ESM Encoder Class Creation

[vratins]

• Add ESMEncoder for pre-computed ESM3 embeddings
• Update encoder interface to return edge features as third output
• Add use_edge_update parameter to GVPEncoder for optional edge updates
• Use constants for defaults
• Update tests

[Copilot]

Pull request overview

Adds a new cached-embedding encoder (ESM) and extends the encoder interface so encoders can optionally return protein–protein edge features, with GVP edge-updates made configurable.

Changes:

• Introduces ESMEncoder that returns precomputed ESM embeddings as scalar node features (no vectors, no edges).
• Updates BaseProteinEncoder.forward to return (s, V, pp_edge_attr) and updates encoder/unit tests accordingly.
• Adds use_edge_update option and cached-edge-feature passthrough/computation changes in the GVP encoder stack.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/test_encoder.py	Updates tests for the new 3-output encoder interface and adds ESM encoder coverage.
src/encoder_base.py	Changes the abstract encoder interface to return optional PP edge features as a third output.
src/gvp_encoder.py	Adds use_edge_update, supports cached edge features, and returns edge features optionally.
src/slae_encoder.py	Updates SLAE encoder to comply with the new interface (returns None for edge features).
src/esm_encoder.py	Adds the new ESM cached-embedding encoder implementation and registration.
src/__init__.py	Updates package-level imports to trigger registration of the new/renamed encoder modules.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[vratins]

In the last commit I made slight formatting changes to files to ensure that ruff/ty/build checks pass. The only files where there are comments that are addressed and functional changes to review are:

• encoder_base.py
• gvp_encoder.py

[marcuscollins]

Lots of comments, but nothing blocking. Please go through and either address them or make issues to track any requests.

[marcuscollins]

None of these as statements are necessary, please remove them.

[vratins]

This would lead to unused import issues when linting -- do you recommend adding noqa comments instead?