aiagents4pharma 1.43.0__py3-none-any.whl → 1.45.0__py3-none-any.whl

aiagents4pharma/talk2biomodels/api/uniprot.py

@@ -1,10 +1,11 @@
 """
 This module contains the API for fetching uniprot database
 """
-from typing import List, Dict
+
 import requests
 
-def search_uniprot_labels(identifiers: List[str]) -> Dict[str, str]:
+
+def search_uniprot_labels(identifiers: list[str]) -> dict[str, str]:
     """
     Fetch protein names or labels for a list of UniProt identifiers by making sequential requests.
 
@@ -24,10 +25,10 @@ def search_uniprot_labels(identifiers: List[str]) -> Dict[str, str]:
             response.raise_for_status()
             data = response.json()
             protein_name = (
-                data.get('proteinDescription', {})
-                .get('recommendedName', {})
-                .get('fullName', {})
-                .get('value', 'Name not found')
+                data.get("proteinDescription", {})
+                .get("recommendedName", {})
+                .get("fullName", {})
+                .get("value", "Name not found")
             )
             results[identifier] = protein_name
         except requests.exceptions.RequestException as e:

aiagents4pharma/talk2biomodels/configs/__init__.py

@@ -1,6 +1,5 @@
-'''
+"""
 Import all the modules in the package
-'''
+"""
 
-from . import agents
-from . import tools
+from . import agents, tools

aiagents4pharma/talk2biomodels/configs/agents/__init__.py

@@ -1,5 +1,5 @@
-'''
+"""
 Import all the modules in the package
-'''
+"""
 
 from . import t2b_agent

aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/__init__.py

@@ -1,3 +1,3 @@
-'''
+"""
 Import all the modules in the package
-'''
+"""

aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/default.yaml

@@ -1,7 +1,7 @@
 _target_: agents.t2b_agent.get_app
 state_modifier: >
   You are Talk2BioModels agent.
-  If the user asks for the uploaded model, 
+  If the user asks for the uploaded model,
   then pass the use_uploaded_model argument
   as True. If the user asks for simulation
   or param_scan or steady state, suggest a

aiagents4pharma/talk2biomodels/configs/config.yaml

@@ -3,4 +3,4 @@ defaults:
   - agents/t2b_agent: default
   - tools/ask_question: default
   - tools/get_annotation: default
-  - tools/custom_plotter: default
+  - tools/custom_plotter: default

aiagents4pharma/talk2biomodels/configs/tools/__init__.py

@@ -1,6 +1,5 @@
-'''
+"""
 Import all the modules in the package
-'''
-from . import ask_question
-from . import get_annotation
-from . import custom_plotter
+"""
+
+from . import ask_question, custom_plotter, get_annotation

aiagents4pharma/talk2biomodels/configs/tools/ask_question/__init__.py

@@ -1,3 +1,3 @@
-'''
+"""
 Import all the modules in the package
-'''
+"""

aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml

@@ -13,7 +13,7 @@ steady_state_prompt: >
   1. If the user wants to know the time taken by the model to reach
   steady state, you should look at the `steady_state_transition_time`
   column of the data for the model species.
-  
+
   2. The highest value in the column `steady_state_transition_time`
   is the time taken by the model to reach steady state.
 
@@ -28,4 +28,3 @@ simulation_prompt: >
   each time point.
 
   3. Please use the units provided below to answer the questions.
-  

aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/__init__.py

@@ -1,3 +1,3 @@
-'''
+"""
 Import all the modules in the package
-'''
+"""

aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/default.yaml

@@ -5,4 +5,4 @@ system_prompt_custom_header: >
   If the user asks for very specific species (for example, using the
   keyword `only` or `exactly` in the question), set this attribute to
   correspond strictly to the species available in the simulation results,
-  otherwise set it to None.
+  otherwise set it to None.

aiagents4pharma/talk2biomodels/configs/tools/get_annotation/__init__.py

@@ -1,3 +1,3 @@
-'''
+"""
 Import all the modules in the package
-'''
+"""

aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml

@@ -5,4 +5,4 @@ prompt: >
   If none of the species match the user question, return None.
   If the user asks for all species, return all species.
   If the user does not specify any species or simpley asks for
-  model annotations, return all species.
+  model annotations, return all species.

