aiagents4pharma 1.22.0__py3-none-any.whl → 1.22.2__py3-none-any.whl

aiagents4pharma/talk2biomodels/configs/config.yaml

@@ -2,4 +2,5 @@ defaults:
   - _self_
   - agents/t2b_agent: default
   - tools/ask_question: default
-  - tools/get_annotation: default
+  - tools/get_annotation: default
+  - tools/custom_plotter: default

aiagents4pharma/talk2biomodels/configs/tools/__init__.py

@@ -3,3 +3,4 @@ Import all the modules in the package
 '''
 from . import ask_question
 from . import get_annotation
+from . import custom_plotter

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

@@ -0,0 +1,3 @@
+'''
+Import all the modules in the package
+'''

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

@@ -0,0 +1,8 @@
+system_prompt_custom_header: >
+  You are custom plotter tool. You can extract species from the given
+  list of species names based on user question. If no species is relevant,
+  set the attribute `relevant_species` to None.
+  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.

aiagents4pharma/talk2biomodels/models/basico_model.py

@@ -21,7 +21,8 @@ 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[int] = Field(None, description="BioModels model ID to download and load")
+    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")
@@ -57,19 +58,24 @@ class BasicoModel(SysBioModel):
             # check if the param_name is not None
             if param_name is None:
                 continue
-            # if param is a kinetic parameter
+            # Extract all parameters and species from the model
             df_all_params = basico.model_info.get_parameters(model=self.copasi_model)
+            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)
             # if param is a species
-            else:
+            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)
+            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:
         """

aiagents4pharma/talk2biomodels/tests/test_basico_model.py

@@ -26,8 +26,15 @@ def test_with_biomodel_id(model):
     assert df_parameters.loc['KmPFKF6P', 'initial_value'] == 1.5
     # check if the simulation results are a pandas DataFrame object
     assert isinstance(model.simulate(duration=2, interval=2), pd.DataFrame)
+    # Pass a None value to the update_parameters method
+    # and it should not raise an error
     model.update_parameters(parameters={None: None})
+    # check if the model description is updated
     assert model.description == basico.biomodels.get_model_info(model.biomodel_id)["description"]
+    # check if an error is raised if an invalid species/parameter (`Pyruv`)
+    # is passed and it should raise a ValueError
+    with pytest.raises(ValueError):
+        model.update_parameters(parameters={'Pyruv': 0.5})
 
 def test_with_sbml_file():
     """

aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py

@@ -55,3 +55,34 @@ def test_model_with_no_species():
                 test_condition = True
                 break
     assert test_condition
+
+def test_model_with_no_parameters():
+    '''
+    Test the get_modelinfo tool with a model that does not
+    return any parameters.
+
+    This should raise a tool error.
+    '''
+    unique_id = 12345
+    app = get_app(unique_id)
+    config = {"configurable": {"thread_id": unique_id}}
+    prompt = "Extract all parameters from model 10"
+    # Test the tool get_modelinfo
+    app.invoke(
+                {"messages": [HumanMessage(content=prompt)]},
+                config=config
+            )
+    current_state = app.get_state(config)
+    reversed_messages = current_state.values["messages"][::-1]
+    # Loop through the reversed messages until a
+    # ToolMessage is found.
+    test_condition = False
+    for msg in reversed_messages:
+        # Check if the message is a ToolMessage from the get_modelinfo tool
+        if isinstance(msg, ToolMessage) and msg.name == "get_modelinfo":
+            # Check if the message is an error message
+            if (msg.status == "error" and
+                "ValueError('Unable to extract parameters from the model.')" in msg.content):
+                test_condition = True
+                break
+    assert test_condition

aiagents4pharma/talk2biomodels/tests/test_integration.py

@@ -20,7 +20,7 @@ def test_integration():
     # ##########################################
     # ## Test simulate_model tool
     # ##########################################
-    prompt = '''Simulate the model 537 for 100 hours and time intervals
+    prompt = '''Simulate the model BIOMD0000000537 for 100 hours and time intervals
     100 with an initial concentration of `DoseQ2W` set to 300 and `Dose`
     set to 0. Reset the concentration of `Ab{serum}` to 100 every 25 hours.'''
     # Test the tool get_modelinfo
@@ -51,12 +51,12 @@ def test_integration():
     assert '211' in assistant_msg
 
