fix mypy errors

pymatgen/core/trajectory.py

@@ -8,7 +8,7 @@
 import warnings
 from fnmatch import fnmatch
 from pathlib import Path
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, cast
 
 import numpy as np
 from monty.io import zopen
@@ -20,10 +20,11 @@
 
 if TYPE_CHECKING:
     from collections.abc import Iterator
+    from typing import Any
 
     from typing_extensions import Self
 
-    from pymatgen.util.typing import Matrix3D, SitePropsType, Vector3D
+    from pymatgen.util.typing import Matrix3D, PathLike, SitePropsType, Vector3D
 
 
 __author__ = "Eric Sivonxay, Shyam Dwaraknath, Mingjian Wen, Evan Spotte-Smith"
@@ -167,7 +168,10 @@ def __len__(self) -> int:
         """Number of frames in the trajectory."""
         return len(self.coords)
 
-    def __getitem__(self, frames: int | slice | list[int]) -> Molecule | Structure | Self:
+    def __getitem__(
+        self,
+        frames: int | slice | list[int],
+    ) -> Molecule | Structure | Self:
         """Get a subset of the trajectory.
 
         The output depends on the type of the input `frames`. If an int is given, return
@@ -189,29 +193,24 @@ def __getitem__(self, frames: int | slice | list[int]) -> Molecule | Structure |
                 raise IndexError(f"Frame index {frames} out of range.")
 
             if self.lattice is None:
-                charge = 0
-                if self.charge is not None:
-                    charge = int(self.charge)
-
-                spin = None
-                if self.spin_multiplicity is not None:
-                    spin = int(self.spin_multiplicity)
+                charge = int(self.charge) if self.charge is not None else 0
+                spin = None if self.spin_multiplicity is None else int(self.spin_multiplicity)
 
                 return Molecule(
                     self.species,
                     self.coords[frames],
                     charge=charge,
                     spin_multiplicity=spin,
-                    site_properties=self._get_site_props(frames),  # type: ignore
+                    site_properties=self._get_site_props(frames),  # type: ignore[arg-type]
                 )
 
-            lattice = self.lattice if self.constant_lattice else self.lattice[frames]  # type: ignore
+            lattice = self.lattice if self.constant_lattice else self.lattice[frames]
 
             return Structure(
                 Lattice(lattice),
                 self.species,
                 self.coords[frames],
-                site_properties=self._get_site_props(frames),  # type: ignore
+                site_properties=self._get_site_props(frames),  # type: ignore[arg-type]
                 to_unit_cell=True,
             )
 
@@ -247,7 +246,7 @@ def __getitem__(self, frames: int | slice | list[int]) -> Molecule | Structure |
                     base_positions=self.base_positions,
                 )
 
-            lattice = self.lattice if self.constant_lattice else self.lattice[selected]  # type: ignore
+            lattice = self.lattice if self.constant_lattice else self.lattice[selected]
 
             return type(self)(
                 species=self.species,
@@ -398,7 +397,7 @@ def extend(self, trajectory: Trajectory) -> None:
 
     def write_Xdatcar(
         self,
-        filename: str | Path = "XDATCAR",
+        filename: PathLike = "XDATCAR",
         system: str | None = None,
         significant_figures: int = 6,
     ) -> None:
@@ -408,7 +407,7 @@ def write_Xdatcar(
         Xdatcar_from_structs.get_str method and are passed through directly.
 
         Args:
-            filename: Name of file to write.  It's prudent to end the filename with
+            filename: File to write. It's prudent to end the filename with
                 'XDATCAR', as most visualization and analysis software require this
                 for autodetection.
             system: Description of system (e.g. 2D MoS2).
@@ -435,7 +434,7 @@ def write_Xdatcar(
             if idx == 0 or not self.constant_lattice:
                 lines.extend([system, "1.0"])
 
-                _lattice = self.lattice if self.constant_lattice else self.lattice[idx]  # type: ignore
+                _lattice = self.lattice if self.constant_lattice else self.lattice[idx]
 
                 for latt_vec in _lattice:
                     lines.append(f'{" ".join(map(str, latt_vec))}')
@@ -498,15 +497,15 @@ def from_structures(
         else:
             lattice = np.array([structure.lattice.matrix for structure in structures])
 
-        species = structures[0].species
+        species: list[Element | Species] = structures[0].species
         coords = [structure.frac_coords for structure in structures]
         site_properties = [structure.site_properties for structure in structures]
 
         return cls(
-            species=species,  # type: ignore
+            species=species,  # type: ignore[arg-type]
             coords=coords,
             lattice=lattice,
-            site_properties=site_properties,  # type: ignore
+            site_properties=site_properties,
             constant_lattice=constant_lattice,
             **kwargs,
         )
@@ -529,11 +528,11 @@ def from_molecules(cls, molecules: list[Molecule], **kwargs) -> Self:
         site_properties = [mol.site_properties for mol in molecules]
 
         return cls(
-            species=species,  # type: ignore
+            species=species,  # type: ignore[arg-type]
             coords=coords,
             charge=int(molecules[0].charge),
             spin_multiplicity=int(molecules[0].spin_multiplicity),
-            site_properties=site_properties,  # type: ignore
+            site_properties=site_properties,
             **kwargs,
         )
 
@@ -571,7 +570,7 @@ def from_file(
                 from ase.io.trajectory import Trajectory as AseTrajectory
 
                 ase_traj = AseTrajectory(filename)
-                # periodic boundary conditions should be the same for all frames so just check the first
+                # Periodic boundary conditions should be the same for all frames so just check the first
                 pbc = ase_traj[0].pbc
                 if any(pbc):
                     structures = [AseAtomsAdaptor.get_structure(atoms) for atoms in ase_traj]
@@ -635,18 +634,18 @@ def _combine_site_props(
         assert prop1 is None or isinstance(prop1, (list, dict))
         assert prop2 is None or isinstance(prop2, (list, dict))
 
-        p1_candidates = {
+        p1_candidates: dict[str, Any] = {
             "NoneType": [None] * len1,
             "dict": [prop1] * len1,
             "list": prop1,
         }
-        p2_candidates = {
+        p2_candidates: dict[str, Any] = {
             "NoneType": [None] * len2,
             "dict": [prop2] * len2,
             "list": prop2,
         }
-        p1_selected: list = p1_candidates[type(prop1).__name__]  # type: ignore
-        p2_selected: list = p2_candidates[type(prop2).__name__]  # type: ignore
+        p1_selected: list = p1_candidates[type(prop1).__name__]
+        p2_selected: list = p2_candidates[type(prop2).__name__]
 
         return p1_selected + p2_selected
 
@@ -661,10 +660,10 @@ def _combine_frame_props(
         if prop1 is prop2 is None:
             return None
         if prop1 is None:
-            return [None] * len1 + list(prop2)  # type: ignore
+            return [None] * len1 + list(cast(list[dict], prop2))
         if prop2 is None:
-            return list(prop1) + [None] * len2  # type: ignore
-        return list(prop1) + list(prop2)  # type:ignore
+            return list(prop1) + [None] * len2
+        return list(prop1) + list(prop2)
 
     def _check_site_props(self, site_props: SitePropsType | None) -> None:
         """Check data shape of site properties.