fix all pydocstyle D202 (#2715)

No blank lines allowed after function docstring

pymatgen/alchemy/transmuters.py

@@ -60,7 +60,6 @@ def __init__(
                 Uses multiprocessing.Pool. Default is None, which implies
                 serial.
         """
-
         self.transformed_structures = transformed_structures
         self.ncores = ncores
         if transformations is not None:
@@ -288,7 +287,6 @@ def from_filenames(filenames, transformations=None, primitive=True, extend_colle
             primitive: Same meaning as in __init__.
             extend_collection: Same meaning as in __init__.
         """
-
         allcifs = []
         for fname in filenames:
             with open(fname) as f:

pymatgen/analysis/adsorption.py

@@ -164,7 +164,6 @@ def find_surface_sites_by_height(self, slab, height=0.9, xy_tol=0.05):
         Returns:
             list of sites selected to be within a threshold of the highest
         """
-
         # Get projection of coordinates along the miller index
         m_projs = np.array([np.dot(site.coords, self.mvec) for site in slab.sites])
 
@@ -482,7 +481,6 @@ def adsorb_both_surfaces(
             find_args (dict): dictionary of arguments to be passed to the
                 call to self.find_adsorption_sites, e.g. {"distance":2.0}
         """
-
         # Get the adsorbed surfaces first
         find_args = find_args or {}
         ad_slabss = self.generate_adsorption_structures(
@@ -545,7 +543,6 @@ def generate_substitution_structures(
             dist_from_surf (float): Distance from the surface to find viable
                 substitution sites, defaults to 0 to substitute at the surface
         """
-
         target_species = target_species or []
 
         # Get symmetrized structure in case we want to substitute both sides

pymatgen/analysis/bond_dissociation.py

@@ -59,7 +59,6 @@ def __init__(
                                                        of self.expected_charges below for more specific information.
             multibreak (bool): If True, additionally attempt to break pairs of bonds. Defaults to False.
         """
-
         self.molecule_entry = molecule_entry
         self.filter_fragment_entries(fragment_entries)
         print(str(len(self.filtered_entries)) + " filtered entries")

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -383,7 +383,6 @@ def __len__(self):
 
     def compute_periodicity(self, algorithm="all_simple_paths"):
         """
-
         Args:
             algorithm ():
 
@@ -399,7 +398,6 @@ def compute_periodicity(self, algorithm="all_simple_paths"):
 
     def compute_periodicity_all_simple_paths_algorithm(self):
         """
-
         Returns:
         """
         self_loop_nodes = list(nx.nodes_with_selfloops(self._connected_subgraph))
@@ -487,7 +485,6 @@ def compute_periodicity_all_simple_paths_algorithm(self):
 
     def compute_periodicity_cycle_basis(self):
         """
-
         Returns:
         """
         my_simple_graph = nx.Graph(self._connected_subgraph)
@@ -534,7 +531,6 @@ def compute_periodicity_cycle_basis(self):
 
     def make_supergraph(self, multiplicity):
         """
-
         Args:
             multiplicity ():
 
@@ -545,7 +541,6 @@ def make_supergraph(self, multiplicity):
 
     def show_graph(self, graph=None, save_file=None, drawing_type="internal", pltshow=True):
         """
-
         Args:
             graph ():
             save_file ():
@@ -597,15 +592,13 @@ def graph(self):
     @property
     def is_periodic(self):
         """
-
         Returns:
         """
         return not self.is_0d
 
