aiagents4pharma 1.5.4__tar.gz → 1.6.1__tar.gz

{aiagents4pharma-1.5.4 → aiagents4pharma-1.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.5.4
+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
@@ -10,6 +10,7 @@ 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: joblib==1.4.2
@@ -18,6 +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
@@ -25,10 +27,14 @@ Requires-Dist: plotly==5.24.1
 Requires-Dist: pydantic==2.9.2
 Requires-Dist: pylint==3.3.1
 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==2.5.1
+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
@@ -46,8 +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.
 
 ---
 
@@ -61,7 +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-1.5.4 → 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-1.6.1/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/__init__.py

@@ -0,0 +1,6 @@
+'''
+This file is used to import all the models in the package.
+'''
+from . import embeddings
+from . import sentence_transformer
+from . import huggingface

aiagents4pharma-1.6.1/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/embeddings.py

@@ -0,0 +1,77 @@
+"""
+Embeddings interface from LangChain Core.
+https://github.com/langchain-ai/langchain/blob/master/libs/core/langchain_core/embeddings/embeddings.py
+"""
+from abc import ABC, abstractmethod
+from langchain_core.runnables.config import run_in_executor
+
+class Embeddings(ABC):
+    """Interface for embedding models.
+
+    This is an interface meant for implementing text embedding models.
+
+    Text embedding models are used to map text to a vector (a point in n-dimensional
+    space).
+
+    Texts that are similar will usually be mapped to points that are close to each
+    other in this space. The exact details of what's considered "similar" and how
+    "distance" is measured in this space are dependent on the specific embedding model.
+
+    This abstraction contains a method for embedding a list of documents and a method
+    for embedding a query text. The embedding of a query text is expected to be a single
+    vector, while the embedding of a list of documents is expected to be a list of
+    vectors.
+
+    Usually the query embedding is identical to the document embedding, but the
+    abstraction allows treating them independently.
+
+    In addition to the synchronous methods, this interface also provides asynchronous
+    versions of the methods.
+
+    By default, the asynchronous methods are implemented using the synchronous methods;
+    however, implementations may choose to override the asynchronous methods with
+    an async native implementation for performance reasons.
+    """
+    @abstractmethod
+    def embed_documents(self, texts: list[str]) -> list[list[float]]:
+        """Embed search docs.
+
+        Args:
+            texts: List of text to embed.
+
+        Returns:
+            List of embeddings.
+        """
+
+    @abstractmethod
+    def embed_query(self, text: str) -> list[float]:
+        """Embed query text.
+
+        Args:
+            text: Text to embed.
+
+        Returns:
+            Embedding.
+        """
+
+    async def aembed_documents(self, texts: list[str]) -> list[list[float]]:
+        """Asynchronous Embed search docs.
+
+        Args:
+            texts: List of text to embed.
+
+        Returns:
+            List of embeddings.
+        """
+        return await run_in_executor(None, self.embed_documents, texts)
+
+    async def aembed_query(self, text: str) -> list[float]:
+        """Asynchronous Embed query text.
+
+        Args:
+            text: Text to embed.
+
+        Returns:
+            Embedding.
+        """
+        return await run_in_executor(None, self.embed_query, text)

aiagents4pharma-1.6.1/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/huggingface.py

