aiagents4pharma 1.43.0__py3-none-any.whl → 1.45.0__py3-none-any.whl

aiagents4pharma/talk2scholars/docker-compose/cpu/docker-compose.yml

@@ -0,0 +1,90 @@
+version: "1.0.0"
+
+services:
+  # talk2scholars
+  talk2scholars:
+    container_name: talk2scholars
+    image: vpatientengine/talk2scholars:latest
+    platform: linux/amd64
+    ports:
+      - "8501:8501"
+    environment:
+      - MILVUS_HOST=milvus-standalone
+      - MILVUS_PORT=19530
+    env_file:
+      - .env
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:8501/health"]
+      interval: 30s
+      timeout: 10s
+      retries: 3
+      start_period: 30s
+    depends_on:
+      milvus-standalone:
+        condition: service_healthy
+
+  # Milvus Dependencies
+  etcd:
+    container_name: milvus-etcd
+    image: quay.io/coreos/etcd:v3.5.18
+    environment:
+      - ETCD_AUTO_COMPACTION_MODE=revision
+      - ETCD_AUTO_COMPACTION_RETENTION=1000
+      - ETCD_QUOTA_BACKEND_BYTES=4294967296
+      - ETCD_SNAPSHOT_COUNT=50000
+    volumes:
+      - ${DOCKER_VOLUME_DIRECTORY:-.}/volumes/etcd:/etcd
+    command: etcd -advertise-client-urls=http://etcd:2379 -listen-client-urls http://0.0.0.0:2379 --data-dir /etcd
+    healthcheck:
+      test: ["CMD", "etcdctl", "endpoint", "health"]
+      interval: 30s
+      timeout: 20s
+      retries: 3
+
+  minio:
+    container_name: milvus-minio
+    image: minio/minio:RELEASE.2024-05-28T17-19-04Z
+    environment:
+      MINIO_ACCESS_KEY: minioadmin
+      MINIO_SECRET_KEY: minioadmin
+    ports:
+      - "9001:9001"
+      - "9000:9000"
+    volumes:
+      - ${DOCKER_VOLUME_DIRECTORY:-.}/volumes/minio:/minio_data
+    command: minio server /minio_data --console-address ":9001"
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:9000/minio/health/live"]
+      interval: 30s
+      timeout: 20s
+      retries: 3
+
+  # Milvus Vector Database (CPU-only)
+  milvus-standalone:
+    container_name: milvus-standalone
+    image: milvusdb/milvus:v2.5.14
+    command: ["milvus", "run", "standalone"]
+    security_opt:
+      - seccomp:unconfined
+    environment:
+      MINIO_REGION: us-east-1
+      ETCD_ENDPOINTS: etcd:2379
+      MINIO_ADDRESS: minio:9000
+    volumes:
+      - ${DOCKER_VOLUME_DIRECTORY:-.}/volumes/milvus:/var/lib/milvus
+    ports:
+      - "19530:19530"
+      - "9091:9091"
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:9091/healthz"]
+      interval: 30s
+      start_period: 90s
+      timeout: 20s
+      retries: 3
+    depends_on:
+      - "etcd"
+      - "minio"
+
+networks:
+  milvus:
+    name: milvus

aiagents4pharma/talk2scholars/docker-compose/gpu/.env.example

@@ -0,0 +1,21 @@
+# .env.example (DO NOT put actual API keys here, read the README.md)
+
+# OPENAI API KEY
+OPENAI_API_KEY=your_openai_api_key_here
+
+# LangSmith API KEY
+LANGCHAIN_TRACING_V2=true
+LANGCHAIN_API_KEY=your_langchain_api_key_heres
+
+# NVIDIA API KEY
+NVIDIA_API_KEY=your_nvidia_api_key_here
+
+# ZOTERO API KEY
+ZOTERO_API_KEY=your_zotero_api_key_here
+ZOTERO_USER_ID=your_zotero_user_id_here
+
+# Set environment variables for data loader
+MILVUS_HOST=milvus-standalone
+MILVUS_PORT=19530
+MILVUS_DB_NAME=pdf_rag_db
+MILVUS_COLLECTION_NAME=pdf_rag_documents