     ##########################################
-    # Test custom_plotter tool when the
+    # Test the custom_plotter tool when the
     # simulation results are available but
     # the species is not available
     ##########################################
     prompt = """Call the custom_plotter tool to make a plot
-        showing only species `TP53` and `Pyruvate`. Let me
+        showing only species 'Infected cases'. Let me
         know if these species were not found. Do not
         invoke any other tool."""
     # Update state
@@ -117,7 +117,7 @@ def test_integration():
             # These may contain additional visuals that
             # need to be displayed to the user.
             if msg.name == "custom_plotter":
-                predicted_artifact = msg.artifact
+                predicted_artifact = msg.artifact['dic_data']
                 break
     # Convert the artifact into a pandas dataframe
     # for easy comparison

aiagents4pharma/talk2biomodels/tests/test_load_biomodel.py

@@ -0,0 +1,32 @@
+'''
+Test cases for Talk2Biomodels.
+'''
+
+import pytest
+from ..tools.load_biomodel import ModelData
+
+def test_model_data_valid_biomodel_id():
+    '''
+    Test the ModelData class with valid
+    biomodel
+    '''
+    # Test with string biomodel_id starting with 'BIOMD'
+    model_data = ModelData(biomodel_id='BIOMD0000000537')
+    assert model_data.biomodel_id == 'BIOMD0000000537'
+
+    # Test with string biomodel_id starting with 'MODEL'
+    model_data = ModelData(biomodel_id='MODEL0000000537')
+    assert model_data.biomodel_id == 'MODEL0000000537'
+
+def test_model_data_invalid_biomodel_id():
+    '''
+    Test the ModelData class with invalid
+    biomodel
+    '''
+    # Test with invalid string biomodel_id
+    with pytest.raises(ValueError):
+        ModelData(biomodel_id='12345')
+
+    # Test with float biomodel_id
+    with pytest.raises(ValueError):
+        ModelData(biomodel_id=123.45)

aiagents4pharma/talk2biomodels/tests/test_search_models.py

@@ -2,7 +2,7 @@
 Test cases for Talk2Biomodels search models tool.
 '''
 
-from langchain_core.messages import HumanMessage
+from langchain_core.messages import HumanMessage, ToolMessage
 from langchain_nvidia_ai_endpoints import ChatNVIDIA
 from ..agents.t2b_agent import get_app
 
@@ -22,9 +22,15 @@ def test_search_models_tool():
                         {"messages": [HumanMessage(content=prompt)]},
                         config=config
                     )
-    assistant_msg = response["messages"][-1].content
-    # Check if the assistant message is a string
-    assert isinstance(assistant_msg, str)
-    # Check if the assistant message contains the
-    # biomodel id BIO0000000537
-    assert "BIOMD0000000537" in assistant_msg
+    # Extract the assistant artifact which contains
+    # all the search results
+    found_model_537 = False
+    for msg in response["messages"]:
+        if isinstance(msg, ToolMessage) and msg.name == "search_models":
+            msg_artifact = msg.artifact
+            for model in msg_artifact["dic_data"]:
+                if model["id"] == "BIOMD0000000537":
+                    found_model_537 = True
+            break
+    # Check if the model BIOMD0000000537 is found
+    assert found_model_537

aiagents4pharma/talk2biomodels/tools/custom_plotter.py

@@ -1,25 +1,81 @@
 #!/usr/bin/env python3
 
 """
-Tool for plotting a custom figure.
+Tool for plotting a custom y-axis of a simulation plot.
 """
 
 import logging
 from typing import Type, Annotated, List, Tuple, Union, Literal
 from pydantic import BaseModel, Field
+import hydra
 import pandas as pd
 from langchain_core.tools import BaseTool
+from langchain_core.prompts import ChatPromptTemplate
 from langgraph.prebuilt import InjectedState
+from .load_biomodel import ModelData, load_biomodel
+from .utils import get_model_units
 
