aiagents4pharma 1.44.0__py3-none-any.whl → 1.45.1__py3-none-any.whl

{aiagents4pharma-1.44.0.dist-info → aiagents4pharma-1.45.1.dist-info}/METADATA

@@ -1,71 +1,91 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.44.0
+Version: 1.45.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
-Classifier: Programming Language :: Python :: 3
+License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.12
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: copasi_basico==0.84
+Requires-Dist: anndata==0.11.3
+Requires-Dist: beautifulsoup4==4.13.4
+Requires-Dist: cell2sentence==1.1.0
+Requires-Dist: cloudscraper==1.2.71
+Requires-Dist: copasi-basico==0.84
 Requires-Dist: coverage==7.6.4
+Requires-Dist: datasets==4.0.0
 Requires-Dist: einops==0.8.0
 Requires-Dist: gdown==5.2.0
 Requires-Dist: gravis==0.1.0
-Requires-Dist: huggingface_hub==0.26.5
+Requires-Dist: gseapy==1.1.8
+Requires-Dist: h5py==3.13.0
+Requires-Dist: huggingface-hub==0.34.4
 Requires-Dist: hydra-core==1.3.2
+Requires-Dist: igraph==0.11.8
+Requires-Dist: ipykernel==6.29.5
+Requires-Dist: ipython==8.32.0
 Requires-Dist: joblib==1.4.2
-Requires-Dist: langchain==0.3.7
 Requires-Dist: langchain-community==0.3.5
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-Requires-Dist: langchain-openai==0.2.5
-Requires-Dist: langchain_ollama==0.2.3
-Requires-Dist: langgraph_supervisor==0.0.9
+Requires-Dist: langchain-ollama==0.2.3
+Requires-Dist: langchain-openai==0.3.0
+Requires-Dist: langchain==0.3.7
+Requires-Dist: langgraph-supervisor==0.0.9
+Requires-Dist: langgraph==0.3.34
 Requires-Dist: matplotlib==3.9.2
-Requires-Dist: openai==1.59.4
+Requires-Dist: mkdocs-include-markdown-plugin==7.1.2
+Requires-Dist: mkdocs-jupyter==0.25.1
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+Requires-Dist: openai==1.59.6
+Requires-Dist: openpyxl==3.1.5
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+Requires-Dist: pydantic==2.10.5
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 Requires-Dist: pylint==3.3.1
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-Requires-Dist: pytest==8.3.3
+Requires-Dist: pymilvus==2.5.11
+Requires-Dist: pypdf==6.0.0
 Requires-Dist: pytest-asyncio==0.25.2
+Requires-Dist: pytest==8.3.3
+Requires-Dist: python-magic==0.4.27
 Requires-Dist: pyzotero==1.6.9
-Requires-Dist: pymilvus==2.5.11
-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
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+Requires-Dist: streamlit==1.41.1
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+Requires-Dist: torch==2.8.0
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-Dynamic: license-file
+Requires-Dist: xlsxwriter==3.2.5
+Provides-Extra: dev
+Requires-Dist: bandit==1.8.6; extra == 'dev'
+Requires-Dist: mypy==1.17.1; extra == 'dev'
+Requires-Dist: pip-audit==2.9.0; extra == 'dev'
+Requires-Dist: pre-commit==4.3.0; extra == 'dev'
+Requires-Dist: ruff==0.12.8; extra == 'dev'
+Requires-Dist: safety==3.2.9; extra == 'dev'
+Requires-Dist: twine==6.1.0; extra == 'dev'
+Description-Content-Type: text/markdown
 
 <img src="docs/assets/VPE.png" alt="Virtual Patient Engine Logo" width="150"/>
 
@@ -78,7 +98,7 @@ Dynamic: license-file
 <!--  Deployment Workflows -->
 
 [![Pages Deployment](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment)
-[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml)
+[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs_deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs_deploy.yml)
 [![Docker Build & Push](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml)
 [![Docker Compose Release](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml)
 
@@ -149,12 +169,16 @@ git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma && cd AIAgents
 
 2. **Install dependencies:**
 
-We use Conda as our environment manager, Follow the official [Quickstart](https://www.anaconda.com/docs/getting-started/miniconda/install#quickstart-install-instructions) install instructions provided by anaconda/miniconda.
+We use `uv` for fast and reliable dependency management. Install uv first following the [official installation guide](https://docs.astral.sh/uv/getting-started/installation/).
 
