Optional: build documentation

If you edit your local tomoDRGN source code or documentation, you can re-build documentation pages to reflect your changes. The source pages for documentation are available at $TOMODRGN_SOURCE_DIR/docs/_source/ and are written in reStructuredText (.rst). Documentation is then built with sphinx in the tomodrgn environment as described below.

Note

Building documentation requires a further installation of tomoDRGN’s documentation-building dependencies.

cd $TOMODRGN_SOURCE_DIR
python -m pip install ".[docs]"

Run the following commands to build local documentation.

cd $TOMODRGN_SOURCE_DIR/docs
make clean
rm -rfv docs/_source/api/_autosummary  # this ensures all files from previous builds are removed, including autosummary API files missed by make clean
make html  # note that a large number of warnings about `torch.nn.modules.Module` are expected and can be ignored

Built documentation can be viewed by opening ./docs/_build/html/index.html in a web browser.