More typing cleanups.

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/apps', '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/vis', "src/pymatgen/alchemy"]
 plugins = ["numpy.typing.mypy_plugin"]
 
 [[tool.mypy.overrides]]

src/pymatgen/apps/battery/battery_abc.py

@@ -14,10 +14,11 @@
 from monty.json import MSONable
 from scipy.constants import N_A
 
-from pymatgen.core import Composition, Element
+from pymatgen.core import Composition
 
 if TYPE_CHECKING:
-    from pymatgen.entries.computed_entries import ComputedEntry
+    from pymatgen.entries import Entry
+    from pymatgen.util.typing import SpeciesLike
 
 __author__ = "Anubhav Jain, Shyue Ping Ong"
 __copyright__ = "Copyright 2012, The Materials Project"
@@ -53,7 +54,7 @@ class AbstractVoltagePair(MSONable):
     vol_discharge: float
     frac_charge: float
     frac_discharge: float
-    working_ion_entry: ComputedEntry
+    working_ion_entry: Entry
     framework_formula: str
 
     def __post_init__(self):
@@ -62,7 +63,7 @@ def __post_init__(self):
         self.framework_formula = fw.reduced_formula
 
     @property
-    def working_ion(self) -> Element:
+    def working_ion(self) -> SpeciesLike:
         """Working ion as pymatgen Element object."""
         return self.working_ion_entry.elements[0]
 
@@ -128,7 +129,7 @@ class AbstractElectrode(Sequence, MSONable):
     """
 
     voltage_pairs: tuple[AbstractVoltagePair, ...]
-    working_ion_entry: ComputedEntry
+    working_ion_entry: Entry
     framework_formula: str  # should be made into Composition whenever the as_dict and from dict are fixed
 
     def __post_init__(self):

src/pymatgen/apps/battery/insertion_battery.py

@@ -15,13 +15,15 @@
 from pymatgen.apps.battery.battery_abc import AbstractElectrode, AbstractVoltagePair
 from pymatgen.core import Composition, Element
 from pymatgen.core.units import Charge, Time
-from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
+from pymatgen.entries.computed_entries import ComputedEntry
 
 if TYPE_CHECKING:
     from collections.abc import Iterable
 
     from typing_extensions import Self
 
+    from pymatgen.entries import Entry
+
 __author__ = "Anubhav Jain, Shyue Ping Ong"
 __copyright__ = "Copyright 2012, The Materials Project"
 
@@ -33,14 +35,14 @@ class InsertionElectrode(AbstractElectrode):
     insertion battery electrode.
     """
 
-    stable_entries: Iterable[ComputedEntry]
-    unstable_entries: Iterable[ComputedEntry]
+    stable_entries: Iterable[Entry]
+    unstable_entries: Iterable[Entry]
 
     @classmethod
     def from_entries(
         cls,
-        entries: Iterable[ComputedEntry | ComputedStructureEntry],
-        working_ion_entry: ComputedEntry | ComputedStructureEntry | PDEntry,
+        entries: Iterable[Entry],
+        working_ion_entry: Entry,
         strip_structures: bool = False,
     ) -> Self:
         """Create a new InsertionElectrode.
@@ -80,15 +82,15 @@ def from_entries(
         # Set an artificial high energy for each element for convex hull generation
         element_energy = max(entry.energy_per_atom for entry in entries) + 10
 
-        pdentries: list[ComputedEntry | ComputedStructureEntry | PDEntry] = []
+        pdentries: list[Entry] = []
         pdentries.extend(entries)
         pdentries.extend([PDEntry(Composition({el: 1}), element_energy) for el in elements])
 
         # Make phase diagram to determine which entries are stable vs. unstable.
         # For each working ion concentration, we want one stable entry
         # to use in forming voltage pairs. PhaseDiagram allows for easy comparison
         # of entry energies.
-        pd = PhaseDiagram(pdentries)
+        pd = PhaseDiagram(pdentries)  # type:ignore[arg-type]
 
         def lifrac(e):
             return e.composition.get_atomic_fraction(_working_ion)
@@ -364,7 +366,7 @@ def from_dict_legacy(cls, dct) -> Self:
         Returns:
             InsertionElectrode
         """
-        return InsertionElectrode(
+        return InsertionElectrode(  # type:ignore[return-value,call-arg]
             MontyDecoder().process_decoded(dct["entries"]),
             MontyDecoder().process_decoded(dct["working_ion_entry"]),
         )
@@ -387,7 +389,7 @@ class InsertionVoltagePair(AbstractVoltagePair):
     entry_discharge: ComputedEntry
 
     @classmethod
-    def from_entries(cls, entry1, entry2, working_ion_entry) -> Self:
+    def from_entries(cls, entry1, entry2, working_ion_entry) -> InsertionVoltagePair:
         """
         Args:
             entry1: Entry corresponding to one of the entries in the voltage step.

src/pymatgen/apps/borg/hive.py

@@ -89,7 +89,7 @@ def __init__(
         self,
         inc_structure: bool = False,
         parameters: list[str] | None = None,
-        data: list[str] | None = None,
+        data: dict | None = None,
     ) -> None:
         """
         Args:
@@ -113,7 +113,7 @@ def __init__(
         }
         if parameters:
             self._parameters.update(parameters)
-        self._data = data or []
+        self._data = data or {}
 
     def __str__(self) -> str:
         return "VaspToComputedEntryDrone"
@@ -132,10 +132,9 @@ def assimilate(self, path: PathLike) -> ComputedStructureEntry | ComputedEntry |
             filepath = glob(f"{path}/relax2/vasprun.xml*")[0]
         else:
             vasprun_files = glob(f"{path}/vasprun.xml*")
-            filepath = None
             if len(vasprun_files) == 1:
                 filepath = vasprun_files[0]
-            elif len(vasprun_files) > 1:
+            else:
                 # Since multiple files are ambiguous, we will always read
                 # the last one alphabetically.
                 filepath = max(vasprun_files)
@@ -147,7 +146,7 @@ def assimilate(self, path: PathLike) -> ComputedStructureEntry | ComputedEntry |
             logger.debug(f"error in {filepath}: {exc}")
             return None
 
-        return vasp_run.get_computed_entry(self._inc_structure, parameters=self._parameters, data=self._data)
+        return vasp_run.get_computed_entry(self._inc_structure, parameters=list(self._parameters), data=self._data)
 
         # entry.parameters["history"] = _get_transformation_history(path)
 
@@ -280,7 +279,7 @@ def assimilate(self, path: PathLike) -> ComputedStructureEntry | ComputedEntry |
             initial_vol = poscar.structure.volume
             final_vol = contcar.structure.volume
             delta_volume = final_vol / initial_vol - 1
-            data = {"filename": path, "delta_volume": delta_volume}
+            data: dict[str, Any] = {"filename": path, "delta_volume": delta_volume}
             if "DYNMAT" in files_to_parse:
                 dynmat = Dynmat(files_to_parse["DYNMAT"])
                 data["phonon_frequencies"] = dynmat.get_phonon_frequencies()

src/pymatgen/apps/borg/queen.py

@@ -104,7 +104,7 @@ def save_data(self, filename: PathLike) -> None:
                 or bz2 compression will be applied.
         """
         with zopen(filename, mode="wt", encoding="utf-8") as file:
-            json.dump(list(self._data), file, cls=MontyEncoder)
+            json.dump(list(self._data), file, cls=MontyEncoder)  # type:ignore[arg-type]
 
     def load_data(self, filename: PathLike) -> None:
         """Load assimilated data from a file."""

src/pymatgen/command_line/enumlib_caller.py

@@ -365,7 +365,8 @@ def _get_structures(self, num_structs: int) -> list[Structure]:
             )
             inv_org_latt = np.linalg.inv(original_latt.matrix)
         else:
-            ordered_structure = inv_org_latt = None
+            ordered_structure = None  # type: ignore[assignment]
+            inv_org_latt = None  # type: ignore[assignment]
 
         for file in glob("vasp.*"):
             with open(file, encoding="utf-8") as _file: