Citing Otter

If you use Otter in a scientific publication, please cite Chongbing Qu and Dominik Kraus, Otter, version 0.2.4, computer software (2026), https://github.com/otter-hed/otter.

The same metadata are provided in CITATION.cff and through GitHub’s Cite this repository menu. Model references document scientific provenance; they are not additional software-citation requirements.

The complete reference registry is kept in the repository root: CITATIONS.md.

Runtime citation API

Electronic, ionic, workflow, and mixture configuration objects expose a three-style provenance API:

config.citation(style="plain")   # readable references
config.citation(style="bibtex")  # copyable BibTeX entries
config.citation(style="cite")    # an unevaluated ``\\cite{...}``

The keys are available as config.citation_keys. They are resolved from the packaged otter/literature.bib file, so installed workflows do not need the documentation dependencies. The otter.literature module also provides bibliography_entries and the three formatting helpers for applications that need to build their own reports.

class otter.literature.CitationMixin[source]

Bases: object

Mixin adding the plain/BibTeX/LaTeX citation API to model configs.

citation(style: str = 'plain', comment: str | None = None) → str[source]

Return references for this configured model.

Parameters:

  • style – "plain", "bibtex", or "cite".

  • comment – Optional provenance note appended to plain output or emitted as a BibTeX/LaTeX comment.

otter.literature.bibliography_entries() → dict[str, str][source]

Return the packaged raw BibTeX entries keyed by citation key.

otter.literature.write_citations_markdown(path: str | Path = 'CITATIONS.md') → Path[source]

Write the repository-wide citation policy and complete key registry.

Reference rules for contributors

  • Add a stable key, authors, year, and DOI to src/otter/literature.bib before introducing a new literature reference.

  • Put :cite:p: or :cite:t: beside equations and model descriptions in RST, and add a References section with the canonical key to Python docstrings.

  • Expose the selected keys through citation_keys for every selectable model. Test plain, bibtex, and cite output.

  • Identify Otter-specific discretization, regularization, and convergence choices separately; a paper describing a physical model does not validate every numerical implementation detail.

The HTML bibliography below is generated by Sphinx from the same BibTeX file. It is therefore the authoritative rendered view of the key registry.