@@ -0,0 +1,114 @@
+"""
+Embedding class using HuggingFace model based on LangChain Embeddings class.
+"""
+
+from typing import List
+import torch
+from transformers import AutoModel, AutoTokenizer, AutoConfig
+from .embeddings import Embeddings
+
+class EmbeddingWithHuggingFace(Embeddings):
+    """
+    Embedding class using HuggingFace model based on LangChain Embeddings class.
+    """
+
+    def __init__(
+        self,
+        model_name: str,
+        model_cache_dir: str = None,
+        truncation: bool = True,
+        device: str = "cpu",
+    ):
+        """
+        Initialize the EmbeddingWithHuggingFace class.
+
+        Args:
+            model_name: The name of the HuggingFace model to be used.
+            model_cache_dir: The directory to cache the HuggingFace model.
+            truncation: The truncation flag for the HuggingFace tokenizer.
+            return_tensors: The return_tensors flag for the HuggingFace tokenizer.
+            device: The device to run the model on.
+        """
+
+        # Set parameters
+        self.model_name = model_name
+        self.model_cache_dir = model_cache_dir
+        self.truncation = truncation
+        self.device = device
+
+        # Try to load the model from HuggingFace Hub
+        try:
+            AutoConfig.from_pretrained(self.model_name)
+        except EnvironmentError as e:
+            raise ValueError(
+                f"Model {self.model_name} is not available on HuggingFace Hub."
+            ) from e
+
+        # Load HuggingFace tokenizer and model
+        self.tokenizer = AutoTokenizer.from_pretrained(
+            self.model_name, cache_dir=self.model_cache_dir
+        )
+        self.model = AutoModel.from_pretrained(
+            self.model_name, cache_dir=self.model_cache_dir
+        )
+
+    def meanpooling(self, output, mask) -> torch.Tensor:
+        """
+        Mean Pooling - Take attention mask into account for correct averaging.
+        According to the following documentation:
+        https://huggingface.co/NeuML/pubmedbert-base-embeddings
+
+        Args:
+            output: The output of the model.
+            mask: The mask of the model.
+        """
+        embeddings = output[0] # First element of model_output contains all token embeddings
+        mask = mask.unsqueeze(-1).expand(embeddings.size()).float()
+        return torch.sum(embeddings * mask, 1) / torch.clamp(mask.sum(1), min=1e-9)
+
+    def embed_documents(self, texts: List[str]) -> List[float]:
+        """
+        Generate embedding for a list of input texts using HuggingFace model.
+
+        Args:
+            texts: The list of texts to be embedded.
+
+        Returns:
+            The list of embeddings for the given texts.
+        """
+
+        # Generate the embedding
+        with torch.no_grad():
+            inputs = self.tokenizer(
+                texts,
+                padding=True,
+                truncation=self.truncation,
+                return_tensors="pt",
+            ).to(self.device)
+            outputs = self.model.to(self.device)(**inputs)
+            embeddings = self.meanpooling(outputs, inputs['attention_mask']).cpu()
+
+        return embeddings
+
+    def embed_query(self, text: str) -> List[float]:
+        """
+        Generate embeddings for an input text using HuggingFace model.
+
+        Args:
+            text: A query to be embedded.
+        Returns:
+            The embeddings for the given query.
+        """
+
+        # Generate the embedding
+        with torch.no_grad():
+            inputs = self.tokenizer(
+                text,
+                padding=True,
+                truncation=self.truncation,
+                return_tensors="pt",
+            ).to(self.device)
+            outputs = self.model.to(self.device)(**inputs)
+            embeddings = self.meanpooling(outputs, inputs['attention_mask']).cpu()[0]
+
+        return embeddings

