fix missing types in doc string args

src/pymatgen/alchemy/filters.py

@@ -43,7 +43,7 @@ class ContainsSpecieFilter(AbstractStructureFilter):
     def __init__(self, species, strict_compare=False, AND=True, exclude=False):
         """
         Args:
-            species ([Species/Element]): list of species to look for
+            species (list[SpeciesLike]): species to look for
             AND: whether all species must be present to pass (or fail) filter.
             strict_compare: if true, compares objects by specie or element
                 object if false, compares atomic number
@@ -157,7 +157,7 @@ def from_dict(cls, dct: dict) -> Self:
             dct (dict): Dict representation.
 
         Returns:
-            Filter
+            SpecieProximityFilter
         """
         return cls(**dct["init_args"])
 

src/pymatgen/alchemy/materials.py

@@ -366,13 +366,13 @@ def to_snl(self, authors: list[str], **kwargs) -> StructureNL:
         history = []
         for hist in self.history:
             snl_metadata = hist.pop("_snl", {})
-            history.append(
+            history += [
                 {
                     "name": snl_metadata.pop("name", "pymatgen"),
                     "url": snl_metadata.pop("url", "http://pypi.python.org/pypi/pymatgen"),
                     "description": hist,
                 }
-            )
+            ]
 
         return StructureNL(self.final_structure, authors, history=history, **kwargs)
 

src/pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -373,14 +373,15 @@ def __len__(self):
     def compute_periodicity(self, algorithm="all_simple_paths") -> None:
         """
         Args:
-            algorithm ():
+            algorithm (str): Algorithm to use to compute the periodicity vectors. Can be
+                either "all_simple_paths" or "cycle_basis".
         """
         if algorithm == "all_simple_paths":
             self.compute_periodicity_all_simple_paths_algorithm()
         elif algorithm == "cycle_basis":
             self.compute_periodicity_cycle_basis()
         else:
-            raise ValueError(f"Algorithm {algorithm!r} is not allowed to compute periodicity")
+            raise ValueError(f"{algorithm=} is not allowed to compute periodicity")
         self._order_periodicity_vectors()
 
     def compute_periodicity_all_simple_paths_algorithm(self):
@@ -513,7 +514,7 @@ def compute_periodicity_cycle_basis(self) -> None:
     def make_supergraph(self, multiplicity):
         """
         Args:
-            multiplicity ():
+            multiplicity (int): Multiplicity of the super graph.
 
         Returns:
             nx.MultiGraph: Super graph of the connected component.
@@ -636,7 +637,8 @@ def periodicity(self):
     def elastic_centered_graph(self, start_node=None):
         """
         Args:
-            start_node ():
+            start_node (Node, optional): Node to start the elastic centering from.
+                If not provided, the first node in the graph is used.
 
         Returns:
             nx.MultiGraph: Elastic centered subgraph.

src/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py

@@ -76,8 +76,8 @@ def __init__(
     def environment_subgraph(self, environments_symbols=None, only_atoms=None):
         """
         Args:
-            environments_symbols ():
-            only_atoms ():
+            environments_symbols (list[str]): symbols of the environments to consider.
+            only_atoms (list[str]): atoms to consider.
 
         Returns:
             nx.MultiGraph: The subgraph of the structure connectivity graph
@@ -187,8 +187,8 @@ def setup_environment_subgraph(self, environments_symbols, only_atoms=None):
                         )
                         self._environment_subgraph.add_node(env_node)
                 else:
-                    #  TODO: add the possibility of a "constraint" on the minimum percentage
-                    #        of the atoms on the site
+                    # TODO add the possibility of a "constraint" on the minimum percentage
+                    # of the atoms on the site
                     this_site_elements = [
                         sp.symbol for sp in self.light_structure_environments.structure[isite].species_and_occu
                     ]

src/pymatgen/analysis/cost.py

@@ -118,10 +118,10 @@ def __init__(self):
 class CostAnalyzer:
     """Given a CostDB, figures out the minimum cost solutions via convex hull."""
 
