aiagents4pharma 1.13.1__py3-none-any.whl → 1.14.1__py3-none-any.whl

aiagents4pharma/talk2biomodels/tools/parameter_scan.py

@@ -6,7 +6,7 @@ Tool for parameter scan.
 
 import logging
 from dataclasses import dataclass
-from typing import Type, Union, List, Annotated
+from typing import Type, Union, List, Annotated, Optional
 import pandas as pd
 import basico
 from pydantic import BaseModel, Field
@@ -16,61 +16,37 @@ from langchain_core.tools import BaseTool
 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
 
 # Initialize logger
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-@dataclass
-class TimeData:
-    """
-    Dataclass for storing the time data.
-    """
-    duration: Union[int, float] = 100
-    interval: Union[int, float] = 10
-
-@dataclass
-class SpeciesData:
-    """
-    Dataclass for storing the species data.
-    """
-    species_name: List[str] = Field(description="species name", default=[])
-    species_concentration: List[Union[int, float]] = Field(
-        description="initial species concentration",
-        default=[])
-
-@dataclass
-class TimeSpeciesNameConcentration:
-    """
-    Dataclass for storing the time, species name, and concentration data.
-    """
-    time: Union[int, float] = Field(description="time point where the event occurs")
-    species_name: str = Field(description="species name")
-    species_concentration: Union[int, float] = Field(
-        description="species concentration at the time point")
-
-@dataclass
-class ReocurringData:
-    """
-    Dataclass for species that reoccur. In other words, the concentration
-    of the species resets to a certain value after a certain time interval.
-    """
-    data: List[TimeSpeciesNameConcentration] = Field(
-        description="time, name, and concentration data of species that reoccur",
-        default=[])
-
 @dataclass
 class ParameterScanData(BaseModel):
     """
     Dataclass for storing the parameter scan data.
     """
-    species_names: List[str] = Field(description="species names to scan",
-                              default=[])
-    parameter_name: str = Field(description="Parameter name to scan",
-                                 default_factory=None)
-    parameter_values: List[Union[int, float]] = Field(
-        description="Parameter values to scan",
-        default_factory=None)
+    species_names: List[str] = Field(
+                    description="species to be observed after each scan."
+                    " These are the species whose concentration"
+                    " will be observed after the parameter scan."
+                    " Do not make up this data.",
+                    default=[])
+    species_parameter_name: str = Field(
+                    description="Species or parameter name to be scanned."
+                    " This is the species or parameter whose value will be scanned"
+                    " over a range of values. This does not include the species"
+                    " that are to be observed after the scan."
+                    "Do not make up this data.",
+                    default=None)
+    species_parameter_values: List[Union[int, float]] = Field(
+                    description="Species or parameter values to be scanned."
+                    " These are the values of the species or parameters that will be"
+                    " scanned over a range of values. This does not include the "
+                    "species that are to be observed after the scan."
+                    "Do not make up this data.",
+                    default=None)
 
 @dataclass
 class ArgumentData:
@@ -78,30 +54,20 @@ class ArgumentData:
     Dataclass for storing the argument data.
     """
     time_data: TimeData = Field(description="time data", default=None)
-    species_data: SpeciesData = Field(
-        description="species name and initial concentration data",
-        default=None)
-    reocurring_data: ReocurringData = Field(
-        description="""Concentration and time data of species that reoccur
-            For example, a species whose concentration resets to a certain value
-            after a certain time interval""")
+    species_to_be_analyzed_before_experiment: Optional[SpeciesInitialData] = Field(
+                    description=" This is the initial condition of the model."
+                    " This does not include species that reoccur or the species"
+                    " whose concentration is to be determined/observed at the end"
+                    " of the experiment. This also does not include the species"
+                    " or the parameter that is to be scanned. Do not make up this data.",
+                    default=None)
     parameter_scan_data: ParameterScanData = Field(
-        description="parameter scan data",
-        default=None)
-    scan_name: str = Field(
-        description="""An AI assigned `_` separated name of
-        the parameter scan experiment based on human query""")
-
-def add_rec_events(model_object, reocurring_data):
-    """
-    Add reocurring events to the model.
-    """
-    for row in reocurring_data.data:
-        tp, sn, sc = row.time, row.species_name, row.species_concentration
-        basico.add_event(f'{sn}_{tp}',
-                            f'Time > {tp}',
-                            [[sn, str(sc)]],
-                            model=model_object.copasi_model)
+                    description="parameter scan data",
+                    default=None)
+    experiment_name: str = Field(
+                    description="An AI assigned `_` separated unique name of"
+                    " the parameter scan experiment based on human query."
+                    " This must be unique for each experiment.")
 
