More type fixes.

Author: shyuep

pyproject.toml

@@ -302,7 +302,7 @@ ignore_missing_imports = true
 namespace_packages = true
 no_implicit_optional = false
 disable_error_code = ["annotation-unchecked", "override", "operator", "attr-defined", "union-attr", "misc"] #, "operator", "arg-type", "index", "call-arg", "return-value", "assignment", "attr-defined"]
-exclude = ['src/pymatgen/analysis', 'src/pymatgen/io', 'src/pymatgen/cli', 'src/pymatgen/electronic_structure', 'src/pymatgen/phonon', 'src/pymatgen/vis', "src/pymatgen/alchemy"]
+exclude = ['src/pymatgen/analysis', 'src/pymatgen/io', 'src/pymatgen/cli', 'src/pymatgen/electronic_structure', 'src/pymatgen/phonon', "src/pymatgen/alchemy"]
 plugins = ["numpy.typing.mypy_plugin"]
 
 [[tool.mypy.overrides]]

src/pymatgen/core/spectrum.py

@@ -17,7 +17,7 @@
     from collections.abc import Callable
     from typing import Literal
 
-    from numpy.typing import NDArray
+    from numpy.typing import ArrayLike, NDArray
     from typing_extensions import Self
 
 
@@ -50,7 +50,7 @@ class Spectrum(MSONable):
     XLABEL = "x"
     YLABEL = "y"
 
-    def __init__(self, x: NDArray, y: NDArray, *args, **kwargs) -> None:
+    def __init__(self, x: ArrayLike, y: ArrayLike, *args, **kwargs) -> None:
         """
         Args:
             x (ndarray): A ndarray of N values.
@@ -62,8 +62,8 @@ def __init__(self, x: NDArray, y: NDArray, *args, **kwargs) -> None:
                 etc. operators work properly.
             **kwargs: Same as that for *args.
         """
-        self.x = np.array(x)
-        self.y = np.array(y)
+        self.x = np.asarray(x)
+        self.y = np.asarray(y)
         self.ydim = self.y.shape
         if self.x.shape[0] != self.ydim[0]:
             raise ValueError("x and y values have different first dimension!")

src/pymatgen/electronic_structure/core.py

@@ -13,7 +13,7 @@
 if TYPE_CHECKING:
     from collections.abc import Sequence
 
-    from numpy.typing import NDArray
+    from numpy.typing import ArrayLike, NDArray
     from typing_extensions import Self
 
     from pymatgen.core import Lattice
@@ -127,7 +127,7 @@ class Magmom(MSONable):
     def __init__(
         self,
         moment: MagMomentLike,
-        saxis: tuple[float, float, float] = (0, 0, 1),
+        saxis: ArrayLike = (0, 0, 1),
     ) -> None:
         """
         Args:
@@ -137,10 +137,10 @@ def __init__(
         """
         # Init from another Magmom instance
         if isinstance(moment, type(self)):
-            saxis = moment.saxis  # type: ignore[has-type]
-            moment = moment.moment  # type: ignore[has-type]
+            saxis = moment.saxis
+            moment = moment.moment
 
-        magmom: NDArray = np.array(moment, dtype="d")
+        magmom = np.array(moment, dtype="d")
         if magmom.ndim == 0:
             magmom = magmom * (0, 0, 1)  # (ruff-preview) noqa: PLR6104
 

src/pymatgen/electronic_structure/dos.py

@@ -24,10 +24,9 @@
     np.trapezoid = np.trapz  # noqa: NPY201
 
 if TYPE_CHECKING:
-    from collections.abc import Sequence
     from typing import Any, Literal
 
-    from numpy.typing import NDArray
+    from numpy.typing import ArrayLike, NDArray
     from typing_extensions import Self
 
     from pymatgen.core.sites import PeriodicSite
@@ -48,7 +47,7 @@ class DOS(Spectrum):
     XLABEL = "Energy"
     YLABEL = "Density"
 
-    def __init__(self, energies: Sequence[float], densities: NDArray, efermi: float) -> None:
+    def __init__(self, energies: ArrayLike, densities: ArrayLike, efermi: float) -> None:
         """
         Args:
             energies (Sequence[float]): The Energies.
@@ -181,8 +180,8 @@ class Dos(MSONable):
     def __init__(
         self,
         efermi: float,
-        energies: Sequence[float],
-        densities: dict[Spin, NDArray],
+        energies: ArrayLike,
+        densities: dict[Spin, ArrayLike],
         norm_vol: float | None = None,
     ) -> None:
         """
@@ -196,10 +195,10 @@ def __init__(
                 otherwise will be in states/eV/Angstrom^3.
         """
         self.efermi = efermi
-        self.energies = np.array(energies)
+        self.energies = np.asarray(energies)
         self.norm_vol = norm_vol
         vol = norm_vol or 1
-        self.densities = {k: np.array(d) / vol for k, d in densities.items()}
+        self.densities = {k: np.asarray(d) / vol for k, d in densities.items()}
 
     def __add__(self, other):
         """Add two Dos.

