Fix mypy errors for io.cp2k (#3984)

* ignore mypy override error globally

* standardize CP2K names

* pre-commit auto-fixes

* standarize more CP2K names

* old trick: relocate magic methods to the top

* format tweaks

* fix type errors in cp2k inputs

* remove reimport Sequence

* use list[Kpoint] as getter return type

* remove unnecessary cast

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

pyproject.toml

@@ -285,7 +285,7 @@ ignore_missing_imports = true
 namespace_packages = true
 explicit_package_bases = true
 no_implicit_optional = false
-disable_error_code = "annotation-unchecked"
+disable_error_code = ["annotation-unchecked", "override"]
 
 [[tool.mypy.overrides]]
 module = ["requests.*", "tabulate.*"]

src/pymatgen/analysis/local_env.py

@@ -1490,7 +1490,7 @@ def get_nn_info(self, structure: Structure, n: int):
 
         return siw
 
-    def get_bonded_structure(self, structure: Structure, decorate: bool = False) -> StructureGraph:  # type: ignore[override]
+    def get_bonded_structure(self, structure: Structure, decorate: bool = False) -> StructureGraph:
         """
         Obtain a MoleculeGraph object using this NearNeighbor
         class. Requires the optional dependency networkx
@@ -1637,7 +1637,7 @@ def get_nn_info(self, structure: Structure, n: int):
 
         return siw
 
-    def get_bonded_structure(self, structure: Structure, decorate: bool = False) -> MoleculeGraph:  # type: ignore[override]
+    def get_bonded_structure(self, structure: Structure, decorate: bool = False) -> MoleculeGraph:
         """
         Obtain a MoleculeGraph object using this NearNeighbor class.
 
@@ -4000,7 +4000,7 @@ def get_nn_data(self, structure: Structure, n: int, length=None):
 
         return self.transform_to_length(self.NNData(nn, cn_weights, cn_nninfo), length)
 
-    def get_cn(self, structure: Structure, n: int, **kwargs) -> float:  # type: ignore[override]
+    def get_cn(self, structure: Structure, n: int, **kwargs) -> float:
         """Get coordination number, CN, of site with index n in structure.
 
         Args:
@@ -4306,7 +4306,7 @@ def extend_structure_molecules(self) -> bool:
         """
         return True
 
-    def get_bonded_structure(self, structure: Structure, decorate: bool = False) -> StructureGraph:  # type: ignore[override]
+    def get_bonded_structure(self, structure: Structure, decorate: bool = False) -> StructureGraph:
         """
         Args:
             structure (Structure): Input structure

src/pymatgen/core/interface.py

@@ -166,7 +166,7 @@ def to_str(number: float, rjust: int = 10) -> str:
             outs.append(f"{idx} {site.species_string} {' '.join(to_str(coord, 12) for coord in site.frac_coords)}")
         return "\n".join(outs)
 
-    def copy(self) -> Self:  # type: ignore[override]
+    def copy(self) -> Self:
         """Make a copy of the GrainBoundary."""
         return type(self)(
             self.lattice,
@@ -261,7 +261,7 @@ def coincidents(self) -> list[Site]:
                 coincident_sites.append(self.sites[idx])
         return coincident_sites
 
-    def as_dict(self) -> dict:  # type: ignore[override]
+    def as_dict(self) -> dict:
         """
         Returns:
             Dictionary representation of GrainBoundary object.
@@ -281,7 +281,7 @@ def as_dict(self) -> dict:  # type: ignore[override]
         }
 
     @classmethod
-    def from_dict(cls, dct: dict) -> Self:  # type: ignore[override]
+    def from_dict(cls, dct: dict) -> Self:
         """Generate GrainBoundary from a dict created by as_dict().
 
         Args:
@@ -2580,7 +2580,7 @@ def film(self) -> Structure:
         """A Structure for just the film."""
         return Structure.from_sites(self.film_sites)
 
-    def copy(self) -> Self:  # type: ignore[override]
+    def copy(self) -> Self:
         """Make a copy of the Interface."""
         return type(self).from_dict(self.as_dict())
 
@@ -2689,7 +2689,7 @@ def _update_c(self, new_c: float) -> None:
             site._lattice = new_lattice  # Update the lattice
             site.coords = c_coords  # Put back into original Cartesian space
 
-    def as_dict(self) -> dict:  # type: ignore[override]
+    def as_dict(self) -> dict:
         """MSONable dict."""
         return {
             **super().as_dict(),
@@ -2700,7 +2700,7 @@ def as_dict(self) -> dict:  # type: ignore[override]
         }
 
     @classmethod
-    def from_dict(cls, dct: dict) -> Self:  # type: ignore[override]
+    def from_dict(cls, dct: dict) -> Self:
         """
         Args:
             dct: dict.

src/pymatgen/core/ion.py

@@ -304,7 +304,7 @@ def composition(self) -> Composition:
         """Composition of ion."""
         return Composition(self._data)
 
-    def oxi_state_guesses(  # type: ignore[override]
+    def oxi_state_guesses(
         self,
         oxi_states_override: dict | None = None,
         all_oxi_states: bool = False,

src/pymatgen/core/lattice.py

@@ -443,7 +443,7 @@ def from_dict(
         dct: dict,
         fmt: str | None = None,
         **kwargs,
-    ) -> Self:  # type: ignore[override]
+    ) -> Self:
         """Create a Lattice from a dictionary.
 
