v3.2.1

Changelog v3.2.1

Changes

• Documentation: Updated README table of contents for better navigation
• Code Quality: Removed unused imports to clean up codebase
• SDK Updates: Various improvements and bug fixes to the ESM SDK
• Tutorials: Updated cookbook tutorials with latest examples
• Dependencies: Updated pixi.lock with latest dependency versions

Bug Fixes

• Cleaned up unused imports in forge.py
• Minor fixes and improvements across various SDK modules

Documentation

• Improved README structure and table of contents
• Updated tutorial notebooks with current best practices

This is a maintenance release focused on code quality improvements, documentation updates, and minor SDK enhancements.

v3.2.0

Updates:

• Upgraded biotite version so we're not restricted to numpy < 2.0. this required removing the to_npz / to_npz_string functions (an internal biotite format they no longer support)
• Added MSA support
• Added a globularity function so it's easy to calculate
• Fixed a bug where Inf SASA was encoded as -1, will now be encoded as 1000.

v3.1.6

• gfp notebook updated to use a max num_steps of 20 instead of 229
• updated docstring for batch executor

v3.1.5

We had a few changes:

• extended the pyproject.toml to be pixi-compliant for folks using pixi
• bugfix to the gfp_design.ipynb in the tutorial
• updated cookbook/snippets/esmc.py to include examples of how to call esmc via forge
• updated the default for num_steps in GenerationConfig

v3.1.3

Main changes:

1. Tutorials have been reorganized to be completed in a step-by-step fashion. We added a new tutorial for using ESM C to get protein embeddings.
2. Layer number specification is required when requesting hidden_states of ESM C 6B.
3. SASA track in forward_and_sample API is fixed.

v3.1.2

In this release, we made two changes:

1. Brought Flash Attention and Triton Rotary embedding to the ESM C model
2. Updated forge client to enable the return of ESM C's binary serialized hidden states. (note this the return of ESM3 hidden states are not supported).

v3.1.1

In this release, we made three changes:

1. Updated ESM C tokenizer to no longer depend on ESM3. So now you can use ESM C without having to accept the ESM3 license.
2. Updated the transformer class so it returns hidden states.
3. Pined transformers version to be <4.47.0 to prevent a tokenizer issue. If you are currently seeing tokenizer issues, try reinstalling the new release.

v3.1.0

Releasing the ESM C series of models!

v3.0.8

v3.0.8 (#146)

Co-authored-by: Zeming Lin <[email protected]>

v3.0.7

• Adds model API support for ProteinComplex and associated utilities