Fix coord_list_mapping_pbc() (#2782)

* fix AttributeError: module 'numpy' has no attribute 'int'

* add missing arg descriptions in doc strings

pymatgen/analysis/structure_matcher.py

@@ -8,7 +8,7 @@
 
 import abc
 import itertools
-from typing import Literal, Sequence
+from typing import Literal, Mapping, Sequence
 
 import numpy as np
 from monty.json import MSONable
@@ -441,7 +441,7 @@ def _get_lattices(self, target_lattice, s, supercell_size=1):
         cells in it
 
         Args:
-            target_lattice (Lattice):
+            target_lattice (Lattice): target lattice.
             s (Structure): input structure.
             supercell_size (int): Number of primitive cells in returned lattice
         """
@@ -521,7 +521,7 @@ def _cart_dists(cls, s1, s2, avg_lattice, mask, normalization, lll_frac_tol=None
             normalization (float): inverse normalization length
 
         Returns:
-            Distances from s2 to s1, normalized by (V/Natom) ^ 1/3
+            Distances from s2 to s1, normalized by (V/atom) ^ 1/3
             Fractional translation vector to apply to s2.
             Mapping from s1 to s2, i.e. with numpy slicing, s1[mapping] => s2
         """
@@ -588,20 +588,19 @@ def fit(
         Args:
             struct1 (Structure): 1st structure
             struct2 (Structure): 2nd structure
-            symmetric (Bool): Defaults to False
+            symmetric (bool): Defaults to False
                 If True, check the equality both ways.
                 This only impacts a small percentage of structures
-            skip_structure_reduction (Bool): Defaults to False
+            skip_structure_reduction (bool): Defaults to False
                 If True, skip to get a primitive structure and perform Niggli reduction for struct1 and struct2
 
         Returns:
-            True or False.
+            bool: True if the structures are equivalent
         """
         struct1, struct2 = self._process_species([struct1, struct2])
 
-        if not self._subset and self._comparator.get_hash(struct1.composition) != self._comparator.get_hash(
-            struct2.composition
-        ):
+        hash_match = self._comparator.get_hash(struct1.composition) != self._comparator.get_hash(struct2.composition)
+        if not self._subset and not hash_match:
             return False
 
         if not symmetric:
@@ -727,25 +726,24 @@ def _match(
 
     def _strict_match(
         self,
-        struct1,
-        struct2,
-        fu,
-        s1_supercell=True,
-        use_rms=False,
-        break_on_match=False,
-    ):
+        struct1: Structure,
+        struct2: Structure,
+        fu: int,
+        s1_supercell: bool = True,
+        use_rms: bool = False,
+        break_on_match: bool = False,
+    ) -> tuple[float, float, np.ndarray, float, Mapping] | None:
         """
         Matches struct2 onto struct1 (which should contain all sites in
         struct2).
 
         Args:
-            struct1, struct2 (Structure): structures to be matched
+            struct1 (Structure): structure to match onto
+            struct2 (Structure): structure to match
             fu (int): size of supercell to create
-            s1_supercell (bool): whether to create the supercell of
-                struct1 (vs struct2)
+            s1_supercell (bool): whether to create the supercell of struct1 (vs struct2)
             use_rms (bool): whether to minimize the rms of the matching
-            break_on_match (bool): whether to stop search at first
-                valid match
+            break_on_match (bool): whether to stop search at first match
         """
         if fu < 1:
             raise ValueError("fu cannot be less than 1")
@@ -895,9 +893,9 @@ def from_dict(cls, d):
 
