We use Sphinx to organize the documentation and it is hosted in ReadTheDocs.

Local Build

Please run the following command under docs/ directory for generating the documentation pages locally. Generated files are under docs/build/html/

make clean html


  • clean removes the possible built files.

  • Optionally we can add SPHINXOPTS="-W" to fail on any warnings, but we are currently having document isn't included in any toctree warning and no better solution has been found yet.


There are some recommendations regarding the docs.

  • We prefer markdown files over reStructuredText files as its linting is covered using Prettier.

    Only use reStructuredText (rst) files for some functionalities not supported by markdown, such as

    The conversion between markdown and rst can be done automatically using free online tool Pandoc.

  • When linking to other pages, please use relative paths such as ../getting_started/install.html instead of absolute paths as relative paths are more robust for different version of documentations.

  • To refer a markdown file outside of the source folder, create an rst file and use .. mdinclude:: <makrdown file path> to include the markdown source.

    Check the source code of paired lung CT image registration page as an example.