aiagents4pharma 1.16.0__py3-none-any.whl → 1.17.1__py3-none-any.whl

aiagents4pharma/talk2scholars/tests/test_langgraph.py

@@ -5,12 +5,14 @@ Tests are deterministic and independent of each other.
 """
 
 from unittest.mock import Mock, patch
-
 import pytest
 from langchain_core.messages import AIMessage, HumanMessage
+import hydra
+from hydra.core.global_hydra import GlobalHydra
+from omegaconf import DictConfig, OmegaConf
 
 from ..agents.main_agent import get_app, make_supervisor_node
-from ..state.state_talk2scholars import replace_dict
+from ..state.state_talk2scholars import replace_dict, Talk2Scholars
 from ..tools.s2.display_results import display_results
 from ..tools.s2.multi_paper_rec import get_multi_paper_recommendations
 from ..tools.s2.search import search_tool
@@ -18,6 +20,42 @@ from ..tools.s2.single_paper_rec import get_single_paper_recommendations
 
 # pylint: disable=redefined-outer-name
 
+
+@pytest.fixture(autouse=True)
+def hydra_setup():
+    """Setup and cleanup Hydra for tests."""
+    GlobalHydra.instance().clear()
+    with hydra.initialize(version_base=None, config_path="../configs"):
+        yield
+
+
+@pytest.fixture
+def mock_cfg() -> DictConfig:
+    """Create a mock configuration for testing."""
+    config = {
+        "agents": {
+            "talk2scholars": {
+                "main_agent": {
+                    "state_modifier": "Test prompt for main agent",
+                    "temperature": 0,
+                },
+                "s2_agent": {
+                    "temperature": 0,
+                    "s2_agent": "Test prompt for s2 agent",
+                },
+            }
+        },
+        "tools": {
+            "search": {
+                "api_endpoint": "https://api.semanticscholar.org/graph/v1/paper/search",
+                "default_limit": 2,
+                "api_fields": ["paperId", "title", "abstract", "year", "authors"],
+            }
+        },
+    }
+    return OmegaConf.create(config)
+
+
 # Fixed test data for deterministic results
 MOCK_SEARCH_RESPONSE = {
     "data": [
@@ -45,27 +83,33 @@ MOCK_STATE_PAPER = {
 
 
 @pytest.fixture
-def initial_state():
+def initial_state() -> Talk2Scholars:
     """Create a base state for tests"""
-    return {
-        "messages": [],
-        "papers": {},
-        "is_last_step": False,
-        "current_agent": None,
-        "llm_model": "gpt-4o-mini",
-    }
+    return Talk2Scholars(
+        messages=[],
+        papers={},
+        is_last_step=False,
+        current_agent=None,
+        llm_model="gpt-4o-mini",
+        next="",
+    )
 
 
 class TestMainAgent:
     """Unit tests for main agent functionality"""
 
-    def test_supervisor_routes_search_to_s2(self, initial_state):
+    def test_supervisor_routes_search_to_s2(
+        self, initial_state: Talk2Scholars, mock_cfg
+    ):
         """Verifies that search-related queries are routed to S2 agent"""
         llm_mock = Mock()
         llm_mock.invoke.return_value = AIMessage(content="Search initiated")
 
-        supervisor = make_supervisor_node(llm_mock)
-        state = initial_state.copy()
+        # Extract the main_agent config
+        supervisor = make_supervisor_node(
+            llm_mock, mock_cfg.agents.talk2scholars.main_agent
+        )
+        state = initial_state
         state["messages"] = [HumanMessage(content="search for papers")]
 
         result = supervisor(state)
@@ -73,13 +117,18 @@ class TestMainAgent:
         assert not result.update["is_last_step"]
         assert result.update["current_agent"] == "s2_agent"
 
-    def test_supervisor_routes_general_to_end(self, initial_state):
+    def test_supervisor_routes_general_to_end(
+        self, initial_state: Talk2Scholars, mock_cfg
+    ):
         """Verifies that non-search queries end the conversation"""
         llm_mock = Mock()
         llm_mock.invoke.return_value = AIMessage(content="General response")
 
