structuretoolkit 0.0.43__tar.gz → 0.0.45__tar.gz

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: structuretoolkit
-Version: 0.0.43
+Version: 0.0.45
 Summary: build, analyse and visualise atomistic structures for materials science
 Project-URL: Homepage, https://github.com/pyiron/structuretoolkit
 Project-URL: Documentation, https://github.com/pyiron/structuretoolkit
@@ -46,8 +46,8 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: <3.15,>=3.10
-Requires-Dist: ase<=3.28.0,>=3.24.0
-Requires-Dist: numpy<=2.4.3,>=1.23.5
+Requires-Dist: ase<=3.29.0,>=3.24.0
+Requires-Dist: numpy<=2.4.6,>=1.23.5
 Requires-Dist: scipy<=1.17.1,>=1.15.0
 Provides-Extra: clusters
 Requires-Dist: scikit-learn==1.8.0; extra == 'clusters'
@@ -64,10 +64,10 @@ Requires-Dist: pymatgen==2026.3.23; extra == 'mp-api'
 Provides-Extra: nglview
 Requires-Dist: nglview<=4.0.1,>=2.7.7; extra == 'nglview'
 Provides-Extra: phonopy
-Requires-Dist: phonopy<=3.5.1,>=2.21.2; extra == 'phonopy'
+Requires-Dist: phonopy<=4.0.1,>=2.21.2; extra == 'phonopy'
 Requires-Dist: spglib==2.7.0; extra == 'phonopy'
 Provides-Extra: plotly
-Requires-Dist: plotly<=6.6.0,>=6.0.0; extra == 'plotly'
+Requires-Dist: plotly<=6.8.0,>=6.0.0; extra == 'plotly'
 Provides-Extra: pyscal
 Requires-Dist: pyscal3<=3.3.2,>=3.2.5; extra == 'pyscal'
 Provides-Extra: surface

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["ase", "numpy", "scipy", "hatchling==1.29.0", "hatch-vcs==0.5.0"]
+requires = ["ase", "numpy", "scipy", "hatchling==1.30.1", "hatch-vcs==0.5.0"]
 build-backend = "hatchling.build"
 
 [project]
@@ -23,8 +23,8 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "ase>=3.24.0,<=3.28.0",
-    "numpy>=1.23.5,<=2.4.3",
+    "ase>=3.24.0,<=3.29.0",
+    "numpy>=1.23.5,<=2.4.6",
     "scipy>=1.15.0,<=1.17.1",
 ]
 dynamic = ["version"]
@@ -43,7 +43,7 @@ grainboundary = [
 pyscal = ["pyscal3>=3.2.5,<=3.3.2"]
 nglview = ["nglview>=2.7.7,<=4.0.1"]
 matplotlib = ["matplotlib==3.10.9"]
-plotly = ["plotly>=6.0.0,<=6.6.0"]
+plotly = ["plotly>=6.0.0,<=6.8.0"]
 clusters = ["scikit-learn==1.8.0"]
 symmetry = ["spglib==2.7.0"]
 surface = [
@@ -51,7 +51,7 @@ surface = [
     "pymatgen==2026.3.23",
 ]
 phonopy = [
-    "phonopy>=2.21.2,<=3.5.1",
+    "phonopy>=2.21.2,<=4.0.1",
     "spglib==2.7.0",
 ]
 mp-api = [

structuretoolkit-0.0.45/src/structuretoolkit/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.0.45'
+__version_tuple__ = version_tuple = (0, 0, 45)
+
+__commit_id__ = commit_id = None

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/analyse/dscribe.py

@@ -11,7 +11,7 @@ def soap_descriptor_per_atom(
     rbf: str = "gto",
     weighting: np.ndarray | None = None,
     average: str = "off",
-    compression: dict = None,
+    compression: dict | None = None,
     species: list | None = None,
     periodic: bool = True,
     sparse: bool = False,

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/analyse/neighbors.py

@@ -3,6 +3,7 @@
 
 import itertools
 import warnings
+from typing import Any, cast
 
 import numpy as np
 from ase.atoms import Atoms
@@ -56,18 +57,18 @@ class Tree:
         Args:
             ref_structure (ase.atoms.Atoms): Reference structure.
         """
-        self._distances = None
-        self._vectors = None
-        self._indices = None
+        self._distances: Any = None
+        self._vectors: Any = None
+        self._indices: Any = None
         self._mode = {"filled": True, "ragged": False, "flattened": False}
-        self._extended_positions = None
-        self._positions = None
-        self._wrapped_indices = None
-        self._extended_indices = None
+        self._extended_positions: Any = None
+        self._positions: Any = None
+        self._wrapped_indices: Any = None
+        self._extended_indices: Any = None
         self._ref_structure = ref_structure.copy()
         self.wrap_positions = False
-        self._tree = None
-        self.num_neighbors = None
+        self._tree: Any = None
+        self.num_neighbors: int | None = None
         self.cutoff_radius = np.inf
         self._norm_order = 2
 
@@ -91,6 +92,7 @@ class Tree:
         for k, v in self._mode.items():
             if v:
                 return k
+        raise ValueError("No neighbor representation mode is active")
 
     def _set_mode(self, new_mode: str) -> None:
         """
@@ -172,6 +174,7 @@ class Tree:
             return self._contract(value, ref_vector=ref_vector)
         elif key == "flattened":
             return value[self._distances < np.inf]
+        raise ValueError(f"Unknown neighbor representation mode: {key}")
 
     @property
     def distances(self) -> np.ndarray:
@@ -257,7 +260,7 @@ class Tree:
             + " with the correct norm_order value"
         )
 
-    def _get_max_length(self, ref_vector: np.ndarray | None = None) -> int:
+    def _get_max_length(self, ref_vector: np.ndarray | None = None) -> int | None:
         """
         Get the maximum length of the reference vector.
 