     def _anonymous_match(
         self,
-        struct1,
-        struct2,
-        fu,
+        struct1: Structure,
+        struct2: Structure,
+        fu: int,
         s1_supercell=True,
         use_rms=False,
         break_on_match=False,
@@ -906,7 +904,14 @@ def _anonymous_match(
         """
         Tries all permutations of matching struct1 to struct2.
         Args:
-            struct1, struct2 (Structure): Preprocessed input structures
+            struct1 (Structure): First structure
+            struct2 (Structure): Second structure
+            fu (int): Factor of unit cell of struct1 to match to struct2
+            s1_supercell (bool): whether to create the supercell of struct1 (vs struct2)
+            use_rms (bool): Whether to minimize the rms of the matching
+            break_on_match (bool): Whether to break search on first match
+            single_match (bool): Whether to return only the best match
+
         Returns:
             List of (mapping, match)
         """
@@ -1062,8 +1067,8 @@ def fit_anonymous(
         Args:
             struct1 (Structure): 1st structure
             struct2 (Structure): 2nd structure
-            niggli (Bool): If true, perform Niggli reduction for struct1 and struct2
-            skip_structure_reduction (Bool): Defaults to False
+            niggli (bool): If true, perform Niggli reduction for struct1 and struct2
+            skip_structure_reduction (bool): Defaults to False
                 If True, skip to get a primitive structure and perform Niggli reduction for struct1 and struct2
 
         Returns:

pymatgen/io/lobster/lobsterenv.py

@@ -64,8 +64,9 @@ def __init__(
         id_blist_sg2="ICOBI",
     ):
         """
+
         Args:
-            are_coops: (Bool) if True, the file is a ICOOPLIST.lobster and not a ICOHPLIST.lobster; only tested for
+            are_coops: (bool) if True, the file is a ICOOPLIST.lobster and not a ICOHPLIST.lobster; only tested for
             ICOHPLIST.lobster so far
             filename_ICOHP: (str) Path to ICOHPLIST.lobster
             valences: (list of integers/floats) gives valence/charge for each element
@@ -215,7 +216,7 @@ def molecules_allowed(self):
 
     def get_anion_types(self):
         """
-        will return the types of anions present in crystal structure
+        Return the types of anions present in crystal structure
         Returns:
         """
         if self.valences is None:
@@ -251,8 +252,9 @@ def get_nn_info(self, structure: Structure, n, use_weights=False):
 
     def get_light_structure_environment(self, only_cation_environments=False, only_indices=None):
         """
-        will return a LobsterLightStructureEnvironments object
+        Return a LobsterLightStructureEnvironments object
         if the structure only contains coordination environments smaller 13
+
         Args:
             only_cation_environments: only data for cations will be returned
             only_indices: will only evaluate the list of isites in this list
@@ -359,7 +361,8 @@ def get_light_structure_environment(self, only_cation_environments=False, only_i
 
     def get_info_icohps_to_neighbors(self, isites=None, onlycation_isites=True):
         """
-        this method will return information of cohps of neighbors
+        this method Return information of cohps of neighbors
+
         Args:
             isites: list of site ids, if isite==None, all isites will be used to add the icohps of the neighbors
             onlycation_isites: will only use cations, if isite==[]
@@ -415,7 +418,8 @@ def plot_cohps_of_neighbors(
         integrated=False,
     ):
         """
-        will plot summed cohps (please be careful in the spin polarized case (plots might overlap (exactly!))
+        Will plot summed cohps (please be careful in the spin polarized case (plots might overlap (exactly!))
+
         Args:
             isites: list of site ids, if isite==[], all isites will be used to add the icohps of the neighbors
             onlycation_isites: bool, will only use cations, if isite==[]
@@ -464,7 +468,8 @@ def get_info_cohps_to_neighbors(
         summed_spin_channels=False,
     ):
         """
-        will return info about the cohps from all sites mentioned in isites with neighbors
+        Return info about the cohps from all sites mentioned in isites with neighbors
+
         Args:
             path_to_COHPCAR: str, path to COHPCAR
             isites: list of int that indicate the number of the site
@@ -588,7 +593,8 @@ def _get_plot_label(self, atoms, per_bond):
 
     def get_info_icohps_between_neighbors(self, isites=None, onlycation_isites=True):
         """
-        will return infos about interactions between neighbors of a certain atom
+        Return infos about interactions between neighbors of a certain atom
+
         Args:
             isites: list of site ids, if isite==None, all isites will be used
             onlycation_isites: will only use cations, if isite==None
@@ -699,6 +705,7 @@ def _evaluate_ce(
         adapt_extremum_to_add_cond=False,
     ):
         """
+
         Args:
             lowerlimit: lower limit which determines the ICOHPs that are considered for the determination of the
             neighbors
@@ -824,7 +831,8 @@ def _evaluate_ce(
 