aiagents4pharma-1.6.1/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py

@@ -0,0 +1,71 @@
+#!/usr/bin/env python3
+
+"""
+Embedding class using SentenceTransformer model based on LangChain Embeddings class.
+"""
+
+from typing import List
+from sentence_transformers import SentenceTransformer
+from .embeddings import Embeddings
+
+
+class EmbeddingWithSentenceTransformer(Embeddings):
+    """
+    Embedding class using SentenceTransformer model based on LangChain Embeddings class.
+    """
+
+    def __init__(
+        self,
+        model_name: str,
+        model_cache_dir: str = None,
+        trust_remote_code: bool = True,
+    ):
+        """
+        Initialize the EmbeddingWithSentenceTransformer class.
+
+        Args:
+            model_name: The name of the SentenceTransformer model to be used.
+            model_cache_dir: The directory to cache the SentenceTransformer model.
+            trust_remote_code: Whether to trust the remote code of the model.
+        """
+
+        # Set parameters
+        self.model_name = model_name
+        self.model_cache_dir = model_cache_dir
+        self.trust_remote_code = trust_remote_code
+
+        # Load the model
+        self.model = SentenceTransformer(self.model_name,
+                                         cache_folder=self.model_cache_dir,
+                                         trust_remote_code=self.trust_remote_code)
+
+    def embed_documents(self, texts: List[str]) -> List[float]:
+        """
+        Generate embedding for a list of input texts using SentenceTransformer model.
+
+        Args:
+            texts: The list of texts to be embedded.
+
+        Returns:
+            The list of embeddings for the given texts.
+        """
+
+        # Generate the embedding
+        embeddings = self.model.encode(texts, show_progress_bar=False)
+
+        return embeddings
+
+    def embed_query(self, text: str) -> List[float]:
+        """
+        Generate embeddings for an input text using SentenceTransformer model.
+
+        Args:
+            text: A query to be embedded.
+        Returns:
+            The embeddings for the given query.
+        """
+
+        # Generate the embedding
+        embeddings = self.model.encode(text, show_progress_bar=False)
+
+        return embeddings

aiagents4pharma-1.6.1/aiagents4pharma/talk2knowledgegraphs/utils/kg_utils.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python3
+
+'''A utility module for knowledge graph operations'''
+
+from typing import Tuple
+import networkx as nx
+import pandas as pd
+
+def kg_to_df_pandas(kg: nx.DiGraph) -> Tuple[pd.DataFrame, pd.DataFrame]:
+    """
+    Convert a directed knowledge graph to a pandas DataFrame.
+
+    Args:
+        kg: The directed knowledge graph in networkX format.
+
+    Returns:
+        df_nodes: A pandas DataFrame of the nodes in the knowledge graph.
+        df_edges: A pandas DataFrame of the edges in the knowledge graph.
+    """
+
+    # Create a pandas DataFrame of the nodes
+    df_nodes = pd.DataFrame.from_dict(kg.nodes, orient='index')
+
+    # Create a pandas DataFrame of the edges
+    df_edges = nx.to_pandas_edgelist(kg,
+                                    source='node_source',
+                                    target='node_target')
+
+    return df_nodes, df_edges
+
+def df_pandas_to_kg(df: pd.DataFrame,
+                    df_nodes_attrs: pd.DataFrame,
+                    node_source: str,
+                    node_target: str
+                    ) -> nx.DiGraph:
+    """
+    Convert a pandas DataFrame to a directed knowledge graph.
+
+    Args:
+        df: A pandas DataFrame of the edges in the knowledge graph.
+        df_nodes_attrs: A pandas DataFrame of the nodes in the knowledge graph.
+        node_source: The column name of the source node in the df.
+        node_target: The column name of the target node in the df.
+
+    Returns:
+        kg: The directed knowledge graph in networkX format.
+    """
+
+    # Assert if the columns node_source and node_target are in the df
+    assert node_source in df.columns, f'{node_source} not in df'
+    assert node_target in df.columns, f'{node_target} not in df'
+
+    # Assert that the nodes in the index of the df_nodes_attrs
+    # are present in the source and target columns of the df
+    assert set(df_nodes_attrs.index).issubset(set(df[node_source]).\
+                                        union(set(df[node_target]))), \
+                                        'Nodes in index of df_nodes not found in df_edges'
+
+    # Create a knowledge graph from the dataframes
+    # Add edges and nodes to the knowledge graph
+    kg = nx.from_pandas_edgelist(df,
+                                source=node_source,
+                                target=node_target,
+                                create_using=nx.DiGraph,
+                                edge_attr=True)
+    kg.add_nodes_from(df_nodes_attrs.to_dict('index').items())
+
+    return kg

{aiagents4pharma-1.5.4 → aiagents4pharma-1.6.1}/aiagents4pharma.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.5.4
+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
@@ -10,6 +10,7 @@ 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: joblib==1.4.2
@@ -18,6 +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
@@ -25,10 +27,14 @@ Requires-Dist: plotly==5.24.1
 Requires-Dist: pydantic==2.9.2
 Requires-Dist: pylint==3.3.1
 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==2.5.1
+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
@@ -46,8 +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.
 
