fix double spaces in doc strings

found with regex \b\s{2,}\b[^\d]

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -51,7 +51,9 @@ def __init__(self, initial_environment_symbol, expected_final_environment_symbol
         self.abstract_geometry = AbstractGeometry.from_cg(self.coordination_geometry)
 
     @classmethod
-    def simple_expansion(cls, initial_environment_symbol, expected_final_environment_symbol, neighbors_indices):
+    def simple_expansion(
+        cls, initial_environment_symbol, expected_final_environment_symbol, neighbors_indices
+    ) -> CoordinationEnvironmentMorphing:
         """Simple expansion of a coordination environment.
 
         Args:

dev_scripts/update_spacegroup_data.py

@@ -30,7 +30,7 @@ def convert_symmops_to_sg_encoding(symbol: str) -> str:
     Args:
         symbol (str): "hermann_mauguin" or "universal_h_m" key of symmops.json
     Returns:
-        symbol in the format of SYMM_DATA["space_group_encoding"] keys
+        str: symbol in the format of SYMM_DATA["space_group_encoding"] keys
     """
     symbol_representation = symbol.split(":")
     representation = ":" + "".join(symbol_representation[1].split(" ")) if len(symbol_representation) > 1 else ""
@@ -51,7 +51,7 @@ def remove_identity_from_full_hermann_mauguin(symbol: str) -> str:
     Args:
         symbol (str): "hermann_mauguin" key of symmops.json
     Returns:
-        short "hermann_mauguin" key
+        str: short "hermann_mauguin" key
     """
     if symbol in ("P 1", "C 1", "P 1 "):
         return symbol

src/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py

@@ -373,7 +373,7 @@ def from_dict(cls, dct, structure: Structure, detailed_voronoi) -> Self:
             the structure and the DetailedVoronoiContainer.
 
             As an inner (nested) class, the NeighborsSet is not supposed to be used anywhere else that inside the
-            StructureEnvironments. The from_dict method is thus using the structure and  detailed_voronoi when
+            StructureEnvironments. The from_dict method is thus using the structure and detailed_voronoi when
             reconstructing itself. These two are both in the StructureEnvironments object.
 
             Args:

src/pymatgen/analysis/interface_reactions.py

@@ -111,7 +111,7 @@ def __init__(
 
         # Factor is the compositional ratio between composition self.c1 and
         # processed composition self.comp1. For example, the factor for
-        # Composition('SiO2') and  Composition('O') is 2.0. This factor will be used
+        # Composition('SiO2') and Composition('O') is 2.0. This factor will be used
         # to convert mixing ratio in self.comp1 - self.comp2 tie line to that in
         # self.c1 - self.c2 tie line.
         self.factor1 = 1.0

src/pymatgen/analysis/local_env.py

@@ -1984,7 +1984,7 @@ def get_okeeffe_distance_prediction(el1, el2):
     """Get an estimate of the bond valence parameter (bond length) using
     the derived parameters from 'Atoms Sizes and Bond Lengths in Molecules
     and Crystals' (O'Keeffe & Brese, 1991). The estimate is based on two
-    experimental parameters: r and c. The value for r  is based off radius,
+    experimental parameters: r and c. The value for r is based off radius,
     while c is (usually) the Allred-Rochow electronegativity. Values used
     are *not* generated from pymatgen, and are found in
     'okeeffe_params.json'.

src/pymatgen/analysis/magnetism/analyzer.py

@@ -476,7 +476,7 @@ def ordering(self) -> Ordering:
         ferro/ferrimagnetic is self.threshold_ordering and defaults to 1e-8.
 
         Returns:
-            Ordering: Enum  with values FM: ferromagnetic, FiM: ferrimagnetic,
+            Ordering: Enum with values FM: ferromagnetic, FiM: ferrimagnetic,
                 AFM: antiferromagnetic, NM: non-magnetic or Unknown. Unknown is
                 returned if magnetic moments are not defined or structure is not collinear
                 (in which case a warning is issued).

src/pymatgen/analysis/molecule_matcher.py

@@ -589,7 +589,7 @@ def fit(self, mol1, mol2):
             mol2: Second molecule. OpenBabel OBMol or pymatgen Molecule object
 
         Returns:
-            bool: Whether two molecules are the same.
+            bool: True if two molecules are the same.
         """
         return self.get_rmsd(mol1, mol2) < self._tolerance
 
@@ -598,7 +598,7 @@ def get_rmsd(self, mol1, mol2):
 
         Returns:
             RMSD if topology of the two molecules are the same
-            Infinite if  the topology is different
+            Infinite if the topology is different
         """
         label1, label2 = self._mapper.uniform_labels(mol1, mol2)
         if label1 is None or label2 is None:

src/pymatgen/analysis/phase_diagram.py

@@ -853,7 +853,7 @@ def get_decomp_and_phase_separation_energy(
             **kwargs: Passed to get_decomp_and_e_above_hull.
 
