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Documentation Guide

Documentation of BioSegment is done through:

  • This GitHub Pages site
    • built using Material for MkDocs
    • features a general overview, tutorial, User Guide, contribution guide and Developer Guide.
  • Markdown files in the BioSegment repository
    • e.g.
  • docstrings in the BioSegment source code
  • the backend API
    • OpenAPI/ReDoc documentation generated by FastAPI backend

Add mkdocs documentation

Via GitHub

You can directly edit the documentation by clicking the pencil icon . This takes you to GitHub and lets you edit the documention's Markdown file located in /docs. Apply your changes and make a Pull request describing your change.


Setup your environment using the Material for MkDocs installation guide.

Run a hot-reload server for the documentation and edit the files.

conda env create -f environment_documentation.yaml --prune
conda activate biosegment_documentation
mkdocs serve

When the changes are merged into main, the CI configuration will update the GitHub Pages site.