aiagents4pharma 1.8.1__tar.gz → 1.8.2__tar.gz

{aiagents4pharma-1.8.1 → aiagents4pharma-1.8.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.8.1
+Version: 1.8.2
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -17,10 +17,10 @@ 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==0.3.15
+Requires-Dist: langchain-core==0.3.31
 Requires-Dist: langchain-experimental==0.3.3
 Requires-Dist: langchain-openai==0.2.5
-Requires-Dist: langgraph==0.2.62
+Requires-Dist: langgraph==0.2.66
 Requires-Dist: matplotlib==3.9.2
 Requires-Dist: openai==1.59.4
 Requires-Dist: pandas==2.2.3

aiagents4pharma-1.8.2/aiagents4pharma/talk2biomodels/agents/__init__.py

@@ -0,0 +1,5 @@
+'''
+This file is used to import all the modules in the package.
+'''
+# import everything from the module
+from . import t2b_agent

aiagents4pharma-1.8.2/aiagents4pharma/talk2biomodels/agents/t2b_agent.py

@@ -0,0 +1,93 @@
+#/usr/bin/env python3
+
+'''
+This is the agent file for the Talk2BioModels agent.
+'''
+
+import logging
+from typing import Annotated
+import hydra
+from langchain_openai import ChatOpenAI
+from langgraph.checkpoint.memory import MemorySaver
+from langgraph.graph import START, StateGraph
+from langgraph.prebuilt import create_react_agent, ToolNode, InjectedState
+from ..tools.search_models import SearchModelsTool
+from ..tools.get_modelinfo import GetModelInfoTool
+from ..tools.simulate_model import SimulateModelTool
+from ..tools.custom_plotter import CustomPlotterTool
+from ..tools.ask_question import AskQuestionTool
+from ..states.state_talk2biomodels import Talk2Biomodels
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+def get_app(uniq_id, llm_model='gpt-4o-mini'):
+    '''
+    This function returns the langraph app.
+    '''
+    def agent_t2b_node(state: Annotated[dict, InjectedState]):
+        '''
+        This function calls the model.
+        '''
+        logger.log(logging.INFO, "Calling t2b_agent node with thread_id %s", uniq_id)
+        response = model.invoke(state, {"configurable": {"thread_id": uniq_id}})
+        return response
+
+    # Define the tools
+    simulate_model = SimulateModelTool()
+    custom_plotter = CustomPlotterTool()
+    ask_question = AskQuestionTool()
+    search_model = SearchModelsTool()
+    get_modelinfo = GetModelInfoTool()
+    tools = ToolNode([
+                    simulate_model,
+                    ask_question,
+                    custom_plotter,
+                    search_model,
+                    get_modelinfo
+                    ])
+
+    # Define the model
+    llm = ChatOpenAI(model=llm_model, temperature=0)
+    # Load hydra configuration
+    logger.log(logging.INFO, "Load Hydra configuration for Talk2BioModels agent.")
+    with hydra.initialize(version_base=None, config_path="../../../configs"):
+        cfg = hydra.compose(config_name='config',
+                            overrides=['aiagents4pharma/talk2biomodels/agents/t2b_agent=default'])
+        cfg = cfg.aiagents4pharma.talk2biomodels.agents.t2b_agent
+    logger.log(logging.INFO, "state_modifier: %s", cfg.state_modifier)
+    # Create the agent
+    model = create_react_agent(
+                llm,
+                tools=tools,
+                state_schema=Talk2Biomodels,
+                state_modifier=cfg.state_modifier,
+                checkpointer=MemorySaver()
+            )
+
+    # Define a new graph
+    workflow = StateGraph(Talk2Biomodels)
+
+    # Define the two nodes we will cycle between
+    workflow.add_node("agent_t2b", agent_t2b_node)
+
+    # Set the entrypoint as the first node
+    # This means that this node is the first one called
+    workflow.add_edge(START, "agent_t2b")
+
+    # Initialize memory to persist state between graph runs
+    checkpointer = MemorySaver()
+
+    # Finally, we compile it!
+    # This compiles it into a LangChain Runnable,
+    # meaning you can use it as you would any other runnable.
+    # Note that we're (optionally) passing the memory
+    # when compiling the graph
+    app = workflow.compile(checkpointer=checkpointer)
+    logger.log(logging.INFO,
+               "Compiled the graph with thread_id %s and llm_model %s",
+               uniq_id,
+               llm_model)
+
+    return app