@@ -277,9 +280,7 @@ class Tree:
             return None
         return max(len(dd[dd < np.inf]) for dd in ref_vector)
 
-    def _contract(
-        self, value: np.ndarray, ref_vector: np.ndarray | None = None
-    ) -> np.ndarray:
+    def _contract(self, value: np.ndarray, ref_vector: np.ndarray | None = None):
         """
         Contract the given value based on the specified reference vector.
 
@@ -297,7 +298,7 @@ class Tree:
             for vv, dist in zip(value, self.filled.distances, strict=True)
         ]
 
-    def _allow_ragged_to_mode(self, new_bool: bool) -> str:
+    def _allow_ragged_to_mode(self, new_bool: bool | None) -> str:
         """
         Set the representation mode based on the value of new_bool.
 
@@ -504,6 +505,8 @@ class Tree:
         if self.num_neighbors is None:
             self.num_neighbors = num_neighbors
             self.cutoff_radius = cutoff_radius
+        assert num_neighbors is not None
+        assert self.num_neighbors is not None
         if num_neighbors > self.num_neighbors:
             warnings.warn(
                 "Taking a larger search area after initialization has the risk of "
@@ -582,7 +585,7 @@ class Tree:
     def _get_neighborhood(
         self,
         positions: np.ndarray,
-        num_neighbors: int = 12,
+        num_neighbors: int | None = 12,
         cutoff_radius: float = np.inf,
         exclude_self: bool = False,
         width_buffer: float = 1.2,
@@ -611,7 +614,7 @@ class Tree:
             cutoff_radius=cutoff_radius,
             width_buffer=width_buffer,
         )
-        if num_neighbors is not None:
+        if num_neighbors is not None and self.num_neighbors is not None:
             self.num_neighbors -= 1
         max_column = np.sum(distances < np.inf, axis=-1).max()
         self._distances = distances[..., start_column:max_column]
@@ -620,7 +623,7 @@ class Tree:
         self._positions = positions
         return self
 
-    def _check_width(self, width: float, pbc: list[bool, bool, bool]) -> bool:
+    def _check_width(self, width: float, pbc: np.ndarray) -> bool:
         """
         Check if the width of the layer exceeds the specified value.
 
@@ -706,26 +709,19 @@ class Tree:
         radius. For automated uses, see Atoms.analyse.pyscal_steinhardt_parameter()
         """
         random_rotation = Rotation.from_mrp(np.random.random(3)).as_matrix()
-        return np.sqrt(
-            4
-            * np.pi
-            / (2 * l + 1)
-            * np.sum(
-                [
-                    np.absolute(
-                        self.get_spherical_harmonics(
-                            l=l,
-                            m=m,
-                            cutoff_radius=cutoff_radius,
-                            rotation=random_rotation,
-                        )
-                    )
-                    ** 2
-                    for m in np.arange(-l, l + 1)
-                ],
-                axis=0,
+        harmonic_values: list[np.ndarray] = [
+            np.absolute(
+                self.get_spherical_harmonics(
+                    l=l,
+                    m=m,
+                    cutoff_radius=cutoff_radius,
+                    rotation=random_rotation,
+                )
             )
-        )
+            ** 2
+            for m in np.arange(-l, l + 1)
+        ]
+        return np.sqrt(4 * np.pi / (2 * l + 1) * np.sum(harmonic_values, axis=0))
 
     @staticmethod
     def _get_all_possible_pairs(l: int) -> np.ndarray:
@@ -827,8 +823,8 @@ class Neighbors(Tree):
         """
         super().__init__(ref_structure=ref_structure)
         self._tolerance = tolerance
-        self._cluster_vecs = None
-        self._cluster_dist = None
+        self._cluster_vecs: Any = None
+        self._cluster_dist: Any = None
 
     def __repr__(self):
         """
@@ -1072,7 +1068,7 @@ class Neighbors(Tree):
 
     def find_neighbors_by_vector(
         self, vector: np.ndarray, return_deviation: bool = False
-    ) -> np.ndarray:
+    ) -> np.ndarray | tuple[np.ndarray, np.ndarray]:
         """
         Args:
             vector (list/np.ndarray): vector by which positions are translated (and neighbors are searched)
@@ -1323,9 +1319,9 @@ class Neighbors(Tree):
         ind_shell = []
         for d, i in zip(dist, ind, strict=True):
             id_list = get_cluster(d[d < radius], i[d < radius])
-            ia_shells_dict = {}
+            ia_shells_dict: dict[str, list[list[int]]] = {}
             for i_shell_list in id_list:
-                ia_shell_dict = {}
+                ia_shell_dict: dict[str, list[int]] = {}
                 for i_s in i_shell_list:
                     el = el_list[i_s]
                     if el not in ia_shell_dict:
@@ -1382,14 +1378,17 @@ def get_neighbors(
     Returns:
         Neighbors: An instance of the Neighbors class with the neighbor indices, distances, and vectors.
     """
-    neigh = _get_neighbors(
-        structure=structure,
-        num_neighbors=num_neighbors,
-        tolerance=tolerance,
-        id_list=id_list,
-        cutoff_radius=cutoff_radius,
-        width_buffer=width_buffer,
-        norm_order=norm_order,
+    neigh = cast(
+        Neighbors,
+        _get_neighbors(
+            structure=structure,
+            num_neighbors=num_neighbors,
+            tolerance=tolerance,
+            id_list=id_list,
+            cutoff_radius=cutoff_radius,
+            width_buffer=width_buffer,
+            norm_order=norm_order,
+        ),
     )
     neigh._set_mode(mode)
     return neigh