 def make_list_dic_scanned_data(dic_param_scan, arg_data, sys_bio_model, tool_call_id):
     """
@@ -125,13 +91,18 @@ def make_list_dic_scanned_data(dic_param_scan, arg_data, sys_bio_model, tool_cal
         # Prepare the list dictionary of scanned data
         # that will be passed to the state of the graph
         list_dic_scanned_data.append({
-            'name': arg_data.scan_name+':'+species_name,
+            'name': arg_data.experiment_name+':'+species_name,
             'source': sys_bio_model.biomodel_id if sys_bio_model.biomodel_id else 'upload',
             'tool_call_id': tool_call_id,
             'data': df_param_scan.to_dict()
         })
     return list_dic_scanned_data
-def run_parameter_scan(model_object, arg_data, dic_species_data, duration, interval) -> dict:
+
+def run_parameter_scan(model_object,
+                       arg_data,
+                       dic_species_data,
+                       duration,
+                       interval) -> dict:
     """
     Run parameter scan on the model.
 
@@ -146,44 +117,61 @@ def run_parameter_scan(model_object, arg_data, dic_species_data, duration, inter
         dict: Dictionary of parameter scan results. Each key is a species name
         and each value is a DataFrame containing the results of the parameter scan.
     """
-    # Extract all parameter names from the model and verify if the given parameter name is valid
+    # 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()
-    if arg_data.parameter_scan_data.parameter_name not in all_parameters:
-        logger.error(
-            "Invalid parameter name: %s", arg_data.parameter_scan_data.parameter_name)
-        raise ValueError(
-            f"Invalid parameter name: {arg_data.parameter_scan_data.parameter_name}")
-    # Extract all species name from the model and verify if the given species name is valid
+
+    # Extract all species name from the model
     df_all_species = basico.model_info.get_species(model=model_object.copasi_model)
     all_species = df_all_species['display_name'].tolist()
+
+    # Verify if the given species or parameter names to be scanned are valid
+    if arg_data.parameter_scan_data.species_parameter_name not in all_parameters + all_species:
+        logger.error(
+            "Invalid species or parameter name: %s",
+            arg_data.parameter_scan_data.species_parameter_name)
+        raise ValueError(
+            "Invalid species or parameter name: "
+            f"{arg_data.parameter_scan_data.species_parameter_name}.")
+
     # Dictionary to store the parameter scan results
     dic_param_scan_results = {}
+
+    # Loop through the species names that are to be observed
     for species_name in arg_data.parameter_scan_data.species_names:
+        # Verify if the given species name to be observed is valid
         if species_name not in all_species:
             logger.error("Invalid species name: %s", species_name)
-            raise ValueError(f"Invalid species name: {species_name}")
+            raise ValueError(f"Invalid species name: {species_name}.")
+
+        # Copy the model object to avoid modifying the original model
+        model_object_copy = model_object.model_copy()
+
         # Update the fixed model species and parameters
         # These are the initial conditions of the model
         # set by the user
-        model_object.update_parameters(dic_species_data)
+        model_object_copy.update_parameters(dic_species_data)
+
         # Initialize empty DataFrame to store results
         # of the parameter scan
         df_param_scan = pd.DataFrame()
-        for param_value in arg_data.parameter_scan_data.parameter_values:
+
+        # Loop through the parameter that are to be scanned
+        for param_value in arg_data.parameter_scan_data.species_parameter_values:
             # Update the parameter value in the model
-            model_object.update_parameters(
-                {arg_data.parameter_scan_data.parameter_name: param_value})
+            model_object_copy.update_parameters(
+                {arg_data.parameter_scan_data.species_parameter_name: param_value})
             # Simulate the model
-            model_object.simulate(duration=duration, interval=interval)
+            model_object_copy.simulate(duration=duration, interval=interval)
             # If the column name 'Time' is not present in the results DataFrame
             if 'Time' not in df_param_scan.columns:
-                df_param_scan['Time'] = model_object.simulation_results['Time']
+                df_param_scan['Time'] = model_object_copy.simulation_results['Time']
             # Add the simulation results to the results DataFrame
-            col_name = f"{arg_data.parameter_scan_data.parameter_name}_{param_value}"
-            df_param_scan[col_name] = model_object.simulation_results[species_name]
+            col_name = f"{arg_data.parameter_scan_data.species_parameter_name}_{param_value}"
+            df_param_scan[col_name] = model_object_copy.simulation_results[species_name]
 