     @property
     def is_0d(self):
         """
-
         Returns:
         """
         if self._periodicity_vectors is None:
@@ -615,7 +608,6 @@ def is_0d(self):
     @property
     def is_1d(self):
         """
-
         Returns:
         """
         if self._periodicity_vectors is None:
@@ -625,7 +617,6 @@ def is_1d(self):
     @property
     def is_2d(self):
         """
-
         Returns:
         """
         if self._periodicity_vectors is None:
@@ -635,7 +626,6 @@ def is_2d(self):
     @property
     def is_3d(self):
         """
-
         Returns:
         """
         if self._periodicity_vectors is None:
@@ -673,7 +663,6 @@ def _order_periodicity_vectors(self):
     @property
     def periodicity_vectors(self):
         """
-
         Returns:
         """
         if self._periodicity_vectors is None:
@@ -683,7 +672,6 @@ def periodicity_vectors(self):
     @property
     def periodicity(self):
         """
-
         Returns:
         """
         if self._periodicity_vectors is None:
@@ -692,7 +680,6 @@ def periodicity(self):
 
     def elastic_centered_graph(self, start_node=None):
         """
-
         Args:
             start_node ():
 
@@ -917,7 +904,6 @@ def from_graph(cls, g):
 
     def description(self, full=False):
         """
-
         Args:
             full ():
 

pymatgen/analysis/chemenv/connectivity/structure_connectivity.py

@@ -79,7 +79,6 @@ def __init__(
 
     def environment_subgraph(self, environments_symbols=None, only_atoms=None):
         """
-
         Args:
             environments_symbols ():
             only_atoms ():
@@ -262,7 +261,6 @@ def setup_environment_subgraph(self, environments_symbols, only_atoms=None):
 
     def setup_connectivity_description(self):
         """
-
         Returns:
         """
 
@@ -283,7 +281,6 @@ def get_connected_components(self, environments_symbols=None, only_atoms=None):
 
     def setup_atom_environment_subgraph(self, atom_environment):
         """
-
         Args:
             atom_environment ():
 
@@ -293,7 +290,6 @@ def setup_atom_environment_subgraph(self, atom_environment):
 
     def setup_environments_subgraph(self, environments_symbols):
         """
-
         Args:
             environments_symbols ():
 
@@ -303,7 +299,6 @@ def setup_environments_subgraph(self, environments_symbols):
 
     def setup_atom_environments_subgraph(self, atoms_environments):
         """
-
         Args:
             atoms_environments ():
 
@@ -313,7 +308,6 @@ def setup_atom_environments_subgraph(self, atoms_environments):
 
     def print_links(self):
         """
-
         Returns:
         """
         nodes = self.environment_subgraph().nodes()
@@ -334,7 +328,6 @@ def print_links(self):
 
     def as_dict(self):
         """
-
         Returns:
         """
         return {
@@ -351,7 +344,6 @@ def as_dict(self):
     @classmethod
     def from_dict(cls, d):
         """
-
         Args:
             d ():
 

pymatgen/analysis/cost.py

@@ -156,7 +156,6 @@ def get_lowest_decomposition(self, composition):
         Returns:
             Decomposition as a dict of {Entry: amount}
         """
-
         entries_list = []
         elements = [e.symbol for e in composition.elements]
         for i in range(len(elements)):
@@ -180,7 +179,6 @@ def get_cost_per_mol(self, comp):
         Returns:
             float of cost/mol
         """
-
         comp = comp if isinstance(comp, Composition) else Composition(comp)
         decomp = self.get_lowest_decomposition(comp)
         return sum(k.energy_per_atom * v * comp.num_atoms for k, v in decomp.items())

pymatgen/analysis/elasticity/elastic.py

@@ -97,7 +97,6 @@ def energy_density(self, strain, convert_GPa_to_eV=True):
     @classmethod
     def from_diff_fit(cls, strains, stresses, eq_stress=None, order=2, tol: float = 1e-10):
         """
-
         Args:
             strains ():
             stresses ():
@@ -155,7 +154,6 @@ def __new__(cls, input_array, tol: float = 1e-4):
 
             tol (float): tolerance for initial symmetry test of tensor
         """
-
         obj = super().__new__(cls, input_array, check_rank=4, tol=tol)
         return obj.view(cls)
 

