aiagents4pharma 1.17.0__tar.gz → 1.17.1__tar.gz

aiagents4pharma-1.17.1/PKG-INFO

@@ -0,0 +1,150 @@
+Metadata-Version: 2.2
+Name: aiagents4pharma
+Version: 1.17.1
+Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: copasi_basico==0.78
+Requires-Dist: coverage==7.6.4
+Requires-Dist: einops==0.8.0
+Requires-Dist: gdown==5.2.0
+Requires-Dist: huggingface_hub==0.26.5
+Requires-Dist: hydra-core==1.3.2
+Requires-Dist: joblib==1.4.2
+Requires-Dist: langchain==0.3.7
+Requires-Dist: langchain-community==0.3.5
+Requires-Dist: langchain-core==0.3.31
+Requires-Dist: langchain-experimental==0.3.3
+Requires-Dist: langchain-openai==0.2.5
+Requires-Dist: langchain_ollama==0.2.2
+Requires-Dist: langgraph==0.2.66
+Requires-Dist: matplotlib==3.9.2
+Requires-Dist: openai==1.59.4
+Requires-Dist: ollama==0.4.6
+Requires-Dist: pandas==2.2.3
+Requires-Dist: plotly==5.24.1
+Requires-Dist: pydantic==2.9.2
+Requires-Dist: pylint==3.3.1
+Requires-Dist: pypdf==5.2.0
+Requires-Dist: pytest==8.3.3
+Requires-Dist: pytest-asyncio==0.25.2
+Requires-Dist: streamlit==1.39.0
+Requires-Dist: sentence_transformers==3.3.1
+Requires-Dist: tabulate==0.9.0
+Requires-Dist: torch==2.2.2
+Requires-Dist: torch_geometric==2.6.1
+Requires-Dist: tqdm==4.66.6
+Requires-Dist: transformers==4.48.0
+Requires-Dist: mkdocs==1.6.1
+Requires-Dist: mkdocs-jupyter==0.25.1
+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
+
+[![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
+[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
+[![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
+[![TESTS Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
+![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+
+## Introduction
+
+Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
+
+Our toolkit currently consists of the following agents:
+
+- **Talk2BioModels** _(v1 released; v2 in progress)_: Engage directly with mathematical models in systems biology.
+- **Talk2KnowledgeGraphs** _(v1 in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Scholars** _(v1 in progress)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Cells** _(v1 in progress)_: Query and analyze sequencing data with ease.
+
+![AIAgents4Pharma](docs/assets/AIAgents4Pharma.png)
+
+## Getting Started
+
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+### 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
+   cd AIAgents4Pharma
+   ```
+2. **Install dependencies:**
+   ```bash
+   pip install .
+   ```
+3. **Initialize OPENAI_API_KEY**
+   ```bash
+   export OPENAI_API_KEY=....
+   ```
+4. **[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 `T2X-xxxx`, where `X` can be `B` (Biomodels), `S` (Scholars),
+`KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will
+default to the name `default`. `xxxx` will be the 4-digit ID created for the
+session._
+
+5. **Launch the app:**
+   ```bash
+   streamlit run app/frontend/streamlit_app_<agent>.py
+   ```
+_Replace <agent> with the agent name you are interested to launch._
+
+For detailed instructions on each agent, please refer to their respective modules.
+
+---
+
+## Contributing
+
+We welcome contributions to AIAgents4Pharma! Here’s how you can help:
+
+1. **Fork the repository**
+2. **Create a new branch** for your feature (`git checkout -b feat/feature-name`)
+3. **Commit your changes** (`git commit -m 'feat: Add new feature'`)
+4. **Push to the branch** (`git push origin feat/feature-name`)
+5. **Open a pull request** and reach out to any one of us below via Discussions:
+
+   _Note: We welcome all contributions, not just programming-related ones. Feel free to open bug reports, suggest new features, or participate as a beta tester. Your support is greatly appreciated!_
+
+- **Talk2Biomodels/Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330) [@lilijap](https://github.com/lilijap) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info) [@gurdeep330](https://github.com/gurdeep330) [@dmccloskey](https://github.com/dmccloskey)
+
+### Current Needs
+
+- **Beta testers** for Talk2BioModels and Talk2Scholars.
+- **Developers** with experience in Python and Bioinformatics and/or knowledge graphs for contributions to AIAgents4Pharma.
+
+Feel free to reach out to us via Discussions.
+
+Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
+
+---
+
+## Feedback
+
+Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Isssues` or `Discussions` 😀

aiagents4pharma-1.17.1/README.md

@@ -0,0 +1,101 @@
+[![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
+[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
+[![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
+[![TESTS Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
+![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+
+## Introduction
+
+Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
+
+Our toolkit currently consists of the following agents:
+
+- **Talk2BioModels** _(v1 released; v2 in progress)_: Engage directly with mathematical models in systems biology.
+- **Talk2KnowledgeGraphs** _(v1 in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Scholars** _(v1 in progress)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Cells** _(v1 in progress)_: Query and analyze sequencing data with ease.
+
+![AIAgents4Pharma](docs/assets/AIAgents4Pharma.png)
+
+## Getting Started
+
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+### 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
+   cd AIAgents4Pharma
+   ```
+2. **Install dependencies:**
+   ```bash
+   pip install .
+   ```
+3. **Initialize OPENAI_API_KEY**
+   ```bash
+   export OPENAI_API_KEY=....
+   ```
+4. **[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 `T2X-xxxx`, where `X` can be `B` (Biomodels), `S` (Scholars),
+`KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will
+default to the name `default`. `xxxx` will be the 4-digit ID created for the
+session._
+
+5. **Launch the app:**
+   ```bash
+   streamlit run app/frontend/streamlit_app_<agent>.py
+   ```
+_Replace <agent> with the agent name you are interested to launch._
+
+For detailed instructions on each agent, please refer to their respective modules.
+
+---
+
+## Contributing
+
+We welcome contributions to AIAgents4Pharma! Here’s how you can help:
+
+1. **Fork the repository**
+2. **Create a new branch** for your feature (`git checkout -b feat/feature-name`)
+3. **Commit your changes** (`git commit -m 'feat: Add new feature'`)
+4. **Push to the branch** (`git push origin feat/feature-name`)
+5. **Open a pull request** and reach out to any one of us below via Discussions:
+
+   _Note: We welcome all contributions, not just programming-related ones. Feel free to open bug reports, suggest new features, or participate as a beta tester. Your support is greatly appreciated!_
+
+- **Talk2Biomodels/Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330) [@lilijap](https://github.com/lilijap) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info) [@gurdeep330](https://github.com/gurdeep330) [@dmccloskey](https://github.com/dmccloskey)
+
+### Current Needs
+
+- **Beta testers** for Talk2BioModels and Talk2Scholars.
+- **Developers** with experience in Python and Bioinformatics and/or knowledge graphs for contributions to AIAgents4Pharma.
+
+Feel free to reach out to us via Discussions.
+
+Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
+
+---
+
+## Feedback
+
+Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Isssues` or `Discussions` 😀

