fhalab/MLDE: 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.A machine-learning package for navigating combinatorial protein fitness landscapes