pymatgen/analysis/elasticity/stress.py

@@ -102,7 +102,6 @@ def piola_kirchoff_2(self, def_grad):
         Args:
             def_grad (3x3 array-like): rate of deformation tensor
         """
-
         def_grad = SquareTensor(def_grad)
         if not self.is_symmetric:
             raise ValueError(

pymatgen/analysis/ewald.py

@@ -453,7 +453,6 @@ def as_dict(self, verbosity: int = 0) -> dict:
             verbosity (int): Verbosity level. Default of 0 only includes the
                 matrix representation. Set to 1 for more details.
         """
-
         d = {
             "@module": type(self).__module__,
             "@class": type(self).__name__,

pymatgen/analysis/ferroelectricity/polarization.py

@@ -208,7 +208,6 @@ def get_pelecs_and_pions(self, convert_to_muC_per_cm2=False):
         convert_to_muC_per_cm2: Convert from electron * Angstroms to microCoulomb
             per centimeter**2
         """
-
         if not convert_to_muC_per_cm2:
             return self.p_elecs, self.p_ions
 
@@ -269,7 +268,6 @@ def get_same_branch_polarization_data(self, convert_to_muC_per_cm2=True, all_in_
             microCoulomb per centimeter**2
         all_in_polar: convert polarization to be in polar (final structure) polarization lattice
         """
-
         p_elec, p_ion = self.get_pelecs_and_pions()
         p_tot = p_elec + p_ion
         p_tot = np.array(p_tot)

pymatgen/analysis/functional_groups.py

@@ -45,7 +45,6 @@ def __init__(self, molecule, optimize=False):
             modified, adding Hydrogens, performing a simple conformer search,
             etc.
         """
-
         self.molgraph = None
 
         if isinstance(molecule, str):
@@ -108,7 +107,6 @@ def get_heteroatoms(self, elements=None):
             functional groups are of interest).
         :return: set of ints representing node indices
         """
-
         heteroatoms = set()
 
         for node in self.molgraph.graph.nodes():
@@ -139,7 +137,6 @@ def get_special_carbon(self, elements=None):
             Default None.
         :return: set of ints representing node indices
         """
-
         specials = set()
 
         # For this function, only carbons are considered
@@ -205,7 +202,6 @@ def link_marked_atoms(self, atoms):
             using other functions in this class.
         :return: list of sets of ints, representing groups of connected atoms
         """
-
         # We will add hydrogens to functional groups
         hydrogens = {n for n in self.molgraph.graph.nodes if str(self.species[n]) == "H"}
 
@@ -241,7 +237,6 @@ def get_basic_functional_groups(self, func_groups=None):
             defined in this function will be sought.
         :return: list of sets of ints, representing groups of connected atoms
         """
-
         strat = OpenBabelNN()
 
         hydrogens = {n for n in self.molgraph.graph.nodes if str(self.species[n]) == "H"}
@@ -306,7 +301,6 @@ def get_all_functional_groups(self, elements=None, func_groups=None, catch_basic
             other methods
         :return: list of sets of ints, representing groups of connected atoms
         """
-
         heteroatoms = self.get_heteroatoms(elements=elements)
         special_cs = self.get_special_carbon(elements=elements)
         groups = self.link_marked_atoms(heteroatoms.union(special_cs))
@@ -325,7 +319,6 @@ def categorize_functional_groups(self, groups):
             where the group occurs in the MoleculeGraph, and how many of each
             type of group there is.
         """
-
         categories = {}
 
         em = iso.numerical_edge_match("weight", 1)  # pylint: disable=E1102

pymatgen/analysis/gb/grain.py

@@ -2089,7 +2089,6 @@ def slab_from_csl(csl, surface, normal, trans_cry, max_search=20, quick_gen=Fals
         Returns:
             t_matrix: a slab lattice ( 3 by 3 integer array):
         """
-
         # set the transform matrix in real space
         trans = trans_cry
         # transform matrix in reciprocal space