 # Initialize logger
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
+def extract_relevant_species(question, species_names, state):
+    """
+    Extract the relevant species from the user question.
+
+    Args:
+        question (str): The user question.
+        species_names (list): The species names available in the simulation results.
+        state (dict): The state of the graph.
+
+    Returns:
+        CustomHeader: The relevant species
+    """
+    # In the following code, we extract the species
+    # from the user question. We use Literal to restrict
+    # the species names to the ones available in the
+    # simulation results.
+    class CustomHeader(BaseModel):
+        """
+        A list of species based on user question.
+
+        This is a Pydantic model that restricts the species
+        names to the ones available in the simulation results.
+        
+        If no species is relevant, set the attribute
+        `relevant_species` to None.
+        """
+        relevant_species: Union[None, List[Literal[*species_names]]] = Field(
+                description="This is a list of species based on the user question."
+                "It is restricted to the species available in the simulation results."
+                "If no species is relevant, set this attribute to None."
+                "If the user asks for very specific species (for example, using the"
+                "keyword `only` in the question), set this attribute to correspond "
+                "to the species available in the simulation results, otherwise set it to None."
+                )
+    # Load hydra configuration
+    with hydra.initialize(version_base=None, config_path="../configs"):
+        cfg = hydra.compose(config_name='config',
+                            overrides=['tools/custom_plotter=default'])
+        cfg = cfg.tools.custom_plotter
+    # Get the system prompt
+    system_prompt = cfg.system_prompt_custom_header
+    # Create an instance of the LLM model
+    logging.log(logging.INFO, "LLM model: %s", state['llm_model'])
+    llm = state['llm_model']
+    llm_with_structured_output = llm.with_structured_output(CustomHeader)
+    prompt = ChatPromptTemplate.from_messages([("system", system_prompt),
+                                               ("human", "{input}")])
+    few_shot_structured_llm = prompt | llm_with_structured_output
+    return few_shot_structured_llm.invoke(question)
+
 class CustomPlotterInput(BaseModel):
     """
-    Input schema for the PlotImage tool.
+    Input schema for the custom plotter tool.
     """
     question: str = Field(description="Description of the plot")
+    sys_bio_model: ModelData = Field(description="model data",
+                                     default=None)
     simulation_name: str = Field(description="Name assigned to the simulation")
     state: Annotated[dict, InjectedState]
 
@@ -31,15 +87,20 @@ class CustomPlotterInput(BaseModel):
 # can lead to unexpected behavior.
 class CustomPlotterTool(BaseTool):
     """
-    Tool for making custom plots
+    Tool for custom plotting the y-axis of a plot.
     """
     name: str = "custom_plotter"
-    description: str = "A tool to make custom plots of the simulation results"
+    description: str = '''A visualization tool designed to extract and display a subset
+                        of the larger simulation plot generated by the simulate_model tool.
+                        It allows users to specify particular species for the y-axis, 
+                        providing a more targeted view of key species without the clutter 
+                        of the full plot.'''
     args_schema: Type[BaseModel] = CustomPlotterInput
     response_format: str = "content_and_artifact"
 
     def _run(self,
              question: str,
+             sys_bio_model: ModelData,
              simulation_name: str,
              state: Annotated[dict, InjectedState]
              ) -> Tuple[str, Union[None, List[str]]]:
@@ -48,12 +109,17 @@ class CustomPlotterTool(BaseTool):
 
         Args:
             question (str): The question about the custom plot.
+            sys_bio_model (ModelData): The model data.
+            simulation_name (str): The name assigned to the simulation.
             state (dict): The state of the graph.
 
         Returns:
             str: The answer to the question
         """
-        logger.log(logging.INFO, "Calling custom_plotter tool %s", question)
+        logger.log(logging.INFO, "Calling custom_plotter tool %s, %s", question, sys_bio_model)
+        # Load the model
+        sbml_file_path = state['sbml_file_path'][-1] if len(state['sbml_file_path']) > 0 else None
+        model_object = load_biomodel(sys_bio_model, sbml_file_path=sbml_file_path)
         dic_simulated_data = {}
         for data in state["dic_simulated_data"]:
             for key in data:
@@ -71,33 +137,9 @@ class CustomPlotterTool(BaseTool):
         # Exclude the time column
         species_names.remove('Time')
         logging.log(logging.INFO, "Species names: %s", species_names)
-        # In the following code, we extract the species
-        # from the user question. We use Literal to restrict
-        # the species names to the ones available in the
-        # simulation results.
-        class CustomHeader(BaseModel):
-            """
-            A list of species based on user question.
-
-            This is a Pydantic model that restricts the species
-            names to the ones available in the simulation results.
-            
-            If no species is relevant, set the attribute
-            `relevant_species` to None.
-            """
-            relevant_species: Union[None, List[Literal[*species_names]]] = Field(
-                    description="This is a list of species based on the user question."
-                    "It is restricted to the species available in the simulation results."
-                    "If no species is relevant, set this attribute to None."
-                    "If the user asks for very specific species (for example, using the"
-                    "keyword `only` in the question), set this attribute to correspond "
-                    "to the species available in the simulation results, otherwise set it to None."
-                    )
-        # Create an instance of the LLM model
-        logging.log(logging.INFO, "LLM model: %s", state['llm_model'])
-        llm = state['llm_model']
-        llm_with_structured_output = llm.with_structured_output(CustomHeader)
-        results = llm_with_structured_output.invoke(question)
+        # Extract the relevant species from the user question
+        results = extract_relevant_species(question, species_names, state)
+        print (results)
         if results.relevant_species is None:
             raise ValueError("No species found in the simulation results \
                              that matches the user prompt.")
@@ -110,4 +152,6 @@ class CustomPlotterTool(BaseTool):
         logging.info("Extracted species: %s", extracted_species)
         # Include the time column
         extracted_species.insert(0, 'Time')
-        return f"Custom plot {simulation_name}", df[extracted_species].to_dict(orient='records')
+        return f"Custom plot {simulation_name}",{
+                            'dic_data': df[extracted_species].to_dict(orient='records')
+                            }| get_model_units(model_object)

