Cleanup.

Author: shyuep

src/pymatgen/analysis/adsorption.py

@@ -57,7 +57,7 @@ class AdsorbateSiteFinder:
 
     def __init__(
         self,
-        slab: Slab,
+        slab: Slab | Structure,
         selective_dynamics: bool = False,
         height: float = 0.9,
         mi_vec: ArrayLike | None = None,
@@ -613,8 +613,7 @@ def get_rot(slab: Slab) -> SymmOp:
     new_y = np.cross(new_z, new_x)
     x, y, z = np.eye(3)
     rot_matrix = np.array([np.dot(*el) for el in itertools.product([x, y, z], [new_x, new_y, new_z])]).reshape(3, 3)
-    rot_matrix = np.transpose(rot_matrix)
-    return SymmOp.from_rotation_and_translation(rot_matrix)
+    return SymmOp.from_rotation_and_translation(np.transpose(rot_matrix))
 
 
 def put_coord_inside(lattice, cart_coordinate):

src/pymatgen/core/interface.py

@@ -31,7 +31,7 @@
     from numpy.typing import ArrayLike, NDArray
     from typing_extensions import Self
 
-    from pymatgen.core import Element
+    from pymatgen.core import Element, Species
     from pymatgen.util.typing import CompositionLike
 
 logger = logging.getLogger(__name__)
@@ -250,7 +250,7 @@ def bottom_grain(self) -> Structure:
         return Structure.from_sites(bottom_sites)
 
     @property
-    def coincidents(self) -> list[Site]:
+    def coincidents(self) -> list[PeriodicSite]:
         """A list of coincident sites."""
         coincident_sites = []
         for idx, tag in enumerate(self.site_properties["grain_label"]):
@@ -810,7 +810,7 @@ def gb_from_parameters(
             _rotation_axis,
             rotation_angle,
             _plane,
-            join_plane,
+            join_plane,  # type: ignore[arg-type]
             self.initial_structure,
             vacuum_thickness,
             ab_shift,
@@ -2087,7 +2087,7 @@ def slab_from_csl(
         trans_cry: NDArray,
         max_search: int = 20,
         quick_gen: bool = False,
-    ) -> Sequence[Sequence[float, float, float], Sequence[float, float, float], Sequence[float, float, float]]:
+    ) -> NDArray:
         """By linear operation of csl lattice vectors to get the best corresponding
         slab lattice. That is the area of a,b vectors (within the surface plane)
         is the smallest, the c vector first, has shortest length perpendicular
@@ -2159,14 +2159,14 @@ def slab_from_csl(
         if len(miller_nonzero) > 1:
             t_matrix[2] = csl[c_index]
             index_len = len(miller_nonzero)
-            lcm_miller = []
+            lcm_miller = []  # type: ignore[assignment]
             for i in range(index_len):
                 for j in range(i + 1, index_len):
                     com_gcd = math.gcd(miller_nonzero[i], miller_nonzero[j])
                     mil1 = round(miller_nonzero[i] / com_gcd)
                     mil2 = round(miller_nonzero[j] / com_gcd)
                     lcm_miller.append(max(abs(mil1), abs(mil2)))
-            lcm_sorted = sorted(lcm_miller)
+            lcm_sorted = sorted(lcm_miller)  # type: ignore[call-overload]
             max_j = lcm_sorted[0] if index_len == 2 else lcm_sorted[1]
         else:
             if not normal:
@@ -2576,7 +2576,7 @@ def substrate_indices(self) -> list[int]:
         return [i for i, tag in enumerate(self.site_properties["interface_label"]) if "substrate" in tag]
 
     @property
-    def substrate_sites(self) -> list[Site]:
+    def substrate_sites(self) -> list[PeriodicSite]:
         """The site objects in the substrate."""
         return [
             site for site, tag in zip(self, self.site_properties["interface_label"], strict=True) if "substrate" in tag
@@ -2593,7 +2593,7 @@ def film_indices(self) -> list[int]:
         return [i for i, tag in enumerate(self.site_properties["interface_label"]) if "film" in tag]
 
     @property
-    def film_sites(self) -> list[Site]:
+    def film_sites(self) -> list[PeriodicSite]:
         """The film sites of the interface."""
         return [site for site, tag in zip(self, self.site_properties["interface_label"], strict=True) if "film" in tag]
 
@@ -2905,7 +2905,7 @@ def label_termination(slab: Structure, ftol: float = 0.25, t_idx: int | None = N
     z = linkage(condensed_m)
     clusters = fcluster(z, ftol, criterion="distance")
 
