Merge pull request #167 from HolobiomicsLab/doc_update_2604

Refactor MetaboT documentation and update demo links
Thanks for reviewing it @madina1203

Author: lfnothias

README.md

@@ -34,7 +34,7 @@ Create a ChatLiteLLM instance based on the model id and configuration from [app/
 **Parameters:**
 - `config` (configparser.SectionProxy): The configuration section from params.ini that contains model settings:
 
-  - Required: "id" - model identifier (e.g., "gpt-4", "deepseek/...")
+  - Required: "id" - model identifier (e.g., "gpt-4o", "deepseek/...")
   - Optional: "temperature", "max_retries", "base_url", "api_base"
 
 **Returns:**

docs/api-reference/core.md

@@ -1,116 +1,84 @@
-# Contributing to 🧪 MetaboT 🍵 📝
+# Contributing
 
-We appreciate your interest in contributing to 🧪 MetaboT 🍵! Below are the guidelines to help you get started.
+Thank you for helping improve MetaboT. Contributions are welcome across code, prompts, evaluation, examples, and documentation.
 
----
+## Development Workflow
 
-## How to Contribute 🤝
+1. Fork the repository.
+2. Clone your fork locally.
+3. Create a feature branch from `main`.
+4. Make and test your changes.
+5. Open a pull request back to `main`.
 
-### Fork the Repository
-
-Fork the [MetaboT repository](https://github.com/holobiomicslab/MetaboT) to your GitHub account.
-
-Clone your forked repository to your local machine:
-
-- Fork the repository on GitHub.
-- Clone your fork and check out a new branch from the [`dev` branch](https://github.com/holobiomicslab/MetaboT/tree/dev).
+Example:
 
 ```bash
 git clone https://github.com/<your-username>/MetaboT.git
 cd MetaboT
-git checkout -b dev
+git checkout -b my-feature
 ```
 
-### Create a Branch
-
-Create a new branch for your feature or bugfix. For example, if you're working on a new feature, you might create a branch off the [`dev` branch](https://github.com/holobiomicslab/MetaboT/tree/dev).
-
-#### Development Process
-
-**Making Changes**
-
-- Make your changes ensuring all references to files (e.g., configuration files like [app/config/params.ini](https://github.com/holobiomicslab/MetaboT/blob/main/app/config/params.ini)) are updated as needed.
-- Commit your changes with clear, meaningful commit messages.
-- Push your feature branch and open a pull request against the [`dev` branch](https://github.com/holobiomicslab/MetaboT/tree/dev).
-
-
-### Code Guidelines
-
-- Follow the existing code style (Google DocString).
-- Write clear and concise commit messages.
-- Include comments and docstrings where necessary.
-
----
+## What We Appreciate Most
 
-#### Code Standards 
+- bug fixes and reliability improvements
+- clearer prompts and better agent coordination
+- documentation improvements
+- new examples and benchmarks
+- portability improvements for new knowledge graphs
 
-- Follow **PEP8** for Python code. See the [Python Style Guide (PEP 8)](https://www.python.org/dev/peps/pep-0008/).
-- Include detailed documentation and inline comments where applicable.
+## Code Style
 
----
+- Follow standard Python style and keep changes readable.
+- Add comments where they clarify non-obvious logic.
+- Prefer small, focused pull requests over large mixed changes.
+- Update docs when behavior, configuration, or setup changes.
 
