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]>

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:

pymatgen/cli/pmg_analyze.py

@@ -111,13 +111,13 @@ def get_magnetizations(dir: str, ion_list: list[int]):
                     fullpath = os.path.join(parent, file)
                     outcar = Outcar(fullpath)
                     mags = outcar.magnetization
-                    mags = [m["tot"] for m in mags]
-                    all_ions = list(range(len(mags)))
+                    _mags: list = [m["tot"] for m in mags]
+                    all_ions = list(range(len(_mags)))
                     row.append(fullpath.lstrip("./"))
                     if ion_list:
                         all_ions = ion_list
                     for ion in all_ions:
-                        row.append(str(mags[ion]))
+                        row.append(str(_mags[ion]))
                     data.append(row)
                     if len(all_ions) > max_row:
                         max_row = len(all_ions)

pymatgen/command_line/vampire_caller.py

@@ -131,8 +131,8 @@ def __init__(
 
         # Call Vampire
         with subprocess.Popen(["vampire-serial"], stdout=subprocess.PIPE, stderr=subprocess.PIPE) as process:
-            stdout, stderr = process.communicate()
-            stdout = stdout.decode()
+            _stdout, stderr = process.communicate()
+            stdout: str = _stdout.decode()
 
         if stderr:
             van_helsing = stderr.decode()

pymatgen/core/interface.py

@@ -244,7 +244,7 @@ def coincidents(self) -> list[Site]:
                 coincident_sites.append(self.sites[idx])
         return coincident_sites
 
-    def __str__(self):
+    def __str__(self) -> str:
         comp = self.composition
         outs = [
             f"Gb Summary ({comp.formula})",

pymatgen/core/structure.py

@@ -2860,7 +2860,7 @@ def from_str(  # type: ignore[override]
         elif fmt_low == "poscar":
             from pymatgen.io.vasp import Poscar
 
-            struct = Poscar.from_str(input_string, default_names=False, read_velocities=False, **kwargs).structure
+            struct = Poscar.from_str(input_string, default_names=None, read_velocities=False, **kwargs).structure
         elif fmt_low == "cssr":
             from pymatgen.io.cssr import Cssr
 

pymatgen/ext/cod.py

@@ -90,7 +90,7 @@ def get_structure_by_id(self, cod_id, **kwargs):
         Returns:
             A Structure.
         """
-        response = requests.get(f"http://{self.url}/cod/{cod_id}.cif")
+        response = requests.get(f"http://{self.url}/cod/{cod_id}.cif", timeout=60)
         return Structure.from_str(response.text, fmt="cif", **kwargs)
 
     @requires(which("mysql"), "mysql must be installed to use this query.")
@@ -112,7 +112,7 @@ def get_structure_by_formula(self, formula: str, **kwargs) -> list[dict[str, str
         for line in text:
             if line.strip():
                 cod_id, sg = line.split("\t")
-                response = requests.get(f"http://www.crystallography.net/cod/{cod_id.strip()}.cif")
+                response = requests.get(f"http://www.crystallography.net/cod/{cod_id.strip()}.cif", timeout=60)
                 try:
                     struct = Structure.from_str(response.text, fmt="cif", **kwargs)
                     structures.append({"structure": struct, "cod_id": int(cod_id), "sg": sg})

pymatgen/ext/matproj_legacy.py

@@ -1570,7 +1570,7 @@ def _check_get_download_info_url_by_task_id(self, prefix, task_ids) -> list[str]
 
     @staticmethod
     def _check_nomad_exist(url) -> bool:
-        response = requests.get(url=url)
+        response = requests.get(url=url, timeout=60)
         if response.status_code != 200:
             return False
         content = json.loads(response.text)

pymatgen/io/abinit/abitimer.py

@@ -85,11 +85,11 @@ def walk(cls, top=".", ext=".abo"):
     def __init__(self):
         """Initialize object."""
         # List of files that have been parsed.
-        self._filenames = []
+        self._filenames: list = []
 