-    def __init__(self, costdb):
+    def __init__(self, costdb: CostDB) -> None:
         """
         Args:
-            costdb (): Cost database.
+            costdb (CostDB): Cost database to use.
         """
         self.costdb = costdb
 

src/pymatgen/analysis/diffraction/xrd.py

@@ -101,7 +101,7 @@ def __init__(self, wavelength="CuKa", symprec: float = 0, debye_waller_factors=N
         """Initialize the XRD calculator with a given radiation.
 
         Args:
-            wavelength (str/float): The wavelength can be specified as either a
+            wavelength (str | float): The wavelength can be specified as either a
                 float or a string. If it is a string, it must be one of the
                 supported definitions in the AVAILABLE_RADIATION class
                 variable, which provides useful commonly used wavelengths.

src/pymatgen/analysis/elasticity/elastic.py

@@ -55,9 +55,9 @@ class NthOrderElasticTensor(Tensor):
     def __new__(cls, input_array, check_rank=None, tol: float = 1e-4) -> Self:
         """
         Args:
-            input_array ():
-            check_rank ():
-            tol ():
+            input_array (np.ndarray): input array for tensor
+            check_rank (int): rank of tensor to check
+            tol (float): tolerance for initial symmetry test of tensor
         """
         obj = super().__new__(cls, input_array, check_rank=check_rank)
         if obj.rank % 2 != 0:
@@ -524,7 +524,7 @@ class ComplianceTensor(Tensor):
     def __new__(cls, s_array) -> Self:
         """
         Args:
-            s_array ():
+            s_array (np.ndarray): input array for tensor
         """
         vscale = np.ones((6, 6))
         vscale[3:] *= 2

src/pymatgen/analysis/eos.py

@@ -38,8 +38,8 @@ class EOSBase(ABC):
     def __init__(self, volumes, energies):
         """
         Args:
-            volumes (list/numpy.array): volumes in Ang^3
-            energies (list/numpy.array): energy in eV.
+            volumes (Sequence[float]): in Ang^3.
+            energies (Sequence[float]): in eV.
         """
         self.volumes = np.array(volumes)
         self.energies = np.array(energies)
@@ -561,8 +561,8 @@ def fit(self, volumes, energies):
         """Fit energies as function of volumes.
 
         Args:
-            volumes (list/np.array)
-            energies (list/np.array)
+            volumes (Sequence[float]): in Ang^3
+            energies (Sequence[float]): in eV
 
         Returns:
             EOSBase: EOSBase object

src/pymatgen/analysis/molecule_structure_comparator.py

@@ -194,7 +194,7 @@ def are_equal(self, mol1, mol2) -> bool:
     def get_13_bonds(priority_bonds):
         """
         Args:
-            priority_bonds ():
+            priority_bonds (list[tuple]): 12 bonds
 
         Returns:
             tuple: 13 bonds

src/pymatgen/analysis/nmr.py

@@ -122,9 +122,9 @@ def from_maryland_notation(cls, sigma_iso, omega, kappa) -> Self:
         Initialize from Maryland notation.
 
         Args:
-            sigma_iso ():
-            omega ():
-            kappa ():
+            sigma_iso (float): isotropic chemical shielding
+            omega (float): anisotropy
+            kappa (float): asymmetry parameter
 
         Returns:
             ChemicalShielding

src/pymatgen/analysis/pourbaix_diagram.py

@@ -85,10 +85,9 @@ class PourbaixEntry(MSONable, Stringify):
     def __init__(self, entry, entry_id=None, concentration=1e-6):
         """
         Args:
-            entry (ComputedEntry/ComputedStructureEntry/PDEntry/IonEntry): An
-                entry object
-            entry_id ():
-            concentration ():
+            entry (ComputedEntry | ComputedStructureEntry | PDEntry | IonEntry): An entry object
+            entry_id (str): A string id for the entry
+            concentration (float): Concentration of the entry in M. Defaults to 1e-6.
         """
         self.entry = entry
         if isinstance(entry, IonEntry):
@@ -102,7 +101,7 @@ def __init__(self, entry, entry_id=None, concentration=1e-6):
         self.uncorrected_energy = entry.energy
         if entry_id is not None:
             self.entry_id = entry_id
-        elif hasattr(entry, "entry_id") and entry.entry_id:
+        elif getattr(entry, "entry_id", None):
             self.entry_id = entry.entry_id
         else:
             self.entry_id = None

src/pymatgen/analysis/reaction_calculator.py

@@ -139,7 +139,7 @@ def normalize_to_element(self, element: Species | Element, factor: float = 1) ->
         Another factor can be specified.
 