aiagents4pharma/talk2biomodels/tools/get_modelinfo.py

@@ -100,6 +100,8 @@ class GetModelInfoTool(BaseTool):
         # Extract parameters from the model
         if requested_model_info.parameters:
             df_parameters = basico.model_info.get_parameters(model=model_obj.copasi_model)
+            if df_parameters is None:
+                raise ValueError("Unable to extract parameters from the model.")
             # Convert index into a column
             df_parameters.reset_index(inplace=True)
             dic_results['Parameters'] = df_parameters[

aiagents4pharma/talk2biomodels/tools/load_biomodel.py

@@ -4,15 +4,25 @@
 Function for loading the BioModel.
 """
 
-from dataclasses import dataclass
+from typing import Annotated, Any, Union
+from pydantic import BaseModel, BeforeValidator
 from ..models.basico_model import BasicoModel
 
-@dataclass
-class ModelData:
+def ensure_biomodel_id(value: Any) -> Any:
     """
-    Dataclass for storing the model data.
+    Ensure that the biomodel_id is an integer or a string starting with 'BIOMD' or 'MODEL'.
     """
-    biomodel_id: int = None
+    if isinstance(value, int):
+        return value
+    if isinstance(value, str) and (value.startswith("BIOMD") or value.startswith("MODEL")):
+        return value
+    raise ValueError("biomodel_id must be an integer or a string starting with 'BIOMD' or 'MODEL'.")
+
+class ModelData(BaseModel):
+    """
+    Base model for the model data.
+    """
+    biomodel_id: Annotated[Union[int, str], BeforeValidator(ensure_biomodel_id)] = None
     # sbml_file_path: Optional[str] = None
     use_uploaded_sbml_file: bool = False
 

aiagents4pharma/talk2biomodels/tools/parameter_scan.py

@@ -17,6 +17,7 @@ from langchain_core.messages import ToolMessage
 from langchain_core.tools.base import InjectedToolCallId
 from .load_biomodel import ModelData, load_biomodel
 from .load_arguments import TimeData, SpeciesInitialData
+from .utils import get_model_units
 
 # Initialize logger
 logging.basicConfig(level=logging.INFO)
@@ -119,7 +120,11 @@ def run_parameter_scan(model_object,
     """
     # Extract all parameter names from the model
     df_all_parameters = basico.model_info.get_parameters(model=model_object.copasi_model)
-    all_parameters = df_all_parameters.index.tolist()
+    all_parameters = []
+    if df_all_parameters is not None:
+        # For example model 10 in the BioModels database
+        # has no parameters
+        all_parameters = df_all_parameters.index.tolist()
 
     # Extract all species name from the model
     df_all_species = basico.model_info.get_species(model=model_object.copasi_model)
@@ -280,7 +285,8 @@ class ParameterScanTool(BaseTool):
                 "messages": [
                     ToolMessage(
                         content=f"Parameter scan results of {arg_data.experiment_name}",
-                        tool_call_id=tool_call_id
+                        tool_call_id=tool_call_id,
+                        artifact=get_model_units(model_object)
                         )
                     ],
                 }

aiagents4pharma/talk2biomodels/tools/search_models.py

@@ -7,11 +7,12 @@ Tool for searching models based on search query.
 from typing import Type, Annotated
 import logging
 from pydantic import BaseModel, Field
+import pandas as pd
 from basico import biomodels
+from langgraph.types import Command
 from langchain_core.tools import BaseTool
-from langchain_core.output_parsers import StrOutputParser
-from langchain_core.prompts import ChatPromptTemplate
-from langgraph.prebuilt import InjectedState
+from langchain_core.messages import ToolMessage
+from langchain_core.tools.base import InjectedToolCallId
 
