From 2215da3d2850aeeead8fd02ceabd79e2ab8c7964 Mon Sep 17 00:00:00 2001
From: ryanDing26 <ryding@ucsd.edu>
Date: Sun, 19 Oct 2025 11:02:09 -0700
Subject: [PATCH 1/3] Add HuggingFace support

---
 biomni/llm.py | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/biomni/llm.py b/biomni/llm.py
index 61747b685..1b3c67132 100644
--- a/biomni/llm.py
+++ b/biomni/llm.py
@@ -6,7 +6,7 @@
 if TYPE_CHECKING:
     from biomni.config import BiomniConfig
 
-SourceType = Literal["OpenAI", "AzureOpenAI", "Anthropic", "Ollama", "Gemini", "Bedrock", "Groq", "Custom"]
+SourceType = Literal["OpenAI", "AzureOpenAI", "Anthropic", "Ollama", "Gemini", "Bedrock", "Groq", "HuggingFace", "Custom"]
 ALLOWED_SOURCES: set[str] = set(SourceType.__args__)
 
 
@@ -26,7 +26,7 @@ def get_llm(
         model (str): The model name to use
         temperature (float): Temperature setting for generation
         stop_sequences (list): Sequences that will stop generation
-        source (str): Source provider: "OpenAI", "AzureOpenAI", "Anthropic", "Ollama", "Gemini", "Bedrock", or "Custom"
+        source (str): Source provider: "OpenAI", "AzureOpenAI", "Anthropic", "Ollama", "Gemini", "Bedrock", "HuggingFace", or "Custom"
                       If None, will attempt to auto-detect from model name
         base_url (str): The base URL for custom model serving (e.g., "http://localhost:8000/v1"), default is None
         api_key (str): The API key for the custom llm
@@ -196,7 +196,21 @@ def get_llm(
             stop_sequences=stop_sequences,
             region_name=os.getenv("AWS_REGION", "us-east-1"),
         )
-
+    elif source == "HuggingFace":
+        try:
+            from langchain_huggingface import ChatHuggingFace, HuggingFaceEndpoint 
+        except ImportError:
+            raise ImportError(  # noqa: B904
+                "langchain-huggingface package is required for HuggingFace models. Install with: pip install langchain-huggingface"
+            )
+        return ChatHuggingFace(
+            llm = HuggingFaceEndpoint(
+                repo_id=model,
+                temperature=temperature,
+                stop_sequences=stop_sequences,
+                huggingfacehub_api_token=os.getenv("HUGGINGFACE_API_KEY")
+            )
+        )
     elif source == "Custom":
         try:
             from langchain_openai import ChatOpenAI

From e6cc6ccbfba9416dd0b7fa54c8bfef84ba8779cf Mon Sep 17 00:00:00 2001
From: ryanDing26 <ryding@ucsd.edu>
Date: Sun, 19 Oct 2025 11:07:22 -0700
Subject: [PATCH 2/3] Add pip installation to new software script

---
 biomni_env/new_software_v007.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/biomni_env/new_software_v007.sh b/biomni_env/new_software_v007.sh
index 4cdcb4ae0..6bdae5c2c 100644
--- a/biomni_env/new_software_v007.sh
+++ b/biomni_env/new_software_v007.sh
@@ -8,4 +8,5 @@ pip install fair-esm
 pip install nnunet nibabel nilearn
 pip install mi-googlesearch-python
 pip install git+https://github.com/pylabrobot/pylabrobot.git
+pip install langchain-huggingface
 conda install weasyprint

From e1a9cc3372eb6ebb798a550ba6944521481c4fc5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 19 Oct 2025 18:25:34 +0000
Subject: [PATCH 3/3] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 biomni/llm.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/biomni/llm.py b/biomni/llm.py
index 1b3c67132..d28e6d657 100644
--- a/biomni/llm.py
+++ b/biomni/llm.py
@@ -6,7 +6,9 @@
 if TYPE_CHECKING:
     from biomni.config import BiomniConfig
 
-SourceType = Literal["OpenAI", "AzureOpenAI", "Anthropic", "Ollama", "Gemini", "Bedrock", "Groq", "HuggingFace", "Custom"]
+SourceType = Literal[
+    "OpenAI", "AzureOpenAI", "Anthropic", "Ollama", "Gemini", "Bedrock", "Groq", "HuggingFace", "Custom"
+]
 ALLOWED_SOURCES: set[str] = set(SourceType.__args__)
 
 
@@ -198,17 +200,17 @@ def get_llm(
         )
     elif source == "HuggingFace":
         try:
-            from langchain_huggingface import ChatHuggingFace, HuggingFaceEndpoint 
+            from langchain_huggingface import ChatHuggingFace, HuggingFaceEndpoint
         except ImportError:
             raise ImportError(  # noqa: B904
                 "langchain-huggingface package is required for HuggingFace models. Install with: pip install langchain-huggingface"
             )
         return ChatHuggingFace(
-            llm = HuggingFaceEndpoint(
+            llm=HuggingFaceEndpoint(
                 repo_id=model,
                 temperature=temperature,
                 stop_sequences=stop_sequences,
-                huggingfacehub_api_token=os.getenv("HUGGINGFACE_API_KEY")
+                huggingfacehub_api_token=os.getenv("HUGGINGFACE_API_KEY"),
             )
         )
     elif source == "Custom":