aiagents4pharma 1.6.0__tar.gz → 1.6.1__tar.gz

{aiagents4pharma-1.6.0 → aiagents4pharma-1.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.6.0
+Version: 1.6.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -19,6 +19,7 @@ Requires-Dist: langchain-community==0.3.5
 Requires-Dist: langchain-core==0.3.15
 Requires-Dist: langchain-experimental==0.3.3
 Requires-Dist: langchain-openai==0.2.5
+Requires-Dist: langgraph==0.2.62
 Requires-Dist: matplotlib==3.9.2
 Requires-Dist: openai==1.59.4
 Requires-Dist: pandas==2.2.3
@@ -51,8 +52,8 @@ Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://
 Our toolkit currently consists of three intelligent agents, each designed to simplify and enhance access to specialized data in biology:
 
 - **Talk2BioModels**: Engage directly with mathematical models in systems biology.
-- **Talk2Cells** *(Coming soon)*: Query and analyze sequencing data with ease.
-- **Talk2KnowledgeGraphs** *(Coming soon)*: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Cells** *(Work in progress)*: Query and analyze sequencing data with ease.
+- **Talk2KnowledgeGraphs** *(Work in progress)*: Access and explore complex biological knowledge graphs for insightful data connections.
 
 ---
 
@@ -66,7 +67,7 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 - Adjust parameters within the model to simulate different conditions.
 - Query simulation results.
 
-### 2. Talk2Cells *(Coming soon)*
+### 2. Talk2Cells *(Work in Progress)*
 
 **Talk2Cells** is being developed to provide direct access to and analysis of sequencing data, such as RNA-Seq or DNA-Seq, using natural language.
 

{aiagents4pharma-1.6.0 → aiagents4pharma-1.6.1}/README.md

@@ -7,8 +7,8 @@ Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://
 Our toolkit currently consists of three intelligent agents, each designed to simplify and enhance access to specialized data in biology:
 
 - **Talk2BioModels**: Engage directly with mathematical models in systems biology.
-- **Talk2Cells** *(Coming soon)*: Query and analyze sequencing data with ease.
-- **Talk2KnowledgeGraphs** *(Coming soon)*: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Cells** *(Work in progress)*: Query and analyze sequencing data with ease.
+- **Talk2KnowledgeGraphs** *(Work in progress)*: Access and explore complex biological knowledge graphs for insightful data connections.
 
 ---
 
@@ -22,7 +22,7 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 - Adjust parameters within the model to simulate different conditions.
 - Query simulation results.
 
-### 2. Talk2Cells *(Coming soon)*
+### 2. Talk2Cells *(Work in Progress)*
 
 **Talk2Cells** is being developed to provide direct access to and analysis of sequencing data, such as RNA-Seq or DNA-Seq, using natural language.
 

aiagents4pharma-1.6.1/aiagents4pharma/talk2cells/__init__.py

@@ -0,0 +1,6 @@
+'''
+This file is used to import the models and tools.
+'''
+from . import agents
+from . import states
+from . import tools

aiagents4pharma-1.6.1/aiagents4pharma/talk2cells/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 scp_agent

aiagents4pharma-1.6.1/aiagents4pharma/talk2cells/agents/scp_agent.py

@@ -0,0 +1,85 @@
+#/usr/bin/env python3
+
+'''
+This is the agent file for the Talk2Cells graph.
+'''
+
+import logging
+import os
+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
+from ..tools.scp_agent.search_studies import search_studies
+from ..tools.scp_agent.display_studies import display_studies
+from ..states.state_talk2cells import Talk2Cells
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+def get_app(uniq_id):
+    '''
+    This function returns the langraph app.
+    '''
+    def agent_scp_node(state: Talk2Cells):
+        '''
+        This function calls the model.
+        '''
+        logger.log(logging.INFO, "Creating SCP_Agent node with thread_id %s", uniq_id)
+        # Get the messages from the state
+        # messages = state['messages']
+        # Call the model
+        # inputs = {'messages': messages}
+        response = model.invoke(state, {"configurable": {"thread_id": uniq_id}})
+        # The response is a list of messages and may contain `tool calls`
+        # We return a list, because this will get added to the existing list
+        # return {"messages": [response]}
+        return response
+
+    # Define the tools
+    # tools = [search_studies, display_studies]
+    tools = ToolNode([search_studies, display_studies])
+
+    # Create the LLM
+    # And bind the tools to it
+    # model = ChatOpenAI(model="gpt-4o-mini", temperature=0).bind_tools(tools)
+
+    # Create an environment variable to store the LLM model
+    # Check if the environment variable AIAGENTS4PHARMA_LLM_MODEL is set
+    # If not, set it to 'gpt-4o-mini'
+    llm_model = os.getenv('AIAGENTS4PHARMA_LLM_MODEL', 'gpt-4o-mini')
+    # print (f'LLM model: {llm_model}')
+    # llm = ChatOpenAI(model="gpt-4o-mini", temperature=0)
+    llm = ChatOpenAI(model=llm_model, temperature=0)
+    model = create_react_agent(
+                            llm,
+                            tools=tools,
+                            state_schema=Talk2Cells,
+                            state_modifier=(
+                                            "You are Talk2Cells agent."
+                                            ),
+                            checkpointer=MemorySaver()
+                        )
+
+    # Define a new graph
+    workflow = StateGraph(Talk2Cells)
+
+    # Define the two nodes we will cycle between
+    workflow.add_node("agent_scp", agent_scp_node)
+
+    # Set the entrypoint as `agent`
+    # This means that this node is the first one called
+    workflow.add_edge(START, "agent_scp")
+
+    # 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")
+
+    return app