aiagents4pharma/talk2scholars/docker-compose/gpu/docker-compose.yml

@@ -0,0 +1,105 @@
+version: "1.0.0"
+
+services:
+  # talk2scholars
+  talk2scholars:
+    container_name: talk2scholars
+    image: vpatientengine/talk2scholars:latest
+    platform: linux/amd64
+    ports:
+      - "8501:8501"
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              capabilities: ["gpu"]
+              device_ids: ["0"]
+    environment:
+      - MILVUS_HOST=milvus-standalone
+      - MILVUS_PORT=19530
+    env_file:
+      - .env
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:8501/health"]
+      interval: 30s
+      timeout: 10s
+      retries: 3
+      start_period: 30s
+    depends_on:
+      milvus-standalone:
+        condition: service_healthy
+
+  # Milvus Dependencies
+  etcd:
+    container_name: milvus-etcd
+    image: quay.io/coreos/etcd:v3.5.18
+    environment:
+      - ETCD_AUTO_COMPACTION_MODE=revision
+      - ETCD_AUTO_COMPACTION_RETENTION=1000
+      - ETCD_QUOTA_BACKEND_BYTES=4294967296
+      - ETCD_SNAPSHOT_COUNT=50000
+    volumes:
+      - ${DOCKER_VOLUME_DIRECTORY:-.}/volumes/etcd:/etcd
+    command: etcd -advertise-client-urls=http://etcd:2379 -listen-client-urls http://0.0.0.0:2379 --data-dir /etcd
+    healthcheck:
+      test: ["CMD", "etcdctl", "endpoint", "health"]
+      interval: 30s
+      timeout: 20s
+      retries: 3
+
+  minio:
+    container_name: milvus-minio
+    image: minio/minio:RELEASE.2023-03-20T20-16-18Z
+    environment:
+      MINIO_ACCESS_KEY: minioadmin
+      MINIO_SECRET_KEY: minioadmin
+    ports:
+      - "9001:9001"
+      - "9000:9000"
+    volumes:
+      - ${DOCKER_VOLUME_DIRECTORY:-.}/volumes/minio:/minio_data
+    command: minio server /minio_data --console-address ":9001"
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:9000/minio/health/live"]
+      interval: 30s
+      timeout: 20s
+      retries: 3
+
+  # Milvus Vector Database (GPU-enabled)
+  milvus-standalone:
+    container_name: milvus-standalone
+    image: milvusdb/milvus:v2.6.0-rc1-gpu
+    command: ["milvus", "run", "standalone"]
+    security_opt:
+      - seccomp:unconfined
+    environment:
+      MINIO_REGION: us-east-1
+      ETCD_ENDPOINTS: etcd:2379
+      MINIO_ADDRESS: minio:9000
+      MQ_TYPE: woodpecker
+    volumes:
+      - ${DOCKER_VOLUME_DIRECTORY:-.}/volumes/milvus:/var/lib/milvus
+    ports:
+      - "19530:19530"
+      - "9091:9091"
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              capabilities: ["gpu"]
+              device_ids: ["0"]
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:9091/healthz"]
+      interval: 30s
+      start_period: 90s
+      timeout: 20s
+      retries: 3
+    depends_on:
+      - "etcd"
+      - "minio"
+
+networks:
+  milvus:
+    name: milvus

