esm 3.1.3 release (#184)

Author: tina-z-jia

CONTRIBUTIONS.md

@@ -27,30 +27,25 @@ python -c 'from huggingface_hub import login; login()'
 
 # Ensure package can correctly interact with forge.
 # This will require an API key from forge.evolutionaryscale.ai
-ESM_API_KEY=$ESM_API_KEY PYTHONPATH='.' python examples/forge_generate.py
-
+ESM_API_KEY=$ESM_API_KEY PYTHONPATH='.' python cookbook/snippets/esm3.py
 
 
 ```
 
 1. Ensure the following scripts run without errors. Most have a pip install command installing the published `esm` package - comment this out so your release candidate version is tested and not the already published version.
 
 ```bash
-ESM_API_KEY=$ESM_API_KEY PYTHONPATH='.' python examples/forge_generate.py
+ESM_API_KEY=$ESM_API_KEY PYTHONPATH='.' python cookbook/snippets/esm3.py
 pip install treon
-treon examples/esmprotein.ipynb
-treon examples/gfp_design.ipynb
+treon cookbook/tutorials/1_esmprotein.ipynb
+treon cookbook/tutorials/2_embed.ipynb
+treon cookbook/tutorials/3_gfp_design.ipynb
+treon cookbook/tutorials/4_forge_generate.ipynb
 
 # requires a GPU
-treon examples/generate.ipynb
-python examples/local_generate.py
-python examples/raw_forwards.py
+python cookbook/snippets/esm3.py
+python cookbook/snippets/esmc.py
+python cookbook/local/raw_forwards.py
 
 
 ```
-
-`examples/esmprotein.ipynb` works. Remember to skip running the first cell - it will reinstall stock esm instead of your deployed version.
-
-3. Ensure `examples/generate.ipynb` works. Note this notebook will require a node with a GPU that can fit ESM3 small open.
-
-4. Ensure

LICENSE.md

@@ -11,3 +11,26 @@ Here are the different licenses that govern access to the ESM codebase and the m
 | Governed by API Agreements (See Below)             | API access to all models, including API-only models (ESM3 family, ESM C 6B) |
 | [Forge API Terms of Use](https://www.evolutionaryscale.ai/policies/terms-of-use)                                          | Free non-commercial API access via Forge to all models including API-only models (ESM3 family, ESM C 6B) |
 | [Cambrian Inference Clickthrough License Agreement](https://www.evolutionaryscale.ai/policies/cambrian-inference-clickthrough-license-agreement)    | Commercial Inference via SageMaker for all ESM C models |
+
+
+# How can I access the models and which licenses apply?
+
+The models can be accessed in three different ways, each with its own licensing terms.
+
+1. **Code and weights** via GitHub and HuggingFace are available under either a [non-commercial](https://www.evolutionaryscale.ai/policies/cambrian-non-commercial-license-agreement) (ESM C 600M, ESM3-small-open) or an [open license](https://www.evolutionaryscale.ai/policies/cambrian-open-license-agreement) (codebase, ESM C 300M).
+    * **Building with ESM encouraged**: You can use embeddings, model predictions, fine-tune the models and use components of both the models and code. We strongly encourage anyone to build on ESM C and ESM3! Just remember to maintain the same license terms and release under the ESM name.
+2. **Free non-commercial inference API** via Forge. All models are available this way, with free credits granted to students and researchers. We want to enable academics under [non-commercial Terms of Use](https://www.evolutionaryscale.ai/policies/terms-of-use), which mirrors the non-commercial license.
+3. **Paid commercial Inference API** for commercial use via SageMaker (Forge coming soon). All ESM C models are available this way to commercial entities for commercial use under a [clickthrough license agreement](https://www.evolutionaryscale.ai/policies/cambrian-inference-clickthrough-license-agreement) with few restrictions.
+    * In broad strokes: standard commercial use like developing molecules and developing downstream ML models and methods with the model is allowed, while training competing models on the API outputs is not.
+    * Note: For ESM3 commercial use, reach out to [[email protected]](mailto:[email protected])
+
+### What changed with the release of ESM C?
+
+We introduced a [clickthrough license agreement](https://www.evolutionaryscale.ai/policies/cambrian-inference-clickthrough-license-agreement) to enable frictionless commercial use of ESM C.
+
+We introduced the new [Cambrian Open License](https://www.evolutionaryscale.ai/policies/cambrian-open-license-agreement) for ESM C 300M, and at the same time moved all code in the [`esm` repo](https://github.com/evolutionaryscale/esm) under that permissive license.
+
+The [Cambrian non-commercial license](https://www.evolutionaryscale.ai/policies/cambrian-non-commercial-license-agreement) is largely based on the original [ESM3 Community License Agreement](https://www.evolutionaryscale.ai/policies/community-license-agreement), but removed the clause that restricted drug development, added the naming requirement, and extended the meaning of “Derivative Work” to allow training on model outputs. Just remember to release models and methods built on ESM under the same license.
+These changes are meant to remove potential gray areas and points of friction for researchers building with ESM.
+
+Finally, The ESM3-open-small model has been moved under the [Cambrian non-commercial license](https://www.evolutionaryscale.ai/policies/cambrian-non-commercial-license-agreement).