Average-minimum-distance

Changed

- Earth Mover's distance changed to calculate to 8 decimal places.

Changed

- ``nearest_neighbours_data()`` changed in line with ``nearest_neighbours()``.

- Improved docs and formatting.

Changed

- Core function ``nearest_neighbours()`` and other code in the ``_nearest_neighbours`` module has changed significantly. ``nearest_neighbours()`` no longer returns ``cloud`` or ``inds``; this behaviour is now given by ``nearest_neighbours_data()``. ``nearest_neighbours()`` has been fixed to not exclude the first nearest neighbours of points in the query set ``x``. Use of ``KDTree`` has been removed. Integer lattice points are stored in a cache.

- Changes to attribute names in ``amd.PeriodicSet``: ``wyckoff_multiplicities`` --> ``multiplicities`` and ``asymmetric_unit`` --> ``asym_unit``.

- Default backend reader changed to `gemmi` for faster CIF reads; removed `ase` as a dependency and added `gemmi`. Reads should be identical to before, but this may turn out to be false. The only known difference is that the `gemmi` parser cannot handle some characters (e.g. �), and does not allow cifs with repeated headers.

- Readers in the ``io`` module give attributes of ``PeriodicSet``s smaller ``dtypes`` where appropriate: ``np.int32`` for ``asym_unit`` and ``multiplicities``, ``np.uint8`` for ``types``.

- ``amd.AMD()``, ``amd.PDD()`` and other functions in ``amd.calculate`` which accept a periodic set no longer accept a tuple, only ``amd.PeriodicSet``. A tuple can be converted before passing, e.g. replace ``amd.AMD((motif, cell), k)`` with ``amd.AMD(amd.PeriodicSet(motif, cell), k)``.

- `verbose` parameter added to `amd.CifReader()` and `amd.CSDReader()`.

Added

- CIF/CSD Reader internals have been improved (expanding the asymmetric unit to the full motif is ~10x faster, giving to an overall reading improvement of ~3x).

- `utils.cell_to_cellpar` and `utils.cell_to_cellpar_2D` have been improved with `numba`.

- Removed `_ETA` class and added dependency `tqdm` for progress bars.

- Changes to converter functions in the `io` module have decoupled them from depending on other packages, e.g. `periodicset_from_pymatgen_cifblock()` now has no dependency on `ase`, just `pymatgen`.

- Cleaned/added more documentation, docstrings, PEP8, type hints. Moved be pyproject.toml only and use a src layout instead of flat.

Changed

- Fixed issue with ccdc reader where atoms with missing coordinates would throw a ParseError where they should have been removed.

- Fixed `molecular_centres` parameter to work correctly in `amd.compare`.

Added

- Parameter `nearest` added to `amd.compare`, which finds a number of nearest neighbours in one set from the other. `amd.compare` can now also be used from the command line.

- `pymatgen` and `gemmi` added as options for the backend to `CifReader`.

- Several converter functions now exist in the `io` module to get `PeriodicSet` objects from `ase`, `pymatgen`, `gemmi` or `ccdc`: , `periodicset_from_ase_cifblock`, `periodicset_from_ase_atoms`, `periodicset_from_pymatgen_cifblock`, `periodicset_from_pymatgen_structure`, `periodicset_from_ccdc_entry`, `periodicset_from_ccdc_crystal`, and `periodicset_from_gemmi_block`. The functions involving `ccdc` no longer depend on `ase`.

Changed

- Read option ``molecular_centres`` now yields `PeriodicSet` objects whose motif consists of the molecular centres, instead of adding an attribute ``.molecular_centres`` containing the centres. The original motif is no longer kept.

Removed

- Removed `.entry()` and `.family()` from `CSDReader`, instead new `CSDReader` objects should be made each time.