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/analyse/phonopy.py

@@ -47,4 +47,6 @@ def get_equivalent_atoms(
     ops = spglib.get_symmetry(
         cell=unitcell.totuple(), symprec=symprec, angle_tolerance=angle_tolerance
     )
+    if ops is None:
+        raise RuntimeError("spglib could not determine symmetry")
     return ops["equivalent_atoms"]

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/analyse/pyscal.py

@@ -27,7 +27,7 @@ def get_steinhardt_parameters(
     n_clusters: int | None = 2,
     q: tuple | None = None,
     averaged: bool = False,
-) -> tuple[np.ndarray] | tuple[np.ndarray, np.ndarray]:
+) -> np.ndarray | tuple[np.ndarray, np.ndarray]:
     """
     Calculate Steinhardts parameters
 
@@ -162,7 +162,7 @@ def get_diamond_structure_descriptors(
 
 def get_adaptive_cna_descriptors(
     structure: Atoms, mode: str = "total", ovito_compatibility: bool = False
-) -> np.ndarray:
+) -> dict | np.ndarray:
     """
     Use common neighbor analysis
 

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/analyse/snap.py

@@ -63,7 +63,7 @@ def get_snap_descriptors_per_atom(
     structure: Atoms,
     atom_types: list[str],
     twojmax: int = 6,
-    element_radius: list[int] = None,
+    element_radius: list[float] | None = None,
     rcutfac: float = 1.0,
     rfac0: float = 0.99363,
     rmin0: float = 0.0,
@@ -114,7 +114,7 @@ def get_snap_descriptor_derivatives(
     structure: Atoms,
     atom_types: list[str],
     twojmax: int = 6,
-    element_radius: list[int] = None,
+    element_radius: list[float] | None = None,
     rcutfac: float = 1.0,
     rfac0: float = 0.99363,
     rmin0: float = 0.0,
@@ -161,7 +161,7 @@ def get_snap_descriptor_derivatives(
     )
 
 
-def get_snap_descriptor_names(twojmax: int) -> np.ndarray:
+def get_snap_descriptor_names(twojmax: int) -> list[list[float]]:
     """
     Get names of the SNAP descriptors
 
@@ -268,8 +268,8 @@ def _set_ase_structure(lmp, structure: Atoms):
     elem_all = np.array([el_dict[el] + 1 for el in structure.get_chemical_symbols()])
     lmp.create_atoms(
         n=len(structure),
-        id=None,
-        type=(len(elem_all) * c_int)(*elem_all),
+        atomid=None,
+        atype=(len(elem_all) * c_int)(*elem_all),
         x=(len(positions) * c_double)(*positions),
         v=None,
         image=None,
@@ -547,16 +547,16 @@ def _extract_computes_snap(
     Returns:
         np.ndarray: Output of the LAMMPS compute command
     """
-    lmp_atom_ids = lmp.numpy.extract_atom_iarray("id", num_atoms).flatten()
-    cond = np.all(lmp_atom_ids == 1 + np.arange(num_atoms))
+    lmp_atom_ids = lmp.numpy.extract_atom(name="id", nelem=num_atoms).flatten()
+    cond = bool(np.all(lmp_atom_ids == 1 + np.arange(num_atoms)))
     assert cond, "LAMMPS seems to have lost atoms"
 
     # Extract types
-    lmp_types = lmp.numpy.extract_atom_iarray(name="type", nelem=num_atoms).flatten()
+    lmp_types = lmp.numpy.extract_atom(name="type", nelem=num_atoms).flatten()
     lmp_volume = lmp.get_thermo("vol")
 
     # Extract Bsum
-    _extract_compute_np(lmp, "b_sum", 0, 1, (n_coeff))
+    _extract_compute_np(lmp, "b_sum", 0, 1, (n_coeff,))
 
     # Extract B
     lmp_barr = _extract_compute_np(lmp, "b", 1, 2, (num_atoms, n_coeff))
@@ -571,13 +571,13 @@ def _extract_computes_snap(
 
     lmp_dbarr = _extract_compute_np(lmp, "db", 1, 2, (num_atoms, num_types, 3, n_coeff))
     lmp_dbsum = _extract_compute_np(lmp, "db_sum", 0, 1, (num_types, 3, n_coeff))
-    cond = np.allclose(lmp_dbsum, lmp_dbarr.sum(axis=0), rtol=1e-12, atol=1e-12)
+    cond = bool(np.allclose(lmp_dbsum, lmp_dbarr.sum(axis=0), rtol=1e-12, atol=1e-12))
     assert cond, "db_sum doesn't match sum of db"
     db_atom = np.transpose(lmp_dbarr, (0, 2, 1, 3))
 
     lmp_vbarr = _extract_compute_np(lmp, "vb", 1, 2, (num_atoms, num_types, 6, n_coeff))
     lmp_vbsum = _extract_compute_np(lmp, "vb_sum", 0, 1, (num_types, 6, n_coeff))
-    cond = np.allclose(lmp_vbsum, lmp_vbarr.sum(axis=0), rtol=1e-12, atol=1e-12)
+    cond = bool(np.allclose(lmp_vbsum, lmp_vbarr.sum(axis=0), rtol=1e-12, atol=1e-12))
     assert cond, "vb_sum doesn't match sum of vb"
     vb_sum = np.transpose(lmp_vbsum, (1, 0, 2)) / lmp_volume * eV_div_A3_to_bar
 

