aiagents4pharma 1.4.1__py3-none-any.whl → 1.4.3__py3-none-any.whl

aiagents4pharma/talk2biomodels/models/basico_model.py

@@ -6,6 +6,8 @@ using the basico package.
 """
 
 from typing import Optional, Dict, Union
+from time import sleep
+from urllib.error import URLError
 from pydantic import Field, model_validator
 import pandas as pd
 import basico
@@ -33,7 +35,17 @@ class BasicoModel(SysBioModel):
         if not self.model_id and not self.sbml_file_path:
             raise ValueError("Either model_id or sbml_file_path must be provided.")
         if self.model_id:
-            self.copasi_model = basico.load_biomodel(self.model_id)
+            attempts = 0
+            max_retries = 5
+            while attempts < max_retries:
+                try:
+                    self.copasi_model = basico.load_biomodel(self.model_id)
+                    break
+                except URLError as e:
+                    attempts += 1
+                    sleep(10*attempts)
+                    if attempts >= max_retries:
+                        raise e
             self.description = basico.biomodels.get_model_info(self.model_id)["description"]
         elif self.sbml_file_path:
             self.copasi_model = basico.load_model(self.sbml_file_path)

aiagents4pharma/talk2biomodels/tools/__init__.py

@@ -1,7 +1,10 @@
 '''
 This file is used to import all the modules in the package.
 '''
+# import everything from the module
+from . import ask_question
 from . import simulate_model
+from . import custom_plotter
+from . import fetch_parameters
 from . import model_description
-from . import ask_question
-from . import plot_figure
+from . import search_models

aiagents4pharma/talk2biomodels/tools/fetch_parameters.py

@@ -4,6 +4,8 @@
 Tool for fetching species and parameters from the model.
 """
 
+from urllib.error import URLError
+from time import sleep
 from typing import Type
 import basico
 from pydantic import BaseModel, Field
@@ -47,14 +49,36 @@ class FetchParametersTool(BaseTool):
         # Extract species from the model
         species = []
         if fetch_species:
-            df_species = basico.model_info.get_species(model=model_obj.copasi_model)
+            df_species = self.get_species_and_parameters(model_obj, fetch_species=True)
             species = df_species.index.tolist()
             species = ','.join(species)
 
         # Extract parameters from the model
         parameters = []
         if fetch_parameters:
-            df_parameters = basico.model_info.get_parameters(model=model_obj.copasi_model)
+            df_parameters = self.get_species_and_parameters(model_obj, fetch_species=False)
             parameters = df_parameters.index.tolist()
             parameters = ','.join(parameters)
         return {'Species': species, 'Parameters': parameters}
+
+    def get_species_and_parameters(self,
+                                   model_obj,
+                                   fetch_species: bool):
+        """
+        Get the species from the model.
+        """
+        attempts = 0
+        max_retries = 3
+        while attempts < max_retries:
+            try:
+                if fetch_species:
+                    df = basico.model_info.get_species(model=model_obj.copasi_model)
+                else:
+                    df = basico.model_info.get_parameters(model=model_obj.copasi_model)
+                break
+            except URLError as e:
+                attempts += 1
+                sleep(10)
+                if attempts >= max_retries:
+                    raise e
+        return df

aiagents4pharma/talk2biomodels/tools/search_models.py

@@ -4,6 +4,8 @@
 Tool for searching models based on search query.
 """
 
+from urllib.error import URLError
+from time import sleep
 from typing import Type
 from pydantic import BaseModel, Field
 from basico import biomodels
@@ -39,7 +41,17 @@ class SearchModelsTool(BaseTool):
         Returns:
             str: The answer to the question.
         """
-        search_results = biomodels.search_for_model(query)
+        attempts = 0
+        max_retries = 3
+        while attempts < max_retries:
+            try:
+                search_results = biomodels.search_for_model(query)
+                break
+            except URLError as e:
+                attempts += 1
+                sleep(10)
+                if attempts >= max_retries:
+                    raise e
         llm = ChatOpenAI(model="gpt-4o-mini")
         # Check if run_manager's metadata has the key 'prompt_content'
         prompt_content = f'''

{aiagents4pharma-1.4.1.dist-info → aiagents4pharma-1.4.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.4.1
+Version: 1.4.3
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -90,7 +90,7 @@ Check out the tutorials on each agent for detailed instrcutions.
 
 2. **Install dependencies:**
    ```bash
-   pip install -r requirements.txt
+   pip install .
    ```
 
 3. **Initialize OPENAI_API_KEY**

{aiagents4pharma-1.4.1.dist-info → aiagents4pharma-1.4.3.dist-info}/RECORD

@@ -1,18 +1,17 @@
 aiagents4pharma/__init__.py,sha256=OF-rmtiLauF4NIlzEvMrWhNiX-mo5NJ4vrUtQbcLwts,93
 aiagents4pharma/talk2biomodels/__init__.py,sha256=MueXwbnuiQyiju7mW6NepFUiZJdodMzmUK3TkQT7iPk,99
 aiagents4pharma/talk2biomodels/models/__init__.py,sha256=5fTHHm3PVloYPNKXbgNlcPgv3-u28ZquxGydFYDfhJA,122
-aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=SC9rFzLWzNxcQueAduL3dBmDh-lTtP1agH-TXjucOkw,4199
+aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=UzTj6EUS7GiaNJogRUY5LkEYv-mUw2kO10v1NW89nPw,4597
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py,sha256=xN-ZXCpIxNkEXuDIvi_AW6LpCyPqXReGyhLPyJIXNqs,1980
-aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=AM03pbYT3nOzI5jf_CJmSDaDwrI-IZ0Zq9hLA2tOXpw,182
+aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=qO3MYCJmXpoUlZYtSW3VxTXdt-yUNHyH-Ua578pdyhg,280
 aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=o9ae4s3wsDFr_pGBU1cSxKhJ7E2yjybIzG1Y4z6957Y,4534
 aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=CdgJjlHAkdyjnwPD6nHARsJXnx_CE0MWg5VOz4oBjY0,2910
-aiagents4pharma/talk2biomodels/tools/fetch_parameters.py,sha256=levr42F-m53Oya8VTbLlvLJt1snNgnIlSHs4JDiNAv8,2063
+aiagents4pharma/talk2biomodels/tools/fetch_parameters.py,sha256=WdLGPdJi4DwGwYMoReByGE9O1Msv68jkVd02F8L2liM,2864
 aiagents4pharma/talk2biomodels/tools/model_description.py,sha256=lcVKVvh50wJ4BmB7xMnTZOtWjCmQUnkh6TQJsX-IjGw,5338
-aiagents4pharma/talk2biomodels/tools/plot_figure.py,sha256=S_d8nNy7NVSBIqnDhg6ex_AdaMqUmVX8D1qOjRGe3r8,5594
-aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=5qmgQcwlICYAFG11y-aEhBSeYYT6Lu6AKGL2V-p1ggQ,2685
+aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=cqsK_ApjrAyjEiXWsXTebDpuvEnA5nb6WYiUGayRkW4,3034
 aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=MxlAy62SuonBbEbKmoUz0HcdfTWvk-x9WMSo17dBU9U,7552
-aiagents4pharma-1.4.1.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.4.1.dist-info/METADATA,sha256=Fh-G93O_d49FDuMV7nqQ0sGhwglioxFYiAJUTOWTPwI,6640
-aiagents4pharma-1.4.1.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-aiagents4pharma-1.4.1.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.4.1.dist-info/RECORD,,
+aiagents4pharma-1.4.3.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.4.3.dist-info/METADATA,sha256=i7KyLyZ8Lkp38BuHOt2eQ44uHqWtLr1xZ83u0HuzCOo,6622
+aiagents4pharma-1.4.3.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+aiagents4pharma-1.4.3.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.4.3.dist-info/RECORD,,

{aiagents4pharma-1.4.1.dist-info → aiagents4pharma-1.4.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