aiagents4pharma-1.8.2/aiagents4pharma/talk2biomodels/states/__init__.py

@@ -0,0 +1,5 @@
+'''
+This file is used to import all the modules in the package.
+'''
+# import everything from the module
+from . import state_talk2biomodels

aiagents4pharma-1.8.2/aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+
+'''
+This is the state file for the Talk2BioModels agent.
+'''
+
+from typing import Annotated
+import operator
+from langgraph.prebuilt.chat_agent_executor import AgentState
+
+class Talk2Biomodels(AgentState):
+    """
+    The state for the Talk2BioModels agent.
+    """
+    model_id: Annotated[list, operator.add]
+    # sbml_file_path: str
+    # A StateGraph may receive a concurrent updates
+    # which is not supported by the StateGraph.
+    # Therefore, we need to use Annotated to specify
+    # the operator for the sbml_file_path field.
+    # https://langchain-ai.github.io/langgraph/troubleshooting/errors/INVALID_CONCURRENT_GRAPH_UPDATE/
+    sbml_file_path: Annotated[list, operator.add]
+    dic_simulated_data: dict
+    llm_model: str

aiagents4pharma-1.8.2/aiagents4pharma/talk2cells/tools/scp_agent/__init__.py

@@ -0,0 +1,6 @@
+'''
+This file is used to import all the modules in the package.
+'''
+# import everything from the module
+from . import display_studies
+from . import search_studies

aiagents4pharma-1.8.2/aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+
+'''
+This tool is used to display the table of studies.
+'''
+
+import logging
+from typing import Annotated
+from langchain_core.tools import tool
+from langgraph.prebuilt import InjectedState
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+@tool('display_studies')
+def display_studies(state: Annotated[dict, InjectedState]):
+    """
+    Display the table of studies.
+
+    Args:
+        state (dict): The state of the agent.
+    """
+    logger.log(logging.INFO, "Calling the tool display_studies")
+    return state["search_table"]

aiagents4pharma-1.8.2/aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python3
+
+'''
+A tool to fetch studies from the Single Cell Portal.
+'''
+
+import logging
+from typing import Annotated
+import requests
+from langchain_core.tools import tool
+from langchain_core.tools.base import InjectedToolCallId
+from langchain_core.messages import ToolMessage
+from langgraph.types import Command
+import pandas as pd
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+@tool('search_studies')
+def search_studies(search_term: str,
+                   tool_call_id: Annotated[str, InjectedToolCallId],
+                   limit: int = 5):
+    """
+    Fetch studies from single cell portal
+
+    Args:
+        search_term (str): The search term to use. Example: "COVID-19", "cancer", etc.
+        limit (int): The number of papers to return. Default is 5.
+
+    """
+    logger.log(logging.INFO, "Calling the tool search_studies")
+    scp_endpoint = 'https://singlecell.broadinstitute.org/single_cell/api/v1/search?type=study'
+    # params = {'terms': search_term, 'facets': 'MONDO_0005011'}
+    params = {'terms': search_term}
+    status_code = 0
+    while status_code != 200:
+        # Make a GET request to the single cell portal
+        search_response = requests.get(scp_endpoint,
+                                       params=params,
+                                       timeout=10,
+                                       verify=False)
+        status_code = search_response.status_code
+        logger.log(logging.INFO, "Status code %s received from SCP")
+
+    # Select the columns to display in the table
+    selected_columns = ["study_source", "name", "study_url", "gene_count", "cell_count"]
+
+    # Extract the data from the response
+    # with the selected columns
+    df = pd.DataFrame(search_response.json()['studies'])[selected_columns]
+
+    # Convert column 'Study Name' into clickable
+    # hyperlinks from the column 'Study URL'
+    scp_api_url = 'https://singlecell.broadinstitute.org'
+    df['name'] = df.apply(
+            lambda x: f"<a href=\"{scp_api_url}/{x['study_url']}\">{x['name']}</a>",
+            axis=1)
+
+    # Excldue the column 'Study URL' from the dataframe
+    df = df.drop(columns=['study_url'])
+
+    # Add a new column a the beginning of the dataframe with row numbers
+    df.insert(0, 'S/N', range(1, 1 + len(df)))
+
+    # Update the state key 'search_table' with the dataframe in markdown format
+    return Command(
+        update={
+            # update the state keys
+            "search_table": df.to_markdown(tablefmt="grid"),
+            # update the message history
+            "messages": [
+                ToolMessage(
+                    f"Successfully fetched {limit} studies on {search_term}.",
+                    tool_call_id=tool_call_id
+                )
+            ],
+        }
+    )

