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Contributing

Thank you for helping improve MetaboT. Contributions are welcome across code, prompts, evaluation, examples, and documentation.

Development Workflow

  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.

Example:

git clone https://github.com/<your-username>/MetaboT.git
cd MetaboT
git checkout -b my-feature

What We Appreciate Most

  • bug fixes and reliability improvements
  • clearer prompts and better agent coordination
  • documentation improvements
  • new examples and benchmarks
  • portability improvements for new knowledge graphs

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 and Validation

Relevant code and tests live under:

  • app/core/
  • app/tests/
  • docs/

Before opening a pull request, run the checks that make sense for your change. At minimum, a lightweight smoke test is helpful:

python -m app.core.main -q 1

If you change prompts, routing, or SPARQL behavior, include a short note in the pull request explaining what you validated.

Documentation Changes

Documentation is part of the product. If you change:

  • setup steps
  • environment variables
  • CLI behavior
  • agent roles
  • endpoint assumptions

please update the corresponding pages in docs/ and, when relevant, README.md.

Pull Requests

When you open a pull request:

  • 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.

Community

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