-        supervisor = make_supervisor_node(llm_mock)
-        state = initial_state.copy()
+        # Extract the main_agent config
+        supervisor = make_supervisor_node(
+            llm_mock, mock_cfg.agents.talk2scholars.main_agent
+        )
+        state = initial_state
         state["messages"] = [HumanMessage(content="What is ML?")]
 
         result = supervisor(state)
@@ -90,9 +139,9 @@ class TestMainAgent:
 class TestS2Tools:
     """Unit tests for individual S2 tools"""
 
-    def test_display_results_shows_papers(self, initial_state):
+    def test_display_results_shows_papers(self, initial_state: Talk2Scholars):
         """Verifies display_results tool correctly returns papers from state"""
-        state = initial_state.copy()
+        state = initial_state
         state["papers"] = MOCK_STATE_PAPER
         result = display_results.invoke(input={"state": state})
         assert result == MOCK_STATE_PAPER
@@ -199,40 +248,6 @@ class TestS2Tools:
         assert "papers" in result.update
         assert len(result.update["messages"]) == 1
 
-    @patch("requests.get")
-    def test_single_paper_rec_empty_response(self, mock_get):
-        """Tests single paper recommendations with empty response"""
-        mock_get.return_value.json.return_value = {"recommendedPapers": []}
-        mock_get.return_value.status_code = 200
-
-        result = get_single_paper_recommendations.invoke(
-            input={
-                "paper_id": "123",
-                "limit": 1,
-                "tool_call_id": "test123",
-                "id": "test123",
-            }
-        )
-        assert "papers" in result.update
-        assert len(result.update["papers"]) == 0
-
-    @patch("requests.post")
-    def test_multi_paper_rec_empty_response(self, mock_post):
-        """Tests multi-paper recommendations with empty response"""
-        mock_post.return_value.json.return_value = {"recommendedPapers": []}
-        mock_post.return_value.status_code = 200
-
-        result = get_multi_paper_recommendations.invoke(
-            input={
-                "paper_ids": ["123", "456"],
-                "limit": 1,
-                "tool_call_id": "test123",
-                "id": "test123",
-            }
-        )
-        assert "papers" in result.update
-        assert len(result.update["papers"]) == 0
-
 
 def test_state_replace_dict():
     """Verifies state dictionary replacement works correctly"""
@@ -244,11 +259,13 @@ def test_state_replace_dict():
 
 
 @pytest.mark.integration
-def test_end_to_end_search_workflow(initial_state):
+def test_end_to_end_search_workflow(initial_state: Talk2Scholars, mock_cfg):
     """Integration test: Complete search workflow"""
     with (
         patch("requests.get") as mock_get,
         patch("langchain_openai.ChatOpenAI") as mock_llm,
+        patch("hydra.compose", return_value=mock_cfg),
+        patch("hydra.initialize"),
     ):
         mock_get.return_value.json.return_value = MOCK_SEARCH_RESPONSE
         mock_get.return_value.status_code = 200
@@ -258,7 +275,7 @@ def test_end_to_end_search_workflow(initial_state):
         mock_llm.return_value = llm_instance
 
         app = get_app("test_integration")
-        test_state = initial_state.copy()
+        test_state = initial_state
         test_state["messages"] = [HumanMessage(content="search for ML papers")]
 
         config = {

aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py

@@ -8,7 +8,7 @@ multi_paper_rec: Tool for getting recommendations
 import json
 import logging
 from typing import Annotated, Any, Dict, List, Optional
-
+import hydra
 import pandas as pd
 import requests
 from langchain_core.messages import ToolMessage
@@ -40,6 +40,14 @@ class MultiPaperRecInput(BaseModel):
     model_config = {"arbitrary_types_allowed": True}
 
 
+# Load hydra configuration
+with hydra.initialize(version_base=None, config_path="../../configs"):
+    cfg = hydra.compose(
+        config_name="config", overrides=["tools/multi_paper_recommendation=default"]
+    )
+    cfg = cfg.tools.multi_paper_recommendation
+
+
 @tool(args_schema=MultiPaperRecInput)
 def get_multi_paper_recommendations(
     paper_ids: List[str],
@@ -62,12 +70,12 @@ def get_multi_paper_recommendations(
     """
     logging.info("Starting multi-paper recommendations search.")
 
-    endpoint = "https://api.semanticscholar.org/recommendations/v1/papers"
-    headers = {"Content-Type": "application/json"}
+    endpoint = cfg.api_endpoint
+    headers = cfg.headers
     payload = {"positivePaperIds": paper_ids, "negativePaperIds": []}
     params = {
         "limit": min(limit, 500),
-        "fields": "paperId,title,abstract,year,authors,citationCount,url",
+        "fields": ",".join(cfg.api_fields),
     }
 
     # Add year parameter if provided
@@ -80,7 +88,7 @@ def get_multi_paper_recommendations(
         headers=headers,
         params=params,
         data=json.dumps(payload),
-        timeout=10,
+        timeout=cfg.request_timeout,
     )
     logging.info(
         "API Response Status for multi-paper recommendations: %s", response.status_code

aiagents4pharma/talk2scholars/tools/s2/search.py

@@ -6,7 +6,7 @@ This tool is used to search for academic papers on Semantic Scholar.
 
 import logging
 from typing import Annotated, Any, Dict, Optional
-
+import hydra
 import pandas as pd
 import requests
 from langchain_core.messages import ToolMessage
@@ -34,6 +34,12 @@ class SearchInput(BaseModel):
     tool_call_id: Annotated[str, InjectedToolCallId]
 
 
+# Load hydra configuration
+with hydra.initialize(version_base=None, config_path="../../configs"):
+    cfg = hydra.compose(config_name="config", overrides=["tools/search=default"])
+    cfg = cfg.tools.search
+
+
 @tool(args_schema=SearchInput)
 def search_tool(
     query: str,
@@ -55,13 +61,13 @@ def search_tool(
         Dict[str, Any]: The search results and related information.
     """
     print("Starting paper search...")
-    endpoint = "https://api.semanticscholar.org/graph/v1/paper/search"
+    endpoint = cfg.api_endpoint
     params = {
         "query": query,
         "limit": min(limit, 100),
         # "fields": "paperId,title,abstract,year,authors,
         # citationCount,url,publicationTypes,openAccessPdf",
-        "fields": "paperId,title,abstract,year,authors,citationCount,url",
+        "fields": ",".join(cfg.api_fields),
     }
 
     # Add year parameter if provided

aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py

@@ -6,7 +6,7 @@ This tool is used to return recommendations for a single paper.
 
 import logging
 from typing import Annotated, Any, Dict, Optional
-
+import hydra
 import pandas as pd
 import requests
 from langchain_core.messages import ToolMessage
@@ -41,6 +41,14 @@ class SinglePaperRecInput(BaseModel):
     model_config = {"arbitrary_types_allowed": True}
 
 
+# Load hydra configuration
+with hydra.initialize(version_base=None, config_path="../../configs"):
+    cfg = hydra.compose(
+        config_name="config", overrides=["tools/single_paper_recommendation=default"]
+    )
+    cfg = cfg.tools.single_paper_recommendation
+
+
 @tool(args_schema=SinglePaperRecInput)
 def get_single_paper_recommendations(
     paper_id: str,
@@ -63,20 +71,18 @@ def get_single_paper_recommendations(
     """
     logger.info("Starting single paper recommendations search.")
 
-    endpoint = (
-        f"https://api.semanticscholar.org/recommendations/v1/papers/forpaper/{paper_id}"
-    )
+    endpoint = f"{cfg.api_endpoint}/{paper_id}"
     params = {
         "limit": min(limit, 500),  # Max 500 per API docs
-        "fields": "paperId,title,abstract,year,authors,citationCount,url",
-        "from": "all-cs",  # Using all-cs pool as specified in docs
+        "fields": ",".join(cfg.api_fields),
+        "from": cfg.recommendation_params.from_pool,
     }
 
     # Add year parameter if provided
     if year:
         params["year"] = year
 
-    response = requests.get(endpoint, params=params, timeout=10)
+    response = requests.get(endpoint, params=params, timeout=cfg.request_timeout)
     data = response.json()
     papers = data.get("data", [])
     response = requests.get(endpoint, params=params, timeout=10)

aiagents4pharma-1.17.1.dist-info/METADATA

@@ -0,0 +1,150 @@
+Metadata-Version: 2.2
+Name: aiagents4pharma
+Version: 1.17.1
+Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: copasi_basico==0.78
+Requires-Dist: coverage==7.6.4
+Requires-Dist: einops==0.8.0
+Requires-Dist: gdown==5.2.0
+Requires-Dist: huggingface_hub==0.26.5
+Requires-Dist: hydra-core==1.3.2
+Requires-Dist: joblib==1.4.2
+Requires-Dist: langchain==0.3.7
+Requires-Dist: langchain-community==0.3.5
+Requires-Dist: langchain-core==0.3.31
+Requires-Dist: langchain-experimental==0.3.3
+Requires-Dist: langchain-openai==0.2.5
+Requires-Dist: langchain_ollama==0.2.2
+Requires-Dist: langgraph==0.2.66
+Requires-Dist: matplotlib==3.9.2
+Requires-Dist: openai==1.59.4
+Requires-Dist: ollama==0.4.6
+Requires-Dist: pandas==2.2.3
+Requires-Dist: plotly==5.24.1
+Requires-Dist: pydantic==2.9.2
+Requires-Dist: pylint==3.3.1
+Requires-Dist: pypdf==5.2.0
+Requires-Dist: pytest==8.3.3
+Requires-Dist: pytest-asyncio==0.25.2
+Requires-Dist: streamlit==1.39.0
+Requires-Dist: sentence_transformers==3.3.1
+Requires-Dist: tabulate==0.9.0
+Requires-Dist: torch==2.2.2
+Requires-Dist: torch_geometric==2.6.1
+Requires-Dist: tqdm==4.66.6
+Requires-Dist: transformers==4.48.0
+Requires-Dist: mkdocs==1.6.1
+Requires-Dist: mkdocs-jupyter==0.25.1
+Requires-Dist: mkdocs-material==9.5.47
+Requires-Dist: mkdocstrings-python==1.12.2
+Requires-Dist: mkdocs-include-markdown-plugin==7.1.2
+Requires-Dist: mkdocstrings==0.27.0
+Requires-Dist: streamlit-feedback
+
+[![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
+[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
+[![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
+[![TESTS Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
+![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+
+## Introduction
+
+Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
+
+Our toolkit currently consists of the following agents:
+
+- **Talk2BioModels** _(v1 released; v2 in progress)_: Engage directly with mathematical models in systems biology.
+- **Talk2KnowledgeGraphs** _(v1 in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Scholars** _(v1 in progress)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Cells** _(v1 in progress)_: Query and analyze sequencing data with ease.
+
+![AIAgents4Pharma](docs/assets/AIAgents4Pharma.png)
+
+## Getting Started
+
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+### Installation
