Add type annotations for io.vasp.inputs/optics (#3740)

* some easy mypy fixes

* ruff check pymatgen/io/vasp --select ANN204 --unsafe-fixes --fix

* add type for io.vasp.help

* add timeout 60 sec for requests.get

* pre-commit auto-fixes

* add timeout 60 sec for requests.get

* fix default value of default_names

* finish poscar.from_str

* finish Poscar

* finish Incar

* temp save for potcarsingle

* put dunder methods close and to the top

* put properties close and to the top

* put properties close and to the top

* replace str with PathLike

* add types for optics

* suppress some overload

* remove None type from completely untyped classes

* pre-commit auto-fixes

* fix type error outside io.vasp

* check for None in Incar init

* ruff fix

* allow None

* fix types

* replace `defaultdict` with specific type

* revert accidental changes

* fix test

* fix tests

---------

Co-authored-by: Janosh Riebesell <[email protected]>

Author: DanielYang59

dev_scripts/update_pt_data.py

@@ -234,7 +234,7 @@ def gen_iupac_ordering():
 def add_electron_affinities():
     """Update the periodic table data file with electron affinities."""
 
-    req = requests.get("https://wikipedia.org/wiki/Electron_affinity_(data_page)")
+    req = requests.get("https://wikipedia.org/wiki/Electron_affinity_(data_page)", timeout=60)
     soup = BeautifulSoup(req.text, "html.parser")
     table = None
     for table in soup.find_all("table"):

pymatgen/alchemy/filters.py

@@ -244,7 +244,7 @@ def __init__(self, existing_structures, structure_matcher=None, symprec=None):
                 structure matcher is used. A recommended value is 1e-5.
         """
         self.symprec = symprec
-        self.structure_list = []
+        self.structure_list: list = []
         self.existing_structures = existing_structures
         if isinstance(structure_matcher, dict):
             self.structure_matcher = StructureMatcher.from_dict(structure_matcher)

pymatgen/alchemy/transmuters.py

@@ -244,7 +244,7 @@ def __init__(self, cif_string, transformations=None, primitive=True, extend_coll
         """
         transformed_structures = []
         lines = cif_string.split("\n")
-        structure_data = []
+        structure_data: list = []
         read_data = False
         for line in lines:
             if re.match(r"^\s*data", line):

pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -908,7 +908,7 @@ def __init__(self, permutations_safe_override=False, only_symbols=None):
 
         self.minpoints = {}
         self.maxpoints = {}
-        self.separations_cg = {}
+        self.separations_cg: dict[int, dict] = {}
         for cn in range(6, 21):
             for cg in self.get_implemented_geometries(coordination=cn):
                 if only_symbols is not None and cg.ce_symbol not in only_symbols:

pymatgen/analysis/chemenv/coordination_environments/structure_environments.py

@@ -2085,7 +2085,7 @@ def __init__(self, coord_geoms=None):
             coord_geoms: coordination geometries to be added to the chemical environment.
         """
         if coord_geoms is None:
-            self.coord_geoms = {}
+            self.coord_geoms: dict = {}
         else:
             raise NotImplementedError(
                 "Constructor for ChemicalEnvironments with the coord_geoms argument is not yet implemented"

pymatgen/analysis/ewald.py

@@ -540,7 +540,7 @@ def __init__(self, matrix, m_list, num_to_return=1, algo=ALGO_FAST):
         if algo == EwaldMinimizer.ALGO_COMPLETE:
             raise NotImplementedError("Complete algo not yet implemented for EwaldMinimizer")
 
-        self._output_lists = []
+        self._output_lists: list = []
         # Tag that the recurse function looks at each level. If a method
         # sets this to true it breaks the recursion and stops the search.
         self._finished = False

pymatgen/analysis/structure_prediction/substitution_probability.py

@@ -79,7 +79,7 @@ def __init__(self, lambda_table=None, alpha=-5):
 
         # create Z and px
         self.Z = 0
-        self._px = defaultdict(float)
+        self._px: dict[Species, float] = defaultdict(float)
         for s1, s2 in itertools.product(self.species, repeat=2):
             value = math.exp(self.get_lambda(s1, s2))
             self._px[s1] += value / 2

pymatgen/analysis/wulff.py

@@ -90,8 +90,8 @@ def __init__(self, normal, e_surf, normal_pt, dual_pt, index, m_ind_orig, miller
         self.index = index
         self.m_ind_orig = m_ind_orig
         self.miller = miller
-        self.points = []
-        self.outer_lines = []
+        self.points: list = []
+        self.outer_lines: list = []
 
 
 class WulffShape:

pymatgen/apps/battery/plotter.py

@@ -2,11 +2,16 @@
 
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import matplotlib.pyplot as plt
 import plotly.graph_objects as go
 
 from pymatgen.util.plotting import pretty_plot
 
+if TYPE_CHECKING:
+    from pymatgen.apps.battery.battery_abc import AbstractElectrode
+
 __author__ = "Shyue Ping Ong"
 __copyright__ = "Copyright 2012, The Materials Project"
 __version__ = "0.1"
@@ -18,7 +23,7 @@
 class VoltageProfilePlotter:
     """A plotter to make voltage profile plots for batteries."""
 
-    def __init__(self, xaxis="capacity", hide_negative=False):
+    def __init__(self, xaxis: str = "capacity", hide_negative: bool = False) -> None:
         """
         Args:
             xaxis: The quantity to use as the xaxis. Can be either
@@ -28,11 +33,11 @@ def __init__(self, xaxis="capacity", hide_negative=False):
             - frac_x: the atomic fraction of the working ion
             hide_negative: If True only plot the voltage steps above zero.
         """
-        self._electrodes = {}
+        self._electrodes: dict[str, AbstractElectrode] = {}
         self.xaxis = xaxis
         self.hide_negative = hide_negative
 
-    def add_electrode(self, electrode, label=None):
+    def add_electrode(self, electrode: AbstractElectrode, label: str | None = None) -> None:
         """Add an electrode to the plot.
 
         Args:
@@ -41,11 +46,11 @@ def add_electrode(self, electrode, label=None):
             label: A label for the electrode. If None, defaults to a counting
                 system, i.e. 'Electrode 1', 'Electrode 2', ...
         """
-        if not label:
+        if label is None:
             label = f"Electrode {len(self._electrodes) + 1}"
         self._electrodes[label] = electrode
 
-    def get_plot_data(self, electrode, term_zero=True):
+    def get_plot_data(self, electrode: AbstractElectrode, term_zero: bool = True) -> tuple[list, list]:
         """
         Args:
             electrode: Electrode object
@@ -82,7 +87,7 @@ def get_plot_data(self, electrode, term_zero=True):
             y.append(0)
         return x, y
 
-    def get_plot(self, width=8, height=8, term_zero=True, ax: plt.Axes = None):
+    def get_plot(self, width: float = 8, height: float = 8, term_zero: bool = True, ax: plt.Axes = None) -> plt.Axes:
         """Returns a plot object.
 
         Args:
@@ -112,12 +117,12 @@ def get_plot(self, width=8, height=8, term_zero=True, ax: plt.Axes = None):
 
     def get_plotly_figure(
         self,
-        width=800,
-        height=600,
-        font_dict=None,
-        term_zero=True,
+        width: float = 800,
+        height: float = 600,
+        font_dict: dict | None = None,
+        term_zero: bool = True,
         **kwargs,
-    ):
+    ) -> plt.Figure:
         """Return plotly Figure object.
 
         Args:
@@ -163,28 +168,28 @@ def get_plotly_figure(
         fig.update_layout(template="plotly_white", title_x=0.5)
         return fig
 
-    def _choose_best_x_label(self, formula, work_ion_symbol):
+    def _choose_best_x_label(self, formula: set[str], work_ion_symbol: set[str]) -> str:
         if self.xaxis in {"capacity", "capacity_grav"}:
             return "Capacity (mAh/g)"
         if self.xaxis == "capacity_vol":
             return "Capacity (Ah/l)"
 
-        formula = formula.pop() if len(formula) == 1 else None
+        _formula: str | None = formula.pop() if len(formula) == 1 else None
 
-        work_ion_symbol = work_ion_symbol.pop() if len(work_ion_symbol) == 1 else None
+        _work_ion_symbol: str | None = work_ion_symbol.pop() if len(work_ion_symbol) == 1 else None
 
         if self.xaxis == "x_form":
-            if formula and work_ion_symbol:
-                return f"x in {work_ion_symbol}<sub>x</sub>{formula}"
+            if _formula and _work_ion_symbol:
+                return f"x in {_work_ion_symbol}<sub>x</sub>{_formula}"
             return "x Work Ion per Host F.U."
 
         if self.xaxis == "frac_x":
-            if work_ion_symbol:
-                return f"Atomic Fraction of {work_ion_symbol}"
+            if _work_ion_symbol:
+                return f"Atomic Fraction of {_work_ion_symbol}"
             return "Atomic Fraction of Working Ion"
         raise RuntimeError("No xaxis label can be determined")
 
-    def show(self, width=8, height=6):
+    def show(self, width: float = 8, height: float = 6) -> None:
         """Show the voltage profile plot.
 
         Args:

pymatgen/apps/borg/queen.py

@@ -44,7 +44,7 @@ def __init__(self, drone, rootpath=None, number_of_drones=1):
         """
         self._drone = drone
         self._num_drones = number_of_drones
-        self._data = []
+        self._data: list = []
 
         if rootpath:
             if number_of_drones > 1: