aiagents4pharma 1.4.2__tar.gz → 1.5.3__tar.gz

{aiagents4pharma-1.4.2 → aiagents4pharma-1.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.4.2
+Version: 1.5.3
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -10,13 +10,16 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: copasi_basico==0.78
 Requires-Dist: coverage==7.6.4
+Requires-Dist: gdown==5.2.0
+Requires-Dist: huggingface_hub==0.26.5
+Requires-Dist: joblib==1.4.2
 Requires-Dist: langchain==0.3.7
 Requires-Dist: langchain-community==0.3.5
 Requires-Dist: langchain-core==0.3.15
 Requires-Dist: langchain-experimental==0.3.3
 Requires-Dist: langchain-openai==0.2.5
 Requires-Dist: matplotlib==3.9.2
-Requires-Dist: openai==1.55.3
+Requires-Dist: openai==1.59.4
 Requires-Dist: pandas==2.2.3
 Requires-Dist: plotly==5.24.1
 Requires-Dist: pydantic==2.9.2
@@ -24,6 +27,7 @@ Requires-Dist: pylint==3.3.1
 Requires-Dist: pytest==8.3.3
 Requires-Dist: streamlit==1.39.0
 Requires-Dist: tabulate==0.9.0
+Requires-Dist: torch==2.5.1
 Requires-Dist: tqdm==4.66.6
 Requires-Dist: mkdocs==1.6.1
 Requires-Dist: mkdocs-jupyter==0.25.1
@@ -90,7 +94,7 @@ 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-1.4.2 → aiagents4pharma-1.5.3}/README.md

@@ -55,7 +55,7 @@ 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-1.5.3/aiagents4pharma/__init__.py

@@ -0,0 +1,7 @@
+'''
+This file is used to import aiagents4pharma modules.
+'''
+
+from . import talk2biomodels
+from . import talk2cells
+from . import talk2knowledgegraphs

{aiagents4pharma-1.4.2 → aiagents4pharma-1.5.3}/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-1.4.2 → aiagents4pharma-1.5.3}/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-1.4.2 → aiagents4pharma-1.5.3}/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-1.5.3/aiagents4pharma/talk2knowledgegraphs/__init__.py

@@ -0,0 +1,4 @@
+'''
+This file is used to import the datasets, utils, and tools.
+'''
+from . import datasets

aiagents4pharma-1.5.3/aiagents4pharma/talk2knowledgegraphs/datasets/__init__.py

@@ -0,0 +1,7 @@
+'''
+This file is used to import all the models in the package.
+'''
+from . import dataset
+from . import primekg
+from . import starkqa_primekg
+from . import biobridge_primekg