         logger.log(logging.INFO, "Parameter scan results with shape %s", df_param_scan.shape)
+
         # Add the results of the parameter scan to the dictionary
         dic_param_scan_results[species_name] = df_param_scan
     # return df_param_scan
@@ -210,8 +198,9 @@ class ParameterScanTool(BaseTool):
     Tool for parameter scan.
     """
     name: str = "parameter_scan"
-    description: str = """A tool to perform parameter scan
-        of a list of parameter values for a given species."""
+    description: str = """A tool to perform scanning of a given
+    parameter over a range of values and observe the effect on
+    the concentration of a given species"""
     args_schema: Type[BaseModel] = ParameterScanInput
 
     def _run(self,
@@ -245,12 +234,18 @@ class ParameterScanTool(BaseTool):
         dic_species_data = {}
         if arg_data:
             # Prepare the dictionary of species data
-            if arg_data.species_data is not None:
-                dic_species_data = dict(zip(arg_data.species_data.species_name,
-                                            arg_data.species_data.species_concentration))
-            # Add reocurring events (if any) to the model
-            if arg_data.reocurring_data is not None:
-                add_rec_events(model_object, arg_data.reocurring_data)
+            if arg_data.species_to_be_analyzed_before_experiment is not None:
+                dic_species_data = dict(
+                    zip(
+                        arg_data.species_to_be_analyzed_before_experiment.species_name,
+                        arg_data.species_to_be_analyzed_before_experiment.species_concentration
+                        )
+                    )
+
+            # # Add reocurring events (if any) to the model
+            # if arg_data.reocurring_data is not None:
+            #     add_rec_events(model_object, arg_data.reocurring_data)
+
             # Set the duration and interval
             if arg_data.time_data is not None:
                 duration = arg_data.time_data.duration
@@ -284,7 +279,7 @@ class ParameterScanTool(BaseTool):
                 # update the message history
                 "messages": [
                     ToolMessage(
-                        content=f"Parameter scan results of {arg_data.scan_name}",
+                        content=f"Parameter scan results of {arg_data.experiment_name}",
                         tool_call_id=tool_call_id
                         )
                     ],

aiagents4pharma/talk2biomodels/tools/simulate_model.py

@@ -5,9 +5,7 @@ Tool for simulating a model.
 """
 
 import logging
-from dataclasses import dataclass
-from typing import Type, Union, List, Annotated
-import basico
+from typing import Type, Annotated
 from pydantic import BaseModel, Field
 from langgraph.types import Command
 from langgraph.prebuilt import InjectedState
@@ -15,76 +13,12 @@ from langchain_core.tools import BaseTool
 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
 