         If fmt is None, the dict should contain the a, b, c,

src/pymatgen/core/sites.py

@@ -84,7 +84,7 @@ def __getattr__(self, attr: str) -> Any:
             return props[attr]
         raise AttributeError(f"{attr=} not found on {type(self).__name__}")
 
-    def __getitem__(self, el: Element) -> float:  # type: ignore[override]
+    def __getitem__(self, el: Element) -> float:
         """Get the occupancy for element."""
         return self.species[el]
 
@@ -102,7 +102,7 @@ def __eq__(self, other: object) -> bool:
             and self.properties == other.properties
         )
 
-    def __hash__(self) -> int:  # type: ignore[override]
+    def __hash__(self) -> int:
         """Minimally effective hash function that just distinguishes between Sites
         with different elements.
         """

src/pymatgen/core/structure.py

@@ -104,7 +104,7 @@ def __len__(self) -> Literal[3]:
         """Make neighbor Tuple-like to retain backwards compatibility."""
         return 3
 
-    def __getitem__(self, idx: int) -> Self | float:  # type: ignore[override]
+    def __getitem__(self, idx: int) -> Self | float:
         """Make neighbor Tuple-like to retain backwards compatibility."""
         return (self, self.nn_distance, self.index)[idx]
 
@@ -170,7 +170,7 @@ def __len__(self) -> Literal[4]:
         """Make neighbor Tuple-like to retain backwards compatibility."""
         return 4
 
-    def __getitem__(self, idx: int | slice):  # type: ignore[override]
+    def __getitem__(self, idx: int | slice):
         """Make neighbor Tuple-like to retain backwards compatibility."""
         return (self, self.nn_distance, self.index, self.image)[idx]
 
@@ -179,12 +179,12 @@ def coords(self) -> NDArray:
         """Cartesian coords."""
         return self._lattice.get_cartesian_coords(self._frac_coords)
 
-    def as_dict(self) -> dict:  # type: ignore[override]
+    def as_dict(self) -> dict:
         """Note that method calls the super of Site, which is MSONable itself."""
         return super(Site, self).as_dict()
 
     @classmethod
-    def from_dict(cls, dct: dict) -> Self:  # type: ignore[override]
+    def from_dict(cls, dct: dict) -> Self:
         """Get a PeriodicNeighbor from a dict.
 
         Args:
@@ -2960,7 +2960,7 @@ def from_id(cls, id_: str, source: StructureSources = "Materials Project", **kwa
         raise ValueError(f"Invalid source: {source}")
 
     @classmethod
-    def from_str(  # type: ignore[override]
+    def from_str(
         cls,
         input_string: str,
         fmt: FileFormats,
@@ -3044,7 +3044,7 @@ def from_str(  # type: ignore[override]
         return cls.from_sites(struct, properties=struct.properties)
 
     @classmethod
-    def from_file(  # type: ignore[override]
+    def from_file(
         cls,
         filename: PathLike,
         primitive: bool = False,
@@ -3774,7 +3774,7 @@ def to(self, filename: str = "", fmt: str = "") -> str | None:
         return str(writer)
 
     @classmethod
-    def from_str(  # type: ignore[override]
+    def from_str(
         cls,
         input_string: str,
         fmt: Literal["xyz", "gjf", "g03", "g09", "com", "inp", "json", "yaml"],
@@ -3821,7 +3821,7 @@ def from_str(  # type: ignore[override]
         return cls.from_sites(mol, properties=mol.properties)
 
     @classmethod
-    def from_file(cls, filename: PathLike) -> Self | None:  # type: ignore[override]
+    def from_file(cls, filename: PathLike) -> Self | None:
         """Read a molecule from a file. Supported formats include xyz,
         gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and
         pymatgen's JSON-serialized molecules. Using openbabel,
@@ -3933,7 +3933,7 @@ def __init__(
 
         self._sites: list[PeriodicSite] = list(self._sites)  # type: ignore[assignment]
 
-    def __setitem__(  # type: ignore[override]
+    def __setitem__(
         self,
         idx: int | slice | Sequence[int] | SpeciesLike,
         site: SpeciesLike | PeriodicSite | Sequence | dict[SpeciesLike, float],
@@ -4018,7 +4018,7 @@ def lattice(self, lattice: ArrayLike | Lattice) -> None:
         for site in self:
             site.lattice = lattice
 
-    def append(  # type: ignore[override]
+    def append(
         self,
         species: CompositionLike,
         coords: ArrayLike,
@@ -4049,7 +4049,7 @@ def append(  # type: ignore[override]
             properties=properties,
         )
 
-    def insert(  # type: ignore[override]
+    def insert(
         self,
         idx: int,
         species: CompositionLike,
@@ -4765,7 +4765,7 @@ def __init__(
         )
         self._sites: list[Site] = list(self._sites)
 
-    def __setitem__(  # type: ignore[override]
+    def __setitem__(
         self,
         idx: int | slice | Sequence[int] | SpeciesLike,
         site: SpeciesLike | Site | Sequence,
@@ -4810,7 +4810,7 @@ def __delitem__(self, idx: SupportsIndex | slice) -> None:
         """Deletes a site from the Structure."""
         self._sites.__delitem__(idx)
 
-    def append(  # type: ignore[override]
+    def append(
         self,
         species: CompositionLike,
         coords: ArrayLike,
@@ -4874,7 +4874,7 @@ def set_charge_and_spin(
 
         return self
 
-    def insert(  # type: ignore[override]
+    def insert(
         self,
         idx: int,
         species: CompositionLike,

src/pymatgen/core/surface.py

@@ -218,7 +218,7 @@ def surface_area(self) -> float:
         return np.linalg.norm(np.cross(matrix[0], matrix[1]))
 
     @classmethod
-    def from_dict(cls, dct: dict[str, Any]) -> Self:  # type: ignore[override]
+    def from_dict(cls, dct: dict[str, Any]) -> Self:
         """
         Args:
             dct: dict.
@@ -242,7 +242,7 @@ def from_dict(cls, dct: dict[str, Any]) -> Self:  # type: ignore[override]
             energy=dct["energy"],
         )
 
-    def as_dict(self, **kwargs) -> dict:  # type: ignore[override]
+    def as_dict(self, **kwargs) -> dict:
         """MSONable dict."""
         dct = super().as_dict(**kwargs)
         dct["@module"] = type(self).__module__
@@ -255,7 +255,7 @@ def as_dict(self, **kwargs) -> dict:  # type: ignore[override]
         dct["energy"] = self.energy
         return dct
 
-    def copy(self, site_properties: dict[str, Any] | None = None) -> Self:  # type: ignore[override]
+    def copy(self, site_properties: dict[str, Any] | None = None) -> Self:
         """Get a copy of the Slab, with options to update site properties.
 
         Args:

src/pymatgen/electronic_structure/bandstructure.py

@@ -1037,7 +1037,7 @@ def get_projection_on_elements(self) -> dict[Spin, list]:
 
     def get_projections_on_elements_and_orbitals(
         self,
-        el_orb_spec: dict[Element, list],  # type: ignore[override]
+        el_orb_spec: dict[Element, list],
     ) -> dict[Spin, list]:
         """Get projections on elements and specific orbitals.
 

src/pymatgen/electronic_structure/dos.py

@@ -1397,7 +1397,7 @@ def as_dict(self) -> dict[str, Any]:
 class LobsterCompleteDos(CompleteDos):
     """Extended CompleteDos for LOBSTER."""
 
-    def get_site_orbital_dos(self, site: PeriodicSite, orbital: str) -> Dos:  # type: ignore[override]
+    def get_site_orbital_dos(self, site: PeriodicSite, orbital: str) -> Dos:
         """Get the DOS for a particular orbital of a particular site.
 
         Args:
@@ -1448,7 +1448,7 @@ def get_site_t2g_eg_resolved_dos(
             "e_g": Dos(self.efermi, self.energies, functools.reduce(add_densities, eg_dos)),
         }
 
-    def get_spd_dos(self) -> dict[str, Dos]:  # type: ignore[override]
+    def get_spd_dos(self) -> dict[str, Dos]:
         """Get orbital projected DOS.
 
         For example, if 3s and 4s are included in the basis of some element,
@@ -1469,7 +1469,7 @@ def get_spd_dos(self) -> dict[str, Dos]:  # type: ignore[override]
 
         return {orb: Dos(self.efermi, self.energies, densities) for orb, densities in spd_dos.items()}  # type: ignore[misc]
 
-    def get_element_spd_dos(self, el: SpeciesLike) -> dict[str, Dos]:  # type: ignore[override]
+    def get_element_spd_dos(self, el: SpeciesLike) -> dict[str, Dos]:
         """Get element and s/p/d projected DOS.
 
         Args:

src/pymatgen/entries/compatibility.py

@@ -837,7 +837,7 @@ def get_explanation_dict(self, entry: ComputedEntry) -> dict[str, Any]:
         dct["corrections"] = corrections
         return dct
 
-    def explain(self, entry: ComputedEntry) -> None:  # type: ignore[override]
+    def explain(self, entry: ComputedEntry) -> None:
         """Print an explanation of the corrections that are being applied for a
         given compatibility scheme. Inspired by the "explain" methods in many
         database methodologies.

src/pymatgen/entries/mixing_scheme.py

@@ -114,7 +114,7 @@ def __init__(
             if hasattr(compat, "check_potcar"):
                 compat.check_potcar = check_potcar  # type: ignore[union-attr]
 
-    def process_entries(  # type: ignore[override]
+    def process_entries(
         self,
         entries: AnyComputedEntry | list[AnyComputedEntry],
         clean: bool = True,