         Returns:
-            tuple[decomp, energy]: The decomposition  is given as a dict of {PDEntry, amount}
+            tuple[decomp, energy]: The decomposition is given as a dict of {PDEntry, amount}
                 for all entries in the decomp reaction where amount is the amount of the
                 fractional composition. The phase separation energy is given per atom.
         """
@@ -1547,7 +1547,7 @@ class PatchedPhaseDiagram(PhaseDiagram):
             Note that this does not mean that all these entries are actually used in
             the phase diagram. For example, this includes the positive formation energy
             entries that are filtered out before Phase Diagram construction.
-        min_entries (list[PDEntry]): List of the  lowest energy entries for each composition
+        min_entries (list[PDEntry]): List of the lowest energy entries for each composition
             in the data provided for Phase Diagram construction.
         el_refs (list[PDEntry]): List of elemental references for the phase diagrams.
             These are entries corresponding to the lowest energy element entries for

src/pymatgen/analysis/quasiharmonic.py

@@ -146,7 +146,7 @@ def optimize_gibbs_free_energy(self):
     def optimizer(self, temperature):
         """Evaluate G(V, T, P) at the given temperature(and pressure) and minimize it w.r.t. V.
 
-        1. Compute the  vibrational Helmholtz free energy, A_vib.
+        1. Compute the vibrational Helmholtz free energy, A_vib.
         2. Compute the Gibbs free energy as a function of volume, temperature
             and pressure, G(V,T,P).
         3. Perform an equation of state fit to get the functional form of
@@ -248,7 +248,7 @@ def debye_temperature(self, volume: float) -> float:
     @staticmethod
     def debye_integral(y):
         """
-        Debye integral. Eq(5) in  doi.org/10.1016/j.comphy.2003.12.001.
+        Debye integral. Eq(5) in doi.org/10.1016/j.comphy.2003.12.001.
 
         Args:
             y (float): Debye temperature / T, upper limit

src/pymatgen/analysis/structure_matcher.py

@@ -53,7 +53,7 @@ def are_equal(self, sp1, sp2) -> bool:
                 definition in Site and PeriodicSite.
 
         Returns:
-            bool: Whether species are considered equal.
+            bool: True if species are considered equal.
         """
         return False
 
@@ -122,7 +122,7 @@ def are_equal(self, sp1, sp2) -> bool:
                 definition in Site and PeriodicSite.
 
         Returns:
-            bool: Whether species are equal.
+            bool: True if species are equal.
         """
         return sp1 == sp2
 
@@ -151,7 +151,7 @@ def are_equal(self, sp1, sp2) -> bool:
                 definition in Site and PeriodicSite.
 
         Returns:
-            bool: Whether species are equal.
+            bool: True if species are equal.
         """
         for s1 in sp1:
             spin1 = getattr(s1, "spin", 0) or 0
@@ -188,7 +188,7 @@ def are_equal(self, sp1, sp2) -> bool:
                 definition in Site and PeriodicSite.
 
         Returns:
-            bool: Whether species are the same based on element and amounts.
+            bool: True if species are the same based on element and amounts.
         """
         comp1 = Composition(sp1)
         comp2 = Composition(sp2)
@@ -1051,7 +1051,7 @@ def fit_anonymous(
                 If True, skip to get a primitive structure and perform Niggli reduction for struct1 and struct2
 
         Returns:
-            bool: Whether a species mapping can map struct1 to struct2
+            bool: True if a species mapping can map struct1 to struct2
         """
         struct1, struct2 = self._process_species([struct1, struct2])
         struct1, struct2, fu, s1_supercell = self._preprocess(struct1, struct2, niggli, skip_structure_reduction)

src/pymatgen/core/bonds.py

@@ -103,7 +103,7 @@ def is_bonded(
                 bond length. If None, a ValueError will be thrown.
 
         Returns:
-            bool: whether two sites are bonded.
+            bool: True if two sites are bonded.
         """
         sp1 = next(iter(site1.species))
         sp2 = next(iter(site2.species))

src/pymatgen/core/composition.py

@@ -536,7 +536,7 @@ def contains_element_type(self, category: str) -> bool:
                 "actinoid", "radioactive", "quadrupolar", "s-block", "p-block", "d-block", "f-block".
 
         Returns:
-            bool: Whether any elements in Composition match category.
+            bool: True if any elements in Composition match category.
         """
         allowed_categories = [element.value for element in ElementType]
 

src/pymatgen/core/interface.py

@@ -1768,7 +1768,7 @@ def enum_sigma_ort(
                 e.g. mu:lam:mv = c2,None,a2, means b2 is irrational.
 