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/analyse/spatial.py

@@ -2,6 +2,7 @@
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
 from collections.abc import Callable
+from typing import Any
 
 import numpy as np
 from ase.atoms import Atoms
@@ -74,10 +75,10 @@ def create_gridpoints(
     """
     cell = get_vertical_length(structure=structure)
     n_points = (n_gridpoints_per_angstrom * cell).astype(int)
-    positions = np.meshgrid(
+    grids = np.meshgrid(
         *[np.linspace(0, 1, n_points[i], endpoint=False) for i in range(3)]
     )
-    positions = np.stack(positions, axis=-1).reshape(-1, 3)
+    positions = np.stack(grids, axis=-1).reshape(-1, 3)
     return np.einsum("ji,nj->ni", structure.cell, positions)
 
 
@@ -226,7 +227,7 @@ class Interstitials:
         q_eps: float = 0.3,
         var_ratio: float = 5.0,
         min_samples: int | None = None,
-        neigh_args: dict = None,
+        neigh_args: dict | None = None,
         **kwargs,
     ):
         """
@@ -266,7 +267,7 @@ class Interstitials:
         self._neigh = get_neighbors(
             structure=structure, num_neighbors=num_neighbors, **neigh_args
         )
-        self.workflow = [
+        self.workflow: list[dict[str, Any]] = [
             {
                 "f": remove_too_close,
                 "kwargs": {"structure": structure, "min_distance": min_distance},
@@ -290,7 +291,7 @@ class Interstitials:
                 },
             },
         ]
-        self._positions = None
+        self._positions: np.ndarray | None = None
         self.structure = structure
 
     def run_workflow(
@@ -312,7 +313,8 @@ class Interstitials:
         if positions is None:
             positions = self.initial_positions.copy()
         for ii, ww in enumerate(self.workflow):
-            positions = ww["f"](positions=positions, **ww["kwargs"])
+            f: Callable[..., np.ndarray] = ww["f"]
+            positions = f(positions=positions, **ww["kwargs"])
             if ii == steps:
                 return positions
         return positions
@@ -338,6 +340,7 @@ class Interstitials:
         if self._positions is None:
             self._positions = self.run_workflow()
             self._neigh = self.neigh.get_neighborhood(self._positions)
+        assert self._positions is not None
         return self._positions
 
     @property
@@ -408,7 +411,7 @@ def get_interstitials(
     q_eps: float = 0.3,
     var_ratio: float = 5.0,
     min_samples: int | None = None,
-    neigh_args: dict = None,
+    neigh_args: dict | None = None,
     **kwargs,
 ) -> Interstitials:
     """
@@ -449,9 +452,9 @@ def get_interstitials(
     )
 
 
-get_interstitials.__doc__ = (
-    Interstitials.__doc__.replace("Class", "Function") + Interstitials.__init__.__doc__
-)
+get_interstitials.__doc__ = (Interstitials.__doc__ or "").replace(
+    "Class", "Function"
+) + (Interstitials.__init__.__doc__ or "")
 
 
 def get_layers(
@@ -459,8 +462,8 @@ def get_layers(
     distance_threshold: float = 0.01,
     id_list: list[int] | None = None,
     wrap_atoms: bool = True,
-    planes: np.ndarray = None,
-    cluster_method: str = None,
+    planes: np.ndarray | None = None,
+    cluster_method: Any | None = None,
 ) -> np.ndarray:
     """
     Get an array of layer numbers.
@@ -512,10 +515,10 @@ def get_layers(
             structure=structure, width=distance_threshold, return_indices=True
         )
         if id_list is not None:
-            id_list = np.arange(len(structure))[np.array(id_list)]
-            id_list = np.any(id_list[:, np.newaxis] == indices[np.newaxis, :], axis=0)
-            positions = positions[id_list]
-            indices = indices[id_list]
+            id_arr = np.arange(len(structure))[np.array(id_list)]
+            id_mask = np.any(id_arr[:, np.newaxis] == indices[np.newaxis, :], axis=0)
+            positions = positions[id_mask]
+            indices = indices[id_mask]
     else:
         positions = structure.positions
         if id_list is not None:
@@ -694,7 +697,7 @@ def get_cluster_positions(
     eps: float = 1.0,
     buffer_width: float | None = None,
     return_labels: bool = False,
-) -> np.ndarray:
+) -> np.ndarray | tuple[np.ndarray, np.ndarray]:
     """
     Cluster positions according to the distances. Clustering algorithm uses DBSCAN:
 

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/analyse/strain.py

@@ -1,3 +1,5 @@
+from typing import Union
+
 import numpy as np
 from ase.atoms import Atoms
 from scipy.spatial.transform import Rotation
@@ -47,18 +49,19 @@ class Strain:
         """
         self.structure = structure
         self.ref_structure = ref_structure
-        self._num_neighbors = num_neighbors
+        self._num_neighbors: int | None = num_neighbors
         self.only_bulk_type = only_bulk_type
-        self._crystal_phase = None
-        self._ref_coord = None
-        self._coords = None
-        self._rotations = None
+        self._crystal_phase: str | None = None
+        self._ref_coord: np.ndarray | None = None
+        self._coords: np.ndarray | None = None
+        self._rotations: np.ndarray | None = None
 
     @property
     def num_neighbors(self) -> int:
         """Number of neighbors to consider the local frame. Should be the coordination number."""
         if self._num_neighbors is None:
             self._num_neighbors = self._get_number_of_neighbors(self.crystal_phase)
+        assert self._num_neighbors is not None
         return self._num_neighbors
 