         # timers[filename][mpi_rank]
         # contains the timer extracted from the file filename associated to the MPI rank mpi_rank.
-        self._timers = {}
+        self._timers: dict = {}
 
     def __iter__(self):
         return iter(self._timers)

pymatgen/io/abinit/pseudos.py

@@ -1033,10 +1033,10 @@ class PseudoParser:
 
     def __init__(self):
         # List of files that have been parsed successfully.
-        self._parsed_paths = []
+        self._parsed_paths: list = []
 
         # List of files that could not been parsed.
-        self._wrong_paths = []
+        self._wrong_paths: list = []
 
     def scan_directory(self, dirname, exclude_exts=(), exclude_fnames=()):
         """
@@ -1228,14 +1228,14 @@ def __init__(self, filepath):
         # In this way, we know that only the first two bound states (with f and n attributes)
         # should be used for constructing an initial guess for the wave functions.
 
-        self.valence_states = {}
+        self.valence_states: dict = {}
         for node in root.find("valence_states"):
             attrib = AttrDict(node.attrib)
             assert attrib.id not in self.valence_states
             self.valence_states[attrib.id] = attrib
 
         # Parse the radial grids
-        self.rad_grids = {}
+        self.rad_grids: dict = {}
         for node in root.findall("radial_grid"):
             grid_params = node.attrib
             gid = grid_params["id"]

pymatgen/io/cp2k/outputs.py

@@ -57,15 +57,15 @@ def __init__(self, filename, verbose=False, auto_load=False):
         # IO Info
         self.filename = filename
         self.dir = os.path.dirname(filename)
-        self.filenames = {}
+        self.filenames: dict = {}
         self.parse_files()
-        self.data = {}
+        self.data: dict = {}
 
         # Material properties/results
         self.input = self.initial_structure = self.lattice = self.final_structure = self.composition = None
         self.efermi = self.vbm = self.cbm = self.band_gap = None
-        self.structures = []
-        self.ionic_steps = []
+        self.structures: list = []
+        self.ionic_steps: list = []
 
         # parse the basic run parameters always
         self.parse_cp2k_params()
@@ -171,7 +171,7 @@ def calculation_type(self):
     @property
     def project_name(self) -> str:
         """What project name was used for this calculation."""
-        return self.data.get("global").get("project_name")
+        return self.data.get("global", {}).get("project_name")
 
     @property
     def spin_polarized(self) -> bool:
@@ -1259,12 +1259,12 @@ def parse_dos(self, dos_file=None, pdos_files=None, ldos_files=None):
             self.data["cdos"] = CompleteDos(self.final_structure, total_dos=tdos, pdoss=_ldoss)
 
     @property
-    def complete_dos(self) -> CompleteDos:
+    def complete_dos(self) -> CompleteDos | None:
         """Returns complete dos object if it has been parsed."""
         return self.data.get("cdos")
 
     @property
-    def band_structure(self) -> BandStructure:
+    def band_structure(self) -> BandStructure | None:
         """Returns band structure object if it has been parsed."""
         return self.data.get("band_structure")
 

pymatgen/io/pwscf.py

@@ -522,7 +522,7 @@ def __init__(self, filename):
             filename (str): Filename.
         """
         self.filename = filename
-        self.data = defaultdict(list)
+        self.data: dict[str, list[float] | float] = defaultdict(list)
         self.read_pattern(PWOutput.patterns)
         for k, v in self.data.items():
             if k == "energies":

pymatgen/io/qchem/inputs.py

@@ -243,8 +243,8 @@ def get_str(self) -> str:
         """Return a string representation of an entire input file."""
         return str(self)
 
-    def __str__(self):
-        combined_list = []
+    def __str__(self) -> str:
+        combined_list: list = []
         # molecule section
         combined_list.extend((self.molecule_template(self.molecule), "", self.rem_template(self.rem), ""))
         # opt section