         Args:
-            element (Element/Species): Element to normalize to.
+            element (SpeciesLike): Element to normalize to.
             factor (float): Factor to normalize to. Defaults to 1.
         """
         all_comp = self._all_comp
@@ -152,7 +152,7 @@ def get_el_amount(self, element: Element | Species) -> float:
         """Get the amount of the element in the reaction.
 
         Args:
-            element (Element/Species): Element in the reaction
+            element (SpeciesLike): Element in the reaction
 
         Returns:
             Amount of that element in the reaction.

src/pymatgen/analysis/structure_prediction/substitution_probability.py

@@ -20,6 +20,8 @@
 if TYPE_CHECKING:
     from typing_extensions import Self
 
+    from pymatgen.util.typing import SpeciesLike
+
 __author__ = "Will Richards, Geoffroy Hautier"
 __copyright__ = "Copyright 2012, The Materials Project"
 __version__ = "1.2"
@@ -84,22 +86,22 @@ def __init__(self, lambda_table=None, alpha=-5):
     def get_lambda(self, s1, s2):
         """
         Args:
-            s1 (Element/Species/str/int): Describes Ion in 1st Structure
-            s2 (Element/Species/str/int): Describes Ion in 2nd Structure.
+            s1 (SpeciesLike): Ion in 1st structure.
+            s2 (SpeciesLike): Ion in 2nd structure.
 
         Returns:
             Lambda values
         """
         key = frozenset([get_el_sp(s1), get_el_sp(s2)])
         return self._l.get(key, self.alpha)
 
-    def get_px(self, sp):
+    def get_px(self, sp: SpeciesLike) -> float:
         """
         Args:
-            sp (Species/Element): Species.
+            sp (SpeciesLike): Species.
 
         Returns:
-            Probability
+            float: Probability
         """
         return self._px[get_el_sp(sp)]
 
@@ -185,7 +187,7 @@ class SubstitutionPredictor:
     def __init__(self, lambda_table=None, alpha=-5, threshold=1e-3):
         """
         Args:
-            lambda_table (): Input lambda table.
+            lambda_table (dict): Input lambda table.
             alpha (float): weight function for never observed substitutions
             threshold (float): Threshold to use to identify high probability structures.
         """

src/pymatgen/core/composition.py

@@ -507,7 +507,7 @@ def get_atomic_fraction(self, el: SpeciesLike) -> float:
         """Calculate atomic fraction of an Element or Species.
 
         Args:
-            el (Element/Species): Element or Species to get fraction for.
+            el (SpeciesLike): Element or Species to get fraction for.
 
         Returns:
             Atomic fraction for element el in Composition

src/pymatgen/core/interface.py

@@ -83,8 +83,8 @@ def __init__(
         """A Structure with additional information and methods pertaining to GBs.
 
         Args:
-            lattice (Lattice/3x3 array): The lattice, either as an instance or
-                any 2D array. Each row should correspond to a lattice vector.
+            lattice (Lattice | np.ndarray): The lattice, either as an instance or
+                a 3x3 array. Each row should correspond to a lattice vector.
             species ([Species]): Sequence of species on each site. Can take in
                 flexible input, including:
 
@@ -2390,7 +2390,7 @@ def symm_group_cubic(mat: NDArray) -> list:
     """Obtain cubic symmetric equivalents of the list of vectors.
 
     Args:
-        mat (n by 3 array/matrix): lattice matrix
+        mat (np.ndarray): n x 3 lattice matrix
 
 
     Returns:
@@ -2451,9 +2451,8 @@ def __init__(
         and methods pertaining to interfaces.
 