 # Initialize logger
 logging.basicConfig(level=logging.INFO)
@@ -22,7 +23,10 @@ class SearchModelsInput(BaseModel):
     Input schema for the search models tool.
     """
     query: str = Field(description="Search models query", default=None)
-    state: Annotated[dict, InjectedState]
+    num_query: int = Field(description="Top number of models to search",
+                           default=10,
+                           le=100)
+    tool_call_id: Annotated[str, InjectedToolCallId]
 
 # Note: It's important that every field has type hints. BaseTool is a
 # Pydantic class and not having type hints can lead to unexpected behavior.
@@ -31,50 +35,51 @@ class SearchModelsTool(BaseTool):
     Tool for returning the search results based on the search query.
     """
     name: str = "search_models"
-    description: str = "Search models in the BioMmodels database based on keywords."
+    description: str = "Search for only manually curated models in "
+    "the BioMmodels database based on keywords."
     args_schema: Type[BaseModel] = SearchModelsInput
     return_direct: bool = False
 
     def _run(self,
-             query: str,
-             state: Annotated[dict, InjectedState]) -> dict:
+             tool_call_id: Annotated[str, InjectedToolCallId],
+             query: str = None,
+             num_query: int = 10) -> dict:
         """
         Run the tool.
 
         Args:
             query (str): The search query.
+            num_query (int): The number of models to search.
+            tool_call_id (str): The tool call ID.
 
         Returns:
             dict: The answer to the question in the form of a dictionary.
         """
-        logger.log(logging.INFO, "Searching models with the query and model: %s, %s",
-                   query, state['llm_model'])
-        search_results = biomodels.search_for_model(query)
-        llm = state['llm_model']
-        # Check if run_manager's metadata has the key 'prompt_content'
-        prompt_content = f'''
-                        Convert the input into a table.
-
-                        The table must contain the following columns:
-                        - #
-                        - BioModel ID
-                        - BioModel Name
-                        - Format
-                        - Submission Date
-
-                        Additional Guidelines:
-                        - The column # must contain the row number starting from 1.
-                        - Embed the url for each BioModel ID in the table 
-                        in the first column in the markdown format.
-                        - The Submission Date must be in the format YYYY-MM-DD.
-
-                        Input:
-                        {input}.
-                        '''
-        prompt_template = ChatPromptTemplate.from_messages(
-            [("system", prompt_content),
-             ("user", "{input}")]
-        )
-        parser = StrOutputParser()
-        chain = prompt_template | llm | parser
-        return chain.invoke({"input": search_results})
+        logger.log(logging.INFO, "Searching models with the query and number %s, %s",
+                   query, num_query)
+        # Search for models based on the query
+        search_results = biomodels.search_for_model(query, num_results=num_query)
+        # Convert the search results to a pandas DataFrame
+        df = pd.DataFrame(search_results)
+        # Prepare a message to return
+        first_n = min(3, len(search_results))
+        content = f"Found {len(search_results)} manually curated models"
+        content += f" for the query: {query}."
+        # Pass the first 3 models to the LLM
+        # to avoid hallucinations
+        content += f" Here is the summary of the first {first_n} models:"
+        for i in range(first_n):
+            content += f"\nModel {i+1}: {search_results[i]['name']} (ID: {search_results[i]['id']})"
+        # Return the updated state of the tool
+        return Command(
+                update={
+                    # update the message history
+                    "messages": [
+                        ToolMessage(
+                            content=content,
+                            tool_call_id=tool_call_id,
+                            artifact={'dic_data': df.to_dict(orient='records')}
+                            )
+                        ],
+                    }
+            )

aiagents4pharma/talk2biomodels/tools/simulate_model.py

@@ -14,6 +14,7 @@ from langchain_core.messages import ToolMessage
 from langchain_core.tools.base import InjectedToolCallId
 from .load_biomodel import ModelData, load_biomodel
 from .load_arguments import ArgumentData, add_rec_events
+from .utils import get_model_units
 