-#### Tests 
+## Tests and Validation
 
-You can find our test suite in the [app/core/tests/](https://github.com/holobiomicslab/MetaboT/tree/main/app/core/tests) directory.
-
-#### Documentation
-
-Update the documentation to reflect your changes. This includes:
-
-- Docstrings in the code.
-- Relevant Markdown files in the [docs/ directory](https://github.com/holobiomicslab/MetaboT/tree/main/docs), including:
-
-    - [API Reference](https://github.com/holobiomicslab/MetaboT/tree/main/docs/api-reference)
-      - [User Guide](https://github.com/holobiomicslab/MetaboT/tree/main/docs/user-guide)
-      - [Examples](https://github.com/holobiomicslab/MetaboT/tree/main/docs/examples)
-      - [Getting Started](https://github.com/holobiomicslab/MetaboT/tree/main/docs/getting-started)
-
----
-
-## Submitting Your Changes 📤
-
-### Commit Your Changes
-
-Commit your changes with a descriptive message:
-
-```bash
-git add .
-git commit -m "Add new feature X"
-```
+Relevant code and tests live under:
 
-### Push to Your Fork
+- `app/core/`
+- `app/tests/`
+- `docs/`
 
-Push your changes to your forked repository:
+Before opening a pull request, run the checks that make sense for your change. At minimum, a lightweight smoke test is helpful:
 
 ```bash
-git push origin my-feature-branch
+python -m app.core.main -q 1
 ```
 
-### Open a Pull Request
+If you change prompts, routing, or SPARQL behavior, include a short note in the pull request explaining what you validated.
 
-Open a pull request from your branch to the [`dev` branch](https://github.com/holobiomicslab/MetaboT/tree/dev) of the original repository. Provide a clear description of your changes and any relevant information.
+## Documentation Changes
 
----
+Documentation is part of the product. If you change:
 
-### Code Review
+- setup steps
+- environment variables
+- CLI behavior
+- agent roles
+- endpoint assumptions
 
-Your pull request to the [`dev` branch](https://github.com/holobiomicslab/MetaboT/tree/dev) will be reviewed by an AI-agent and then by the maintainers. They may request changes or provide feedback. Please be responsive and address any comments or suggestions.
+please update the corresponding pages in `docs/` and, when relevant, `README.md`.
 
----
+## Pull Requests
 
-## Community 👥
+When you open a pull request:
 
-- You are welcome to use, reuse, and enrich 🧪 MetaboT 🍵.
-- Be respectful and considerate in your interactions.
-- Help others and share your knowledge.
-- Check our [examples](https://github.com/holobiomicslab/MetaboT/tree/main/docs/examples) for guidance.
+- explain the user-facing motivation
+- summarize the main changes
+- mention how you tested them
+- link related issues or discussions when available
 
----
+Clear PR descriptions make review much faster.
 
-## Additional Resource 📚
+## Community
 
-- [Writing Good Commit Messages](https://chris.beams.io/posts/git-commit/)
+Please be respectful, generous, and constructive in discussion and review. MetaboT sits at the intersection of AI, knowledge graphs, and metabolomics, so clear collaboration matters a lot.
 
----
+## Useful References
 
-Thank you for contributing to 🧪 MetaboT 🍵! Your efforts help make this project better for everyone.
+- [Documentation Home](index.md)
+- [Installation](getting-started/installation.md)
+- [Quick Start](getting-started/quickstart.md)
+- [Examples](examples/basic-usage.md)

docs/assets/images/metabot-overview.png

@@ -67,7 +67,7 @@ from app.core.main import llm_creation
 from app.core.workflow.langraph_workflow import create_workflow
 # Initialize components
 endpoint_url = "https://enpkg.commons-lab.org/graphdb/repositories/ENPKG"
-models = llm_creation()  # [llm_creation](https://github.com/nothiasl/MetaboT/blob/main/app/core/main.py)
+models = llm_creation()  # See app/core/main.py
 # Create workflow
 workflow = create_workflow(
     models=models,
@@ -84,7 +84,7 @@ from app.core.workflow.langraph_workflow import process_workflow
 
 # Process a custom query
 query = "What are the chemical structure ISDB annotations for Lovoa trichilioides?"
-process_workflow(workflow, query)  # [process_workflow](https://github.com/nothiasl/MetaboT/blob/main/app/core/workflow/langraph_workflow.py)
+process_workflow(workflow, query)  # See app/core/workflow/langraph_workflow.py
 ```
 
 ### Batch Processing