fix missing types in doc string args

Author: janosh

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