     @property
@@ -66,6 +69,7 @@ class Strain:
         """Majority crystal phase calculated via common neighbor analysis."""
         if self._crystal_phase is None:
             self._crystal_phase = self._get_majority_phase(self.ref_structure)
+        assert self._crystal_phase is not None
         return self._crystal_phase
 
     @property
@@ -79,7 +83,8 @@ class Strain:
                 than the bulk.
         """
         return np.array(
-            self.structure.analyse.pyscal_cna_adaptive(mode="str") != self.crystal_phase
+            get_adaptive_cna_descriptors(structure=self.structure, mode="str")
+            != self.crystal_phase
         )
 
     def _get_perpendicular_unit_vectors(
@@ -197,6 +202,7 @@ class Strain:
             w_second = self.ref_coord[dist.argmin(axis=1)].copy()
             second_rot = self._get_rotation_from_vectors(v, w_second, all_vecs[:, 0])
             self._rotations = np.einsum("nij,njk->nik", second_rot, first_rot)
+        assert self._rotations is not None
         return self._rotations
 
     @staticmethod
@@ -219,7 +225,7 @@ class Strain:
         return np.argmin(distances, axis=-1)
 
     @staticmethod
-    def _get_majority_phase(structure: Atoms) -> np.ndarray:
+    def _get_majority_phase(structure: Atoms) -> str:
         """
         Get the majority crystal phase in the structure based on the common neighbor analysis (CNA) descriptors.
 
@@ -227,10 +233,12 @@ class Strain:
             structure (ase.atoms.Atoms): The structure to analyze.
 
         Returns:
-            np.ndarray: The crystal phase with the highest count.
+            str: The crystal phase with the highest count.
         """
         cna = get_adaptive_cna_descriptors(structure=structure)
-        return np.asarray(list(cna.keys()))[np.argmax(list(cna.values()))]
+        if not isinstance(cna, dict):
+            raise TypeError("Expected CNA descriptors as a dictionary")
+        return str(np.asarray(list(cna.keys()))[np.argmax(list(cna.values()))])
 
     @staticmethod
     def _get_number_of_neighbors(crystal_phase: str) -> int:
@@ -265,6 +273,7 @@ class Strain:
             self._ref_coord = get_neighbors(
                 structure=self.ref_structure, num_neighbors=self.num_neighbors
             ).vecs[0]
+        assert self._ref_coord is not None
         return self._ref_coord
 
     @property
@@ -279,6 +288,7 @@ class Strain:
             self._coords = get_neighbors(
                 structure=self.structure, num_neighbors=self.num_neighbors
             ).vecs
+        assert self._coords is not None
         return self._coords
 
     @property
@@ -320,7 +330,7 @@ def get_strain(
     num_neighbors: int | None = None,
     only_bulk_type: bool = False,
     return_object: bool = False,
-):
+) -> Union[np.ndarray, "Strain"]:
     """
     Calculate local strain of each atom following the Lagrangian strain tensor:
 

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/analyse/symmetry.py

@@ -63,7 +63,7 @@ class Symmetry(dict):
         self._symprec = symprec
         self._angle_tolerance = angle_tolerance
         self.epsilon = epsilon
-        self._permutations = None
+        self._permutations: np.ndarray | None = None
         for k, v in self._get_symmetry(
             symprec=symprec, angle_tolerance=angle_tolerance
         ).items():
@@ -209,6 +209,7 @@ class Symmetry(dict):
             if np.ptp(distances) > self._symprec:
                 raise AssertionError("Neighbor search failed")
             self._permutations = self._permutations.argsort(axis=-1)
+        assert self._permutations is not None
         return self._permutations
 
     def symmetrize_vectors(
@@ -369,12 +370,12 @@ class Symmetry(dict):
         )
         if space_group is None:
             raise SymmetryError(spglib.error.get_error_message())
-        space_group = space_group.split()
-        if len(space_group) == 1:
-            return {"Number": ast.literal_eval(space_group[0])}
+        parts = space_group.split()
+        if len(parts) == 1:
+            return {"Number": ast.literal_eval(parts[0])}
         return {
-            "InternationalTableSymbol": space_group[0],
-            "Number": ast.literal_eval(space_group[1]),
+            "InternationalTableSymbol": parts[0],
+            "Number": ast.literal_eval(parts[1]),
         }
 
     def get_primitive_cell(
@@ -442,7 +443,7 @@ class Symmetry(dict):
         mesh: np.ndarray,
         is_shift: np.ndarray = np.zeros(3, dtype="intc"),
         is_time_reversal: bool = True,
-    ) -> np.ndarray:
+    ) -> tuple[np.ndarray, np.ndarray]:
         """
         Get the irreducible reciprocal mesh points.
 
@@ -452,21 +453,21 @@ class Symmetry(dict):
             is_time_reversal (bool, optional): Whether to consider time reversal symmetry. Defaults to True.
 
         Returns:
-            ndarray: The irreducible reciprocal mesh points.
+            tuple: The irreducible reciprocal mesh points (mapping, grid_points).
 
         Raises:
             SymmetryError: If the irreducible reciprocal mesh points cannot be obtained.
         """
-        mesh = spglib.get_ir_reciprocal_mesh(
+        result = spglib.get_ir_reciprocal_mesh(
             mesh=mesh,
             cell=self._get_spglib_cell(),
             is_shift=is_shift,
             is_time_reversal=is_time_reversal,
             symprec=self._symprec,
         )
-        if mesh is None:
+        if result is None:
             raise SymmetryError(spglib.error.get_error_message())
-        return mesh
+        return result
 
 
 def _get_inner_slicer(n: int, i: int) -> tuple:
@@ -481,7 +482,7 @@ def _get_inner_slicer(n: int, i: int) -> tuple:
         tuple: Inner slicer tuple.
 
