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", "call-overload"]
-exclude = ['src/pymatgen/analysis', 'src/pymatgen/phonon', 'src/pymatgen/io/lobster', 'src/pymatgen/io/cp2k', 'src/pymatgen/io/lammps']
+exclude = ['src/pymatgen/analysis', 'src/pymatgen/phonon', 'src/pymatgen/io/cp2k', 'src/pymatgen/io/lammps']
 plugins = ["numpy.typing.mypy_plugin"]
 
 [[tool.mypy.overrides]]

src/pymatgen/io/lobster/inputs.py

@@ -512,7 +512,7 @@ def write_KPOINTS(
         # For now, we are setting MAGMOM to zero. (Taken from INCAR class)
         cell = matrix, positions, zs, magmoms
         # TODO: what about this shift?
-        mapping, grid = spglib.get_ir_reciprocal_mesh(mesh, cell, is_shift=[0, 0, 0])
+        mapping, grid = spglib.get_ir_reciprocal_mesh(mesh, cell, is_shift=[0, 0, 0])  # type:ignore[arg-type]
 
         # Get the KPOINTS for the grid
         if isym == -1:
@@ -530,7 +530,7 @@ def write_KPOINTS(
             weights = []
             all_labels = []
             newlist = [list(gp) for gp in list(grid)]
-            mapping = []
+            mapping = []  # type:ignore[assignment]
             for gp in newlist:
                 minus_gp = [-k for k in gp]
                 if minus_gp in newlist and minus_gp != [0, 0, 0]:
@@ -590,7 +590,7 @@ def from_file(cls, lobsterin: PathLike) -> Self:
             Lobsterin object
         """
         with zopen(lobsterin, mode="rt", encoding="utf-8") as file:
-            lines = file.read().split("\n")
+            lines: list[str] = file.read().split("\n")  # type:ignore[arg-type,assignment]
         if not lines:
             raise RuntimeError("lobsterin file contains no data.")
 
@@ -640,7 +640,7 @@ def _get_potcar_symbols(POTCAR_input: PathLike) -> list[str]:
         Returns:
             list[str]: names of the species
         """
-        potcar = Potcar.from_file(POTCAR_input)
+        potcar = Potcar.from_file(POTCAR_input)  # type:ignore[arg-type]
         for pot in potcar:
             if pot.potential_type != "PAW":
                 raise ValueError("Lobster only works with PAW! Use different POTCARs")

src/pymatgen/io/lobster/lobsterenv.py

@@ -204,7 +204,7 @@ def __init__(
             else:
                 bv_analyzer = BVAnalyzer()
                 try:
-                    self.valences = bv_analyzer.get_valences(structure=self.structure)
+                    self.valences = bv_analyzer.get_valences(structure=self.structure)  # type:ignore[arg-type]
                 except ValueError as exc:
                     self.valences = None
                     if additional_condition in {1, 3, 5, 6}:
@@ -311,7 +311,7 @@ def get_light_structure_environment(
             LobsterLightStructureEnvironments
         """
         lgf = LocalGeometryFinder()
-        lgf.setup_structure(structure=self.structure)
+        lgf.setup_structure(structure=self.structure)  # type:ignore[arg-type]
         list_ce_symbols = []
         list_csm = []
         list_permut = []
@@ -342,7 +342,7 @@ def get_light_structure_environment(
                     list_ce_symbol=list_ce_symbols,
                     list_csm=list_csm,
                     list_permutation=list_permut,
-                    list_neighsite=self.list_neighsite,
+                    list_neighsite=self.list_neighsite,  # type:ignore[arg-type]
                     list_neighisite=self.list_neighisite,
                     structure=self.structure,
                     valences=self.valences,
@@ -384,7 +384,7 @@ def get_light_structure_environment(
             list_ce_symbol=new_list_ce_symbols,
             list_csm=new_list_csm,
             list_permutation=new_list_permut,
-            list_neighsite=new_list_neighsite,
+            list_neighsite=new_list_neighsite,  # type:ignore[arg-type]
             list_neighisite=new_list_neighisite,
             structure=self.structure,
             valences=self.valences,
@@ -436,7 +436,7 @@ def get_info_icohps_to_neighbors(
             if idx in isites:
                 for key, icohpsum in zip(self.list_keys[idx], self.list_icohps[idx], strict=True):
                     summed_icohps += icohpsum
-                    list_icohps.append(icohpsum)
+                    list_icohps.append(icohpsum)  # type:ignore[arg-type]
                     labels.append(key)
                     atoms.append(
                         [
@@ -617,7 +617,7 @@ def get_info_cohps_to_neighbors(
 
                 summed_cohp = None
 
-        return plot_label, summed_cohp
+        return plot_label, summed_cohp  # type:ignore[return-value]
 
     def _get_plot_label(self, atoms: list[list[str]], per_bond: bool) -> str:
         """Count the types of bonds and append a label."""
@@ -682,8 +682,8 @@ def get_info_icohps_between_neighbors(
                         unitcell1 = self._determine_unit_cell(n_site)
                         unitcell2 = self._determine_unit_cell(n_site2)
 
-                        index_n_site = self._get_original_site(self.structure, n_site)
-                        index_n_site2 = self._get_original_site(self.structure, n_site2)
+                        index_n_site = self._get_original_site(self.structure, n_site)  # type:ignore[arg-type]
+                        index_n_site2 = self._get_original_site(self.structure, n_site2)  # type:ignore[arg-type]
 
                         if index_n_site < index_n_site2:
                             translation = list(np.array(unitcell1) - np.array(unitcell2))
@@ -913,7 +913,7 @@ def _find_environments(
         Returns:
             Tuple of ICOHPs, keys, lengths, neighisite, neighsite, coords.
         """
-        list_icohps: list[list[IcohpValue]] = []
+        list_icohps: list[list[float]] = []
         list_keys: list[list[str]] = []
         list_lengths: list[list[float]] = []
         list_neighisite: list[list[int]] = []
@@ -1013,7 +1013,7 @@ def _find_environments(
                 list_lengths.append([])
                 list_keys.append([])
                 list_coords.append([])
-        return (
+        return (  # type:ignore[return-value]
             list_icohps,
             list_keys,
             list_lengths,
@@ -1027,7 +1027,7 @@ def _find_relevant_atoms_additional_condition(
         site_idx: int,
         icohps: dict[str, IcohpValue],
         additional_condition: Literal[0, 1, 2, 3, 4, 5, 6],
-    ) -> tuple[list[str], list[float], list[int], list[IcohpValue]]:
+    ) -> tuple[list[str], list[float], list[int], list[float]]:
         """Find all relevant atoms that fulfill the additional condition.
 
         Args:
@@ -1041,7 +1041,7 @@ def _find_relevant_atoms_additional_condition(
         keys_from_ICOHPs: list[str] = []
         lengths_from_ICOHPs: list[float] = []
         neighbors_from_ICOHPs: list[int] = []
-        icohps_from_ICOHPs: list[IcohpValue] = []
+        icohps_from_ICOHPs: list[float] = []
 
         for key, icohp in icohps.items():
             atomnr1 = self._get_atomnumber(icohp._atom1)
@@ -1443,15 +1443,15 @@ def from_Lobster(
 
             if list_neighisite[site_idx] is not None:
                 nb_set = cls.NeighborsSet(
-                    structure=structure,
+                    structure=structure,  # type:ignore[arg-type]
                     isite=site_idx,
                     all_nbs_sites=all_nbs_sites,
                     all_nbs_sites_indices=all_nbs_sites_indices[site_idx],
                 )
 
             else:
                 nb_set = cls.NeighborsSet(
-                    structure=structure,
+                    structure=structure,  # type:ignore[arg-type]
                     isite=site_idx,
                     all_nbs_sites=[],
                     all_nbs_sites_indices=[],

src/pymatgen/io/lobster/outputs.py

@@ -55,6 +55,11 @@
 )
 
 
+def _get_lines(filename) -> list[str]:
+    with zopen(filename, mode="rt", encoding="utf-8") as file:
+        return file.read().split("\n")  # type:ignore[return-value,arg-type]
+
+
 class Cohpcar:
     """Read COXXCAR.lobster/COXXCAR.LCFO.lobster files generated by LOBSTER.
 