aiagents4pharma/talk2scholars/install.md

@@ -0,0 +1,122 @@
+# Talk2Scholars
+
+## Installation
+
+- [nvidia-cuda-toolkit](https://developer.nvidia.com/cuda-toolkit)
+- [nvidia-container-toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/1.17.8/install-guide.html) (required for GPU support with Docker; enables containers to access NVIDIA GPUs for accelerated computing). After installing `nvidia-container-toolkit`, please restart Docker to ensure GPU support is enabled.
+
+### Docker (stable-release)
+
+**Prerequisites**
+
+- [Milvus](https://milvus.io) (for a vector database)
+
+---
+
+#### 1. Download files
+
+Choose the appropriate version of the `docker-compose.yml` file based on your system:
+
+**For GPU:**
+
+```sh
+wget https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2scholars/docker-compose/gpu/docker-compose.yml \
+     https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2scholars/docker-compose/gpu/.env.example
+```
+
+**For CPU:**
+
+```sh
+wget https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2scholars/docker-compose/cpu/docker-compose.yml \
+     https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2scholars/docker-compose/cpu/.env.example
+```
+
+#### 2. Setup environment variables
+
+```sh
+cp .env.example .env
+```
+
+Edit `.env` with your API keys:
+
+```env
+# .env.example (DO NOT put actual API keys here, read the README.md)
+
+# OPENAI API KEY
+OPENAI_API_KEY=your_openai_api_key_here
+
+# LangSmith API KEY
+LANGCHAIN_TRACING_V2=true
+LANGCHAIN_API_KEY=your_langchain_api_key_heres
+
+# NVIDIA API KEY
+NVIDIA_API_KEY=your_nvidia_api_key_here
+
+# ZOTERO API KEY
+ZOTERO_API_KEY=your_zotero_api_key_here
+ZOTERO_USER_ID=your_zotero_user_id_here
+
+# Set environment variables for data loader
+MILVUS_HOST=milvus-standalone
+MILVUS_PORT=19530
+MILVUS_DB_NAME=pdf_rag_db
+MILVUS_COLLECTION_NAME=pdf_rag_documents
+```
+
+---
+
+#### 3. Start the agent
+
+```sh
+docker compose up -d
+```
+
+---
+
+### Access the Web UI
+
+Once started, open:
+
+```
+http://localhost:8501
+```
+
+> In the background, the BioBridge multimodal embeddings will be inserted into the Milvus database, and the `talk2scholars` service will start. Once the data is fully inserted, the application will be in a healthy state and accessible at the above address.
+>
+> You can monitor the process using:
+>
+> ```sh
+> docker logs -f talk2scholars
+> ```
+
+---
+
+## Get Key
+
+- `NVIDIA_API_KEY` – required (obtain a free key at [https://build.nvidia.com/explore/discover](https://build.nvidia.com/explore/discover))
+- `ZOTERO_API_KEY` – required (generate at [https://www.zotero.org/user/login#applications](https://www.zotero.org/user/login#applications))
+
+  **LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
+
+_Please note that this will create a new tracing project in your Langsmith
+account with the name `T2X-xxxx`, where `X` can be `KG` (KnowledgeGraphs).
+If you skip the previous step, it will default to the name `default`.
+`xxxx` will be the 4-digit ID created for the session._
+
+---
+
+## Notes for Windows Users
+
+If you are using Windows, it is recommended to install [**Git Bash**](https://git-scm.com/downloads) for a smoother experience when running the bash commands in this guide.
+
+- For applications that use **Docker Compose**, Git Bash is **required**.
+- For applications that use **docker run** manually, Git Bash is **optional**, but recommended for consistency.
+
+You can download Git Bash here: [Git for Windows](https://git-scm.com/downloads).
+
+When using Docker on Windows, make sure you **run Docker with administrative privileges** if you face permission issues.
+
+To resolve permission issues, you can:
+
+- Review the official Docker documentation on [Windows permission requirements](https://docs.docker.com/desktop/setup/install/windows-permission-requirements/).
+- Alternatively, follow the community discussion and solutions on [Docker Community Forums](https://forums.docker.com/t/error-when-trying-to-run-windows-containers-docker-client-must-be-run-with-elevated-privileges/136619).

aiagents4pharma/talk2scholars/state/state_talk2scholars.py

@@ -8,7 +8,7 @@ across agent interactions.
 
 import logging
 from collections.abc import Mapping
-from typing import Annotated, Any, Dict
+from typing import Annotated, Any
 
 from langchain_core.embeddings import Embeddings
 from langchain_core.language_models import BaseChatModel
@@ -19,7 +19,7 @@ logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
 
-def merge_dict(existing: Dict[str, Any], new: Dict[str, Any]) -> Dict[str, Any]:
+def merge_dict(existing: dict[str, Any], new: dict[str, Any]) -> dict[str, Any]:
     """
     Merges the existing dictionary with a new dictionary.
 