 # Initialize logger
 logging.basicConfig(level=logging.INFO)
@@ -116,7 +117,8 @@ class SimulateModelTool(BaseTool):
                 "messages": [
                     ToolMessage(
                         content=f"Simulation results of {arg_data.experiment_name}",
-                        tool_call_id=tool_call_id
+                        tool_call_id=tool_call_id,
+                        artifact=get_model_units(model_object)
                         )
                     ],
                 }

aiagents4pharma/talk2biomodels/tools/steady_state.py

@@ -134,6 +134,7 @@ class SteadyStateTool(BaseTool):
         # Run the parameter scan
         df_steady_state = run_steady_state(model_object,
                                            dic_species_to_be_analyzed_before_experiment)
+        print (df_steady_state)
         # Prepare the dictionary of scanned data
         # that will be passed to the state of the graph
         dic_steady_state_data = {
@@ -160,7 +161,8 @@ class SteadyStateTool(BaseTool):
                         content=f"Steady state analysis of"
                                 f" {arg_data.experiment_name}"
                                 " was successful.",
-                        tool_call_id=tool_call_id
+                        tool_call_id=tool_call_id,
+                        artifact={'dic_data': df_steady_state.to_dict(orient='records')}
                         )
                     ],
                 }

aiagents4pharma/talk2biomodels/tools/utils.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+
+"""
+Utility functions for T2B tools.
+"""
+
+import basico
+
+def get_model_units(model_object):
+    """
+    Get the units of the model.
+
+    Args:
+        model_object: The model object.
+
+    Returns:
+        dict: The units of the model.
+    """
+    model_units = basico.model_info.get_model_units(model=model_object.copasi_model)
+    model_units_y = model_units['quantity_unit']
+    model_units_x = model_units['time_unit']
+    return {'y_axis_label': model_units_y, 'x_axis_label': model_units_x}

{aiagents4pharma-1.22.0.dist-info → aiagents4pharma-1.22.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.22.0
+Version: 1.22.2
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License

