aiagents4pharma 1.6.0__py3-none-any.whl → 1.6.2__py3-none-any.whl

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/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/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/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/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/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.dist-info → aiagents4pharma-1.6.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.6.0
+Version: 1.6.2
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -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 +52,9 @@ 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.
+- **Talk2Competitors** *(Coming soon)*: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
 
 ---
 
@@ -66,7 +68,7 @@ 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.
 
@@ -74,6 +76,8 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 
 **Talk2KnowledgeGraphs** is an agent designed to enable interaction with biological knowledge graphs (KGs). KGs integrate vast amounts of structured biological data into a format that highlights relationships between entities, such as proteins, genes, and diseases.
 
+### 4. Talk2KnowledgeGraphs *(Coming soon)*
+
 ## Getting Started
 
 ### Prerequisites
@@ -172,6 +176,7 @@ Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
 - **User Interface**: Interactive web UI for all agents.
 - **Talk2Cells**: Integration of sequencing data analysis tools.
 - **Talk2KnowledgeGraphs**: Interface for biological knowledge graph interaction.
+- **Talk2Competitors**
 
 We’re excited to bring AIAgents4Pharma to the bioinformatics and pharmaceutical research community. Together, let’s make data-driven biological research more accessible and insightful. 
 

{aiagents4pharma-1.6.0.dist-info → aiagents4pharma-1.6.2.dist-info}/RECORD

@@ -10,6 +10,12 @@ aiagents4pharma/talk2biomodels/tools/fetch_parameters.py,sha256=WdLGPdJi4DwGwYMo
 aiagents4pharma/talk2biomodels/tools/model_description.py,sha256=lcVKVvh50wJ4BmB7xMnTZOtWjCmQUnkh6TQJsX-IjGw,5338
 aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=cqsK_ApjrAyjEiXWsXTebDpuvEnA5nb6WYiUGayRkW4,3034
 aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=MxlAy62SuonBbEbKmoUz0HcdfTWvk-x9WMSo17dBU9U,7552
+aiagents4pharma/talk2cells/__init__.py,sha256=zmOP5RAhabgKIQP-W4P4qKME2tG3fhAXM3MeO5_H8kE,120
+aiagents4pharma/talk2cells/agents/__init__.py,sha256=38nK2a_lEFRjO3qD6Fo9a3983ZCYat6hmJKWY61y2Mo,128
+aiagents4pharma/talk2cells/agents/scp_agent.py,sha256=gDMfhUNWHa_XWOqm1Ql6yLAdI_7bnIk5sRYn43H2sYk,3090
+aiagents4pharma/talk2cells/states/__init__.py,sha256=e4s8pHZaR6UC42DtmsOzCVms5gxp5QEzLE4bG54YYko,135
+aiagents4pharma/talk2cells/states/state_talk2cells.py,sha256=en5LikmabPZA6lLVpmYXff0Q3Fno0N2PBSMxk3gLWaE,253
+aiagents4pharma/talk2cells/tools/__init__.py,sha256=38nK2a_lEFRjO3qD6Fo9a3983ZCYat6hmJKWY61y2Mo,128
 aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=SW7Ys2A4eXyFtizNPdSw91SHOPVUBGBsrCQ7TqwSUL0,91
 aiagents4pharma/talk2knowledgegraphs/datasets/__init__.py,sha256=L3gPuHskSegmtXskVrLIYr7FXe_ibKgJ2GGr1_Wok6k,173
 aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py,sha256=QlzDXmXREoa9MA6-GwzqRjdzndQeGBAF11Td6NFk_9Y,23426
@@ -22,8 +28,8 @@ aiagents4pharma/talk2knowledgegraphs/utils/embeddings/__init__.py,sha256=xRb0x7S
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/embeddings.py,sha256=1nGznrAj-xT0xuSMBGz2dOujJ7M_IwSR84njxtxsy9A,2523
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/huggingface.py,sha256=2vi_elf6EgzfagFAO5QnL3a_aXZyN7B1EBziu44MTfM,3806
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py,sha256=36iKlisOpMtGR5xfTAlSHXWvPqVC_Jbezod8kbBBMVg,2136
-aiagents4pharma-1.6.0.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
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-aiagents4pharma-1.6.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.6.0.dist-info/RECORD,,
+aiagents4pharma-1.6.2.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
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