Changelog

Fixed variable shadowing in polyhedra_from_atom_indices that caused only the first polyhedron to receive correct vertices.
Invalid atom indices passed to polyhedra_from_atom_indices now raise ValueError with a descriptive message instead of a raw KeyError.

polyhedra_from_atom_indices now uses precomputed index-to-atom mappings for O(1) lookups instead of repeated linear scans.

Expanded test coverage across configuration, coordination_polyhedron, orientation_parameters, polyhedra_recipe, trajectory, and utils modules.

The progress parameter on Trajectory.from_structures(), Trajectory.from_xdatcar(), and Trajectory.from_xdatcars() is now bool instead of bool | str. The "notebook" option has been removed; tqdm.auto now handles automatic terminal/Jupyter detection. Replace progress="notebook" with progress=True. Passing a non-bool now raises TypeError with a migration hint.
Renamed SymmetryMeasure.string attribute to SymmetryMeasure.name.
Removed unused verbose parameter from Trajectory.from_structures(), from_xdatcar(), and from_xdatcars().
Removed unused offset parameter from Trajectory.extend().

Trajectory.extend() now extends both structures and configurations. Previously only configurations were extended, causing the two lists to fall out of sync.

Comprehensive documentation overhaul with narrative pages, guides, and grouped API reference.
Added getting started guide and core concepts page.
Added guides for polyhedra recipes, continuous symmetry measures, neighbour analysis, and trajectory analysis.
Replaced auto-generated module stubs with a single grouped API reference page.
Added citing and changelog pages.
Modernised Sphinx configuration: replaced deprecated recommonmark with myst-parser, added intersphinx cross-references to pymatgen, numpy, scipy, and matplotlib.
Filled ~30 missing docstrings across the codebase.

Cached symmetry_measure property on CoordinationPolyhedron to avoid redundant CSM calculations on repeated access.
edge_graph and symmetry_measure now return defensive copies to prevent callers from corrupting the internal cache.
Replaced N! permutation loop in RotationAnalyser with symmetry-reduced approach using bsym, giving ~50x speedup for octahedral geometries.

Fixed OrientationDict.all_rotational_distances type annotation (np.ndarray, not float).

Removed dependency on pymatgen.analysis.chemenv. CSM (continuous symmetry measure) calculation and reference geometry data are now implemented internally.
minimum_symmetry_measure() now takes distorted_points: np.ndarray instead of AbstractGeometry.
oct_rotational_order_parameter() now takes points: np.ndarray instead of AbstractGeometry.
Removed abstract_geometry property and construct_abstract_geometry() method from CoordinationPolyhedron.

Added polyhedral_analysis.csm module with internal continuous_symmetry_measure() function using SVD-based Procrustes analysis.
Added polyhedral_analysis.reference_geometries module with hardcoded ideal vertex coordinates for 17 reference geometries (CN 4-8).

Migrated from setup.py to pyproject.toml.
Removed requirements.txt, .coveragerc, and .mypy.ini (consolidated into pyproject.toml).
Version now read at runtime via importlib.metadata.
Updated type hints to modern Python 3.11+ syntax.
Updated README with description, features, installation, and quick start example.

Reduced CSM (continuous symmetry measure) permutations using symmetry equivalence via bsym. Only symmetry-inequivalent vertex permutations are evaluated, giving 12-49x speedups depending on geometry symmetry.

Removed duplicate “Dodecahedron with triangular faces” entry from CN=8 geometry list.
Fixed mypy errors across codebase.

Initial release.