fix missing arguments in doc strings in pymatgen/entries

remove unused verbose flag from get_mixing_state_data()

metadata.yml

@@ -430,7 +430,7 @@ developers:
   first_name: Francesco
   last_name: Ricci
   orcid: 0000-0002-2677-7227
-- affiliations: [University of Cambridge]
+- affiliations: [University of Cambridge, Lawrence Berkeley National Laboratory]
   first_name: Janosh
   last_name: Riebesell
   orcid: 0000-0001-5233-3462

pymatgen/analysis/adsorption.py

@@ -207,11 +207,11 @@ def get_extended_surface_mesh(self, repeat=(5, 5, 1)):
 
     @property
     def surface_sites(self):
-        """convenience method to return a list of surface sites."""
+        """Convenience method to return a list of surface sites."""
         return [site for site in self.slab.sites if site.properties["surface_properties"] == "surface"]
 
     def subsurface_sites(self):
-        """convenience method to return list of subsurface sites."""
+        """Convenience method to return list of subsurface sites."""
         return [site for site in self.slab.sites if site.properties["surface_properties"] == "subsurface"]
 
     def find_adsorption_sites(
@@ -607,13 +607,13 @@ def get_rot(slab):
 
 
 def put_coord_inside(lattice, cart_coordinate):
-    """converts a Cartesian coordinate such that it is inside the unit cell."""
+    """Converts a Cartesian coordinate such that it is inside the unit cell."""
     fc = lattice.get_fractional_coords(cart_coordinate)
     return lattice.get_cartesian_coords([c - np.floor(c) for c in fc])
 
 
 def reorient_z(structure):
-    """reorients a structure such that the z axis is concurrent with the normal
+    """Reorients a structure such that the z axis is concurrent with the normal
     to the A-B plane.
     """
     struct = structure.copy()

pymatgen/analysis/wulff.py

@@ -424,9 +424,8 @@ def get_plot(
         import matplotlib.pyplot as plt
         import mpl_toolkits.mplot3d as mpl3
 
-        color_list, color_proxy, color_proxy_on_wulff, miller_on_wulff, e_surf_on_wulff = self._get_colors(
-            color_set, alpha, off_color, custom_colors=custom_colors or {}
-        )
+        colors = self._get_colors(color_set, alpha, off_color, custom_colors=custom_colors or {})
+        color_list, color_proxy, color_proxy_on_wulff, miller_on_wulff, e_surf_on_wulff = colors
 
         if not direction:
             # If direction is not specified, use the miller indices of
@@ -485,11 +484,9 @@ def get_plot(
                     fancybox=True,
                     shadow=False,
                 )
-        ax.set_xlabel("x")
-        ax.set_ylabel("y")
-        ax.set_zlabel("z")
+        ax.set(xlabel="x", ylabel="y", zlabel="z")
 
-        # Add colorbar
+        # Add color bar
         if bar_on:
             cmap = plt.get_cmap(color_set)
             cmap.set_over("0.25")
@@ -503,7 +500,7 @@ def get_plot(
                 ax1,
                 cmap=cmap,
                 norm=norm,
-                boundaries=[0, *bounds] + [10],
+                boundaries=[0, *bounds, 10],
                 extend="both",
                 ticks=bounds[:-1],
                 spacing="proportional",

pymatgen/entries/compatibility.py

@@ -541,6 +541,7 @@ def process_entry(self, entry: ComputedEntry, **kwargs) -> ComputedEntry | None:
 
         Args:
             entry: A ComputedEntry object.
+            **kwargs: Will be passed to process_entries().
 
         Returns:
             An adjusted entry if entry is compatible, else None.
@@ -564,15 +565,14 @@ def process_entries(
         restored by setting entry.energy_adjustments = [].
 
         Args:
-            entries list[ComputedEntry | ComputedStructureEntry]: A sequence of
+            entries (AnyComputedEntry | list[AnyComputedEntry]): A sequence of
                 Computed(Structure)Entry objects.
             clean (bool): Whether to remove any previously-applied energy adjustments.
                 If True, all EnergyAdjustment are removed prior to processing the Entry.
-                Default is True.
+                Defaults to True.
             verbose (bool): Whether to display progress bar for processing multiple entries.
-                Default is False.
-            inplace (bool): Whether to adjust input entries in place.
-                Default is True.
+                Defaults to False.
+            inplace (bool): Whether to adjust input entries in place. Defaults to True.
 
