SCiarella

I don't have a strong opinion on yapf vs ruff, so I totally trust you on this! Go with the one you like the most!

> > * `Pathway` should also compute and report the energy difference between connected sites, and report this information which is more relevant than the total free energy of the...

Once #323 is merged, this issue can be closed. Task 2. has not been addressed and will be left for a future issue if the need arises.

[This issue](https://github.com/JuliaDiff/SparseDiffTools.jl/issues/300) needs to be addressed in order to be able to write custom pullback rules for Enzyme

Not needed anymore after #116