 # Initialize logger
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-@dataclass
-class TimeData:
-    """
-    Dataclass for storing the time data.
-    """
-    duration: Union[int, float] = 100
-    interval: Union[int, float] = 10
-
-@dataclass
-class SpeciesData:
-    """
-    Dataclass for storing the species data.
-    """
-    species_name: List[str] = Field(description="species name", default=None)
-    species_concentration: List[Union[int, float]] = Field(
-        description="initial species concentration",
-        default=None)
-
-@dataclass
-class TimeSpeciesNameConcentration:
-    """
-    Dataclass for storing the time, species name, and concentration data.
-    """
-    time: Union[int, float] = Field(description="time point where the event occurs")
-    species_name: str = Field(description="species name")
-    species_concentration: Union[int, float] = Field(
-        description="species concentration at the time point")
-
-@dataclass
-class RecurringData:
-    """
-    Dataclass for storing the species and time data 
-    on reocurring basis.
-    """
-    data: List[TimeSpeciesNameConcentration] = Field(
-        description="species and time data on reocurring basis",
-        default=None)
-
-@dataclass
-class ArgumentData:
-    """
-    Dataclass for storing the argument data.
-    """
-    time_data: TimeData = Field(description="time data", default=None)
-    species_data: SpeciesData = Field(
-        description="species name and initial concentration data",
-        default=None)
-    recurring_data: RecurringData = Field(
-        description="species and time data on reocurring basis",
-        default=None)
-    simulation_name: str = Field(
-        description="""An AI assigned `_` separated name of
-        the simulation based on human query""")
-
-def add_rec_events(model_object, recurring_data):
-    """
-    Add reocurring events to the model.
-    """
-    for row in recurring_data.data:
-        tp, sn, sc = row.time, row.species_name, row.species_concentration
-        basico.add_event(f'{sn}_{tp}',
-                            f'Time > {tp}',
-                            [[sn, str(sc)]],
-                            model=model_object.copasi_model)
-
 class SimulateModelInput(BaseModel):
     """
     Input schema for the SimulateModel tool.
@@ -138,29 +72,30 @@ class SimulateModelTool(BaseTool):
         # of the BasicoModel class
         duration = 100.0
         interval = 10
-        dic_species_data = {}
+        dic_species_to_be_analyzed_before_experiment = {}
         if arg_data:
             # Prepare the dictionary of species data
-            if arg_data.species_data is not None:
-                dic_species_data = dict(zip(arg_data.species_data.species_name,
-                                            arg_data.species_data.species_concentration))
-            # Add recurring events (if any) to the model
-            if arg_data.recurring_data is not None:
-                add_rec_events(model_object, arg_data.recurring_data)
+            if arg_data.species_to_be_analyzed_before_experiment is not None:
+                dic_species_to_be_analyzed_before_experiment = dict(
+                    zip(arg_data.species_to_be_analyzed_before_experiment.species_name,
+                        arg_data.species_to_be_analyzed_before_experiment.species_concentration))
+            # Add reocurring events (if any) to the model
+            if arg_data.reocurring_data is not None:
+                add_rec_events(model_object, arg_data.reocurring_data)
             # Set the duration and interval
             if arg_data.time_data is not None:
                 duration = arg_data.time_data.duration
                 interval = arg_data.time_data.interval
         # Update the model parameters
-        model_object.update_parameters(dic_species_data)
+        model_object.update_parameters(dic_species_to_be_analyzed_before_experiment)
         logger.log(logging.INFO,
                    "Following species/parameters updated in the model %s",
-                   dic_species_data)
+                   dic_species_to_be_analyzed_before_experiment)
         # Simulate the model
         df = model_object.simulate(duration=duration, interval=interval)
         logger.log(logging.INFO, "Simulation results ready with shape %s", df.shape)
         dic_simulated_data = {
-            'name': arg_data.simulation_name,
+            'name': arg_data.experiment_name,
             'source': sys_bio_model.biomodel_id if sys_bio_model.biomodel_id else 'upload',
             'tool_call_id': tool_call_id,
             'data': df.to_dict()
@@ -177,12 +112,10 @@ class SimulateModelTool(BaseTool):
         # Return the updated state of the tool
         return Command(
                 update=dic_updated_state_for_model|{
-                # update the state keys
-                # "dic_simulated_data": df.to_dict(),
                 # update the message history
                 "messages": [
                     ToolMessage(
-                        content=f"Simulation results of {arg_data.simulation_name}",
+                        content=f"Simulation results of {arg_data.experiment_name}",
                         tool_call_id=tool_call_id
                         )
                     ],

aiagents4pharma/talk2biomodels/tools/steady_state.py

@@ -5,8 +5,7 @@ Tool for parameter scan.
 """
 
 import logging
-from dataclasses import dataclass
-from typing import Type, Union, List, Annotated
+from typing import Type, Annotated
 import basico
 from pydantic import BaseModel, Field
 from langgraph.types import Command
@@ -15,83 +14,20 @@ from langchain_core.tools import BaseTool
 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
 
 # Initialize logger
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-@dataclass
-class TimeData:
-    """
-    Dataclass for storing the time data.
-    """
-    duration: Union[int, float] = 100
-    interval: Union[int, float] = 10
-
-@dataclass
-class SpeciesData:
-    """
-    Dataclass for storing the species data.
-    """
-    species_name: List[str] = Field(description="species name", default=[])
-    species_concentration: List[Union[int, float]] = Field(
-        description="initial species concentration",
-        default=[])
-
-@dataclass
-class TimeSpeciesNameConcentration:
-    """
-    Dataclass for storing the time, species name, and concentration data.
-    """
-    time: Union[int, float] = Field(description="time point where the event occurs")
-    species_name: str = Field(description="species name")
-    species_concentration: Union[int, float] = Field(
-        description="species concentration at the time point")
-
-@dataclass
-class ReocurringData:
-    """
-    Dataclass for species that reoccur. In other words, the concentration
-    of the species resets to a certain value after a certain time interval.
-    """
-    data: List[TimeSpeciesNameConcentration] = Field(
-        description="time, name, and concentration data of species that reoccur",
-        default=[])
-
-@dataclass
-class ArgumentData:
-    """
-    Dataclass for storing the argument data.
-    """
-    time_data: TimeData = Field(description="time data", default=None)
-    species_data: SpeciesData = Field(
-        description="species name and initial concentration data")
-    reocurring_data: ReocurringData = Field(
-        description="""Concentration and time data of species that reoccur
-            For example, a species whose concentration resets to a certain value
-            after a certain time interval""")
-    steadystate_name: str = Field(
-        description="""An AI assigned `_` separated name of
-        the steady state experiment based on human query""")
-
-def add_rec_events(model_object, reocurring_data):
-    """
-    Add reocurring events to the model.
-    """
-    for row in reocurring_data.data:
-        tp, sn, sc = row.time, row.species_name, row.species_concentration
-        basico.add_event(f'{sn}_{tp}',
-                            f'Time > {tp}',
-                            [[sn, str(sc)]],
-                            model=model_object.copasi_model)
-
-def run_steady_state(model_object, dic_species_data):
+def run_steady_state(model_object,
+                     dic_species_to_be_analyzed_before_experiment):
     """
     Run the steady state analysis.
 
     Args:
         model_object: The model object.
-        dic_species_data: Dictionary of species data.
+        dic_species_to_be_analyzed_before_experiment: Dictionary of species data.
 
     Returns:
         DataFrame: The results of the steady state analysis.
@@ -99,7 +35,7 @@ def run_steady_state(model_object, dic_species_data):
     # Update the fixed model species and parameters
     # These are the initial conditions of the model
     # set by the user
-    model_object.update_parameters(dic_species_data)
+    model_object.update_parameters(dic_species_to_be_analyzed_before_experiment)
     logger.log(logging.INFO, "Running steady state analysis")
     # Run the steady state analysis
     output = basico.task_steadystate.run_steadystate(model=model_object.copasi_model)
@@ -108,7 +44,30 @@ def run_steady_state(model_object, dic_species_data):
         raise ValueError("A steady state was not found")
     logger.log(logging.INFO, "Steady state analysis successful")
     # Store the steady state results in a DataFrame
-    df_steady_state = basico.model_info.get_species(model=model_object.copasi_model)
+    df_steady_state = basico.model_info.get_species(model=model_object.copasi_model).reset_index()
+    # print (df_steady_state)
+    # Rename the column name to species_name
+    df_steady_state.rename(columns={'name': 'species_name'},
+                           inplace=True)
+    # Rename the column concentration to steady_state_concentration
+    df_steady_state.rename(columns={'concentration': 'steady_state_concentration'},
+                           inplace=True)
+    # Rename the column transition_time to steady_state_transition_time
+    df_steady_state.rename(columns={'transition_time': 'steady_state_transition_time'},
+                           inplace=True)
+    # Drop some columns
+    df_steady_state.drop(columns=
+                         [
+                            'initial_particle_number',
+                            'initial_expression',
+                            'expression',
+                            'particle_number',
+                            'type',
+                            'particle_number_rate',
+                            'key',
+                            'sbml_id',
+                            'display_name'],
+                            inplace=True)
     logger.log(logging.INFO, "Steady state results with shape %s", df_steady_state.shape)
     return df_steady_state
 