     def _find_environments(self, additional_condition, lowerlimit, upperlimit, only_bonds_to):
         """
-        will find all relevant neighbors based on certain restrictions
+        Will find all relevant neighbors based on certain restrictions
+
         Args:
             additional_condition (int): additional condition (see above)
             lowerlimit (float): lower limit that tells you which ICOHPs are considered
@@ -936,7 +944,8 @@ def _find_environments(self, additional_condition, lowerlimit, upperlimit, only_
 
     def _find_relevant_atoms_additional_condition(self, isite, icohps, additional_condition):
         """
-        will find all relevant atoms that fulfill the additional_conditions
+        Will find all relevant atoms that fulfill the additional_conditions
+
         Args:
             isite: number of site in structure (starts with 0)
             icohps: icohps
@@ -1073,7 +1082,8 @@ def _find_relevant_atoms_additional_condition(self, isite, icohps, additional_co
     @staticmethod
     def _get_icohps(icohpcollection, isite, lowerlimit, upperlimit, only_bonds_to):
         """
-        will return icohp dict for certain site
+        Return icohp dict for certain site
+
         Args:
             icohpcollection: Icohpcollection object
             isite (int): number of a site
@@ -1095,7 +1105,8 @@ def _get_icohps(icohpcollection, isite, lowerlimit, upperlimit, only_bonds_to):
     @staticmethod
     def _get_atomnumber(atomstring):
         """
-        will return the number of the atom within the initial POSCAR (e.g., will return 0 for "Na1")
+        Return the number of the atom within the initial POSCAR (e.g., Return 0 for "Na1")
+
         Args:
             atomstring: string such as "Na1"
 
@@ -1106,11 +1117,10 @@ def _get_atomnumber(atomstring):
     @staticmethod
     def _split_string(s):
         """
-        will split strings such as "Na1" in "Na" and "1" and return "1"
+        Will split strings such as "Na1" in "Na" and "1" and return "1"
+
         Args:
             s (str): string
-
-        Returns:
         """
         head = s.rstrip("0123456789")
         tail = s[len(head) :]
@@ -1119,11 +1129,10 @@ def _split_string(s):
     @staticmethod
     def _determine_unit_cell(site):
         """
-        based on the site it will determine the unit cell, in which this site is based
+        Based on the site it will determine the unit cell, in which this site is based
+
         Args:
             site: site object
-
-        Returns:
         """
         unitcell = []
         for coord in site.frac_coords:
@@ -1142,8 +1151,9 @@ def _get_limit_from_extremum(
         # TODO: adapt this to give the extremum for the correct type of bond
         # TODO add tests
         """
-        will return limits for the evaluation of the icohp values from an icohpcollection
-        will return -100000, min(max_icohp*0.15,-0.1)
+        Return limits for the evaluation of the icohp values from an icohpcollection
+        Return -100000, min(max_icohp*0.15,-0.1)
+
         Args:
             icohpcollection: icohpcollection object
             percentage: will determine which ICOHPs will be considered (only 0.15 from the maximum value)
@@ -1248,7 +1258,8 @@ def from_Lobster(
         valences=None,
     ):
         """
-        will set up a LightStructureEnvironments from Lobster
+        Will set up a LightStructureEnvironments from Lobster
+
         Args:
             structure: Structure object
             list_ce_symbol: list of symbols for coordination environments

pymatgen/util/coord_cython.pyx

@@ -251,7 +251,7 @@ def coord_list_mapping_pbc(subset, superset, atol=1e-8, pbc=(True, True, True)):
     Returns:
         list of indices such that superset[indices] = subset
     """
-    inds = np.zeros(len(subset), dtype=np.int) - 1
+    inds = np.zeros(len(subset)) - 1
     subset = np.atleast_2d(subset)
     superset = np.atleast_2d(superset)