+
+#### Option 1: PyPI
+
+```bash
+pip install aiagents4pharma
+```
+
+Check out the tutorials on each agent for detailed instrcutions.
+
+#### Option 2: git
+
+1. **Clone the repository:**
+   ```bash
+   git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+   cd AIAgents4Pharma
+   ```
+2. **Install dependencies:**
+   ```bash
+   pip install .
+   ```
+3. **Initialize OPENAI_API_KEY**
+   ```bash
+   export OPENAI_API_KEY=....
+   ```
+4. **[Optional] Initialize LANGSMITH_API_KEY**
+   ```bash
+   export LANGCHAIN_TRACING_V2=true
+   export LANGCHAIN_API_KEY=<your-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 `B` (Biomodels), `S` (Scholars),
+`KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will
+default to the name `default`. `xxxx` will be the 4-digit ID created for the
+session._
+
+5. **Launch the app:**
+   ```bash
+   streamlit run app/frontend/streamlit_app_<agent>.py
+   ```
+_Replace <agent> with the agent name you are interested to launch._
+
+For detailed instructions on each agent, please refer to their respective modules.
+
+---
+
+## Contributing
+
+We welcome contributions to AIAgents4Pharma! Here’s how you can help:
+
+1. **Fork the repository**
+2. **Create a new branch** for your feature (`git checkout -b feat/feature-name`)
+3. **Commit your changes** (`git commit -m 'feat: Add new feature'`)
+4. **Push to the branch** (`git push origin feat/feature-name`)
+5. **Open a pull request** and reach out to any one of us below via Discussions:
+
+   _Note: We welcome all contributions, not just programming-related ones. Feel free to open bug reports, suggest new features, or participate as a beta tester. Your support is greatly appreciated!_
+
+- **Talk2Biomodels/Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330) [@lilijap](https://github.com/lilijap) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info) [@gurdeep330](https://github.com/gurdeep330) [@dmccloskey](https://github.com/dmccloskey)
+
+### Current Needs
+
+- **Beta testers** for Talk2BioModels and Talk2Scholars.
+- **Developers** with experience in Python and Bioinformatics and/or knowledge graphs for contributions to AIAgents4Pharma.
+
+Feel free to reach out to us via Discussions.
+
+Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
+
+---
+
+## Feedback
+
+Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Isssues` or `Discussions` 😀

{aiagents4pharma-1.16.0.dist-info → aiagents4pharma-1.17.1.dist-info}/RECORD

@@ -1,22 +1,20 @@
-aiagents4pharma/__init__.py,sha256=nFCe1As_SuRkmhcdZVsU0aYjYccHxk1DbduLpy8XulY,174
-aiagents4pharma/configs/__init__.py,sha256=hNkSrXw1Ix1HhkGn_aaidr2coBYySfM0Hm_pMeRcX7k,76
-aiagents4pharma/configs/config.yaml,sha256=e0w2GOBVWcoPDtX-z4S6yKbv2rja5PfGRBhmTPVIXNU,161
-aiagents4pharma/configs/talk2biomodels/__init__.py,sha256=safyFKhkd5Wlirl9dMZIHWDLTpY2oLw9wjIM7ZtLIHk,88
-aiagents4pharma/configs/talk2biomodels/agents/__init__.py,sha256=_ZoG8snICK2bidWtc2KOGs738LWg9_r66V9mOMnEb-E,71
-aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
-aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/default.yaml,sha256=eLrJIezoPJ6_DvrSYsi3eALl03o0hJhntej3ESoeKKg,551
-aiagents4pharma/configs/talk2biomodels/tools/__init__.py,sha256=B08KWjj7bpizuTETGnnngrEVK4nzdWGREdoCCSw1Sm4,102