         Returns:
-            dict: sigmas  dictionary with keys as the possible integer sigma values
+            dict: sigmas dictionary with keys as the possible integer sigma values
                 and values as list of the possible rotation angles to the
                 corresponding sigma values. e.g. the format as
                 {sigma1: [angle11,angle12,...], sigma2: [angle21, angle22,...],...}

src/pymatgen/core/sites.py

@@ -46,7 +46,7 @@ def __init__(
         Args:
             species: Species on the site. Can be:
                 i.  A Composition-type object (preferred)
-                ii. An  element / species specified either as a string
+                ii. An element / species specified either as a string
                     symbols, e.g. "Li", "Fe2+", "P" or atomic numbers,
                     e.g. 3, 56, or actual Element or Species objects.
                 iii.Dict of elements/species and occupancies, e.g.
@@ -305,7 +305,7 @@ def __init__(
         Args:
             species: Species on the site. Can be:
                 i.  A Composition-type object (preferred)
-                ii. An  element / species specified either as a string
+                ii. An element / species specified either as a string
                     symbols, e.g. "Li", "Fe2+", "P" or atomic numbers,
                     e.g. 3, 56, or actual Element or Species objects.
                 iii.Dict of elements/species and occupancies, e.g.

src/pymatgen/core/surface.py

@@ -290,7 +290,7 @@ def is_symmetric(self, symprec: float = 0.1) -> bool:
             symprec (float): Symmetry precision used for SpaceGroup analyzer.
 
         Returns:
-            bool: Whether surfaces are symmetric.
+            bool: True if surfaces are symmetric.
         """
         spg_analyzer = SpacegroupAnalyzer(self, symprec=symprec)
         symm_ops = spg_analyzer.get_point_group_operations()

src/pymatgen/ext/optimade.py

@@ -500,7 +500,7 @@ def _parse_provider(self, provider: str, provider_url: str) -> dict[str, Provide
         It does not raise exceptions but will instead _logger.warning and provide
         an empty dictionary in the case of invalid data.
 
-        In future, when the specification  is sufficiently well adopted,
+        In future, when the specification is sufficiently well adopted,
         we might be more strict here.
 
         Args:

src/pymatgen/io/fiesta.py

@@ -39,7 +39,7 @@ class Nwchem2Fiesta(MSONable):
 
     If nwchem.nw is the input, nwchem.out the output, and structure.movecs the
     "movecs" file, the syntax to run NWCHEM2FIESTA is: NWCHEM2FIESTA
-    nwchem.nw  nwchem.nwout  structure.movecs > log_n2f
+    nwchem.nw nwchem.nwout structure.movecs > log_n2f
     """
 
     def __init__(self, folder, filename="nwchem", log_file="log_n2f"):

src/pymatgen/io/gaussian.py

@@ -1003,7 +1003,7 @@ def _parse_hessian(self, file, structure):
             structure: structure in the output file
         """
         # read Hessian matrix under "Force constants in Cartesian coordinates"
-        # Hessian matrix is in the input  orientation framework
+        # Hessian matrix is in the input orientation framework
         # WARNING : need #P in the route line
 
         ndf = 3 * len(structure)

src/pymatgen/io/lobster/outputs.py

@@ -1503,7 +1503,7 @@ def has_good_quality_maxDeviation(self, limit_maxDeviation: float = 0.1) -> bool
             limit_maxDeviation: limit of the maxDeviation
 
         Returns:
-            bool: Whether the quality of the projection is good.
+            bool: True if the quality of the projection is good.
         """
         return all(deviation <= limit_maxDeviation for deviation in self.max_deviation)
 
@@ -1525,7 +1525,7 @@ def has_good_quality_check_occupied_bands(
             limit_deviation (float): limit of the maxDeviation
 
         Returns:
-            bool: Whether the quality of the projection is good.
+            bool: True if the quality of the projection is good.
         """
         for matrix in self.band_overlaps_dict[Spin.up]["matrices"]:
             for iband1, band1 in enumerate(matrix):

src/pymatgen/io/xtb/inputs.py

@@ -23,7 +23,7 @@
 
 class CRESTInput(MSONable):
     """
-    An object representing  CREST input files.
+    An object representing CREST input files.
     Because CREST is controlled through command line flags and external
     files, the CRESTInput class mainly consists of methods for containing
     and writing external files.

src/pymatgen/phonon/bandstructure.py

@@ -254,7 +254,7 @@ def asr_breaking(self, tol_eigendisplacements: float = 1e-5) -> np.ndarray | Non
         """Get the breaking of the acoustic sum rule for the three acoustic modes,
         if Gamma is present. None otherwise.
         If eigendisplacements are available they are used to determine the acoustic
-        modes: selects the bands corresponding  to the eigendisplacements that
+        modes: selects the bands corresponding to the eigendisplacements that
         represent to a translation within tol_eigendisplacements. If these are not
         identified or eigendisplacements are missing the first 3 modes will be used
         (indices [:3]).

src/pymatgen/symmetry/analyzer.py

@@ -1346,7 +1346,7 @@ def is_valid_op(self, symm_op: SymmOp) -> bool:
             symm_op (SymmOp): Symmetry operation to test.
 