aiagents4pharma-1.6.1/aiagents4pharma/talk2cells/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_talk2cells

aiagents4pharma-1.6.1/aiagents4pharma/talk2cells/states/state_talk2cells.py

@@ -0,0 +1,13 @@
+#!/usr/bin/env python3
+
+'''
+This is the state file for the Talk2Cells agent.
+'''
+
+from langgraph.prebuilt.chat_agent_executor import AgentState
+
+class Talk2Cells(AgentState):
+    """
+    The state for the Talk2Cells agent.
+    """
+    search_table: str

aiagents4pharma-1.6.1/aiagents4pharma/talk2cells/tools/__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 scp_agent

{aiagents4pharma-1.6.0 → aiagents4pharma-1.6.1}/aiagents4pharma.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.6.0
+Version: 1.6.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -19,6 +19,7 @@ Requires-Dist: langchain-community==0.3.5
 Requires-Dist: langchain-core==0.3.15
 Requires-Dist: langchain-experimental==0.3.3
 Requires-Dist: langchain-openai==0.2.5
+Requires-Dist: langgraph==0.2.62
 Requires-Dist: matplotlib==3.9.2
 Requires-Dist: openai==1.59.4
 Requires-Dist: pandas==2.2.3
@@ -51,8 +52,8 @@ Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://
 Our toolkit currently consists of three intelligent agents, each designed to simplify and enhance access to specialized data in biology:
 
 - **Talk2BioModels**: Engage directly with mathematical models in systems biology.
-- **Talk2Cells** *(Coming soon)*: Query and analyze sequencing data with ease.
-- **Talk2KnowledgeGraphs** *(Coming soon)*: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Cells** *(Work in progress)*: Query and analyze sequencing data with ease.
+- **Talk2KnowledgeGraphs** *(Work in progress)*: Access and explore complex biological knowledge graphs for insightful data connections.
 
 ---
 
@@ -66,7 +67,7 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 - Adjust parameters within the model to simulate different conditions.
 - Query simulation results.
 
-### 2. Talk2Cells *(Coming soon)*
+### 2. Talk2Cells *(Work in Progress)*
 
 **Talk2Cells** is being developed to provide direct access to and analysis of sequencing data, such as RNA-Seq or DNA-Seq, using natural language.
 

{aiagents4pharma-1.6.0 → aiagents4pharma-1.6.1}/aiagents4pharma.egg-info/SOURCES.txt

@@ -19,6 +19,12 @@ aiagents4pharma/talk2biomodels/tools/fetch_parameters.py
 aiagents4pharma/talk2biomodels/tools/model_description.py
 aiagents4pharma/talk2biomodels/tools/search_models.py
 aiagents4pharma/talk2biomodels/tools/simulate_model.py
+aiagents4pharma/talk2cells/__init__.py
+aiagents4pharma/talk2cells/agents/__init__.py
+aiagents4pharma/talk2cells/agents/scp_agent.py
+aiagents4pharma/talk2cells/states/__init__.py
+aiagents4pharma/talk2cells/states/state_talk2cells.py
+aiagents4pharma/talk2cells/tools/__init__.py
 aiagents4pharma/talk2knowledgegraphs/__init__.py
 aiagents4pharma/talk2knowledgegraphs/datasets/__init__.py
 aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py

{aiagents4pharma-1.6.0 → aiagents4pharma-1.6.1}/aiagents4pharma.egg-info/requires.txt

@@ -9,6 +9,7 @@ langchain-community==0.3.5
 langchain-core==0.3.15
 langchain-experimental==0.3.3
 langchain-openai==0.2.5
+langgraph==0.2.62
 matplotlib==3.9.2
 openai==1.59.4
 pandas==2.2.3

{aiagents4pharma-1.6.0 → aiagents4pharma-1.6.1}/pyproject.toml

@@ -24,6 +24,7 @@ dependencies = [
     "langchain-core==0.3.15",
     "langchain-experimental==0.3.3",
     "langchain-openai==0.2.5",
+    "langgraph==0.2.62",
     "matplotlib==3.9.2",
     "openai==1.59.4",
     "pandas==2.2.3",
@@ -58,6 +59,10 @@ packages = ["aiagents4pharma",
             "aiagents4pharma.talk2biomodels",
             "aiagents4pharma.talk2biomodels.models",
             "aiagents4pharma.talk2biomodels.tools",
+            "aiagents4pharma.talk2cells",
+            "aiagents4pharma.talk2cells.agents",
+            "aiagents4pharma.talk2cells.states",
+            "aiagents4pharma.talk2cells.tools",
             "aiagents4pharma.talk2knowledgegraphs",
             "aiagents4pharma.talk2knowledgegraphs.datasets",
             "aiagents4pharma.talk2knowledgegraphs.utils",

aiagents4pharma-1.6.1/release_version.txt

@@ -0,0 +1 @@
+v1.6.1

aiagents4pharma-1.6.0/release_version.txt

@@ -1 +0,0 @@
-v1.6.0