Add type annotations for io.vasp.outputs (#3776)

* remove a lot of ignore tags

* first go: quick look and comment/type tweaks

* remove ALL type: ignore[reportPossiblyUnboundVariable]

* a quick look

* tweak module docstring

* fix/supress PossiblyUnboundVariable

* pre-commit fix

* revert changes from other branch

* [Need Discussion] set IVDW default to 0

* suppress None error for ElementTree searches

* replace dict update with |=

* fix typo in update -> |=, and mypy fixes

* fix another typo in update -> |=

* add DEBUG tag and mypy fixes

* remove DEBUG tag

* more mypy fixes

* more mypy fixes

* mypy fixes

* finish mypy errors

pymatgen/core/trajectory.py

@@ -16,7 +16,6 @@
 
 from pymatgen.core.structure import Composition, DummySpecies, Element, Lattice, Molecule, Species, Structure
 from pymatgen.io.ase import AseAtomsAdaptor
-from pymatgen.io.vasp.outputs import Vasprun, Xdatcar
 
 if TYPE_CHECKING:
     from collections.abc import Iterator
@@ -547,9 +546,13 @@ def from_file(cls, filename: str | Path, constant_lattice: bool = True, **kwargs
         structures = []
 
         if fnmatch(filename, "*XDATCAR*"):
+            from pymatgen.io.vasp.outputs import Xdatcar
+
             structures = Xdatcar(filename).structures
 
         elif fnmatch(filename, "vasprun*.xml*"):
+            from pymatgen.io.vasp.outputs import Vasprun
+
             structures = Vasprun(filename).structures
 
         elif fnmatch(filename, "*.traj"):

pymatgen/entries/computed_entries.py

@@ -291,7 +291,7 @@ def __init__(
         energy_adjustments: list | None = None,
         parameters: dict | None = None,
         data: dict | None = None,
-        entry_id: object | None = None,
+        entry_id: str | None = None,
     ):
         """Initialize a ComputedEntry.
 
@@ -557,7 +557,7 @@ def __init__(
         energy_adjustments: list | None = None,
         parameters: dict | None = None,
         data: dict | None = None,
-        entry_id: object | None = None,
+        entry_id: str | None = None,
     ) -> None:
         """Initialize a ComputedStructureEntry.
 
@@ -647,7 +647,10 @@ def from_dict(cls, dct: dict) -> Self:
             entry_id=dct.get("entry_id"),
         )
 
-    def normalize(self, mode: Literal["formula_unit", "atom"] = "formula_unit") -> ComputedStructureEntry:
+    def normalize(
+        self,
+        mode: Literal["formula_unit", "atom"] = "formula_unit",
+    ) -> ComputedStructureEntry:
         """Normalize the entry's composition and energy. The structure remains unchanged.
 
         Args:
@@ -698,7 +701,7 @@ def __init__(
         energy_adjustments: list | None = None,
         parameters: dict | None = None,
         data: dict | None = None,
-        entry_id: object | None = None,
+        entry_id: str | None = None,
     ):
         """
         Args:

pymatgen/io/lobster/outputs.py

@@ -1380,14 +1380,14 @@ def __init__(
                     iband = 0
                 if line.split()[0] != "#":
                     if linenumber < self.nbands:
-                        if ifilename == 0:
+                        if ifilename == 0 and self.efermi is not None:
                             eigenvals[Spin.up][iband][idx_kpt] = float(line.split()[1]) + self.efermi
 
                         p_eigenvals[Spin.up][iband][idx_kpt][atom_names[ifilename]][orbital_names[ifilename]] = float(
                             line.split()[2]
                         )
                     if linenumber >= self.nbands and self.is_spinpolarized:
-                        if ifilename == 0:
+                        if ifilename == 0 and self.efermi is not None:
                             eigenvals[Spin.down][iband][idx_kpt] = float(line.split()[1]) + self.efermi
                         p_eigenvals[Spin.down][iband][idx_kpt][atom_names[ifilename]][orbital_names[ifilename]] = float(
                             line.split()[2]

pymatgen/io/vasp/optics.py

@@ -72,14 +72,17 @@ class DielectricFunctionCalculator(MSONable):
 
     @classmethod
     def from_vasp_objects(cls, vrun: Vasprun, waveder: Waveder) -> Self:
-        """Construct a DielectricFunction from Vasprun, Kpoint, and Waveder objects.
+        """Construct a DielectricFunction from Vasprun, Kpoint, and Waveder.
 
         Args:
             vrun: Vasprun object
             kpoint: Kpoint object
             waveder: Waveder object
         """
         bands = vrun.eigenvalues
+        if bands is None:
+            raise RuntimeError("eigenvalues cannot be None.")
+
         sspins = [Spin.up, Spin.down]
         eigs = np.stack([bands[spin] for spin in sspins[: vrun.parameters["ISPIN"]]], axis=2)[..., 0]
         eigs = np.swapaxes(eigs, 0, 1)
@@ -95,6 +98,9 @@ def from_vasp_objects(cls, vrun: Vasprun, waveder: Waveder) -> Self:
         if vrun.parameters["ISYM"] != 0:
             raise NotImplementedError("ISYM != 0 is not implemented yet")
 
+        if efermi is None:
+            raise ValueError("efermi cannot be None.")
+
         return cls(
             cder_real=waveder.cder_real,
             cder_imag=waveder.cder_imag,