aiagents4pharma 1.7.0__py3-none-any.whl → 1.8.1__py3-none-any.whl

aiagents4pharma/talk2biomodels/__init__.py

@@ -3,3 +3,5 @@ This file is used to import the models and tools.
 '''
 from . import models
 from . import tools
+from . import agents
+from . import states

aiagents4pharma/talk2biomodels/tools/__init__.py

@@ -6,3 +6,4 @@ from . import simulate_model
 from . import ask_question
 from . import custom_plotter
 from . import get_modelinfo
+from . import load_biomodel

aiagents4pharma/talk2biomodels/tools/custom_plotter.py

@@ -6,11 +6,14 @@ Tool for plotting a custom figure.
 
 import logging
 from typing import Type, List, TypedDict, Annotated, Tuple, Union, Literal
+from typing import Type, List, TypedDict, Annotated, Tuple, Union, Literal
 from pydantic import BaseModel, Field
 import pandas as pd
+import pandas as pd
 from langchain_openai import ChatOpenAI
 from langchain_core.tools import BaseTool
 from langgraph.prebuilt import InjectedState
+from langgraph.prebuilt import InjectedState
 
 # Initialize logger
 logging.basicConfig(level=logging.INFO)
@@ -22,18 +25,23 @@ class CustomPlotterInput(BaseModel):
     """
     question: str = Field(description="Description of the plot")
     state: Annotated[dict, InjectedState]
+    state: Annotated[dict, InjectedState]
 
+# 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.
 # 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 CustomPlotterTool(BaseTool):
     """
-    Tool for plotting a custom plot.
+    Tool for making custom plots
     """
     name: str = "custom_plotter"
-    description: str = "A tool to plot a custom figure."
+    description: str = "A tool to make custom plots of the simulation results"
     args_schema: Type[BaseModel] = CustomPlotterInput
     response_format: str = "content_and_artifact"
+    response_format: str = "content_and_artifact"
 
     def _run(self,
              question: str,
@@ -45,6 +53,8 @@ class CustomPlotterTool(BaseTool):
         Args:
             question (str): The question about the custom plot.
             state (dict): The state of the graph.
+            question (str): The question about the custom plot.
+            state (dict): The state of the graph.
 
         Returns:
             str: The answer to the question
@@ -66,7 +76,7 @@ class CustomPlotterTool(BaseTool):
             A list of species based on user question.
             """
             relevant_species: Union[None, List[Literal[*species_names]]] = Field(
-                                        description="List of species based on user question.")
+                    description="List of species based on user question. If no relevant species are found, it will be None.")
         # Create an instance of the LLM model
         llm = ChatOpenAI(model=state['llm_model'], temperature=0)
         llm_with_structured_output = llm.with_structured_output(CustomHeader)

aiagents4pharma/talk2biomodels/tools/load_biomodel.py

@@ -26,4 +26,3 @@ def load_biomodel(sys_bio_model, sbml_file_path=None):
     elif sbml_file_path:
         model_object = BasicoModel(sbml_file_path=sbml_file_path)
     return model_object
-    # return None

aiagents4pharma/talk2biomodels/tools/search_models.py

@@ -27,7 +27,7 @@ class SearchModelsTool(BaseTool):
     Tool for returning the search results based on the search query.
     """
     name: str = "search_models"
-    description: str = "Search models based on search query."
+    description: str = "Search models in the BioMmodels database based on keywords."
     args_schema: Type[BaseModel] = SearchModelsInput
     return_direct: bool = True
 

aiagents4pharma/talk2biomodels/tools/simulate_model.py

@@ -99,7 +99,7 @@ class SimulateModelTool(BaseTool):
     Tool for simulating a model.
     """
     name: str = "simulate_model"
-    description: str = "A tool to simulate a model."
+    description: str = "A tool to simulate a biomodel"
     args_schema: Type[BaseModel] = SimulateModelInput
 
     def _run(self,

{aiagents4pharma-1.7.0.dist-info → aiagents4pharma-1.8.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.7.0
+Version: 1.8.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License

