pyiron / pyiron_workflow_atomistics / 25741942359
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Cleanup + reorganise: Engine Protocol, topical physics modules, _internal/, README+badges (#30)

Surgical cleanup/reorganisation of pyiron_workflow_atomistics around the same architecture:

- engine/ — single Engine Protocol (@runtime_checkable), EngineOutput dataclass, run(structure, engine) node, subengine/subdir_path helpers for macro-safe sub-engines, ASEEngine consolidated from three duplicate files. Pickle-safe; pure with_working_directory via dataclasses.replace.
- structure/ — generic builders (get_bulk, create_surface_slab), transforms (add_vacuum, create_supercell*, rattle), defects (create_vacancy, substitutional_swap).
- physics/ — topical workflow macros: physics.bulk, physics.surface, physics.point_defect, physics.grain_boundary. physics/__init__.py re-exports nothing by design.
- analysis/ — featurisers (snake_case), GB-plane helpers, derived quantities.
- _internal/ — private plumbing for kwargs / dataclass / workdir helpers.
- Top-level __init__.py only exposes __version__; py.typed marker added.
- 87 unit tests + new tests/unit/physics/ + tests/unit/_internal/; notebook integration test executes all 10 notebooks end-to-end.
- docs/README.md rewritten with Tests / Coverage / PyPI / Python / ReadTheDocs / black / BSD-3-Clause badges and new-API examples.
- CI fixes: lz-GB-code installed in env, ruff/black configs cleaned, pyproject pins bumped to match conda solve.

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861 of 2045 relevant lines covered (42.1%)

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1 25741942359.1 30
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Source Files on build 25741942359