{aiagents4pharma-1.17.0 → aiagents4pharma-1.17.1}/aiagents4pharma/__init__.py

@@ -3,7 +3,6 @@ This file is used to import aiagents4pharma modules.
 """
 
 from . import (
-    configs,
     talk2biomodels,
     talk2cells,
     talk2scholars,

{aiagents4pharma-1.17.0 → aiagents4pharma-1.17.1}/aiagents4pharma/talk2biomodels/__init__.py

@@ -6,3 +6,4 @@ from . import tools
 from . import agents
 from . import states
 from . import api
+from . import configs

{aiagents4pharma-1.17.0 → aiagents4pharma-1.17.1}/aiagents4pharma/talk2biomodels/agents/t2b_agent.py

@@ -55,10 +55,10 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
     llm = ChatOpenAI(model=llm_model, temperature=0)
     # Load hydra configuration
     logger.log(logging.INFO, "Load Hydra configuration for Talk2BioModels agent.")
-    with hydra.initialize(version_base=None, config_path="../../configs"):
+    with hydra.initialize(version_base=None, config_path="../configs"):
         cfg = hydra.compose(config_name='config',
-                            overrides=['talk2biomodels/agents/t2b_agent=default'])
-        cfg = cfg.talk2biomodels.agents.t2b_agent
+                            overrides=['agents/t2b_agent=default'])
+        cfg = cfg.agents.t2b_agent
     logger.log(logging.INFO, "state_modifier: %s", cfg.state_modifier)
     # Create the agent
     model = create_react_agent(

