packages this depends upon; installation should then be done through those)

• adds tutorial as an optional dependency type containing libraries that are only relevant for tutorials

Linting of the file is done automatically using Even Better Toml.

[levtelyatnikov]

One question regarding the dependencies: shouldn't we specify the exact version of each library we use? My primary concern is torch_geometric as it updates often and not always with backward compatibility

[luisfpereira]

@levtelyatnikov, personally I try to keep the code always working with the latest release of a given package (especially the most relevant ones).
This is supported by the fact the latest release of a package is (supposedly) better and more bug free.

When that is not possible, I agree specifying the version is a good practice, though it increases the possibility the package becomes incompatible with some other (the same may happen if we update and others not, but it that case, ours is not the outdated package).

I guess the guidelines may vary among communities though.