-```python
-conda create --name AIAgents4Pharma python=3.12 -y && conda activate AIAgents4Pharma && pip install --upgrade pip && pip install -r requirements.txt
+> **For developers**: See [docs/developer/README.md](docs/developer/README.md) for detailed setup instructions including system prerequisites.
+
+```sh
+uv sync --extra dev --frozen
 ```
 
+> 💡 **Recommended**: Use `--frozen` flag to ensure exact reproducible builds using the pinned versions from `uv.lock`.
+
 3. **Initialize API Keys**
 
 ```env
@@ -168,7 +192,21 @@ export LANGCHAIN_API_KEY=...        # Optional for all agents
 
 4. **Launch the app:**
 
+**Option A: Using UV (recommended)**
+
 ```sh
+uv run streamlit run app/frontend/streamlit_app_<agent>.py
+```
+
+**Option B: Traditional approach**
+
+```sh
+# Activate virtual environment
+source .venv/bin/activate  # Linux/macOS
+# or
+.venv\Scripts\activate     # Windows
+
+# Then run the app
 streamlit run app/frontend/streamlit_app_<agent>.py
 ```
 
@@ -187,6 +225,8 @@ If your machine has NVIDIA GPU(s), please install the following this:
 
 To use the **Agents**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
 
+**Talk2Biomodels** supports integration with multiple LLMs: gpt-4o-mini (via OpenAI API) and open-source llama (3.1 and 3.3) models (via NVIDIA API). An **OpenAI API** key may be generated [here](https://platform.openai.com/settings/organization/api-keys). OpenAI may provide initial free credits for API calls with the API key, after which additional credits may be purchased [here](https://platform.openai.com/settings/organization/billing). More information on pricing is available [here](https://openai.com/api/pricing/).
+
 **Talk2Scholars** and **Talk2KnowledgeGraphs** requires Milvus to be set up as the vector database — install Milvus depending on your setup by following the official instructions for [CPU](https://milvus.io/docs/install_standalone-docker-compose.md) or [GPU](https://milvus.io/docs/install_standalone-docker-compose-gpu.md). You will also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(The Zotero key is only required for Talk2Scholars; all other agents do not need it.)_
 
 > By default, `talk2knowledgegraphs` includes a small subset of the PrimeKG knowledge graph, allowing users to start interacting with it out of the box.
@@ -214,9 +254,19 @@ Check out the tutorials on each agent for detailed instructions.
 
 ## Contributing
 
-We welcome your support to make **AIAgents4Pharma** even better.  
+We welcome your support to make **AIAgents4Pharma** even better.
 All types of contributions are appreciated — whether you're fixing bugs, adding features, improving documentation, or helping with testing, every contribution is valuable.
 
+#### Development Setup
+
+For contributors and developers, we have comprehensive documentation:
+
+- **[Developer Setup Guide](docs/developer/README.md)** - Complete setup instructions with UV, security implementation, and tooling
+- **[Testing & Linting Guide](docs/developer/TESTING_LINTING.md)** - How to run tests, coverage, and code quality checks
+- **[SonarCloud Integration](docs/developer/SONARCLOUD_SETUP.md)** - Code quality analysis and CI/CD integration
+- **[GitHub Workflows](docs/developer/WORKFLOWS.md)** - Understanding our CI/CD pipeline
+- **[Streamlit Security](docs/developer/STREAMLIT_SECURITY.md)** - File upload security implementation
+
 #### How to contribute
 
 1. Star this repository to show your support.
@@ -227,19 +277,33 @@ All types of contributions are appreciated — whether you're fixing bugs, addin
 git checkout -b feat/your-feature-name
 ```
 
-4. Make your changes and commit them:
+4. Set up your development environment:
 
 ```sh
-git commit -m "feat: add a brief description of your change"
+uv sync --extra dev --frozen  # Install development dependencies
+uv run pre-commit install    # Set up code quality hooks
+```
+
+5. Make your changes and run quality checks:
+
+```sh
+uv run ruff check --fix .  # Lint and fix code
+uv run ruff format .  # Format code
+uv run pre-commit run --all-files  # Run all checks (linting, formatting, security)
+
+# Run submodule-specific checks (pylint configuration in pyproject.toml)
+uv run pylint aiagents4pharma/talk2scholars/
+uv run coverage run --include="aiagents4pharma/talk2scholars/*" -m pytest --cache-clear aiagents4pharma/talk2scholars/tests/ && uv run coverage report
 ```
 
-5. Push your branch:
+6. Commit and push your changes:
 
 ```sh
+git commit -m "feat: add a brief description of your change"
 git push origin feat/your-feature-name
 ```
 
-6. Open a Pull Request.
+7. Open a Pull Request.
 
 #### Areas where you can help
 
@@ -253,9 +317,9 @@ git push origin feat/your-feature-name
 - **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi)
 - **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info), [@gurdeep330](https://github.com/gurdeep330)
 
-Please refer to our [CONTRIBUTING.md](CONTRIBUTING.md) for more detailed contribution guidelines.
+Please refer to our [CONTRIBUTING.md](CONTRIBUTING.md) and [developer documentation](docs/developer/) for detailed contribution guidelines and setup instructions.
 
 ## Feedback
 
-If you have questions, bug reports, feature requests, comments, or suggestions, we would love to hear from you.  
+If you have questions, bug reports, feature requests, comments, or suggestions, we would love to hear from you.
 Please open an `issue` or start a `discussion`

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{aiagents4pharma-1.44.0.dist-info → aiagents4pharma-1.45.1.dist-info}/WHEEL

@@ -1,5 +1,4 @@
 Wheel-Version: 1.0
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 Root-Is-Purelib: true
 Tag: py3-none-any
-