aiagents4pharma/talk2biomodels/install.md

@@ -0,0 +1,63 @@
+# Talk2BioModels
+
+## Installation
+
+### Docker (stable-release)
+
+_This agent is available on Docker Hub._
+
+### Run via `docker run`
+
+```sh
+docker run -d \
+  --name talk2biomodels \
+  -e OPENAI_API_KEY=<your_openai_api_key> \
+  -e NVIDIA_API_KEY=<your_nvidia_api_key> \
+  -p 8501:8501 \
+  virtualpatientengine/talk2biomodels
+```
+
+### Access the Web UI
+
+Once started, open:
+
+```
+http://localhost:8501
+```
+
+---
+
+## Environment Variables
+
+- `OPENAI_API_KEY` – required
+- `NVIDIA_API_KEY` – required
+
+---
+
+## Get Key
+
+- `NVIDIA_API_KEY` – required (obtain a free key at [https://build.nvidia.com/explore/discover](https://build.nvidia.com/explore/discover))
+
+**LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_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).
+If you skip the previous step, it will default to the name `default`.
+`xxxx` will be the 4-digit ID created for the session._
+
+---
+
+## Running Multiple Agents
+
+By default, this agent listens on port `8501`. To run another agent on a different port, map a different host port:
+
+```sh
+docker run -d \
+  --name talk2biomodels \
+  -e OPENAI_API_KEY=<your_openai_api_key> \
+  -e NVIDIA_API_KEY=<your_nvidia_api_key> \
+  -p 8502:8501 \
+  virtualpatientengine/talk2biomodels
+```
+
+Then visit: [http://localhost:8502](http://localhost:8502)

aiagents4pharma/talk2biomodels/models/__init__.py

@@ -1,5 +1,5 @@
-'''
+"""
 This file is used to import all the models in the package.
-'''
-from . import basico_model
-from . import sys_bio_model
+"""
+
+from . import basico_model, sys_bio_model

aiagents4pharma/talk2biomodels/models/basico_model.py

@@ -6,30 +6,34 @@ using the basico package.
 """
 
 import logging
-from typing import Optional, Dict, Union
-from pydantic import Field, model_validator
-import pandas as pd
+
 import basico
+import pandas as pd
+from pydantic import Field, model_validator
+
 from .sys_bio_model import SysBioModel
 
 # Initialize logger
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
+
 class BasicoModel(SysBioModel):
     """
     Model that loads and simulates SBML models using the basico package.
     Can load models from an SBML file or download them using a BioModels biomodel_id.
     """
-    biomodel_id: Optional[Union[int, str]] = Field(None,
-                                description="BioModels model ID to download and load")
-    sbml_file_path: Optional[str] = Field(None, description="Path to an SBML file to load")
-    simulation_results: Optional[str] = None
-    name: Optional[str] = Field("", description="Name of the model")
-    description: Optional[str] = Field("", description="Description of the model")
+
+    biomodel_id: int | str | None = Field(
+        None, description="BioModels model ID to download and load"
+    )
+    sbml_file_path: str | None = Field(None, description="Path to an SBML file to load")
+    simulation_results: str | None = None
+    name: str | None = Field("", description="Name of the model")
+    description: str | None = Field("", description="Description of the model")
 
     # Additional attribute not included in the schema
-    copasi_model: Optional[object] = None  # Holds the loaded Copasi model
+    copasi_model: object | None = None  # Holds the loaded Copasi model
 
     @model_validator(mode="after")
     def check_biomodel_id_or_sbml_file_path(self):
@@ -49,7 +53,7 @@ class BasicoModel(SysBioModel):
             self.name = basico.model_info.get_model_name(model=self.copasi_model)
         return self
 
-    def update_parameters(self, parameters: Dict[str, Union[float, int]]) -> None:
+    def update_parameters(self, parameters: dict[str, float | int]) -> None:
         """
         Update model parameters with new values.
         """
@@ -63,35 +67,39 @@ class BasicoModel(SysBioModel):
             df_all_species = basico.model_info.get_species(model=self.copasi_model)
             # if param is a kinetic parameter
             if param_name in df_all_params.index.tolist():
-                basico.model_info.set_parameters(name=param_name,
-                                            exact=True,
-                                            initial_value=param_value,
-                                            model=self.copasi_model)
+                basico.model_info.set_parameters(
+                    name=param_name,
+                    exact=True,
+                    initial_value=param_value,
+                    model=self.copasi_model,
+                )
             # if param is a species
             elif param_name in df_all_species.index.tolist():
-                basico.model_info.set_species(name=param_name,
-                                            exact=True,
-                                            initial_concentration=param_value,
-                                            model=self.copasi_model)
+                basico.model_info.set_species(
+                    name=param_name,
+                    exact=True,
+                    initial_concentration=param_value,
+                    model=self.copasi_model,
+                )
             else:
                 logger.error("Parameter/Species %s not found in the model.", param_name)
                 raise ValueError(f"Parameter/Species {param_name} not found in the model.")
 