-    clustered_sites: dict[int, list[Site]] = {c: [] for c in clusters}
+    clustered_sites: dict[int, list[PeriodicSite]] = {c: [] for c in clusters}
     for idx, cluster in enumerate(clusters):
         clustered_sites[cluster].append(slab[idx])
 
@@ -2923,7 +2923,7 @@ def label_termination(slab: Structure, ftol: float = 0.25, t_idx: int | None = N
     return f"{t_idx}_{form}_{sp_symbol}_{len(top_plane)}"
 
 
-def count_layers(struct: Structure, el: Element | None = None) -> int:
+def count_layers(struct: Structure, el: Element | Species | None = None) -> int:
     """Count the number of layers along the c-axis."""
     el = el or struct.elements[0]
     frac_coords = [site.frac_coords for site in struct if site.species_string == str(el)]

src/pymatgen/core/structure.py

@@ -3191,109 +3191,109 @@ def from_file(  # type:ignore[override]
         fname = os.path.basename(filename)
         with zopen(filename, mode="rt", errors="replace", encoding="utf-8") as file:
             contents = file.read()
-        if fnmatch(fname.lower(), "*.cif*") or fnmatch(fname.lower(), "*.mcif*"):
-            return cls.from_str(
-                contents,
-                fmt="cif",
-                primitive=primitive,
-                sort=sort,
-                merge_tol=merge_tol,
-                **kwargs,
-            )
-        if fnmatch(fname, "*POSCAR*") or fnmatch(fname, "*CONTCAR*") or fnmatch(fname, "*.vasp"):
-            struct = cls.from_str(
-                contents,
-                fmt="poscar",
-                primitive=primitive,
-                sort=sort,
-                merge_tol=merge_tol,
-                **kwargs,
-            )
+            if fnmatch(fname.lower(), "*.cif*") or fnmatch(fname.lower(), "*.mcif*"):
+                return cls.from_str(
+                    contents,
+                    fmt="cif",
+                    primitive=primitive,
+                    sort=sort,
+                    merge_tol=merge_tol,
+                    **kwargs,
+                )
+            if fnmatch(fname, "*POSCAR*") or fnmatch(fname, "*CONTCAR*") or fnmatch(fname, "*.vasp"):
+                struct = cls.from_str(
+                    contents,
+                    fmt="poscar",
+                    primitive=primitive,
+                    sort=sort,
+                    merge_tol=merge_tol,
+                    **kwargs,
+                )
 
