aiagents4pharma 1.3.2__tar.gz → 1.4.0__tar.gz

{aiagents4pharma-1.3.2 → aiagents4pharma-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: aiagents4pharma
-Version: 1.3.2
+Version: 1.4.0
 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-1.3.2 → aiagents4pharma-1.4.0}/README.md

@@ -39,7 +39,14 @@ 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
@@ -56,8 +63,28 @@ 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
    ```
@@ -104,4 +131,9 @@ 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.
+**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-1.3.2 → aiagents4pharma-1.4.0}/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-1.3.2 → aiagents4pharma-1.4.0}/aiagents4pharma.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: aiagents4pharma
-Version: 1.3.2
+Version: 1.4.0
 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-1.3.2 → aiagents4pharma-1.4.0}/aiagents4pharma.egg-info/requires.txt

@@ -21,3 +21,4 @@ mkdocs-material==9.5.47
 mkdocstrings-python==1.12.2
 mkdocs-include-markdown-plugin==7.1.2
 mkdocstrings==0.27.0
+streamlit-feedback

{aiagents4pharma-1.3.2 → aiagents4pharma-1.4.0}/pyproject.toml

@@ -35,7 +35,8 @@ dependencies = [
     "mkdocs-material==9.5.47",
     "mkdocstrings-python==1.12.2",
     "mkdocs-include-markdown-plugin==7.1.2",
-    "mkdocstrings==0.27.0"
+    "mkdocstrings==0.27.0",
+    "streamlit-feedback"
 ]
 dynamic = ["version"]
 

aiagents4pharma-1.4.0/release_version.txt

@@ -0,0 +1 @@
+v1.4.0

aiagents4pharma-1.3.2/release_version.txt

@@ -1 +0,0 @@
-v1.3.2