     """
-    s = [None for _ in range(n)]
+    s: list[None | slice] = [None for _ in range(n)]
     s[0] = slice(None)
     s[i] = slice(None)
     return tuple(s)

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/build/__init__.py

@@ -1,11 +1,13 @@
 from structuretoolkit.build.aimsgb import get_grainboundary_info, grainboundary
 from structuretoolkit.build.compound import B2, C14, C15, C36, D03
-from structuretoolkit.build.mesh import create_mesh
-from structuretoolkit.build.sqs import sqs_structures
 from structuretoolkit.build.materialsproject import (
-    search as materialsproject_search,
     by_id as materialsproject_by_id,
 )
+from structuretoolkit.build.materialsproject import (
+    search as materialsproject_search,
+)
+from structuretoolkit.build.mesh import create_mesh
+from structuretoolkit.build.sqs import sqs_structures
 from structuretoolkit.build.surface import (
     get_high_index_surface_info,
     high_index_surface,

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/build/compound.py

@@ -6,7 +6,7 @@ from ase.spacegroup import crystal
 from structuretoolkit.analyse.neighbors import get_neighbors
 
 
-def B2(element_a: str, element_b: str, a: float | None = None):
+def B2(element_a: str, element_b: str, a: float | None = None) -> Atoms:
     """
     Builds a cubic $AB$ B2 structure of interpenetrating simple cubic lattices.
 
@@ -207,7 +207,7 @@ def D03(element_a: str, element_b: str, a: float | None = None) -> Atoms:
     )
 
 
-def _bcc_lattice_constant_from_nn_distance(element: Atoms):
+def _bcc_lattice_constant_from_nn_distance(element: str) -> float:
     """
     Build a BCC lattice constant by making the BCC have the same nearest neighbour distance as the regular cell.
 

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/build/geometry.py

@@ -51,8 +51,7 @@ def repulse(
     """
     if not inplace:
         structure = structure.copy()
-    if axis is None:
-        axis = slice(None)
+    ax: int | slice = axis if axis is not None else slice(None)
     for _ in range(iterations):
         neigh = get_neighbors(structure, num_neighbors=1)
         dd = neigh.distances[:, 0]
@@ -78,7 +77,7 @@ def repulse(
         disp = np.clip(min_dist - dd[I], 0, step_size)
 
         displacement = disp[:, None] * vv  # (N_close, 3)
-        structure.positions[I, axis] -= displacement[:, axis]
+        structure.positions[I, ax] -= displacement[:, ax]
 
     else:
         raise RuntimeError(f"repulse did not converge within {iterations} iterations")
@@ -86,9 +85,7 @@ def repulse(
     return structure
 
 
-def merge(
-    structure: "ase.Atoms", cutoff: float = 1.8, iterations: int = 10
-) -> "ase.Atoms":
+def merge(structure: Atoms, cutoff: float = 1.8, iterations: int = 10) -> Atoms:
     """Merge pairs of atoms that are closer than ``cutoff`` by collapsing each
     pair to their midpoint and deleting one of the two atoms.
 

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/build/materialsproject.py

@@ -1,6 +1,8 @@
-from typing import Any, Iterable
-from collections.abc import Generator
+from collections.abc import Generator, Iterable
+from typing import Any
+
 from ase.atoms import Atoms
+
 from structuretoolkit.common.pymatgen import pymatgen_to_ase
 
 

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/build/mesh.py

@@ -12,7 +12,7 @@ class MeshInputError(ValueError):
 
 def create_mesh(
     cell: ase.atoms.Atoms | np.ndarray | list | float,
-    n_mesh: int | list[int, int, int] = 10,
+    n_mesh: int | list[int] | None = 10,
     density: float | None = None,
     endpoint: bool = False,
 ):
@@ -32,20 +32,22 @@ def create_mesh(
     Returns:
         (3, n, n, n)-array: mesh
     """
-    cell = get_cell(cell)
+    cell = np.asarray(get_cell(cell), dtype=float)
+    n_arr: np.ndarray
     if n_mesh is None:
         if density is None:
             raise MeshInputError("either n_mesh or density must be specified")
-        n_mesh = np.rint(np.linalg.norm(cell, axis=-1) / density).astype(int)
+        n_arr = np.rint(np.linalg.norm(cell, axis=-1) / density).astype(int)
     elif density is not None:
         raise MeshInputError(
             "You cannot set n_mesh at density at the same time. Set one of them to None"
         )
-    n_mesh = np.atleast_1d(n_mesh).astype(int)
-    if len(n_mesh) == 1:
-        n_mesh = np.repeat(n_mesh, 3)
-    elif len(n_mesh) != 3:
+    else:
+        n_arr = np.atleast_1d(n_mesh).astype(int)
+    if len(n_arr) == 1:
+        n_arr = np.repeat(n_arr, 3)
+    elif len(n_arr) != 3:
         raise MeshInputError("n_mesh must be a 3-dim vector")
-    linspace = [np.linspace(0, 1, nn, endpoint=endpoint) for nn in n_mesh]
+    linspace = [np.linspace(0, 1, nn, endpoint=endpoint) for nn in n_arr]
     x_mesh = np.meshgrid(*linspace, indexing="ij")
     return np.einsum("ixyz,ij->jxyz", x_mesh, cell)