aiagents4pharma/talk2biomodels/tools/plot_figure.py

@@ -1,135 +0,0 @@
-#!/usr/bin/env python3
-
-"""
-Tool for plotting a figure.
-"""
-
-from typing import Type, Optional
-from dataclasses import dataclass
-import matplotlib.pyplot as plt
-from pydantic import BaseModel, Field
-import streamlit as st
-from langchain_openai import ChatOpenAI
-from langchain_core.tools import BaseTool
-from langchain_core.prompts import ChatPromptTemplate
-from langchain_core.output_parsers.openai_tools import JsonOutputKeyToolsParser
-from langchain_experimental.tools import PythonAstREPLTool
-from ..models.basico_model import BasicoModel
-
-@dataclass
-class ModelData:
-    """
-    Dataclass for storing the model data.
-    """
-    modelid: Optional[int] = None
-    sbml_file_path: Optional[str] = None
-    model_object: Optional[BasicoModel] = None
-
-class PlotImageInput(BaseModel):
-    """
-    Input schema for the PlotImage tool.
-    """
-    question: str = Field(description="Description of the plot")
-    sys_bio_model: ModelData = Field(description="model data", default=None)
-
-# 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.
-class PlotImageTool(BaseTool):
-    """
-    Tool for plotting a figure.
-    """
-    name: str = "plot_figure"
-    description: str = "A tool to plot or visualize the simulation results."
-    args_schema: Type[BaseModel] = PlotImageInput
-    st_session_key: str = None
-
-    def _run(self,
-             question: str,
-             sys_bio_model: ModelData = ModelData()) -> str:
-        """
-        Run the tool.
-
-        Args:
-            question (str): The question to ask about the model description.
-            sys_bio_model (ModelData): The model data.
-
-        Returns:
-            str: The answer to the question
-        """
-        st_session_key = self.st_session_key
-        # Check if sys_bio_model is provided
-        if sys_bio_model.modelid or sys_bio_model.sbml_file_path or sys_bio_model.model_object:
-            if sys_bio_model.modelid:
-                model_object = BasicoModel(model_id=sys_bio_model.modelid)
-            elif sys_bio_model.sbml_file_path:
-                model_object = BasicoModel(sbml_file_path=sys_bio_model.sbml_file_path)
-            else:
-                model_object = sys_bio_model.model_object
-            if st_session_key:
-                st.session_state[st_session_key] = model_object
-        else:
-            # If the model_object is not provided,
-            # get it from the Streamlit session state
-            if st_session_key:
-                if st_session_key not in st.session_state:
-                    return f"Session key {st_session_key} not found in Streamlit session state."
-                model_object = st.session_state[st_session_key]
-            else:
-                return "Please provide a valid model object or \
-                    Streamlit session key that contains the model object."
-        if model_object is None:
-            return "Please run the simulation first before plotting the figure."
-        if model_object.simulation_results is None:
-            model_object.simulate()
-        df = model_object.simulation_results
-        tool = PythonAstREPLTool(locals={"df": df})
-        llm = ChatOpenAI(model="gpt-3.5-turbo")
-        llm_with_tools = llm.bind_tools([tool], tool_choice=tool.name)
-        system = f"""
-                    You have access to a pandas dataframe `df`.
-                    Here is the output of `df.head().to_markdown()`:
-                    {df.head().to_markdown()}
-                    Given a user question, write the Python code to
-                    plot a figure of the answer using matplolib.
-                    Return ONLY the valid Python code and nothing else.
-                    The firgure size should be equal or smaller than (2, 2).
-                    Show the grid and legend. The font size of the legend should be 6.
-                    Also write a suitable title for the figure. The font size of the title should be 8.
-                    The font size of the x-axis and y-axis labels should be 8.
-                    The font size of the x-axis and y-axis ticks should be 6.
-                    Make sure that the x-axis has at least 10 tick marks.
-                    Use color-blind friendly colors. The figure must be of high quality.
-                    Don't assume you have access to any libraries other
-                    than built-in Python ones, pandas, streamlit and matplotlib.
-                    """
-        prompt = ChatPromptTemplate.from_messages([("system", system), ("human", "{question}")])
-        parser = JsonOutputKeyToolsParser(key_name=tool.name, first_tool_only=True)
-        code_chain = prompt | llm_with_tools | parser
-        response = code_chain.invoke({"question": question})
-        exec(response['query'], globals(), {"df": df, "plt": plt})
-        # load for plotly
-        fig = plt.gcf()
-        if st_session_key:
-            st.pyplot(fig, use_container_width=False)
-            st.dataframe(df)
-        return "Figure plotted successfully"
-
-    def call_run(self,
-            question: str,
-            sys_bio_model: ModelData = ModelData(),
-            st_session_key: str = None) -> str:
-        """
-        Run the tool.
-        """
-        return self._run(question=question,
-                         sys_bio_model=sys_bio_model,
-                         st_session_key=st_session_key)
-
-    def get_metadata(self):
-        """
-        Get metadata for the tool.
-        """
-        return {
-            "name": self.name,
-            "description": self.description
-        }