         Returns:
             list[AnyComputedEntry]: Adjusted entries. Entries in the original list incompatible with
@@ -1407,6 +1407,8 @@ def process_entries(
                 Default is False.
             verbose (bool): Whether to display progress bar for processing multiple entries.
                 Default is False.
+            inplace (bool): Whether to modify the entries in place. If False, a copy of the
+                entries is made and processed. Default is True.
 
         Returns:
             list[AnyComputedEntry]: Adjusted entries. Entries in the original list incompatible with

pymatgen/entries/computed_entries.py

@@ -753,7 +753,10 @@ def __init__(
             gibbs_model ('SISSO'): Model for Gibbs Free energy. "SISSO", the descriptor
                 created by Bartel et al. (2018) -- see reference in documentation, is
                 currently the only supported) option.
-            correction (float): A correction to be applied to the energy. Defaults to 0
+            composition (Composition): The composition of the entry. Defaults to None.
+            correction (float): A correction to be applied to the energy. Defaults to 0.
+            energy_adjustments (list): A list of energy adjustments to be applied to
+                the energy. Defaults to None.
             parameters (dict): An optional dict of parameters associated with
                 the entry. Defaults to None.
             data (dict): An optional dict of any additional data associated
@@ -910,9 +913,9 @@ def _g_delta_sisso(vol_per_atom, reduced_mass, temp) -> float:
 
         Args:
             vol_per_atom (float): volume per atom [Å^3/atom]
-            reduced_mass (float) - reduced mass as calculated with pair-wise sum formula
+            reduced_mass (float): as calculated with pair-wise sum formula
                 [amu]
-            temp (float) - Temperature [K]
+            temp (float): Temperature [K]
 
         Returns:
             float: G^delta [eV/atom]

pymatgen/entries/mixing_scheme.py

@@ -183,7 +183,7 @@ def process_entries(
         if mixing_state_data is None:
             if verbose:
                 print("  Generating mixing state data from provided entries.")
-            mixing_state_data = self.get_mixing_state_data(entries_type_1 + entries_type_2, verbose=False)
+            mixing_state_data = self.get_mixing_state_data(entries_type_1 + entries_type_2)
 
         if verbose:
             # how many stable entries from run_type_1 do we have in run_type_2?
@@ -458,7 +458,7 @@ def get_adjustments(self, entry, mixing_state_data: pd.DataFrame = None):
                 f"an edge case in {type(self).__name__}. Inspect your input carefully and post a bug report."
             )
 
-    def get_mixing_state_data(self, entries: list[ComputedStructureEntry], verbose: bool = False):
+    def get_mixing_state_data(self, entries: list[ComputedStructureEntry]):
         """
         Generate internal state data to be passed to get_adjustments.
 

pymatgen/io/abinit/abiobjects.py

@@ -497,7 +497,7 @@ def to_abivars(self):
         return {"occopt": self.occopt, "tsmear": self.tsmear}
 
     def as_dict(self):
-        """json friendly dict representation of Smearing"""
+        """JSON-friendly dict representation of Smearing"""
         return {
             "@module": type(self).__module__,
             "@class": type(self).__name__,
@@ -599,7 +599,7 @@ def nspden(self):
         return self.spin_mode.nspden
 
     def as_dict(self):
-        """json friendly dict representation"""
+        """Json friendly dict representation"""
         d = {}
         d["@module"] = type(self).__module__
         d["@class"] = type(self).__name__

pymatgen/io/abinit/inputs.py

@@ -1176,7 +1176,7 @@ def on_all(*args, **kwargs):
         return on_all
 
     def __add__(self, other):
-        """self + other"""
+        """Self + other"""
         if isinstance(other, BasicAbinitInput):
             new_mds = BasicMultiDataset.from_inputs(self)
             new_mds.append(other)

pymatgen/io/feff/outputs.py

@@ -225,7 +225,7 @@ def charge_transfer_from_file(feff_inp_file, ldos_file):
         return cht
 
     def charge_transfer_to_string(self):
-        """returns shrage transfer as string"""
+        """Returns charge transfer as string"""
         ch = self.charge_transfer
         chts = ["\nCharge Transfer\n\nabsorbing atom"]
         for i in range(len(ch)):

pymatgen/io/gaussian.py

@@ -1246,7 +1246,7 @@ def read_scan(self):
         """
 
         def floatList(lst):
-            """return a list of float from a list of string"""
+            """Return a list of float from a list of string"""
             return [float(val) for val in lst]
 
         scan_patt = re.compile(r"^\sSummary of the potential surface scan:")