         Returns:
-            bool: Whether SymmOp is valid for Molecule.
+            bool: True if SymmOp is valid for Molecule.
         """
         coords = self.centered_mol.cart_coords
         for site in self.centered_mol:
@@ -1674,7 +1674,7 @@ def are_symmetrically_equivalent(
                 are symmetrically similar.
 
         Returns:
-            bool: Whether the two sets of sites are symmetrically equivalent.
+            bool: True if the two sets of sites are symmetrically equivalent.
         """
 
         def in_sites(site):

src/pymatgen/symmetry/groups.py

@@ -255,7 +255,7 @@ def __init__(self, int_symbol: str, hexagonal: bool = True) -> None:
                 notation is a LaTeX-like string, with screw axes being
                 represented by an underscore. For example, "P6_3/mmc".
                 Alternative settings can be accessed by adding a ":identifier".
-                For example, the hexagonal setting  for rhombohedral cells can be
+                For example, the hexagonal setting for rhombohedral cells can be
                 accessed by adding a ":H", e.g. "R-3m:H". To find out all
                 possible settings for a spacegroup, use the get_settings()
                 classmethod. Alternative origin choices can be indicated by a

src/pymatgen/transformations/advanced_transformations.py

@@ -820,7 +820,7 @@ def apply_transformation(
             Structure | list[Structure]: Structure(s) after MagOrderTransformation.
         """
         if not structure.is_ordered:
-            raise ValueError("Create an ordered approximation of your  input structure first.")
+            raise ValueError("Create an ordered approximation of your input structure first.")
 
         # retrieve order parameters
         order_parameters = [MagOrderParameterConstraint.from_dict(op_dict) for op_dict in self.order_parameter]

src/pymatgen/transformations/standard_transformations.py

@@ -426,7 +426,7 @@ class OrderDisorderedStructureTransformation(AbstractTransformation):
     these will be treated separately if the difference is above a threshold
     tolerance. currently this is .1
 
-    For example, if a fraction of .25 Li is on sites 0, 1, 2, 3  and .5 on sites
+    For example, if a fraction of .25 Li is on sites 0, 1, 2, 3 and .5 on sites
     4, 5, 6, 7 then 1 site from [0, 1, 2, 3] will be filled and 2 sites from [4, 5, 6, 7]
     will be filled, even though a lower energy combination might be found by
     putting all lithium in sites [4, 5, 6, 7].
@@ -457,7 +457,7 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool |
         """For this transformation, the apply_transformation method will return
         only the ordered structure with the lowest Ewald energy, to be
         consistent with the method signature of the other transformations.
-        However, all structures are stored in the  all_structures attribute in
+        However, all structures are stored in the all_structures attribute in
         the transformation object for easy access.
 
         Args:

src/pymatgen/util/due.py

@@ -8,7 +8,7 @@
 See https://github.com/duecredit/duecredit/blob/master/README.md for examples.
 
 Origin:     Originally a part of the duecredit
-Copyright:  2015-2021  DueCredit developers
+Copyright:  2015-2021 DueCredit developers
 License:    BSD-2
 """
 

src/pymatgen/util/plotting.py

@@ -712,7 +712,7 @@ def wrapper(*args, **kwargs):
         tight_layout      True to call fig.tight_layout (default: False)
         ax_grid           True (False) to add (remove) grid from all axes in fig.
                           Default: None i.e. fig is left unchanged.
-        ax_annotate       Add labels to  subplots e.g. (a), (b).
+        ax_annotate       Add labels to subplots e.g. (a), (b).
                           Default: False
         fig_close         Close figure. Default: False.
         ================  ====================================================

src/pymatgen/vis/structure_vtk.py

@@ -517,7 +517,7 @@ def add_triangle(
             color: Color for triangle as RGB.
             center: The "central atom" of the triangle
             opacity: opacity of the triangle
-            draw_edges: If set to True, the a line will be  drawn at each edge
+            draw_edges: If set to True, the a line will be drawn at each edge
             edges_color: Color of the line for the edges
             edges_linewidth: Width of the line drawn for the edges
         """