@@ -36,7 +36,7 @@ def merge_dict(existing: Dict[str, Any], new: Dict[str, Any]) -> Dict[str, Any]:
     return merged
 
 
-def replace_dict(existing: Dict[str, Any], new: Any) -> Any:
+def replace_dict(existing: dict[str, Any], new: Any) -> Any:
     """
     Replaces the existing dictionary with a new dictionary.
 
@@ -87,12 +87,12 @@ class Talk2Scholars(AgentState):
     # Agent state fields
     # Key controlling UI display: always replace to reference latest output
     # Stores the most recently displayed papers metadata
-    last_displayed_papers: Annotated[Dict[str, Any], replace_dict]
+    last_displayed_papers: Annotated[dict[str, Any], replace_dict]
     # Accumulative keys: merge new entries into existing state
-    papers: Annotated[Dict[str, Any], merge_dict]
-    multi_papers: Annotated[Dict[str, Any], merge_dict]
-    article_data: Annotated[Dict[str, Any], merge_dict]
+    papers: Annotated[dict[str, Any], merge_dict]
+    multi_papers: Annotated[dict[str, Any], merge_dict]
+    article_data: Annotated[dict[str, Any], merge_dict]
     # Approval status: always replace to reflect latest operation
-    zotero_write_approval_status: Annotated[Dict[str, Any], replace_dict]
+    zotero_write_approval_status: Annotated[dict[str, Any], replace_dict]
     llm_model: BaseChatModel
     text_embedding_model: Embeddings

aiagents4pharma/talk2scholars/tests/{test_main_agent.py → test_agents_main_agent.py}

@@ -4,11 +4,15 @@ Tests the supervisor agent's routing logic and state management.
 """
 
 from types import SimpleNamespace
-import pytest
+
 import hydra
+import pytest
 from langchain_core.language_models.chat_models import BaseChatModel
+from langchain_core.messages import AIMessage, HumanMessage
+from langchain_core.outputs import ChatGeneration, ChatResult
 from langchain_openai import ChatOpenAI
 from pydantic import Field
+
 from aiagents4pharma.talk2scholars.agents.main_agent import get_app
 
 # --- Dummy LLM Implementation ---
@@ -19,16 +23,23 @@ class DummyLLM(BaseChatModel):
 
     model_name: str = Field(...)
 
-    def _generate(self, prompt, stop=None):
-        """Generate a response given a prompt."""
-        DummyLLM.called_prompt = prompt
-        return "dummy output"
+    def _generate(self, messages, stop=None, run_manager=None, **kwargs):
+        """generate a dummy response based on the input messages."""
+        DummyLLM.called_prompt = messages[0].content
+        message = AIMessage(content="dummy output")
+        generation = ChatGeneration(message=message)
+        return ChatResult(generations=[generation])
 
     @property
     def _llm_type(self):
         """Return the type of the language model."""
         return "dummy"
 
+    # NEW: public shim to avoid protected access in tests
+    def public_llm_type(self) -> str:
+        """public method to access the LLM type."""
+        return self._llm_type
+
 
 # --- Dummy Workflow and Sub-agent Functions ---
 
@@ -105,17 +116,12 @@ class DummyHydraContext:
 def dict_to_namespace(d):
     """Convert a dictionary to a SimpleNamespace object."""
     return SimpleNamespace(
-        **{
-            key: dict_to_namespace(val) if isinstance(val, dict) else val
-            for key, val in d.items()
-        }
+        **{key: dict_to_namespace(val) if isinstance(val, dict) else val for key, val in d.items()}
     )
 
 
 dummy_config = {
-    "agents": {
-        "talk2scholars": {"main_agent": {"system_prompt": "Dummy system prompt"}}
-    }
+    "agents": {"talk2scholars": {"main_agent": {"system_prompt": "Dummy system prompt"}}}
 }
 
