3.0.0

• Major efficiency updates to most parts of the workflow, mostly implemented as helper functions in
  doped.utils.efficiency and doped.utils.configurations, including:

  • Fast and intelligent structure matching (patching various parts of pymatgen's StructureMatcher code).
  • Voronoi tessellation for interstitial generation
  • Defect generation
  • Wyckoff site detection
  • Defect site detection and matching, including very large supercells.
  • DefectThermodynamics initialisation (and defect grouping by distance between equivalent sites).

• FermiSolver and ChemicalPotentialGrid classes in #46, for
  advanced defect/carrier thermodynamics, allowing various constraints (e.g. mobile/fixed defects / charge
  states etc), with a number of convenience functions (e.g. for scanning temperature / chemical potentials
  etc, optimising output properties over many-dimensional chemical potential spaces etc). Usage
  demonstrated in https://doped.readthedocs.io/en/latest/fermisolver_tutorial.html.

• Add is_shallow DefectEntry property, and DefectThermodynamics._get_in_gap_fermi_level_stability_window
  method. Shallow defect states now automatically excluded from formation energy diagram plots for cleaner
  outputs, controllable with the unstable_entries kwarg. Large charge correction errors for
  shallow/unstable defects (typically higher and a common indication of 'false charge state' behaviour)
  now do not throw a warning during parsing.

• CompetingPhases now compatible with both legacy and new Materials Project APIs, with automatic
  handling (and appropriate warnings) for cases of unstable host materials/compositions.

• Internal overhaul of CompetingPhasesAnalyzer code, using ComputedStructureEntry objects.
  Initialisation now much faster and more convenient, JSON-serializable outputs, further visualisation and
  plotting, and queryability.

• Various robustness improvements, including:

  • Handling mixed-valence systems
  • Handling systems with very large inter-atomic distances.
  • As a robustness test, defect generation for all materials on the Materials Project proceeds
    efficiently and without issue (as performed as part of https://arxiv.org/abs/2412.19330).
  • Improved eigenvalue parsing and comparisons (for automated shallow defect detection).
  • Dynamic adjustment of symprec for edge cases.

• Miscellaneous convenience updates.

• Docs, tutorials and tests updates.

• BETA: Add doped.utils.configurations functions to quickly generate CC diagram structures / initial
  NEB paths for defect transformations, ensuring correct initial orientations (to give shortest path).