-    def simulate(self, duration: Union[int, float] = 10, interval: int = 10) -> pd.DataFrame:
+    def simulate(self, duration: int | float = 10, interval: int = 10) -> pd.DataFrame:
         """
         Simulate the COPASI model over a specified range of time points.
-        
+
         Args:
             duration: Duration of the simulation in time units.
             interval: Interval between time points in the simulation.
-        
+
         Returns:
             Pandas DataFrame with time-course simulation results.
         """
         # Run the simulation and return results
-        df_result = basico.run_time_course(model=self.copasi_model,
-                                        intervals=interval,
-                                        duration=duration)
+        df_result = basico.run_time_course(
+            model=self.copasi_model, intervals=interval, duration=duration
+        )
         # # Replace curly braces in column headers with square brackets
         # # Because curly braces in the world of LLMS are used for
         # # structured output
@@ -104,14 +112,14 @@ class BasicoModel(SysBioModel):
         # Return copy of the simulation results
         return df_result.copy()
 
-    def get_model_metadata(self) -> Dict[str, Union[str, int]]:
+    def get_model_metadata(self) -> dict[str, str | int]:
         """
         Retrieve metadata specific to the COPASI model.
-        
+
         Returns:
             Dictionary of model metadata.
         """
         return {
             "Model Type": "SBML Model (COPASI)",
-            "Parameter Count": len(basico.get_parameters())
+            "Parameter Count": len(basico.get_parameters()),
         }

aiagents4pharma/talk2biomodels/models/sys_bio_model.py

@@ -1,21 +1,23 @@
-'''
+"""
 An abstract base class for BioModels in the BioModels repository.
-'''
+"""
 
 from abc import ABC, abstractmethod
-from typing import List, Dict, Union, Optional
+
 from pydantic import BaseModel, Field, model_validator
 
+
 class SysBioModel(ABC, BaseModel):
     """
     Abstract base class for BioModels in the BioModels repository.
     This class serves as a general structure for models, allowing
     different mathematical approaches to be implemented in subclasses.
     """
-    biomodel_id: Optional[int] = Field(None, description="BioModel ID of the model")
-    sbml_file_path: Optional[str] = Field(None, description="Path to an SBML file")
-    name: Optional[str] = Field(..., description="Name of the model")
-    description: Optional[str] = Field("", description="Description of the model")
+
+    biomodel_id: int | None = Field(None, description="BioModel ID of the model")
+    sbml_file_path: str | None = Field(None, description="Path to an SBML file")
+    name: str | None = Field(..., description="Name of the model")
+    description: str | None = Field("", description="Description of the model")
 
     @model_validator(mode="after")
     def check_biomodel_id_or_sbml_file_path(self):
@@ -27,7 +29,7 @@ class SysBioModel(ABC, BaseModel):
         return self
 
     @abstractmethod
-    def get_model_metadata(self) -> Dict[str, Union[str, int]]:
+    def get_model_metadata(self) -> dict[str, str | int]:
         """
         Abstract method to retrieve metadata of the model.
         This method should return a dictionary containing model metadata.
@@ -35,8 +37,9 @@ class SysBioModel(ABC, BaseModel):
         Returns:
             dict: Dictionary with model metadata
         """
+
     @abstractmethod
-    def update_parameters(self, parameters: Dict[str, Union[float, int]]) -> None:
+    def update_parameters(self, parameters: dict[str, float | int]) -> None:
         """
         Abstract method to update model parameters.
 
@@ -45,7 +48,7 @@ class SysBioModel(ABC, BaseModel):
         """
 
     @abstractmethod
-    def simulate(self, duration: Union[int, float]) -> List[float]:
+    def simulate(self, duration: int | float) -> list[float]:
         """
         Abstract method to run a simulation of the model.
 

aiagents4pharma/talk2biomodels/states/__init__.py

@@ -1,5 +1,6 @@
-'''
+"""
 This file is used to import all the modules in the package.
-'''
+"""
+
 # import everything from the module
 from . import state_talk2biomodels

aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py

@@ -1,33 +1,37 @@
 #!/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
-from langchain_core.language_models import BaseChatModel
+from typing import Annotated
+
 from langchain_core.embeddings import Embeddings
+from langchain_core.language_models import BaseChatModel
+from langgraph.prebuilt.chat_agent_executor import AgentState
+
 
 def add_data(data1: dict, data2: dict) -> dict:
     """
     A reducer function to merge two dictionaries.
     """
-    left_idx_by_name = {data['name']: idx for idx, data in enumerate(data1)}
+    left_idx_by_name = {data["name"]: idx for idx, data in enumerate(data1)}
     merged = data1.copy()
     for data in data2:
-        idx = left_idx_by_name.get(data['name'])
+        idx = left_idx_by_name.get(data["name"])
         if idx is not None:
             merged[idx] = data
         else:
             merged.append(data)
     return merged
 
+
 class Talk2Biomodels(AgentState):
     """
     The state for the Talk2BioModels agent.
     """
+
     llm_model: BaseChatModel
     text_embedding_model: Embeddings
     pdf_file_name: str
@@ -41,4 +45,4 @@ class Talk2Biomodels(AgentState):
     dic_simulated_data: Annotated[list[dict], add_data]
     dic_scanned_data: Annotated[list[dict], add_data]
     dic_steady_state_data: Annotated[list[dict], add_data]
-    dic_annotations_data : Annotated[list[dict], add_data]
+    dic_annotations_data: Annotated[list[dict], add_data]