{aiagents4pharma-1.17.0/aiagents4pharma/configs/talk2biomodels → aiagents4pharma-1.17.1/aiagents4pharma/talk2biomodels/configs}/agents/t2b_agent/default.yaml

@@ -1,4 +1,4 @@
-_target_: talk2biomodels.agents.t2b_agent.get_app
+_target_: agents.t2b_agent.get_app
 state_modifier: >
   You are Talk2BioModels agent.
   If the user asks for the uploaded model, 

{aiagents4pharma-1.17.0/aiagents4pharma/configs/talk2biomodels → aiagents4pharma-1.17.1/aiagents4pharma/talk2biomodels/configs}/tools/ask_question/default.yaml

@@ -1,4 +1,4 @@
-_target_: talk2biomodels.tools.ask_question.AskQuestionTool
+_target_: tools.ask_question.AskQuestionTool
 steady_state_prompt: >
   Following are header columns of the data:
   `species_name`: Name of the species,

{aiagents4pharma-1.17.0/aiagents4pharma/configs/talk2biomodels → aiagents4pharma-1.17.1/aiagents4pharma/talk2biomodels/configs}/tools/get_annotation/default.yaml

@@ -1,4 +1,4 @@
-_target_: talk2biomodels.tools.get_annotation.GetAnnotationTool
+_target_: tools.get_annotation.GetAnnotationTool
 prompt: >
   Given the user question, extract the relevant species names.
   If the user aks for a specific species, extract that species.

{aiagents4pharma-1.17.0 → aiagents4pharma-1.17.1}/aiagents4pharma/talk2biomodels/tools/ask_question.py

@@ -66,10 +66,10 @@ class AskQuestionTool(BaseTool):
                    question_context,
                    experiment_name)
         # Load hydra configuration
-        with hydra.initialize(version_base=None, config_path="../../configs"):
+        with hydra.initialize(version_base=None, config_path="../configs"):
             cfg = hydra.compose(config_name='config',
-                                overrides=['talk2biomodels/tools/ask_question=default'])
-            cfg = cfg.talk2biomodels.tools.ask_question
+                                overrides=['tools/ask_question=default'])
+            cfg = cfg.tools.ask_question
         # Get the context of the question
         # and based on the context, get the data
         # and prompt content to ask the question
@@ -111,5 +111,6 @@ class AskQuestionTool(BaseTool):
                         verbose=True,
                         prefix=prompt_content)
         # Invoke the agent with the question
-        llm_result = df_agent.invoke(question)
+        llm_result = df_agent.invoke(question, stream_mode=None)
+        # print (llm_result)
         return llm_result["output"]

{aiagents4pharma-1.17.0 → aiagents4pharma-1.17.1}/aiagents4pharma/talk2biomodels/tools/get_annotation.py

@@ -34,10 +34,10 @@ def extract_relevant_species_names(model_object, arg_data, state):
     Extract relevant species names based on the user question.
     """
     # Load hydra configuration
-    with hydra.initialize(version_base=None, config_path="../../configs"):
+    with hydra.initialize(version_base=None, config_path="../configs"):
         cfg = hydra.compose(config_name='config',
-                            overrides=['talk2biomodels/tools/get_annotation=default'])
-        cfg = cfg.talk2biomodels.tools.get_annotation
+                            overrides=['tools/get_annotation=default'])
+        cfg = cfg.tools.get_annotation
     logger.info("Loaded the following system prompt for the LLM"
                 " to get a structured output: %s", cfg.prompt)
 

{aiagents4pharma-1.17.0 → aiagents4pharma-1.17.1}/aiagents4pharma/talk2biomodels/tools/search_models.py