 ---
 
@@ -61,7 +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-1.5.4 → aiagents4pharma-1.6.1}/aiagents4pharma.egg-info/SOURCES.txt

@@ -19,9 +19,21 @@ 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/talk2knowledgegraphs/datasets/dataset.py
 aiagents4pharma/talk2knowledgegraphs/datasets/primekg.py
-aiagents4pharma/talk2knowledgegraphs/datasets/starkqa_primekg.py
+aiagents4pharma/talk2knowledgegraphs/datasets/starkqa_primekg.py
+aiagents4pharma/talk2knowledgegraphs/utils/__init__.py
+aiagents4pharma/talk2knowledgegraphs/utils/kg_utils.py
+aiagents4pharma/talk2knowledgegraphs/utils/embeddings/__init__.py
+aiagents4pharma/talk2knowledgegraphs/utils/embeddings/embeddings.py
+aiagents4pharma/talk2knowledgegraphs/utils/embeddings/huggingface.py
+aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py

{aiagents4pharma-1.5.4 → aiagents4pharma-1.6.1}/aiagents4pharma.egg-info/requires.txt

@@ -1,5 +1,6 @@
 copasi_basico==0.78
 coverage==7.6.4
+einops==0.8.0
 gdown==5.2.0
 huggingface_hub==0.26.5
 joblib==1.4.2
@@ -8,6 +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
@@ -15,10 +17,14 @@ plotly==5.24.1
 pydantic==2.9.2
 pylint==3.3.1
 pytest==8.3.3
+pytest-asyncio==0.25.2
 streamlit==1.39.0
+sentence_transformers==3.3.1
 tabulate==0.9.0
-torch==2.5.1
+torch==2.2.2
+torch_geometric==2.6.1
 tqdm==4.66.6
+transformers==4.48.0
 mkdocs==1.6.1
 mkdocs-jupyter==0.25.1
 mkdocs-material==9.5.47

{aiagents4pharma-1.5.4 → aiagents4pharma-1.6.1}/pyproject.toml

@@ -15,6 +15,7 @@ classifiers = [
 dependencies = [
     "copasi_basico==0.78",
     "coverage==7.6.4",
+    "einops==0.8.0",
     "gdown==5.2.0",
     "huggingface_hub==0.26.5",
     "joblib==1.4.2",
@@ -23,6 +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",
@@ -30,10 +32,14 @@ dependencies = [
     "pydantic==2.9.2",
     "pylint==3.3.1",
     "pytest==8.3.3",
+    "pytest-asyncio==0.25.2",
     "streamlit==1.39.0",
+    "sentence_transformers==3.3.1",
     "tabulate==0.9.0",
-    "torch==2.5.1",
+    "torch==2.2.2",
+    "torch_geometric==2.6.1",
     "tqdm==4.66.6",
+    "transformers==4.48.0",
     "mkdocs==1.6.1",
     "mkdocs-jupyter==0.25.1",
     "mkdocs-material==9.5.47",
@@ -53,8 +59,14 @@ 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.datasets",
+            "aiagents4pharma.talk2knowledgegraphs.utils",
+            "aiagents4pharma.talk2knowledgegraphs.utils.embeddings"]
 
 # [tool.setuptools.packages.find]
 # where = ["aiagents4pharma", "aiagents4pharma.talk2biomodels"]

aiagents4pharma-1.6.1/release_version.txt

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

aiagents4pharma-1.5.4/release_version.txt

@@ -1 +0,0 @@
-v1.5.4