Sphinx source for the docs published on GitHub Pages.

• docs/pages/ — hand-authored content, tracked in git.
• docs/src/ — generated by sphinx-apidoc + build_defaults_rst.py. Not tracked, rebuilt every time.
• docs/titles.yaml — page titles for docs/src/ content.
• docs/figs/ — images used by docs/pages/.

pip install -e '.[dev,docs]'
cd docs
make html
open ../haddock3-docs/pages/index.html

make html runs sphinx-apidoc + sphinx-build (see docs/Makefile), same as CI. make linkcheck checks for broken links.

Napoleon (docs/conf.py) supports NumPy and Google style. NumPy style example:

def identify_unknown_hetatms(pdb_file: FilePath) -> list[str]:
    """Return residue names in a PDB that are not in the supported residues.

    Parameters
    ----------
    pdb_file : FilePath
        Path to the PDB file to inspect.

    Returns
    -------
    list[str]
        Unique residue names not found in the supported residues set.
    """