@@ -29,7 +29,7 @@ class SearchModelsTool(BaseTool):
     name: str = "search_models"
     description: str = "Search models in the BioMmodels database based on keywords."
     args_schema: Type[BaseModel] = SearchModelsInput
-    return_direct: bool = True
+    return_direct: bool = False
 
     def _run(self,
              query: str,

aiagents4pharma-1.17.1/aiagents4pharma.egg-info/PKG-INFO

@@ -0,0 +1,150 @@
+Metadata-Version: 2.2
+Name: aiagents4pharma
+Version: 1.17.1
+Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: copasi_basico==0.78
+Requires-Dist: coverage==7.6.4
+Requires-Dist: einops==0.8.0
+Requires-Dist: gdown==5.2.0
+Requires-Dist: huggingface_hub==0.26.5
+Requires-Dist: hydra-core==1.3.2
+Requires-Dist: joblib==1.4.2
+Requires-Dist: langchain==0.3.7
+Requires-Dist: langchain-community==0.3.5
+Requires-Dist: langchain-core==0.3.31
+Requires-Dist: langchain-experimental==0.3.3
+Requires-Dist: langchain-openai==0.2.5
+Requires-Dist: langchain_ollama==0.2.2
+Requires-Dist: langgraph==0.2.66
+Requires-Dist: matplotlib==3.9.2
+Requires-Dist: openai==1.59.4
+Requires-Dist: ollama==0.4.6
+Requires-Dist: pandas==2.2.3
+Requires-Dist: plotly==5.24.1
+Requires-Dist: pydantic==2.9.2
+Requires-Dist: pylint==3.3.1
+Requires-Dist: pypdf==5.2.0
+Requires-Dist: pytest==8.3.3
+Requires-Dist: pytest-asyncio==0.25.2
+Requires-Dist: streamlit==1.39.0
+Requires-Dist: sentence_transformers==3.3.1
+Requires-Dist: tabulate==0.9.0
+Requires-Dist: torch==2.2.2
+Requires-Dist: torch_geometric==2.6.1
+Requires-Dist: tqdm==4.66.6
+Requires-Dist: transformers==4.48.0
+Requires-Dist: mkdocs==1.6.1
+Requires-Dist: mkdocs-jupyter==0.25.1
+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
+
+[![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
+[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
+[![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
+[![TESTS Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
+![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+
+## Introduction
+
+Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
+
+Our toolkit currently consists of the following agents:
+
+- **Talk2BioModels** _(v1 released; v2 in progress)_: Engage directly with mathematical models in systems biology.
+- **Talk2KnowledgeGraphs** _(v1 in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Scholars** _(v1 in progress)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Cells** _(v1 in progress)_: Query and analyze sequencing data with ease.
+
+![AIAgents4Pharma](docs/assets/AIAgents4Pharma.png)
+
+## Getting Started
+
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+### 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
+   cd AIAgents4Pharma
+   ```
+2. **Install dependencies:**
+   ```bash
+   pip install .
+   ```
+3. **Initialize OPENAI_API_KEY**
+   ```bash
+   export OPENAI_API_KEY=....
+   ```
+4. **[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 `T2X-xxxx`, where `X` can be `B` (Biomodels), `S` (Scholars),
+`KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will
+default to the name `default`. `xxxx` will be the 4-digit ID created for the
+session._
+
+5. **Launch the app:**
+   ```bash
+   streamlit run app/frontend/streamlit_app_<agent>.py
+   ```
+_Replace <agent> with the agent name you are interested to launch._
+
+For detailed instructions on each agent, please refer to their respective modules.
+
+---
+
+## Contributing
+
+We welcome contributions to AIAgents4Pharma! Here’s how you can help:
+
+1. **Fork the repository**
+2. **Create a new branch** for your feature (`git checkout -b feat/feature-name`)
+3. **Commit your changes** (`git commit -m 'feat: Add new feature'`)
+4. **Push to the branch** (`git push origin feat/feature-name`)
+5. **Open a pull request** and reach out to any one of us below via Discussions:
+
+   _Note: We welcome all contributions, not just programming-related ones. Feel free to open bug reports, suggest new features, or participate as a beta tester. Your support is greatly appreciated!_
+