{aiagents4pharma-1.8.1 → aiagents4pharma-1.8.2}/aiagents4pharma.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.8.1
+Version: 1.8.2
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -17,10 +17,10 @@ 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==0.3.15
+Requires-Dist: langchain-core==0.3.31
 Requires-Dist: langchain-experimental==0.3.3
 Requires-Dist: langchain-openai==0.2.5
-Requires-Dist: langgraph==0.2.62
+Requires-Dist: langgraph==0.2.66
 Requires-Dist: matplotlib==3.9.2
 Requires-Dist: openai==1.59.4
 Requires-Dist: pandas==2.2.3

{aiagents4pharma-1.8.1 → aiagents4pharma-1.8.2}/aiagents4pharma.egg-info/SOURCES.txt

@@ -9,9 +9,13 @@ aiagents4pharma.egg-info/dependency_links.txt
 aiagents4pharma.egg-info/requires.txt
 aiagents4pharma.egg-info/top_level.txt
 aiagents4pharma/talk2biomodels/__init__.py
+aiagents4pharma/talk2biomodels/agents/__init__.py
+aiagents4pharma/talk2biomodels/agents/t2b_agent.py
 aiagents4pharma/talk2biomodels/models/__init__.py
 aiagents4pharma/talk2biomodels/models/basico_model.py
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py
+aiagents4pharma/talk2biomodels/states/__init__.py
+aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py
 aiagents4pharma/talk2biomodels/tools/__init__.py
 aiagents4pharma/talk2biomodels/tools/ask_question.py
 aiagents4pharma/talk2biomodels/tools/custom_plotter.py
@@ -25,6 +29,9 @@ aiagents4pharma/talk2cells/agents/scp_agent.py
 aiagents4pharma/talk2cells/states/__init__.py
 aiagents4pharma/talk2cells/states/state_talk2cells.py
 aiagents4pharma/talk2cells/tools/__init__.py
+aiagents4pharma/talk2cells/tools/scp_agent/__init__.py
+aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py
+aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py
 aiagents4pharma/talk2knowledgegraphs/__init__.py
 aiagents4pharma/talk2knowledgegraphs/datasets/__init__.py
 aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py

{aiagents4pharma-1.8.1 → aiagents4pharma-1.8.2}/aiagents4pharma.egg-info/requires.txt

@@ -7,10 +7,10 @@ hydra-core==1.3.2
 joblib==1.4.2
 langchain==0.3.7
 langchain-community==0.3.5
-langchain-core==0.3.15
+langchain-core==0.3.31
 langchain-experimental==0.3.3
 langchain-openai==0.2.5
-langgraph==0.2.62
+langgraph==0.2.66
 matplotlib==3.9.2
 openai==1.59.4
 pandas==2.2.3

{aiagents4pharma-1.8.1 → aiagents4pharma-1.8.2}/pyproject.toml

@@ -22,10 +22,10 @@ dependencies = [
     "joblib==1.4.2",
     "langchain==0.3.7",
     "langchain-community==0.3.5",
-    "langchain-core==0.3.15",
+    "langchain-core==0.3.31",
     "langchain-experimental==0.3.3",
     "langchain-openai==0.2.5",
-    "langgraph==0.2.62",
+    "langgraph==0.2.66",
     "matplotlib==3.9.2",
     "openai==1.59.4",
     "pandas==2.2.3",
@@ -60,10 +60,13 @@ packages = ["aiagents4pharma",
             "aiagents4pharma.talk2biomodels",
             "aiagents4pharma.talk2biomodels.models",
             "aiagents4pharma.talk2biomodels.tools",
+            "aiagents4pharma.talk2biomodels.agents",
+            "aiagents4pharma.talk2biomodels.states",
             "aiagents4pharma.talk2cells",
             "aiagents4pharma.talk2cells.agents",
             "aiagents4pharma.talk2cells.states",
             "aiagents4pharma.talk2cells.tools",
+            "aiagents4pharma.talk2cells.tools.scp_agent",
             "aiagents4pharma.talk2knowledgegraphs",
             "aiagents4pharma.talk2knowledgegraphs.datasets",
             "aiagents4pharma.talk2knowledgegraphs.utils",

aiagents4pharma-1.8.2/release_version.txt

@@ -0,0 +1 @@
+v1.8.2

aiagents4pharma-1.8.1/release_version.txt

@@ -1 +0,0 @@
-v1.8.1