aiagents4pharma 1.3.3__py3-none-any.whl → 1.4.1__py3-none-any.whl

aiagents4pharma/talk2biomodels/tools/model_description.py

@@ -20,7 +20,7 @@ class ModelData:
     """
     Dataclass for storing the model data.
     """
-    modelid: Optional[int] = None
+    model_id: Optional[int] = None
     sbml_file_path: Optional[str] = None
     model_object: Optional[BasicoModel] = None
 
@@ -73,12 +73,11 @@ class ModelDescriptionTool(BaseTool):
             str: The answer to the question.
         """
         st_session_key = self.st_session_key
-        print (st_session_key, 'st_session_key')
         # Check if sys_bio_model is provided in the input schema
-        if sys_bio_model.modelid or sys_bio_model.sbml_file_path \
+        if sys_bio_model.model_id or sys_bio_model.sbml_file_path \
             or sys_bio_model.model_object not in [None, "", {}]:
-            if sys_bio_model.modelid:
-                model_object = BasicoModel(model_id=sys_bio_model.modelid)
+            if sys_bio_model.model_id:
+                model_object = BasicoModel(model_id=sys_bio_model.model_id)
             elif sys_bio_model.sbml_file_path:
                 model_object = BasicoModel(sbml_file_path=sys_bio_model.sbml_file_path)
             else:

aiagents4pharma/talk2biomodels/tools/simulate_model.py

@@ -4,13 +4,13 @@
 Tool for simulating a model.
 """
 
-from typing import Type, Union, List, Optional, Tuple
-import basico
+from typing import Type, Union, List, Optional
 from dataclasses import dataclass
+import basico
 from pydantic import BaseModel, Field
 from langchain_core.tools import BaseTool
 import streamlit as st
-import plotly.express as px
+# import plotly.express as px
 from ..models.basico_model import BasicoModel
 
 @dataclass
@@ -91,33 +91,36 @@ class SimulateModelTool(BaseTool):
         Returns:
             str: The result of the simulation.
         """
-        st_session_key = self.st_session_key
+        # st_session_key = self.st_session_key
         # Retrieve the model ID, duration, and interval
         modelid = model_data.modelid if model_data is not None else None
-        duration = time_data.duration if time_data is not None else 100.0
-        interval = time_data.interval if time_data is not None else 10
+        # duration = time_data.duration if time_data is not None else 100.0
+        # interval = time_data.interval if time_data is not None else 10
         # Prepare the dictionary of species data
         # that will be passed to the simulate method
         # of the BasicoModel class
-        dic_species_data = None
-        if species_data is not None:
-            dic_species_data = dict(zip(species_data.species_name,
-                                    species_data.species_concentration))
+        # dic_species_data = None
+        # if species_data is not None:
+        #     dic_species_data = dict(zip(species_data.species_name,
+        #                             species_data.species_concentration))
+        dic_species_data = dict(zip(species_data.species_name, \
+            species_data.species_concentration)) \
+                if species_data is not None else None
         # Retrieve the SBML file path from the Streamlit session state
         # otherwise retrieve it from the model_data object if the user
         # has provided it.
         sbml_file_path = model_data.sbml_file_path if model_data is not None else None
-        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."
+        if self.st_session_key:
+            if self.st_session_key not in st.session_state:
+                return f"Session key {self.st_session_key} not found in Streamlit session state."
             if 'sbml_file_path' in st.session_state:
                 sbml_file_path = st.session_state.sbml_file_path
         # Check if both modelid and sbml_file_path are None
         if modelid is None and sbml_file_path is None:
             # Then load the model from the Streamlit session state
             # if the streamlit session exists
-            if st_session_key:
-                model_object = st.session_state[st_session_key]
+            if self.st_session_key:
+                model_object = st.session_state[self.st_session_key]
                 # If this model object is None, then return an error message
                 if model_object is None:
                     return "Please provide a BioModels ID or an SBML file path for simulation."
@@ -131,13 +134,13 @@ class SimulateModelTool(BaseTool):
             # model_object = BasicoModel(model_id=modelid)
             model_object = BasicoModel(model_id=modelid)
             # Save the model object in the Streamlit session state
-            st.session_state[st_session_key] = model_object
+            st.session_state[self.st_session_key] = model_object
         elif sbml_file_path:
             # Create a BasicoModel object with the SBML file path
             model_object = BasicoModel(sbml_file_path=sbml_file_path)
             modelid = model_object.model_id
             # Save the model object in the Streamlit session state
-            st.session_state[st_session_key] = model_object
+            st.session_state[self.st_session_key] = model_object
         # Add recurring events (if any) to the model
         if recurring_data is not None:
             for row in recurring_data.data:
@@ -149,29 +152,30 @@ class SimulateModelTool(BaseTool):
                 # print (f'Added event {sn}_{tp} at time {tp} \
                 #        for species {sn} with concentration {sc}')
         # Simulate the model
-        df = model_object.simulate(parameters=dic_species_data,
-                                    duration=duration,
-                                    interval=interval)
+        df = model_object.simulate(
+            parameters=dic_species_data,
+            duration=time_data.duration if time_data is not None else 100.0,
+            interval=time_data.interval if time_data is not None else 10)
         # Convert the DataFrame to long format for plotting
         # and ignore the index column
         df = df.melt(id_vars='Time',
                     var_name='Species',
                     value_name='Concentration')
         # Plot the simulation results using Plotly
-        fig = px.line(df,
-                        x='Time',
-                        y='Concentration',
-                        color='Species',
-                        title=f"Concentration of Species over Time in the model {modelid}",
-                        height=600,
-                        width=800
-        )
+        # fig = px.line(df,
+        #                 x='Time',
+        #                 y='Concentration',
+        #                 color='Species',
+        #                 title=f"Concentration of Species over Time in the model {modelid}",
+        #                 height=600,
+        #                 width=800
+        # )
         # Display the plot in Streamlit
         # st.plotly_chart(fig, use_container_width = False)
-        if modelid is None:
-            modelid = "internal"
-        content = f"Simulation results for the model {modelid}."
-        return content
+        # if modelid is None:
+        #     modelid = "internal"
+        # return f"Simulation results for the model {modelid}."
+        return "Simulation results for the model."
 