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/build/sqs/_interface.py

@@ -1,18 +1,21 @@
 from __future__ import annotations
-from ase.atoms import Atoms
+
+from collections.abc import Iterator
 from threading import Event, Thread
-from typing import overload, Literal, TypeVar, Generic, Any, Iterator
+from typing import Any, Generic, Literal, TypeVar, cast, overload
+
+from ase.atoms import Atoms
 
 from ._types import (
     Composition,
-    ShellWeights,
-    ShellRadii,
-    SublatticeMode,
     IterationMode,
+    LogLevel,
     Prec,
+    ShellRadii,
+    ShellWeights,
     SqsResultInteract,
     SqsResultSplit,
-    LogLevel,
+    SublatticeMode,
 )
 
 R = TypeVar("R", SqsResultInteract, SqsResultSplit)
@@ -21,12 +24,12 @@ T = TypeVar("T")
 
 class _SqsResultProxy(Generic[R]):
     def __init__(self, result: R):
-        self._result = result
+        self._result: R = result
 
     def atoms(self) -> Atoms:
         from sqsgenerator import to_ase
 
-        return to_ase(self._result.structure())
+        return to_ase(cast(Any, self._result).structure())
 
     def __getattr__(self, item: str) -> Any:
         return getattr(self._result, item)
@@ -186,24 +189,28 @@ def sqs_structures(
 
     from sqsgenerator import parse_config
     from sqsgenerator.core import (
-        ParseError,
         LogLevel as SqsLogLevel,
+    )
+    from sqsgenerator.core import (
+        ParseError,
         SqsCallbackContext,
+    )
+    from sqsgenerator.core import (
         optimize as sqs_optimize,
     )
 
-    config = dict(
-        prec=precision,
-        iteration_mode=iteration_mode,
-        sublattice_mode=sublattice_mode,
-        structure=dict(
-            lattice=structure.cell.array.tolist(),
-            coords=structure.get_scaled_positions().tolist(),
-            species=structure.get_atomic_numbers().tolist(),
-        ),
-        iterations=iterations,
-        max_results_per_objective=max_results_per_objective,
-    )
+    config: dict[str, Any] = {
+        "prec": precision,
+        "iteration_mode": iteration_mode,
+        "sublattice_mode": sublattice_mode,
+        "structure": {
+            "lattice": structure.cell.array.tolist(),
+            "coords": structure.get_scaled_positions().tolist(),
+            "species": structure.get_atomic_numbers().tolist(),
+        },
+        "iterations": iterations,
+        "max_results_per_objective": max_results_per_objective,
+    }
     if atol is not None:
         config["atol"] = atol
     if rtol is not None:
@@ -216,7 +223,7 @@ def sqs_structures(
                 f"Invalid supercell: {supercell}. All dimensions must be positive integers."
             )
 
-    def _preprocess_for_mode(v: T | list[T] | None) -> list[T] | None:
+    def _preprocess_for_mode(v: T | list[T] | None) -> T | list[T] | None:
         match sublattice_mode:
             case "interact":
                 return v
@@ -227,15 +234,20 @@ def sqs_structures(
                     f"Invalid sublattice mode: {sublattice_mode}. Use 'interact' or 'split'."
                 )
 
-    if (composition := _preprocess_for_mode(composition)) is not None:
-        config["composition"] = composition
-    if (shell_weights := _preprocess_for_mode(shell_weights)) is not None:
-        config["shell_weights"] = shell_weights
-    if (shell_radii := _preprocess_for_mode(shell_radii)) is not None:
-        config["shell_radii"] = shell_radii
+    composition_processed = cast(Any, _preprocess_for_mode(composition))
+    if composition_processed is not None:
+        config["composition"] = composition_processed
+    shell_weights_processed = cast(Any, _preprocess_for_mode(shell_weights))
+    if shell_weights_processed is not None:
+        config["shell_weights"] = shell_weights_processed
+    shell_radii_processed = cast(Any, _preprocess_for_mode(shell_radii))
+    if shell_radii_processed is not None:
+        config["shell_radii"] = shell_radii_processed
     if objective is None:
-        objective = 0.0 if sublattice_mode == "interact" else [0.0] * len(composition)
-    config["target_objective"] = _preprocess_for_mode(objective)
+        objective = (
+            0.0 if sublattice_mode == "interact" else [0.0] * len(composition_processed)
+        )
+    config["target_objective"] = cast(Any, _preprocess_for_mode(objective))
 
     if num_threads is not None:
         if num_threads > 0:

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/build/sqs/_types.py

@@ -1,6 +1,7 @@
+from typing import Literal, Protocol, TypeAlias, overload
+
 import numpy as np
 from ase import Atoms
-from typing import Literal, TypeAlias, Protocol, overload, Union
 
 Shell: TypeAlias = int
 
@@ -124,11 +125,11 @@ Element = Literal[
     "Fl",
 ]
 
-Site = Union[str, list[int]]
+Site = str | list[int]
 
 Prec = Literal["single", "double"]
 
-Composition = dict[Element | Literal["sites"], Union[int, Site]]
+Composition = dict[Element | Literal["sites"], int | Site]
 
 ShellWeights = dict[Shell, float]
 
@@ -137,7 +138,7 @@ ShellRadii = list[float]
 LogLevel = Literal["warn", "info", "debug", "error", "trace"]
 
 
-class SroParameter:
+class SroParameter(Protocol):
     @property
     def i(self) -> int: ...
 

