Cell Systems Publication Accompaniment

Major changes include:

1. Major overhaul to the underlying package structure.
2. Support for deriving encodings from ESM and ProtTrans.
3. Support for zero-shot prediction of combinatorial library fitness. Currently supported strategies are EVmutation, DeepSequence, and masked-token prediction with models from ESM and ProtTrans.
4. Script support for replicating simulated MLDE experiments.