Contributing

Development setup

uv sync
uv run pytest
uv run ruff check .

Documentation

uv sync --group docs
uv run mkdocs serve
uv run mkdocs build --strict

Build a PDF copy of the user guide with Pandoc and a LaTeX engine:

python scripts/build_user_guide_pdf.py

The generated file is written to docs/_build/molscope-user-guide.pdf.

Guidelines

• Keep the core package dependency-light.
• Prefer clear, small APIs over framework-specific abstractions.
• Add tests for new readers, descriptors, graph exporters, or coarse-graining behavior.
• Document limitations when behavior is intentionally simple or prototype-oriented.