raven-docs

Documentation site for RAVEN (the MATLAB toolbox) and raven-toolbox (the Python port) for genome-scale metabolic model reconstruction, analysis and visualization. Built with MkDocs + Material and published on Read the Docs.

The site combines:

• a side-by-side API reference auto-generated from the function comments of both toolboxes (via mkdocstrings with its Python and MATLAB handlers);
• the RAVEN tutorials; and
• a complete, worked GEM reconstruction protocol (the Hansenula polymorpha hanpo-GEM example).

The source repositories are tracked as git submodules pinned to their main branches: RAVEN, raven-toolbox and hanpo-GEM.

Building locally

# clone with submodules
git clone --recurse-submodules https://github.com/edkerk/raven-docs.git
cd raven-docs
# (if already cloned: git submodule update --init --recursive)

python -m venv .venv
source .venv/Scripts/activate      # Windows; use .venv/bin/activate on macOS/Linux
pip install -r requirements.txt

mkdocs serve     # live preview at http://127.0.0.1:8000
mkdocs build     # static site into ./site

The API reference pages are generated at build time by scripts/gen_api_pages.py, which walks the two toolbox submodules and pairs their functions. No MATLAB runtime or installed Python package is required — docstrings are collected statically from source.