{aiagents4pharma-1.22.0.dist-info → aiagents4pharma-1.22.2.dist-info}/RECORD

@@ -7,45 +7,49 @@ aiagents4pharma/talk2biomodels/api/kegg.py,sha256=QzYDAfJ16E7tbHGxP8ZNWRizMkMRS_
 aiagents4pharma/talk2biomodels/api/ols.py,sha256=qq0Qy-gJDxanQW-HfCChDsTQsY1M41ua8hMlTnfuzrA,2202
 aiagents4pharma/talk2biomodels/api/uniprot.py,sha256=aPUAVBR7UYXDuuhDpKezAK2aTMzo-NxFYFq6C0W5u6U,1175
 aiagents4pharma/talk2biomodels/configs/__init__.py,sha256=safyFKhkd5Wlirl9dMZIHWDLTpY2oLw9wjIM7ZtLIHk,88
-aiagents4pharma/talk2biomodels/configs/config.yaml,sha256=X0CMsnx6hHNvV04wsENQSGXadx0aKIy6mziSopVUdZI,116
+aiagents4pharma/talk2biomodels/configs/config.yaml,sha256=ysp8ONR1DVOazxk63S4VA7g4HP9q8xAJ3oMIdcICxSE,150
 aiagents4pharma/talk2biomodels/configs/agents/__init__.py,sha256=_ZoG8snICK2bidWtc2KOGs738LWg9_r66V9mOMnEb-E,71
 aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/default.yaml,sha256=pSViMKwKyMQDm8LzbfIaGdxph73iHYaXMiv5YOuxM7k,536
-aiagents4pharma/talk2biomodels/configs/tools/__init__.py,sha256=B08KWjj7bpizuTETGnnngrEVK4nzdWGREdoCCSw1Sm4,102
+aiagents4pharma/talk2biomodels/configs/tools/__init__.py,sha256=AzOyyV24G1YQ4Tg4Y5IvntvWaqhoKkE04RIKSLqI_SA,131
 aiagents4pharma/talk2biomodels/configs/tools/ask_question/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml,sha256=7k49GkLbPy4v7w5-zfwkgBUPaH6R1IrRPCXvUiUiCKE,1300
+aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
+aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/default.yaml,sha256=14Aic9IDr1eOyeLo_YGMwZL40CYsgqOXix2j9ucB4EA,464
 aiagents4pharma/talk2biomodels/configs/tools/get_annotation/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml,sha256=o5kqLJ5QGJsLMUhAqotudIMhxxNfPUVcDVH1tdRIutU,304
 aiagents4pharma/talk2biomodels/models/__init__.py,sha256=5fTHHm3PVloYPNKXbgNlcPgv3-u28ZquxGydFYDfhJA,122
-aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=PH25FTOuUjsmw_UUxoRb-4kptOYpicEn4GqS0phS3nk,4807
+aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=4LjeHKGcXsdm1gFxs9SGVNDerajZ7REvCeNch0s2pDg,5242
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py,sha256=JeoiGQAvQABHnG0wKR2XBmmxqQdtgO6kxaLDUTUmr1s,2001
 aiagents4pharma/talk2biomodels/states/__init__.py,sha256=YLg1-N0D9qyRRLRqwqfLCLAqZYDtMVZTfI8Y0b_4tbA,139
 aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=S1UtXvocWR8Y9OVUp6pIDFnmaCcjbwmUbW8u79TuGcg,1508
 aiagents4pharma/talk2biomodels/tests/__init__.py,sha256=Jbw5tJxSrjGoaK5IX3pJWDCNzhrVQ10lkYq2oQ_KQD8,45
 aiagents4pharma/talk2biomodels/tests/test_api.py,sha256=7Kz2r5F5tjmn3F0LoM33oP-21W633936YHiyf5toGg0,1716
 aiagents4pharma/talk2biomodels/tests/test_ask_question.py,sha256=rdForKfj2zj2IXl6ntK9_I0AbgsCv8MXOZ2khBnaPms,1620
-aiagents4pharma/talk2biomodels/tests/test_basico_model.py,sha256=y82fpTJMPHwtXxlle1cGQ_2Bewwpxi0aJSVrVAYLhN0,2060
+aiagents4pharma/talk2biomodels/tests/test_basico_model.py,sha256=-2g7HGHXsJeaE06FUI380Br3uh1Wb-JV51mgqcb3GJw,2423
 aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=GbobfjtCAOV0HddM4pb2o3c49Q05fKIM0Ubnf8BRxHM,8273
-aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py,sha256=Y1sFhoMF4mbvlag7D-dEvv6ytjmAqzMLPvSvaVEI_Qk,2045
-aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=XvQmnkIkAcgjmNwsW4FXiCwMMU7fpCpxfqhG2v2KyF4,5170
+aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py,sha256=CIKeIm5FGTCyW-FR2nIo3Tr5AyAdxBelNngkdUd5-kk,3206
+aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=9nYRqpJ_OtmUypuHm4URzoHhcpKEldCEwKxLzh8jcZU,5193
+aiagents4pharma/talk2biomodels/tests/test_load_biomodel.py,sha256=Th5EVlfowwoM0tAu1R2oPISqW7SFduC-TYa3jIqIvC0,892
 aiagents4pharma/talk2biomodels/tests/test_param_scan.py,sha256=vRbnn4uVWFbfZbU4gVCjHi5WDCUrErut8ElzAPE5y84,2648
 aiagents4pharma/talk2biomodels/tests/test_query_article.py,sha256=lArISS111mQUZmjLY82PkRVPSTcN2h8KNF4gpTTvwL0,3185
-aiagents4pharma/talk2biomodels/tests/test_search_models.py,sha256=ttOzN78b06ixYF_SbSyrhQSnmCgOMlSoeG9Q1FeRAis,1028