-aiagents4pharma/configs/talk2biomodels/tools/ask_question/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
-aiagents4pharma/configs/talk2biomodels/tools/ask_question/default.yaml,sha256=yy-Sq1u4dBlTFi_UeoWYoHkWRDWueJWVNK_rcUCC5bw,1747
-aiagents4pharma/configs/talk2biomodels/tools/get_annotation/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
-aiagents4pharma/configs/talk2biomodels/tools/get_annotation/default.yaml,sha256=8vUlzU5Y3BPggId5bVMo9B23VG4mp2ziTglb4LmLCsc,319
-aiagents4pharma/talk2biomodels/__init__.py,sha256=2ICwVh1u07SZv31Jd2DKHobauOxWNWY29_Gqq3kOnNQ,159
+aiagents4pharma/__init__.py,sha256=Ua9fqYW5gV1SZ0nOyOMd4T3wTlBui1-mrlJzFUQLFgY,161
+aiagents4pharma/talk2biomodels/__init__.py,sha256=1cq1HX2xoi_a0nDPuXYoSTrnL26OHQBW3zXNwwwjFO0,181
 aiagents4pharma/talk2biomodels/agents/__init__.py,sha256=sn5-fREjMdEvb-OUan3iOqrgYGjplNx3J8hYOaW0Po8,128
-aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=5h4n7dF13KuT5f9vzfK7EQTu_b0a0hB7ScLFlTKaNko,3449
+aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=CXlqDRqG_cxb1TUEL6960s2ActFiXblYPraagDDGQpo,3416
 aiagents4pharma/talk2biomodels/api/__init__.py,sha256=_GmDQqDLYpsUPUeE1nBNlT5AI9oTXIcqgOfNfvmonqA,123
 aiagents4pharma/talk2biomodels/api/kegg.py,sha256=QzYDAfJ16E7tbHGxP8ZNWRizMkMRS_HJuucueXEC1Gg,2943
 aiagents4pharma/talk2biomodels/api/ols.py,sha256=qq0Qy-gJDxanQW-HfCChDsTQsY1M41ua8hMlTnfuzrA,2202
 aiagents4pharma/talk2biomodels/api/uniprot.py,sha256=aPUAVBR7UYXDuuhDpKezAK2aTMzo-NxFYFq6C0W5u6U,1175
+aiagents4pharma/talk2biomodels/configs/__init__.py,sha256=safyFKhkd5Wlirl9dMZIHWDLTpY2oLw9wjIM7ZtLIHk,88
+aiagents4pharma/talk2biomodels/configs/agents/__init__.py,sha256=_ZoG8snICK2bidWtc2KOGs738LWg9_r66V9mOMnEb-E,71
+aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
+aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/default.yaml,sha256=pSViMKwKyMQDm8LzbfIaGdxph73iHYaXMiv5YOuxM7k,536
+aiagents4pharma/talk2biomodels/configs/tools/__init__.py,sha256=B08KWjj7bpizuTETGnnngrEVK4nzdWGREdoCCSw1Sm4,102
+aiagents4pharma/talk2biomodels/configs/tools/ask_question/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
+aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml,sha256=pMjs-peecRl8xtIucbEM1Z8Mm_8KGZj0JBrKKD3cMxU,1732
+aiagents4pharma/talk2biomodels/configs/tools/get_annotation/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
+aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml,sha256=o5kqLJ5QGJsLMUhAqotudIMhxxNfPUVcDVH1tdRIutU,304
 aiagents4pharma/talk2biomodels/models/__init__.py,sha256=5fTHHm3PVloYPNKXbgNlcPgv3-u28ZquxGydFYDfhJA,122
 aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=PH25FTOuUjsmw_UUxoRb-4kptOYpicEn4GqS0phS3nk,4807
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py,sha256=JeoiGQAvQABHnG0wKR2XBmmxqQdtgO6kxaLDUTUmr1s,2001
@@ -36,15 +34,15 @@ aiagents4pharma/talk2biomodels/tests/test_simulate_model.py,sha256=GjLE1DZpcKUAF
 aiagents4pharma/talk2biomodels/tests/test_steady_state.py,sha256=zt15KQoQku6jyzvpJXwINGTyhEnQl8wX81ueHlxnUCA,3467
 aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py,sha256=HSmBBViMi0jYf4gWX21IbppAfDzG0nr_S3KtKS9fZVQ,2165
 aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=6H2HWv5Q4NZYEmw-Ti5KZnJlEqhaC2HXSDZa6kiSl-U,350
-aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=hWXg7o0sTMDWH1ZnxtashTALvXpvNoaomfcniEhw-Bw,4684
+aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=ASkqT6VHUWcMdkVAlqqfbwq7_EBVAXdtmlkMFy7-XxI,4698
 aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=HWwKTX3o4dk0GcRVTO2hPrFSu98mtJ4TKC_hbHXOe1c,4018
-aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=l6gN_Urf-EJ5a_ZobIBeJB68BvLznsPUZR5sV04XR70,13420
+aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=Cea0vid_KX1xjI6ZqDygREAcM7sC7wZXNLTkAN8Nk3Y,13387
 aiagents4pharma/talk2biomodels/tools/get_modelinfo.py,sha256=57dkXrBeRpyiaW3dYkoWIfr6zSsFHcWRhvUVNyLcvUs,6363
 aiagents4pharma/talk2biomodels/tools/load_arguments.py,sha256=bffNIlBDTCSFYiZprA73yi8Jbb8z3Oh2decVNh1UnZc,4162
 aiagents4pharma/talk2biomodels/tools/load_biomodel.py,sha256=pyVzLQoMnuJYEwsjeOlqcUrbU1F1Z-pNlgkhFaoKpy0,689
 aiagents4pharma/talk2biomodels/tools/parameter_scan.py,sha256=aNh94LgBgVXBIczuNkbSsOZ9j54YVEdZWmZbZr7Nk8k,12465
 aiagents4pharma/talk2biomodels/tools/query_article.py,sha256=1tpYiE69MYcqiNcRaBgNiYzkkNmuTnlxLuBL_FnRuBU,2058
-aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=Iq2ddofOOfZYtAurCISq3bAq5rbwB3l_rL1lgEFyFCI,2653
+aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=b2OK-Z4ilddbEaJPSQlnZ6sHX3UAWXr_Hq-knoSbbAE,2654
 aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=qXs9lg9XgA7EaRiX3wBS8w_ug8tI-G3pzhcRg6dTRio,5060
 aiagents4pharma/talk2biomodels/tools/steady_state.py,sha256=j3ckuNlUtv7lT922MbN0JhT9H0JpWAdx2mLPwao6uu8,7123
 aiagents4pharma/talk2cells/__init__.py,sha256=zmOP5RAhabgKIQP-W4P4qKME2tG3fhAXM3MeO5_H8kE,120
@@ -82,24 +80,40 @@ aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py,sh
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py,sha256=tW426knki2DBIHcWyF_K04iMMdbpIn_e_TpPmTgz2dI,113
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/enrichments.py,sha256=Bx8x6zzk5614ApWB90N_iv4_Y_Uq0-KwUeBwYSdQMU4,924
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py,sha256=8eoxR-VHo0G7ReQIwje7xEhE-SJlHdef7_wJRpnvFIc,4116
-aiagents4pharma/talk2scholars/__init__.py,sha256=haaikzND3c0Euqq86ndA4fl9q42aOop5rYG_8Zh1D-o,119
+aiagents4pharma/talk2scholars/__init__.py,sha256=gphERyVKZHvOnMQsml7TIHlaIshHJ75R1J3FKExkfuY,120
 aiagents4pharma/talk2scholars/agents/__init__.py,sha256=ykszlVGxz3egLHZAttlNoTPxIrnQJZYva_ssR8fwIFk,117
-aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=HN3MkfHSDDlfzCKP79yAkpf3uyz3ZOCDGNRQ4gRL5RI,3854
-aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=HI037q-bq-bGf5DqtraSCWO493fAzUZ81lOEOCbMAaM,2486
-aiagents4pharma/talk2scholars/config/__init__.py,sha256=HyM6paOpKZ5_tZnyVheSAFmxjT6Mb3PxvWKfP0rz-dE,113
-aiagents4pharma/talk2scholars/config/config.py,sha256=jd4ltMBJyTztm9wT7j3ujOyYxL2SXRgxQJ4OZUBmCG4,5387
+aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=etPQUCjHtD-in-kD7Wg_UD6jRtCHj-mj41y03PYbAQM,4616
+aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=0OlxNb8IEhd7JJNL8rRlr_U67iPgtGjbbAiJo9HFPdY,2737
+aiagents4pharma/talk2scholars/configs/__init__.py,sha256=tf2gz8n7M4ko6xLdX_C925ELVIxoP6SgkPcbeh59ad4,151
+aiagents4pharma/talk2scholars/configs/config.yaml,sha256=a3_jCFAmsVL6gZuvzoRe4jL94mQaSbp0CUXZDUtqhZA,254
+aiagents4pharma/talk2scholars/configs/agents/__init__.py,sha256=yyh7PB2oY_JulnpSQCWS4wwCH_uzIdt47O2Ay48x_oU,75
