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Changelog

0.6.1

Bug fixes

  • 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.

Performance

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

Testing

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

0.6.0

Breaking changes

  • 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().

Bug fixes

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

Documentation

  • 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.

Other changes

  • Switched from tqdm / tqdm.notebook to tqdm.auto for progress bars.
  • Removed unused imports from trajectory module.

0.5.0

Performance

  • 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.

Bug fixes

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

Other changes

  • Removed redundant assert isinstance checks across the codebase.
  • Added input shape validation to RotationAnalyser.discrete_orientation.

0.4.0

Breaking changes

  • 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.

New features

  • 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).

Other changes

  • Split mypy type checking into a separate CI job.

0.3.0

Other changes

  • 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.

0.2.0

Performance

  • 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.

Bug fixes

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

Breaking changes

  • Now requires Python >=3.11 (previously >=3.7).
  • Removed numpy<2.0 version cap; now compatible with numpy 2.x.
  • Minimum pymatgen version bumped to >=2024.7.18.
  • New runtime dependencies: bsym, cmcrameri.

New features

  • Added orientation plotting.
  • Added off-centre displacement calculation.
  • Added octahedral orthogonality metric.
  • Added radial distortion parameter.
  • Added polyhedron centroid methods.
  • Added mapping from global to local vertex indices.
  • Revised vertex distance and vertex pair angle calculations.

Other changes

  • CI updated to test Python 3.11, 3.12, 3.13, 3.14.
  • CI now triggers only on pull requests.

0.1

Initial release.