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/common/helper.py

@@ -53,8 +53,8 @@ def get_extended_positions(
     width /= get_vertical_length(structure=structure, norm_order=norm_order)
     rep = 2 * np.ceil(width).astype(int) * structure.pbc + 1
     rep = [np.arange(r) - int(r / 2) for r in rep]
-    meshgrid = np.meshgrid(rep[0], rep[1], rep[2])
-    meshgrid = np.stack(meshgrid, axis=-1).reshape(-1, 3)
+    rep_grids = np.meshgrid(rep[0], rep[1], rep[2])
+    meshgrid = np.stack(rep_grids, axis=-1).reshape(-1, 3)
     v_repeated = np.einsum("ni,ij->nj", meshgrid, structure.cell)
     v_repeated = v_repeated[:, np.newaxis, :] + positions[np.newaxis, :, :]
     v_repeated = v_repeated.reshape(-1, 3)
@@ -184,7 +184,7 @@ def set_indices(structure: Atoms, indices: np.ndarray) -> Atoms:
     return structure
 
 
-def get_average_of_unique_labels(labels: np.ndarray, values: np.ndarray) -> float:
+def get_average_of_unique_labels(labels: np.ndarray, values: np.ndarray) -> np.ndarray:
     """
 
     This function returns the average values of those elements, which share the same labels
@@ -251,20 +251,20 @@ def apply_strain(
             If `lagrangian`, epsilon is given by `(F^T * F - 1) / 2`. It raises an error if
             the strain is not symmetric (if the shear components are given).
     """
-    epsilon = np.array([epsilon]).flatten()
-    if len(epsilon) == 3 or len(epsilon) == 1:
-        epsilon = epsilon * np.eye(3)
-    epsilon = epsilon.reshape(3, 3)
-    if epsilon.min() < -1.0:
+    eps: np.ndarray = np.array([epsilon]).flatten()
+    if len(eps) == 3 or len(eps) == 1:
+        eps = eps * np.eye(3)
+    eps = eps.reshape(3, 3)
+    if eps.min() < -1.0:
         raise ValueError("Strain value too negative")
     structure_copy = structure.copy() if return_box else structure
     cell = structure_copy.cell.copy()
     if mode == "linear":
-        F = epsilon + np.eye(3)
+        F = eps + np.eye(3)
     elif mode == "lagrangian":
-        if not np.allclose(epsilon, epsilon.T):
+        if not np.allclose(eps, eps.T):
             raise ValueError("Strain must be symmetric if `mode = 'lagrangian'`")
-        E, V = np.linalg.eigh(2 * epsilon + np.eye(3))
+        E, V = np.linalg.eigh(2 * eps + np.eye(3))
         F = np.einsum("ik,k,jk->ij", V, np.sqrt(E), V)
     else:
         raise ValueError("mode must be `linear` or `lagrangian`")

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/visualize.py

@@ -153,7 +153,7 @@ def plot3d(
             spacefill=spacefill,
             particle_size=particle_size,
             background=background,
-            color_scheme=color_scheme,
+            color_scheme=color_scheme if color_scheme is not None else "element",
         )
     else:
         raise ValueError("plot method not recognized")
@@ -453,15 +453,20 @@ def _plot3d(
         vector_field is not None and vector_field is not None
     ):  # WARNING: There must be a bug here...
         try:
-            if vector_color.shape != np.ones((len(structure), 3)).shape:
+            if (
+                vector_color is not None
+                and vector_color.shape != np.ones((len(structure), 3)).shape
+            ):
                 vector_color = np.outer(
                     np.ones(len(structure)),
                     vector_color / np.linalg.norm(vector_color),
                 )
         except AttributeError:
-            vector_color = np.ones((len(structure), 3)) * vector_color
+            if vector_color is not None:
+                vector_color = np.ones((len(structure), 3)) * vector_color
 
     if vector_field is not None:
+        assert vector_color is not None
         for arr, pos, col in zip(vector_field, positions, vector_color, strict=True):
             view.shape.add_arrow(list(pos), list(pos + arr), list(col), 0.2)
 

structuretoolkit-0.0.43/src/structuretoolkit/_version.py

@@ -1,34 +0,0 @@
-# file generated by setuptools-scm
-# don't change, don't track in version control
-
-__all__ = [
-    "__version__",
-    "__version_tuple__",
-    "version",
-    "version_tuple",
-    "__commit_id__",
-    "commit_id",
-]
-
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple
-    from typing import Union
-
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-    COMMIT_ID = Union[str, None]
-else:
-    VERSION_TUPLE = object
-    COMMIT_ID = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-commit_id: COMMIT_ID
-__commit_id__: COMMIT_ID
-
-__version__ = version = '0.0.43'
-__version_tuple__ = version_tuple = (0, 0, 43)
-
-__commit_id__ = commit_id = None

{structuretoolkit-0.0.43 → structuretoolkit-0.0.45}/src/structuretoolkit/build/sqs/__init__.py

@@ -1,19 +1,19 @@
+from ._interface import sqs_structures
 from ._types import (
-    SqsResultSplit,
-    SqsResult,
-    SqsResultInteract,
-    SublatticeMode,
-    IterationMode,
-    Site,
+    Composition,
     Element,
+    IterationMode,
+    Prec,
+    Shell,
     ShellRadii,
     ShellWeights,
-    Shell,
-    Composition,
-    Prec,
+    Site,
+    SqsResult,
+    SqsResultInteract,
+    SqsResultSplit,
     SroParameter,
+    SublatticeMode,
 )
-from ._interface import sqs_structures
 
 __all__ = [
     "Composition",