+- **Talk2Biomodels/Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330) [@lilijap](https://github.com/lilijap) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info) [@gurdeep330](https://github.com/gurdeep330) [@dmccloskey](https://github.com/dmccloskey)
+
+### Current Needs
+
+- **Beta testers** for Talk2BioModels and Talk2Scholars.
+- **Developers** with experience in Python and Bioinformatics and/or knowledge graphs for contributions to AIAgents4Pharma.
+
+Feel free to reach out to us via Discussions.
+
+Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
+
+---
+
+## Feedback
+
+Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Isssues` or `Discussions` 😀

{aiagents4pharma-1.17.0 → aiagents4pharma-1.17.1}/aiagents4pharma.egg-info/SOURCES.txt

@@ -8,17 +8,6 @@ aiagents4pharma.egg-info/SOURCES.txt
 aiagents4pharma.egg-info/dependency_links.txt
 aiagents4pharma.egg-info/requires.txt
 aiagents4pharma.egg-info/top_level.txt
-aiagents4pharma/configs/__init__.py
-aiagents4pharma/configs/config.yaml
-aiagents4pharma/configs/talk2biomodels/__init__.py
-aiagents4pharma/configs/talk2biomodels/agents/__init__.py
-aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/__init__.py
-aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/default.yaml
-aiagents4pharma/configs/talk2biomodels/tools/__init__.py
-aiagents4pharma/configs/talk2biomodels/tools/ask_question/__init__.py
-aiagents4pharma/configs/talk2biomodels/tools/ask_question/default.yaml
-aiagents4pharma/configs/talk2biomodels/tools/get_annotation/__init__.py
-aiagents4pharma/configs/talk2biomodels/tools/get_annotation/default.yaml
 aiagents4pharma/talk2biomodels/__init__.py
 aiagents4pharma/talk2biomodels/agents/__init__.py
 aiagents4pharma/talk2biomodels/agents/t2b_agent.py
@@ -26,6 +15,15 @@ aiagents4pharma/talk2biomodels/api/__init__.py
 aiagents4pharma/talk2biomodels/api/kegg.py
 aiagents4pharma/talk2biomodels/api/ols.py
 aiagents4pharma/talk2biomodels/api/uniprot.py
+aiagents4pharma/talk2biomodels/configs/__init__.py
+aiagents4pharma/talk2biomodels/configs/agents/__init__.py
+aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/__init__.py
+aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/default.yaml
+aiagents4pharma/talk2biomodels/configs/tools/__init__.py
+aiagents4pharma/talk2biomodels/configs/tools/ask_question/__init__.py
+aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml
+aiagents4pharma/talk2biomodels/configs/tools/get_annotation/__init__.py
+aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml
 aiagents4pharma/talk2biomodels/models/__init__.py
 aiagents4pharma/talk2biomodels/models/basico_model.py
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py

{aiagents4pharma-1.17.0 → aiagents4pharma-1.17.1}/pyproject.toml

@@ -67,17 +67,17 @@ include = ["aiagents4pharma*"]
 
 [tool.setuptools.package-data]
 aiagents4pharma = [
-  "configs/*",
-  "configs/talk2biomodels/agents/t2b_agent/*",
-  "configs/talk2biomodels/tools/ask_question/*",
-  "configs/talk2biomodels/tools/get_annotation/*",
-  "talk2scholars/configs/*",
-  "talk2scholars/configs/agents/talk2scholars/main_agent/*",
-  "talk2scholars/configs/agents/talk2scholars/s2_agent/*",
-  "talk2scholars/configs/app/frontend/*",
-  "talk2scholars/configs/tools/multi_paper_recommendation/*",
-  "talk2scholars/configs/tools/search/*",
-  "talk2scholars/configs/tools/single_paper_recommendation/*",
+    "talk2biomodels/configs*",
+    "talk2biomodels/configs/agents/t2b_agent/*",
+    "talk2biomodels/configs/tools/ask_question/*",
+    "talk2biomodels/configs/tools/get_annotation/*",
+    "talk2scholars/configs/*",
+    "talk2scholars/configs/agents/talk2scholars/main_agent/*",
+    "talk2scholars/configs/agents/talk2scholars/s2_agent/*",
+    "talk2scholars/configs/app/frontend/*",
+    "talk2scholars/configs/tools/multi_paper_recommendation/*",
+    "talk2scholars/configs/tools/search/*",
+    "talk2scholars/configs/tools/single_paper_recommendation/*",
 
 ]
 

aiagents4pharma-1.17.1/release_version.txt

@@ -0,0 +1 @@
+v1.17.1