 
@@ -141,9 +147,7 @@ class DummyHydraCompose:
 @pytest.fixture(autouse=True)
 def patch_hydra(monkeypatch):
     """Patch the hydra.initialize and hydra.compose functions to return dummy objects."""
-    monkeypatch.setattr(
-        hydra, "initialize", lambda version_base, config_path: DummyHydraContext()
-    )
+    monkeypatch.setattr(hydra, "initialize", lambda version_base, config_path: DummyHydraContext())
     monkeypatch.setattr(
         hydra, "compose", lambda config_name, overrides: DummyHydraCompose(dummy_config)
     )
@@ -153,9 +157,7 @@ def dummy_paper_download_agent(uniq_id, llm_model):
     """Return a DummyWorkflow for the paper download agent."""
     dummy_paper_download_agent.called_uniq_id = uniq_id
     dummy_paper_download_agent.called_llm_model = llm_model
-    return DummyWorkflow(
-        supervisor_args={"agent": "paper_download", "uniq_id": uniq_id}
-    )
+    return DummyWorkflow(supervisor_args={"agent": "paper_download", "uniq_id": uniq_id})
 
 
 @pytest.fixture(autouse=True)
@@ -186,16 +188,30 @@ def patch_sub_agents_and_supervisor(monkeypatch):
 
 
 def test_dummy_llm_generate():
-    """Test the dummy LLM's generate function."""
+    """Test the dummy LLM's generate function through public interface."""
     dummy = DummyLLM(model_name="test-model")
-    output = getattr(dummy, "_generate")("any prompt")
-    assert output == "dummy output"
+    # Test that the dummy LLM can be used (testing the class works)
+    assert dummy.model_name == "test-model"
+    # Test through public interface that internally calls _generate (covers lines 26-27)
+    # Use invoke which internally calls _generate
+    messages = [HumanMessage(content="test prompt")]
+    result = dummy.invoke(messages)
+    # Verify the internal state was set
+    assert hasattr(DummyLLM, "called_prompt")
+    assert result is not None
+    assert DummyLLM.called_prompt == "test prompt"
 
 
 def test_dummy_llm_llm_type():
-    """Test the dummy LLM's _llm_type property."""
+    """Test the dummy LLM's type identification."""
     dummy = DummyLLM(model_name="test-model")
-    assert getattr(dummy, "_llm_type") == "dummy"
+
+    # Use public shim instead of protected attribute access
+    llm_type = dummy.public_llm_type()
+    assert llm_type == "dummy"
+
+    # Also test the public string representation
+    assert "DummyLLM" in str(dummy.__class__.__name__)
 
 
 def test_get_app_with_gpt4o_mini():
@@ -225,12 +241,14 @@ def test_get_app_with_other_model():
     assert supervisor_args.get("prompt") == "Dummy system prompt"
     assert getattr(app, "name", "") == "Talk2Scholars_MainAgent"
 
+
 def test_dummy_workflow_get_supervisor_args():
     """Test that DummyWorkflow.get_supervisor_args returns the stored args."""
     dummy_args = {"agent": "test", "uniq_id": "id123"}
     wf = DummyWorkflow(supervisor_args=dummy_args)
     assert wf.get_supervisor_args() is dummy_args
 
+
 def test_dummy_hydra_compose_get_config():
     """Test that DummyHydraCompose.get_config returns the raw config."""
     config_dict = {"agents": {"test": {"key": "value"}}}

aiagents4pharma/talk2scholars/tests/{test_paper_download_agent.py → test_agents_paper_agents_download_agent.py}

@@ -1,9 +1,11 @@
 """Unit tests for the paper download agent in Talk2Scholars."""
 
 from unittest import mock
+
 import pytest
-from langchain_core.messages import HumanMessage, AIMessage
 from langchain_core.language_models.chat_models import BaseChatModel
+from langchain_core.messages import AIMessage, HumanMessage
+
 from ..agents.paper_download_agent import get_app
 from ..state.state_talk2scholars import Talk2Scholars
 
@@ -13,9 +15,7 @@ def mock_hydra_fixture():
     """Mocks Hydra configuration for tests."""
     with mock.patch("hydra.initialize"), mock.patch("hydra.compose") as mock_compose:
         cfg_mock = mock.MagicMock()
-        cfg_mock.agents.talk2scholars.paper_download_agent.paper_download_agent = (
-            "Test prompt"
-        )
+        cfg_mock.agents.talk2scholars.paper_download_agent.paper_download_agent = "Test prompt"
         mock_compose.return_value = cfg_mock
         yield mock_compose
 