     def get_metadata(self):
         """
@@ -182,6 +186,5 @@ class SimulateModelTool(BaseTool):
         """
         return {
             "name": self.name,
-            "description": self.description,
-            "return_direct": self.return_direct,
+            "description": self.description
         }

{aiagents4pharma-1.3.3.dist-info → aiagents4pharma-1.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: aiagents4pharma
-Version: 1.3.3
+Version: 1.4.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -31,6 +31,7 @@ Requires-Dist: mkdocs-material==9.5.47
 Requires-Dist: mkdocstrings-python==1.12.2
 Requires-Dist: mkdocs-include-markdown-plugin==7.1.2
 Requires-Dist: mkdocstrings==0.27.0
+Requires-Dist: streamlit-feedback
 
 [![TESTS](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests.yml/badge.svg?branch=feat%2Finitial-setup)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests.yml)
 
@@ -73,7 +74,14 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 - Required libraries specified in `requirements.txt`
 
 ### Installation
+#### Option 1: PyPI
+   ```bash
+   pip install aiagents4pharma
+   ```
 
+Check out the tutorials on each agent for detailed instrcutions.
+
+#### Option 2: git
 1. **Clone the repository:**
    ```bash
    git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
@@ -90,8 +98,28 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
    export OPENAI_API_KEY = ....
    ```
 
-4. **Launch the agent:**
-   To launch the Talk2BioModels agent, run:
+4. **[Optional] Set up login credentials**
+   ```bash
+   vi .streamlit/secrets.toml
+   ```
+   and enter
+   ```
+   password='XXX'
+   ```
+   Please note that the passowrd will be same for all the users.
+
+5. **[Optional] Initialize LANGSMITH_API_KEY**
+   ```bash
+   export LANGCHAIN_TRACING_V2=true
+   export LANGCHAIN_API_KEY=<your-api-key>
+   ```
+   Please note that this will create a new tracing project in your Langsmith 
+   account with the name `<user_name>@<uuid>`, where `user_name` is the name 
+   you provided in the previous step. If you skip the previous step, it will 
+   default to `default`. <uuid> will be the 128 bit unique ID created for the
+   session.
+
+6. **Launch the app:**
    ```bash
    streamlit run app/frontend/streamlit_app.py
    ```
@@ -139,3 +167,8 @@ Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
 We’re excited to bring AIAgents4Pharma to the bioinformatics and pharmaceutical research community. Together, let’s make data-driven biological research more accessible and insightful. 
 
 **Get Started** with AIAgents4Pharma today and transform the way you interact with biological data.
+
+---
+
+## Feedback
+Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use the `Isssues` tab 😀

{aiagents4pharma-1.3.3.dist-info → aiagents4pharma-1.4.1.dist-info}/RECORD

@@ -7,12 +7,12 @@ aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=AM03pbYT3nOzI5jf_CJmSDaD
 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/model_description.py,sha256=MwG3XLw-lrR8iReH6VQ94yuU4VGn-I9pxv8anFxIMVc,5383
+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/simulate_model.py,sha256=n6TbfJRgeo2X_1wXPHGeeCvZoso8LFjLqqfKhfseFVM,7287
-aiagents4pharma-1.3.3.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.3.3.dist-info/METADATA,sha256=fXHllHR_OLjO2VYdU18pFJ1h7_S4v3Dw6aNkUZEFUPA,5698
-aiagents4pharma-1.3.3.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-aiagents4pharma-1.3.3.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.3.3.dist-info/RECORD,,
+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,,