+aiagents4pharma/talk2biomodels/tests/test_search_models.py,sha256=543uNSIPVLrD1mwH0Ru5l1tlTZ452MIr4aIgCssMw3g,1270
 aiagents4pharma/talk2biomodels/tests/test_simulate_model.py,sha256=GjLE1DZpcKUAFSmoHD86vkfK0b5LJPM8a4WYyraazig,1487
 aiagents4pharma/talk2biomodels/tests/test_steady_state.py,sha256=2bzxj74vekazgLG7hiMALRiqP_4sVmue9cN4zCZ42T8,3556
 aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py,sha256=HSmBBViMi0jYf4gWX21IbppAfDzG0nr_S3KtKS9fZVQ,2165
 aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=6H2HWv5Q4NZYEmw-Ti5KZnJlEqhaC2HXSDZa6kiSl-U,350
 aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=NZwKT7DHc4TW9e8LOkHaRG_nqUs_lEandvi89DTXilQ,4640
-aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=DsnQIKebchy6tgzLZnY7VLVesu3Es-OdqLfW61kIn3A,4762
+aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=gzKUEz28Ioz_0L-FRF_EITDXZItix3j0PryyKQyHEEE,6875
 aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=njxUmFuFwlzY3Doq-XlepGXJTMgnYfs88L4RkKSiptw,13438
-aiagents4pharma/talk2biomodels/tools/get_modelinfo.py,sha256=57dkXrBeRpyiaW3dYkoWIfr6zSsFHcWRhvUVNyLcvUs,6363
+aiagents4pharma/talk2biomodels/tools/get_modelinfo.py,sha256=TPXH70CQ6cQ1UpTUPtc2MXKDAm5mfZX4lj-2CLRzv1Y,6482
 aiagents4pharma/talk2biomodels/tools/load_arguments.py,sha256=bffNIlBDTCSFYiZprA73yi8Jbb8z3Oh2decVNh1UnZc,4162
-aiagents4pharma/talk2biomodels/tools/load_biomodel.py,sha256=pyVzLQoMnuJYEwsjeOlqcUrbU1F1Z-pNlgkhFaoKpy0,689
-aiagents4pharma/talk2biomodels/tools/parameter_scan.py,sha256=aNh94LgBgVXBIczuNkbSsOZ9j54YVEdZWmZbZr7Nk8k,12465
+aiagents4pharma/talk2biomodels/tools/load_biomodel.py,sha256=o-Z_ZqpHy2S-HvMfrB4aI3lrFuYIEG5u0z6uDKOJXak,1215
+aiagents4pharma/talk2biomodels/tools/parameter_scan.py,sha256=-0OzZWoZxMImLNrQReT-PLEIu2sPa4zWg_Pd27EhMsE,12715
 aiagents4pharma/talk2biomodels/tools/query_article.py,sha256=6xfirRRMXN-wxqZxYYbKeEMXLMAHKl5IPShfpoOEBcc,2268
-aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=LdvfCNeiO8fU6lszd7UUzk4NXP6ETuMsCRb2SpXcztw,2841
-aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=qXs9lg9XgA7EaRiX3wBS8w_ug8tI-G3pzhcRg6dTRio,5060
-aiagents4pharma/talk2biomodels/tools/steady_state.py,sha256=j3ckuNlUtv7lT922MbN0JhT9H0JpWAdx2mLPwao6uu8,7123
+aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=uJ16fqTqL-SUgVQ1iXyaM8XA4uDwRtuot933XZ28Z3M,3169
+aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=KfQFDQuHF4cwEGqTPMDNmKSjQRRNSdJZsvqlj37W1A4,5159
+aiagents4pharma/talk2biomodels/tools/steady_state.py,sha256=vGF7SH98mYWSbWAKxhYmzi96Gzw9VhzYMvXXPgAqBYk,7245
+aiagents4pharma/talk2biomodels/tools/utils.py,sha256=iI5WlWcsrjE75zY2BoPAoVtS5NhE7vP6OyRnWil7OHY,520
 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
@@ -158,8 +162,8 @@ aiagents4pharma/talk2scholars/tools/s2/query_results.py,sha256=EUfzRh5Qc_tMl5fDI
 aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py,sha256=Lg1L4HQCN2LaQEyWtLD73O67PMoXkPHi-Y8rCzHS0A4,2499
 aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=mnBQWDuQ50UVw6B-bRuL8Ek1av-pEtdgzVMxpEA2BpI,4296
 aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=xgnUj9W9JkeTvB2VJBJUAnia789GGNGqdqgJ_G16v2s,5120
-aiagents4pharma-1.22.0.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.22.0.dist-info/METADATA,sha256=qMCGdj4nouCcxKZOt2SwH53fDMIgPkoUTirEIvk2Mfs,7789
-aiagents4pharma-1.22.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-aiagents4pharma-1.22.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.22.0.dist-info/RECORD,,
+aiagents4pharma-1.22.2.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.22.2.dist-info/METADATA,sha256=OMtzAMhrSQiB7SpK7-waB0SLh8Je5i5HSHE5J9lY7xQ,7789
+aiagents4pharma-1.22.2.dist-info/WHEEL,sha256=nn6H5-ilmfVryoAQl3ZQ2l8SH5imPWFpm1A5FgEuFV4,91
+aiagents4pharma-1.22.2.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.22.2.dist-info/RECORD,,

{aiagents4pharma-1.22.0.dist-info → aiagents4pharma-1.22.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (75.8.1)
 Root-Is-Purelib: true
 Tag: py3-none-any