@@ -120,8 +125,7 @@ def __init__(
             else:
                 self._filename = "COHPCAR.lobster"
 
-        with zopen(self._filename, mode="rt", encoding="utf-8") as file:
-            lines = file.read().split("\n")
+        lines = _get_lines(filename)
 
         # The parameters line is the second line in a COHPCAR file.
         # It contains all parameters that are needed to map the file.
@@ -405,7 +409,7 @@ def __init__(
         # and we don't need the header.
         if self._icohpcollection is None:
             with zopen(self._filename, mode="rt", encoding="utf-8") as file:
-                all_lines = file.read().splitlines()
+                all_lines: list[str] = file.read().splitlines()  # type:ignore[assignment]
 
                 # strip *trailing* blank lines only
                 all_lines = [line for line in all_lines if line.strip()]
@@ -625,7 +629,7 @@ class NciCobiList:
             }
     """
 
-    def __init__(self, filename: PathLike | None = "NcICOBILIST.lobster") -> None:
+    def __init__(self, filename: PathLike = "NcICOBILIST.lobster") -> None:
         """
 
         LOBSTER < 4.1.0: no COBI/ICOBI/NcICOBI
@@ -636,8 +640,7 @@ def __init__(self, filename: PathLike | None = "NcICOBILIST.lobster") -> None:
 
         # LOBSTER list files have an extra trailing blank line
         # and we don't need the header
-        with zopen(filename, mode="rt", encoding="utf-8") as file:
-            lines = file.read().split("\n")[1:-1]
+        lines = _get_lines(filename)[1:-1]
         if len(lines) == 0:
             raise RuntimeError("NcICOBILIST file contains no data.")
 
@@ -927,8 +930,7 @@ def __init__(
         self.loewdin = [] if loewdin is None else loewdin
 
         if self.num_atoms is None:
-            with zopen(filename, mode="rt", encoding="utf-8") as file:
-                lines = file.read().split("\n")[3:-3]
+            lines = _get_lines(filename)[3:-3]  # type:ignore[arg-type,assignment]
             if len(lines) == 0:
                 raise RuntimeError("CHARGES file contains no data.")
 
@@ -1061,8 +1063,7 @@ def __init__(self, filename: PathLike | None, **kwargs) -> None:
                 else:
                     raise ValueError(f"{attr}={val} is not a valid attribute for Lobsterout")
         elif filename:
-            with zopen(filename, mode="rt", encoding="utf-8") as file:
-                lines = file.read().split("\n")
+            lines = _get_lines(filename)
             if len(lines) == 0:
                 raise RuntimeError("lobsterout does not contain any data")
 
@@ -1459,8 +1460,7 @@ def __init__(
             raise ValueError("No FATBAND files in folder or given")
 
         for fname in filenames:
-            with zopen(fname, mode="rt", encoding="utf-8") as file:
-                lines = file.read().split("\n")
+            lines = _get_lines(fname)
 
             atom_names.append(os.path.split(fname)[1].split("_")[1].capitalize())
             parameters = lines[0].split()
@@ -1493,8 +1493,7 @@ def __init__(
         eigenvals: dict = {}
         p_eigenvals: dict = {}
         for ifilename, filename in enumerate(filenames):
-            with zopen(filename, mode="rt", encoding="utf-8") as file:
-                lines = file.read().split("\n")
+            lines = _get_lines(filename)
 
             if ifilename == 0:
                 self.nbands = int(parameters[6])
@@ -1601,7 +1600,7 @@ def get_bandstructure(self) -> LobsterBandStructureSymmLine:
             lattice=self.lattice,
             efermi=self.efermi,  # type: ignore[arg-type]
             labels_dict=self.label_dict,
-            structure=self.structure,
+            structure=self.structure,  # type:ignore[arg-type]
             projections=self.p_eigenvals,
         )
 