@@ -26,9 +26,7 @@ def mock_tools_fixture():
     with mock.patch(
         "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.download_papers"
     ) as mock_download_papers:
-        mock_download_papers.return_value = {
-            "article_data": {"dummy_key": "dummy_value"}
-        }
+        mock_download_papers.return_value = {"article_data": {"dummy_key": "dummy_value"}}
         yield [mock_download_papers]
 
 
@@ -52,9 +50,7 @@ def test_paper_download_agent_invocation():
     """Verifies agent processes queries and updates state correctly."""
     _ = mock_tools_fixture  # Prevents unused-argument warning
     thread_id = "test_thread_paper_dl"
-    mock_state = Talk2Scholars(
-        messages=[HumanMessage(content="Download paper 1234.5678")]
-    )
+    mock_state = Talk2Scholars(messages=[HumanMessage(content="Download paper 1234.5678")])
     llm_mock = mock.Mock(spec=BaseChatModel)
 
     with mock.patch(
@@ -108,9 +104,7 @@ def test_paper_download_agent_tools_assignment(
         # Verify ToolNode was called with download_papers function
         assert mock_toolnode.called
         # Check that ToolNode was called with a list containing the download_papers tool
-        call_args = mock_toolnode.call_args[0][
-            0
-        ]  # Get first positional argument (the tools list)
+        call_args = mock_toolnode.call_args[0][0]  # Get first positional argument (the tools list)
         assert len(call_args) == 1
         # The tool should be a StructuredTool with name 'download_papers'
         tool = call_args[0]
@@ -140,6 +134,6 @@ def test_paper_download_agent_model_failure():
     ):
         with pytest.raises(Exception) as exc_info:
             get_app(thread_id, llm_mock)
-        assert "Mock model failure" in str(
-            exc_info.value
-        ), "Model initialization failure should raise an exception."
+        assert "Mock model failure" in str(exc_info.value), (
+            "Model initialization failure should raise an exception."
+        )

aiagents4pharma/talk2scholars/tests/{test_pdf_agent.py → test_agents_pdf_agent.py}

@@ -3,8 +3,10 @@ Unit Tests for the PDF agent.
 """
 
 from unittest import mock
+
 import pytest
-from langchain_core.messages import HumanMessage, AIMessage
+from langchain_core.messages import AIMessage, HumanMessage
+
 from ..agents.pdf_agent import get_app
 from ..state.state_talk2scholars import Talk2Scholars
 
@@ -29,9 +31,7 @@ def mock_tools_fixture():
             "aiagents4pharma.talk2scholars.agents.pdf_agent.question_and_answer"
         ) as mock_question_and_answer,
     ):
-        mock_question_and_answer.return_value = {
-            "result": "Mock Question and Answer Result"
-        }
+        mock_question_and_answer.return_value = {"result": "Mock Question and Answer Result"}
         yield [mock_question_and_answer]
 
 
@@ -58,9 +58,7 @@ def test_pdf_agent_invocation(mock_llm):
     """Test that the PDF agent processes user input and returns a valid response."""
     thread_id = "test_thread"
     # Create a sample state with a human message.
-    mock_state = Talk2Scholars(
-        messages=[HumanMessage(content="Extract key data from PDF")]
-    )
+    mock_state = Talk2Scholars(messages=[HumanMessage(content="Extract key data from PDF")])
     with mock.patch(
         "aiagents4pharma.talk2scholars.agents.pdf_agent.create_react_agent"
     ) as mock_create:
@@ -95,9 +93,7 @@ def test_pdf_agent_tools_assignment(request, mock_llm):
         mock.patch(
             "aiagents4pharma.talk2scholars.agents.pdf_agent.create_react_agent"
         ) as mock_create,
-        mock.patch(
-            "aiagents4pharma.talk2scholars.agents.pdf_agent.ToolNode"
-        ) as mock_toolnode,
+        mock.patch("aiagents4pharma.talk2scholars.agents.pdf_agent.ToolNode") as mock_toolnode,
     ):
         mock_agent = mock.Mock()
         mock_create.return_value = mock_agent