-        elif fnmatch(fname, "CHGCAR*") or fnmatch(fname, "LOCPOT*"):
-            from pymatgen.io.vasp import Chgcar
-
-            struct = Chgcar.from_file(filename, **kwargs).structure
-        elif fnmatch(fname, "vasprun*.xml*"):
-            from pymatgen.io.vasp import Vasprun
-
-            struct = Vasprun(filename, **kwargs).final_structure
-        elif fnmatch(fname.lower(), "*.cssr*"):
-            return cls.from_str(
-                contents,
-                fmt="cssr",
-                primitive=primitive,
-                sort=sort,
-                merge_tol=merge_tol,
-                **kwargs,
-            )
-        elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
-            return cls.from_str(
-                contents,
-                fmt="json",
-                primitive=primitive,
-                sort=sort,
-                merge_tol=merge_tol,
-                **kwargs,
-            )
-        elif fnmatch(fname, "*.yaml*") or fnmatch(fname, "*.yml*"):
-            return cls.from_str(
-                contents,
-                fmt="yaml",
-                primitive=primitive,
-                sort=sort,
-                merge_tol=merge_tol,
-                **kwargs,
-            )
-        elif fnmatch(fname, "*.xsf"):
-            return cls.from_str(
-                contents,
-                fmt="xsf",
-                primitive=primitive,
-                sort=sort,
-                merge_tol=merge_tol,
-                **kwargs,
-            )
-        elif fnmatch(fname, "input*.xml"):
-            from pymatgen.io.exciting import ExcitingInput
-
-            return ExcitingInput.from_file(fname, **kwargs).structure
-        elif fnmatch(fname, "*rndstr.in*") or fnmatch(fname, "*lat.in*") or fnmatch(fname, "*bestsqs*"):
-            return cls.from_str(
-                contents,
-                fmt="mcsqs",
-                primitive=primitive,
-                sort=sort,
-                merge_tol=merge_tol,
-                **kwargs,
-            )
-        elif fnmatch(fname, "CTRL*"):
-            from pymatgen.io.lmto import LMTOCtrl
-
-            return LMTOCtrl.from_file(filename=filename, **kwargs).structure
-        elif fnmatch(fname, "geometry.in*"):
-            return cls.from_str(
-                contents,
-                fmt="aims",
-                primitive=primitive,
-                sort=sort,
-                merge_tol=merge_tol,
-                **kwargs,
-            )
-        elif fnmatch(fname, "inp*.xml") or fnmatch(fname, "*.in*") or fnmatch(fname, "inp_*"):
-            from pymatgen.io.fleur import FleurInput
+            elif fnmatch(fname, "CHGCAR*") or fnmatch(fname, "LOCPOT*"):
+                from pymatgen.io.vasp import Chgcar
+
+                struct = Chgcar.from_file(filename, **kwargs).structure
+            elif fnmatch(fname, "vasprun*.xml*"):
+                from pymatgen.io.vasp import Vasprun
+
+                struct = Vasprun(filename, **kwargs).final_structure
+            elif fnmatch(fname.lower(), "*.cssr*"):
+                return cls.from_str(
+                    contents,
+                    fmt="cssr",
+                    primitive=primitive,
+                    sort=sort,
+                    merge_tol=merge_tol,
+                    **kwargs,
+                )
+            elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
+                return cls.from_str(
+                    contents,
+                    fmt="json",
+                    primitive=primitive,
+                    sort=sort,
+                    merge_tol=merge_tol,
+                    **kwargs,
+                )
+            elif fnmatch(fname, "*.yaml*") or fnmatch(fname, "*.yml*"):
+                return cls.from_str(
+                    contents,
+                    fmt="yaml",
+                    primitive=primitive,
+                    sort=sort,
+                    merge_tol=merge_tol,
+                    **kwargs,
+                )
+            elif fnmatch(fname, "*.xsf"):
+                return cls.from_str(
+                    contents,
+                    fmt="xsf",
+                    primitive=primitive,
+                    sort=sort,
+                    merge_tol=merge_tol,
+                    **kwargs,
+                )
+            elif fnmatch(fname, "input*.xml"):
+                from pymatgen.io.exciting import ExcitingInput
+
+                return ExcitingInput.from_file(fname, **kwargs).structure
+            elif fnmatch(fname, "*rndstr.in*") or fnmatch(fname, "*lat.in*") or fnmatch(fname, "*bestsqs*"):
+                return cls.from_str(
+                    contents,
+                    fmt="mcsqs",
+                    primitive=primitive,
+                    sort=sort,
+                    merge_tol=merge_tol,
+                    **kwargs,
+                )
+            elif fnmatch(fname, "CTRL*"):
+                from pymatgen.io.lmto import LMTOCtrl
+
+                return LMTOCtrl.from_file(filename=filename, **kwargs).structure
+            elif fnmatch(fname, "geometry.in*"):
+                return cls.from_str(
+                    contents,
+                    fmt="aims",
+                    primitive=primitive,
+                    sort=sort,
+                    merge_tol=merge_tol,
+                    **kwargs,
+                )
+            elif fnmatch(fname, "inp*.xml") or fnmatch(fname, "*.in*") or fnmatch(fname, "inp_*"):
+                from pymatgen.io.fleur import FleurInput
 
-            struct = FleurInput.from_file(filename, **kwargs).structure
-        elif fnmatch(fname, "*.res"):
-            from pymatgen.io.res import ResIO
+                struct = FleurInput.from_file(filename, **kwargs).structure
+            elif fnmatch(fname, "*.res"):
+                from pymatgen.io.res import ResIO
 
-            struct = ResIO.structure_from_file(filename, **kwargs)
-        elif fnmatch(fname.lower(), "*.config*") or fnmatch(fname.lower(), "*.pwmat*"):
-            from pymatgen.io.pwmat import AtomConfig
+                struct = ResIO.structure_from_file(filename, **kwargs)
+            elif fnmatch(fname.lower(), "*.config*") or fnmatch(fname.lower(), "*.pwmat*"):
+                from pymatgen.io.pwmat import AtomConfig
 
-            struct = AtomConfig.from_file(filename, **kwargs).structure
-        else:
-            raise ValueError(f"Unrecognized extension in {filename=}")
+                struct = AtomConfig.from_file(filename, **kwargs).structure
+            else:
+                raise ValueError(f"Unrecognized extension in {filename=}")
         if sort:
             struct = struct.get_sorted_structure()
         if merge_tol: