Development

Project structure

• src/pycardinal/ contains the installable Python package.
• tests/ contains pytest checks built from deterministic simulated spectra and temporary imzML files. No external MSI dataset is required.
• docs/ contains the MkDocs site.
• docs/api-reference.md is the hand-written behavioral guide; docs/generated-api.md is generated from public Python docstrings.
• The original Cardinal authors and publication remain the migration attribution and numerical reference.

Checks

Run these from the repository root after a code or documentation change:

python -m pytest
python -m ruff check src tests
python -m mypy src/pycardinal
python -m mkdocs build --strict

If a future manual integration test uses a large private imzML file, keep it outside the default pytest suite and document its local setup separately.

API documentation conventions

Every public class and function should have a NumPy-style docstring with a summary, parameter descriptions and units, return values, raised exceptions, and a small executable example where practical. Document whether processing is deferred or eager, the orientation of data axes, and any relevant m/z or spatial units. Update the API reference and relevant guide in the same change that adds or changes public behavior.