{aiagents4pharma-1.7.0.dist-info → aiagents4pharma-1.8.1.dist-info}/RECORD

@@ -1,15 +1,15 @@
 aiagents4pharma/__init__.py,sha256=ds5Ft1k2ww2m7N-yv5ZyymBw0LBuHVjwC9TuekQBL_c,151
-aiagents4pharma/talk2biomodels/__init__.py,sha256=MueXwbnuiQyiju7mW6NepFUiZJdodMzmUK3TkQT7iPk,99
+aiagents4pharma/talk2biomodels/__init__.py,sha256=9MuyHb5KTf5ufeyq7fu5xoLEwVT688DFOWuKuzdWG9o,140
 aiagents4pharma/talk2biomodels/models/__init__.py,sha256=5fTHHm3PVloYPNKXbgNlcPgv3-u28ZquxGydFYDfhJA,122
 aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=js7ORLwbJPaIsko5oRToMMCh4l8LsN292OIvFzTfvRg,4946
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py,sha256=ylpPba2SA8kl68q3k1kJbiUdRYplPHykyslTQLDZ19I,1995
-aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=tkNUpUtZOe3hwbKQgp97e4gJ3p2d38G8WFHNO9A83uM,209
+aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=8hAT6z1OO8N9HRylh6fwoqyjYlGdpkngkElBNqH40Zo,237
 aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=UEdT46DIFZHlAOF4cNX4_s7VjHvbbiGpNmEY2-XW2iA,2655
-aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=ESsdV_sz3wdynK9EbqZYhoY9r5zLto3NTZmUYvqS_TU,3282
+aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=BfLSivWqtRVZDeqD7RP5sgZP6B9rET47IWdNrA3gmIE,3825
 aiagents4pharma/talk2biomodels/tools/get_modelinfo.py,sha256=czxjRa9jvjTow-POGU5wSV8_lwfknAezBnzCFA0gQ8E,5189
-aiagents4pharma/talk2biomodels/tools/load_biomodel.py,sha256=QQOBCrDoEEWdSVCIYyBXL2WLSgEs3yB_fDpwALnsl-U,707
-aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=GzF313UgawtrA0fvYEh_AX2HKO9eMV77YH-R__Gw3iY,2630
-aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=Ax9nuHyINMIlqETujfYxqnzUsgLE-TUFV0EY5Qr7rPk,6249
+aiagents4pharma/talk2biomodels/tools/load_biomodel.py,sha256=pyVzLQoMnuJYEwsjeOlqcUrbU1F1Z-pNlgkhFaoKpy0,689
+aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=Iq2ddofOOfZYtAurCISq3bAq5rbwB3l_rL1lgEFyFCI,2653
+aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=hBRrSLVGcaT157FCe8ajVKJZ2fi9CJhGeniGLaZJ-KE,6251
 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
@@ -28,8 +28,8 @@ aiagents4pharma/talk2knowledgegraphs/utils/embeddings/__init__.py,sha256=xRb0x7S
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/embeddings.py,sha256=1nGznrAj-xT0xuSMBGz2dOujJ7M_IwSR84njxtxsy9A,2523
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/huggingface.py,sha256=2vi_elf6EgzfagFAO5QnL3a_aXZyN7B1EBziu44MTfM,3806
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py,sha256=36iKlisOpMtGR5xfTAlSHXWvPqVC_Jbezod8kbBBMVg,2136
-aiagents4pharma-1.7.0.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.7.0.dist-info/METADATA,sha256=Ppwb-9bU-tkQ18AjrX6xmySzOrmcXIIszAL6j-ZpfCw,7988
-aiagents4pharma-1.7.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-aiagents4pharma-1.7.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.7.0.dist-info/RECORD,,
+aiagents4pharma-1.8.1.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.8.1.dist-info/METADATA,sha256=IT0veyP78F4miSANCtd1knzOq5kjmmFn5g2KLhO3Su8,7988
+aiagents4pharma-1.8.1.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+aiagents4pharma-1.8.1.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.8.1.dist-info/RECORD,,