@@ -118,10 +77,10 @@ class SteadyStateInput(BaseModel):
     """
     sys_bio_model: ModelData = Field(description="model data",
                                      default=None)
-    arg_data: ArgumentData = Field(description=
-                                   """time, species, and reocurring data
-                                   as well as the steady state data""",
-                                   default=None)
+    arg_data: ArgumentData = Field(
+        description="time, species, and reocurring data"
+                " that must be set before the steady state analysis"
+                " as well as the experiment name", default=None)
     tool_call_id: Annotated[str, InjectedToolCallId]
     state: Annotated[dict, InjectedState]
 
@@ -129,12 +88,10 @@ class SteadyStateInput(BaseModel):
 # Pydantic class and not having type hints can lead to unexpected behavior.
 class SteadyStateTool(BaseTool):
     """
-    Tool for steady state analysis.
+    Tool to bring a model to steady state.
     """
     name: str = "steady_state"
-    description: str = """A tool to simulate a model and perform
-                        steady state analysisto answer questions
-                        about the steady state of species."""
+    description: str = "A tool to bring a model to steady state."
     args_schema: Type[BaseModel] = SteadyStateInput
 
     def _run(self,
@@ -155,7 +112,7 @@ class SteadyStateTool(BaseTool):
         Returns:
             Command: The updated state of the tool.
         """
-        logger.log(logging.INFO, "Calling steady_state tool %s, %s",
+        logger.log(logging.INFO, "Calling the steady_state tool %s, %s",
                    sys_bio_model, arg_data)
         # print (f'Calling steady_state tool {sys_bio_model}, {arg_data}, {tool_call_id}')
         sbml_file_path = state['sbml_file_path'][-1] if len(state['sbml_file_path']) > 0 else None
@@ -164,21 +121,23 @@ class SteadyStateTool(BaseTool):
         # Prepare the dictionary of species data
         # that will be passed to the simulate method
         # of the BasicoModel class
-        dic_species_data = {}
+        dic_species_to_be_analyzed_before_experiment = {}
         if arg_data:
             # Prepare the dictionary of species data
-            if arg_data.species_data is not None:
-                dic_species_data = dict(zip(arg_data.species_data.species_name,
-                                            arg_data.species_data.species_concentration))
+            if arg_data.species_to_be_analyzed_before_experiment is not None:
+                dic_species_to_be_analyzed_before_experiment = dict(
+                    zip(arg_data.species_to_be_analyzed_before_experiment.species_name,
+                        arg_data.species_to_be_analyzed_before_experiment.species_concentration))
             # Add reocurring events (if any) to the model
             if arg_data.reocurring_data is not None:
                 add_rec_events(model_object, arg_data.reocurring_data)
         # Run the parameter scan
-        df_steady_state = run_steady_state(model_object, dic_species_data)
+        df_steady_state = run_steady_state(model_object,
+                                           dic_species_to_be_analyzed_before_experiment)
         # Prepare the dictionary of scanned data
         # that will be passed to the state of the graph
         dic_steady_state_data = {
-            'name': arg_data.steadystate_name,
+            'name': arg_data.experiment_name,
             'source': sys_bio_model.biomodel_id if sys_bio_model.biomodel_id else 'upload',
             'tool_call_id': tool_call_id,
             'data': df_steady_state.to_dict(orient='records')
@@ -198,9 +157,9 @@ class SteadyStateTool(BaseTool):
                 # Update the message history
                 "messages": [
                 ToolMessage(
-                        content=f'''Steady state analysis of
-                                {arg_data.steadystate_name}
-                                are ready''',
+                        content=f"Steady state analysis of"
+                                f" {arg_data.experiment_name}"
+                                " was successful.",
                         tool_call_id=tool_call_id
                         )
                     ],

{aiagents4pharma-1.13.1.dist-info → aiagents4pharma-1.14.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.13.1
+Version: 1.14.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License