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py,sha256=Tj4urOkjpu2cTlpJl0Fmr_18RZCR88vns-Gt-XquDzs,95
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=77DLch0YDiGslm3HerBaEDqKj1jLqI_jusHFbCchJDU,1617
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=6mgBvjifpHJ20kLwuwWr56UoZqmyf1luZnNWlYR6gnc,3135
+aiagents4pharma/talk2scholars/configs/app/__init__.py,sha256=JoSZV6N669kGMv5zLDszwf0ZjcRHx9TJfIqGhIIdPXE,70
+aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml,sha256=BX-J1zQyb0QJ7hcOFOnkJ8aWoWbjK4WE2VG7OZTOyKU,821
+aiagents4pharma/talk2scholars/configs/tools/__init__.py,sha256=w0BJK0MR6Et8Pw1htP8JV0Lr9F_N68CqvbpV14KBy_8,151
+aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml,sha256=70HSJ8WbS2Qbhur5FpuOPBjrea9g3TioM0gjGn6U1bE,369
+aiagents4pharma/talk2scholars/configs/tools/search/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/search/default.yaml,sha256=NznRVqB6EamMfsFc5hj5s9ygzl6rPuFPiy9ikcpqp68,486
+aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/default.yaml,sha256=4_gTvdVc-hf9GNxBKMGQd72s5h53Zy09j9qeZ9Fys04,578
 aiagents4pharma/talk2scholars/state/__init__.py,sha256=S6SxlszIMZSIMJehjevPF9sKyR-PAwWb5TEdo6xWXE8,103
 aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=nwNRKdhoTXAtBGMMp6coMyUCaQVOnoGNqyjpKKw_FVM,998
 aiagents4pharma/talk2scholars/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
-aiagents4pharma/talk2scholars/tests/test_langgraph.py,sha256=HcnahbazwaLaZg71OyCho2FLZ0ePedmv3XGvARFNe0g,9277
+aiagents4pharma/talk2scholars/tests/test_langgraph.py,sha256=36tWBmdewCZC8Yw1CCIpJxusGLCy21SVHhG1tR5C3TU,9605
 aiagents4pharma/talk2scholars/tools/__init__.py,sha256=YudBDRwaEzDnAcpxGZvEOfyh5-6xd51CTvTKTkywgXw,68
 aiagents4pharma/talk2scholars/tools/s2/__init__.py,sha256=9RQH3efTj6qkXk0ICKSc7Mzpkitt4gRGsQ1pGPrrREU,181
 aiagents4pharma/talk2scholars/tools/s2/display_results.py,sha256=B8JJGohi1Eyx8C3MhO_SiyQP3R6hPyUKJOAzcHmq3FU,584
-aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py,sha256=FYLt47DAk6WOKfEk1Gj9zVvJGNyxA283PCp8IKW9U5M,4262
-aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=pppjrQv5-8ep4fnqgTSBNgnbSnQsVIcNrRrH0p2TP1o,4025
-aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=dAfUQxI7T5eu0eDxK8VAl7-JH0Wnw24CVkOQqwj-hXc,4810
-aiagents4pharma-1.16.0.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.16.0.dist-info/METADATA,sha256=XH5jLQYNhAKOc4ixt5KovsExcjX14eEBrzTp40YluKY,8906
-aiagents4pharma-1.16.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-aiagents4pharma-1.16.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.16.0.dist-info/RECORD,,
+aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py,sha256=0Y3q8TkF_Phng9L7g1kk9Fhyit9UNitWurp03H0GZv8,4455
+aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=CcgFN7YuuQ9Vl1DJcldnnvPrswABKjNxeauK1rABps8,4176
+aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=irS-igdG8BZbVb0Z4VlIjzsyBlUfREd0v0_RlUM-0_U,4994
+aiagents4pharma-1.17.1.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
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+aiagents4pharma-1.17.1.dist-info/RECORD,,

aiagents4pharma/configs/config.yaml

@@ -1,5 +0,0 @@
-defaults:
-  - _self_
-  - talk2biomodels/agents/t2b_agent: default
-  - talk2biomodels/tools/ask_question: default
-  - talk2biomodels/tools/get_annotation: default