Merge 33c8013 into 0b88ab9

Author: maxiallard

.gitignore

@@ -45,7 +45,6 @@ ci/tests/test_output
 
 # mkdocs
 site
-docs/notebooks/
 
 # Keep unit tests data
 !ci/tests/data/*

.readthedocs.yaml

@@ -4,11 +4,6 @@ build:
   tools:
     python: "3.11"
 
-  jobs:
-    pre_build:
-      - "mkdir -p ./docs/notebooks"
-      - "cp ./examples/notebooks/*.ipynb ./docs/notebooks"
-
 mkdocs:
   configuration: mkdocs.yml
   fail_on_warning: false

README.md

@@ -31,7 +31,7 @@ Let’s build the most exciting AI-for-Bio community together!
 
 ## What's new?
 ### Evo2
-We have integrated [Evo2](https://github.com/ArcInstitute/evo2) into our helical package and have made a model card for it in our [Evo2 model folder](helical/helical/models/evo_2/README.md). If you would like to test the model, take a look at our [example notebook](helical/examples/notebooks/Evo-2.ipynb)!
+We have integrated [Evo2](https://github.com/ArcInstitute/evo2) into our helical package and have made a model card for it in our [Evo2 model folder](helical/models/evo_2/README.md). If you would like to test the model, take a look at our [example notebook](examples/notebooks/Evo-2.ipynb)!
 Let us know what you think and we are happy to help you with the larger model (40B parameters!) if needed!
 
 ### 🧬 Introducing Helix-mRNA-v0: Unlocking new frontiers & use cases in mRNA therapy 🧬
@@ -99,8 +99,9 @@ apptainer shell --nv --fakeroot singularity/helical/
 - [Universal Cell Embedding (UCE)](https://helical.readthedocs.io/en/latest/model_cards/uce/)
 
 ### DNA models:
-- [HyenaDNA](https://helical.readthedocs.io/en/latest/model_cards/hyenadna/)
+- [HyenaDNA](https://helical.readthedocs.io/en/latest/model_cards/hyena_dna/)
 - [Caduceus](https://helical.readthedocs.io/en/latest/model_cards/caduceus/)
+- [Evo 2](https://helical.readthedocs.io/en/latest/model_cards/evo_2/)
 
 
 ## Demo & Use Cases

docs/index.md

@@ -10,6 +10,10 @@ We will update this repo on a regular basis with new models, benchmarks, modalit
 Let’s build the most exciting AI-for-Bio community together!
 
 ## What's new?
+### Evo 2
+We have integrated [Evo 2](https://github.com/ArcInstitute/evo2) into our helical package and have made a model card for it in our [Evo 2 model card](./model_cards/evo_2.md). If you would like to test the model, take a look at our [example notebook](./notebooks/Evo-2.ipynb)!
+Let us know what you think and we are happy to help you with the larger model (40B parameters!) if needed!
+
 ### 🧬 Introducing Helix-mRNA-v0: Unlocking new frontiers & use cases in mRNA therapy 🧬
 We’re thrilled to announce the release of our first-ever mRNA Bio Foundation Model, designed to:
 
@@ -75,6 +79,7 @@ apptainer shell --nv --fakeroot singularity/helical/
 ### DNA models:
 - [HyenaDNA](./model_cards/hyenadna.md)
 - [Caduceus](./model_cards/caduceus.md)
+- [Evo 2](./model_cards/evo_2.md)
 
 
 ## Demo & Use Cases

docs/model_cards/caduceus.md

@@ -0,0 +1 @@
+../../helical/models/caduceus/README.md