src/pymatgen/phonon/dos.py

@@ -19,9 +19,7 @@
     np.trapezoid = np.trapz  # noqa: NPY201
 
 if TYPE_CHECKING:
-    from collections.abc import Sequence
-
-    from numpy.typing import NDArray
+    from numpy.typing import ArrayLike, NDArray
     from typing_extensions import Self
 
 BOLTZ_THZ_PER_K = const.value("Boltzmann constant in Hz/K") / const.tera  # Boltzmann constant in THz/K
@@ -31,7 +29,7 @@
 class PhononDos(MSONable):
     """Basic DOS object. All other DOS objects are extended versions of this object."""
 
-    def __init__(self, frequencies: Sequence, densities: Sequence) -> None:
+    def __init__(self, frequencies: ArrayLike, densities: ArrayLike) -> None:
         """
         Args:
             frequencies: A sequence of frequencies in THz
@@ -141,7 +139,7 @@ def __str__(self) -> str:
         return "\n".join(str_arr)
 
     @classmethod
-    def from_dict(cls, dct: dict[str, Sequence]) -> Self:
+    def from_dict(cls, dct: dict[str, ArrayLike]) -> Self:
         """Get PhononDos object from dict representation of PhononDos."""
         return cls(dct["frequencies"], dct["densities"])
 

src/pymatgen/phonon/thermal_displacements.py

@@ -51,10 +51,10 @@ class ThermalDisplacementMatrices(MSONable):
 
     def __init__(
         self,
-        thermal_displacement_matrix_cart: ArrayLike[ArrayLike],
+        thermal_displacement_matrix_cart: ArrayLike,
         structure: Structure,
         temperature: float | None,
-        thermal_displacement_matrix_cif: ArrayLike[ArrayLike] = None,
+        thermal_displacement_matrix_cif: ArrayLike | None = None,
     ) -> None:
         """
         Args:
@@ -89,8 +89,8 @@ def __init__(
 
     @staticmethod
     def get_full_matrix(
-        thermal_displacement: ArrayLike[ArrayLike],
-    ) -> np.ndarray[np.ndarray]:
+        thermal_displacement: ArrayLike,
+    ) -> np.ndarray:
         """Transfers the reduced matrix to the full matrix (order of reduced matrix U11, U22, U33, U23, U13, U12).
 
         Args:
@@ -115,8 +115,8 @@ def get_full_matrix(
 
     @staticmethod
     def get_reduced_matrix(
-        thermal_displacement: ArrayLike[ArrayLike],
-    ) -> np.ndarray[np.ndarray]:
+        thermal_displacement: ArrayLike,
+    ) -> np.ndarray:
         """Transfers the full matrix to reduced matrix (order of reduced matrix U11, U22, U33, U23, U13, U12).
 
         Args:
@@ -420,7 +420,7 @@ def ratio_prolate(self) -> np.ndarray:
     @classmethod
     def from_Ucif(
         cls,
-        thermal_displacement_matrix_cif: ArrayLike[ArrayLike],
+        thermal_displacement_matrix_cif: ArrayLike,
         structure: Structure,
         temperature: float | None = None,
     ) -> Self:

src/pymatgen/vis/structure_vtk.py

@@ -256,7 +256,7 @@ def contains_anion(site):
                     if sp.symbol in self.excluded_bonding_elements or sp == anion:
                         exclude = True
                         break
-                    max_radius = max(max_radius, sp.average_ionic_radius)
+                    max_radius = max(max_radius, sp.average_ionic_radius)  # type:ignore[type-var,assignment]
                     color += occu * np.array(self.el_color_mapping.get(sp.symbol, [0, 0, 0]))
 
                 if not exclude:
@@ -982,7 +982,7 @@ def set_structures(self, structures: Sequence[Structure], tags=None):
             struct_radii = []
             struct_vis_radii = []
             for site in struct:
-                radius = 0
+                radius = 0.0
                 vis_radius = 0.2
                 for species, occu in site.species.items():
                     radius += occu * (