Add HyenaDNA to documents folder

helicalAI · May 22, 2024 · 9d9ec87 · 9d9ec87
1 parent d212ab8
commit 9d9ec87
Show file tree

Hide file tree

Showing 7 changed files with 32 additions and 4 deletions.
diff --git a/_toc.yml b/_toc.yml
@@ -9,6 +9,7 @@ parts:
   - file: docs/Geneformer.rst
   - file: docs/UCE.rst
   - file: docs/scGPT.rst
+  - file: docs/hyena_dna.rst
 - caption: Tutorials🪄
   chapters:
   - file : examples/Geneformer-vs-UCE

diff --git a/docs/_autosummary/helical.constants.rst b/docs/_autosummary/helical.constants.rst
@@ -1,4 +1,4 @@
-helical.constants
+helical.constants
 =================
 
 .. automodule:: helical.constants
@@ -28,4 +28,5 @@ helical.constants
    :recursive:
 
    helical.constants.enums
+   helical.constants.paths
 
diff --git a/docs/_autosummary/helical.models.geneformer.rst b/docs/_autosummary/helical.models.geneformer.rst
@@ -1,4 +1,4 @@
-helical.models.geneformer
+helical.models.geneformer
 =========================
 
 .. automodule:: helical.models.geneformer

diff --git a/docs/_autosummary/helical.models.rst b/docs/_autosummary/helical.models.rst
@@ -29,6 +29,7 @@
 
    helical.models.geneformer
    helical.models.helical
+   helical.models.hyena_dna
    helical.models.scgpt
    helical.models.uce
 
diff --git a/docs/_autosummary/helical.models.scgpt.rst b/docs/_autosummary/helical.models.scgpt.rst
@@ -27,7 +27,17 @@ helical.models.scgpt
    :toctree:
    :recursive:
 
+   helical.models.scgpt.data_collator
+   helical.models.scgpt.data_sampler
+   helical.models.scgpt.loss
    helical.models.scgpt.model
-   helical.models.scgpt.scGPT
+   helical.models.scgpt.model_dir
+   helical.models.scgpt.preprocess
+   helical.models.scgpt.scbank
    helical.models.scgpt.scgpt_config
+   helical.models.scgpt.scgpt_utils
+   helical.models.scgpt.tasks
+   helical.models.scgpt.tokenizer
+   helical.models.scgpt.trainer
+   helical.models.scgpt.utils
 
diff --git a/docs/_autosummary/helical.models.uce.rst b/docs/_autosummary/helical.models.uce.rst
@@ -1,4 +1,4 @@
-helical.models.uce
+helical.models.uce
 ==================
 
 .. automodule:: helical.models.uce

diff --git a/docs/hyena_dna.rst b/docs/hyena_dna.rst
@@ -0,0 +1,15 @@
+Hyena-DNA
+=================
+
+.. currentmodule:: helical.models.hyena_dna
+.. automodule:: helical.models.hyena_dna
+
+.. autosummary::
+   :toctree: _autosummary
+
+   HyenaDNA
+   HyenaDNAConfig
+   HyenaDNA.process_data
+   HyenaDNA.get_embeddings
+
+