@@ -1641,8 +1640,7 @@ def __init__(
         self.max_deviation = [] if max_deviation is None else max_deviation
 
         if not self.band_overlaps_dict:
-            with zopen(filename, mode="rt", encoding="utf-8") as file:
-                lines = file.read().split("\n")
+            lines = _get_lines(filename)
 
             spin_numbers = [0, 1] if lines[0].split()[-1] == "0" else [1, 2]
 
@@ -1786,8 +1784,7 @@ def __init__(
         self.is_lcfo = is_lcfo
         self.list_dict_grosspop = [] if list_dict_grosspop is None else list_dict_grosspop
         if not self.list_dict_grosspop:
-            with zopen(filename, mode="rt", encoding="utf-8") as file:
-                lines = file.read().split("\n")
+            lines = _get_lines(filename)
 
             # Read file to list of dict
             small_dict: dict[str, Any] = {}
@@ -1916,8 +1913,7 @@ def _parse_file(
             imaginary (list[float]): Imaginary parts of wave function.
             distance (list[float]): Distances to the first point in wave function file.
         """
-        with zopen(filename, mode="rt", encoding="utf-8") as file:
-            lines = file.read().split("\n")
+        lines = _get_lines(filename)
 
         points = []
         distances = []
@@ -2086,8 +2082,7 @@ def __init__(
         self.madelungenergies_mulliken = None if madelungenergies_mulliken is None else madelungenergies_mulliken
 
         if self.ewald_splitting is None:
-            with zopen(filename, mode="rt", encoding="utf-8") as file:
-                lines = file.read().split("\n")[5]
+            lines = _get_lines(filename)[5]
             if len(lines) == 0:
                 raise RuntimeError("MadelungEnergies file contains no data.")
 
@@ -2157,8 +2152,7 @@ def __init__(
         self.madelungenergies_mulliken: list | float = madelungenergies_mulliken or []
 
         if self.num_atoms is None:
-            with zopen(filename, mode="rt", encoding="utf-8") as file:
-                lines = file.read().split("\n")
+            lines = _get_lines(filename)
             if len(lines) == 0:
                 raise RuntimeError("SitePotentials file contains no data.")
 
@@ -2311,7 +2305,7 @@ def __init__(
 
         self._filename = str(filename)
         with zopen(self._filename, mode="rt", encoding="utf-8") as file:
-            lines = file.readlines()
+            lines: list[str] = file.readlines()  # type:ignore[assignment]
         if len(lines) == 0:
             raise RuntimeError("Please check provided input file, it seems to be empty")
 
@@ -2454,8 +2448,7 @@ def __init__(
         self.rel_loewdin_pol_vector = {} if rel_loewdin_pol_vector is None else rel_loewdin_pol_vector
 
         if not self.rel_loewdin_pol_vector and not self.rel_mulliken_pol_vector:
-            with zopen(filename, mode="rt", encoding="utf-8") as file:
-                lines = file.read().split("\n")
+            lines = _get_lines(filename)
             if len(lines) == 0:
                 raise RuntimeError("Polarization file contains no data.")
 
@@ -2498,8 +2491,7 @@ def __init__(
         self.bin_width = 0.0 if bin_width is None else bin_width
 
         if not self.bwdf:
-            with zopen(filename, mode="rt", encoding="utf-8") as file:
-                lines = file.read().split("\n")
+            lines = _get_lines(filename)
             if len(lines) == 0:
                 raise RuntimeError("BWDF file contains no data.")
 

src/pymatgen/io/vasp/outputs.py

@@ -3855,7 +3855,7 @@ def write_spin(data_type: str) -> None:
             if count % 5 != 0:
                 file.write(" " + "".join(lines) + " \n")  # type:ignore[arg-type]
 
-            data = self.data_aug.get(data_type, [])
+            data = self.data_aug.get(data_type, []) if self.data_aug is not None else []
             if isinstance(data, Iterable):
                 file.write("".join(data))  # type:ignore[arg-type]