         Args:
-            lattice (Lattice/3x3 array): The lattice, either as a
-                pymatgen.core.Lattice or
-                simply as any 2D array. Each row should correspond to a lattice
+            lattice (Lattice | np.ndarray): The lattice, either as a pymatgen.core.Lattice
+                or a 3x3 array. Each row should correspond to a lattice
                 vector. e.g. [[10,0,0], [20,10,0], [0,0,30]] specifies a
                 lattice with lattice vectors [10,0,0], [20,10,0] and [0,0,30].
             species ([Species]): Sequence of species on each site. Can take in

src/pymatgen/core/periodic_table.py

@@ -1609,9 +1609,8 @@ def get_el_sp(obj: int | SpeciesLike) -> Element | Species | DummySpecies:
     will be attempted.
 
     Args:
-        obj (Element/Species/str/int): An arbitrary object. Supported objects
-            are actual Element/Species objects, integers (representing atomic
-            numbers) or strings (element symbols or species strings).
+        obj (SpeciesLike): An arbitrary object. Supported objects are actual Element/Species,
+            integers (representing atomic numbers) or strings (element symbols or species strings).
 
     Raises:
         ValueError: if obj cannot be converted into an Element or Species.

src/pymatgen/core/structure.py

@@ -1256,7 +1256,7 @@ def from_spacegroup(
         are generated from the spacegroup operations.
 
         Args:
-            sg (str/int): The spacegroup. If a string, it will be interpreted
+            sg (str | int): The spacegroup. If a string, it will be interpreted
                 as one of the notations supported by
                 pymatgen.symmetry.groups.Spacegroup. e.g. "R-3c" or "Fm-3m".
                 If an int, it will be interpreted as an international number.
@@ -1545,7 +1545,7 @@ def matches(
         Basically a convenience method to call structure matching.
 
         Args:
-            other (IStructure/Structure): Another structure.
+            other (IStructure | Structure): Another structure.
             anonymous (bool): Whether to use anonymous structure matching which allows distinct
                 species in one structure to map to another.
             **kwargs: Same **kwargs as in
@@ -1816,7 +1816,7 @@ def get_symmetric_neighbor_list(
 
         Args:
             r (float): Radius of sphere
-            sg (str/int): The spacegroup the symmetry operations of which will be
+            sg (str | int): The spacegroup the symmetry operations of which will be
                 used to classify the neighbors. If a string, it will be interpreted
                 as one of the notations supported by
                 pymatgen.symmetry.groups.Spacegroup. e.g. "R-3c" or "Fm-3m".

src/pymatgen/io/cssr.py

@@ -32,7 +32,7 @@ class Cssr:
     def __init__(self, structure: Structure):
         """
         Args:
-            structure (Structure/IStructure): A structure to create the Cssr object.
+            structure (Structure | IStructure): A structure to create the Cssr object.
         """
         if not structure.is_ordered:
             raise ValueError("Cssr file can only be constructed from ordered structure")

src/pymatgen/io/feff/inputs.py

@@ -375,7 +375,7 @@ def __init__(self, struct, absorbing_atom, radius):
         """
         Args:
             struct (Structure): input structure
-            absorbing_atom (str/int): Symbol for absorbing atom or site index
+            absorbing_atom (str | int): Symbol for absorbing atom or site index
             radius (float): radius of the atom cluster in Angstroms.
         """
         if not struct.is_ordered:
@@ -778,7 +778,7 @@ def __init__(self, struct, absorbing_atom):
         """
         Args:
             struct (Structure): Structure object.
-            absorbing_atom (str/int): Absorbing atom symbol or site index.
+            absorbing_atom (str | int): Absorbing atom symbol or site index.
         """
         if not struct.is_ordered:
             raise ValueError("Structure with partial occupancies cannot be converted into atomic coordinates!")
@@ -984,7 +984,7 @@ def get_absorbing_atom_symbol_index(absorbing_atom, structure):
     """Get the absorbing atom symbol and site index in the given structure.
 
     Args:
-        absorbing_atom (str/int): symbol or site index
+        absorbing_atom (str | int): symbol or site index
         structure (Structure)
 
     Returns: