Unignore flake8 B028 and fix occurrences (#2807)

* un-ignore flake8 B028 error and fix occurrences

* fix pymatgen/analysis/chemenv/coordination_environments/tests/test_coordination_geometries.py:299

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -48,8 +48,15 @@ def prt2(string, printing_volume):
 
 
 # Iterator function for the random permutations
-def random_permutations_iterator(initial_permutation, npermutations):
-    for _ in range(npermutations):
+def random_permutations_iterator(initial_permutation, n_permutations):
+    """
+    It takes a list and returns an iterator that yields random permutations of that list
+
+    Args:
+        initial_permutation: the initial permutation of the data
+        n_permutations: the number of permutations to generate
+    """
+    for _ in range(n_permutations):
         shuffle(initial_permutation)
         yield initial_permutation
 
@@ -157,7 +164,7 @@ def random_permutations_iterator(initial_permutation, npermutations):
 
         cg = all_cg[cg_symbol]
 
-        print(f'Getting explicit permutations for geometry "{cg.name}" (symbol : "{cg_symbol}")\n')
+        print(f"Getting explicit permutations for geometry {cg.name!r} (symbol : {cg_symbol!r})\n")
 
         # Setup of the local geometry finder
         lgf = LocalGeometryFinder()
@@ -274,8 +281,8 @@ def random_permutations_iterator(initial_permutation, npermutations):
 
         while True:
             test = input(
-                f'Get the explicit optimized permutations for geometry "{cg.name}" (symbol : '
-                f'"{cg_symbol}") ? ("y" to confirm, "q" to quit)\n'
+                f"Get the explicit optimized permutations for geometry {cg.name!r} (symbol : "
+                f'{cg_symbol!r}) ? ("y" to confirm, "q" to quit)\n'
             )
             if test not in ["y", "q"]:
                 print("Wrong key, try again")
@@ -285,7 +292,7 @@ def random_permutations_iterator(initial_permutation, npermutations):
             elif test == "q":
                 exit()
         # 2. Optimization of the permutations
-        print(f'Getting explicit optimized permutations for geometry "{cg.name}" (symbol : "{cg_symbol}")\n')
+        print(f"Getting explicit optimized permutations for geometry {cg.name!r} (symbol : {cg_symbol!r})\n")
         perms_used_algos = [dict() for algo in cg.algorithms]
 
         # Loop on algorithms
@@ -424,7 +431,7 @@ def random_permutations_iterator(initial_permutation, npermutations):
                 algo.explicit_optimized_permutations = np.array(explicit_optimized_permutations)
 
         test = input(
-            f'Save coordination geometry "{cg.name}" (symbol "{cg_symbol}") and new explicit and optimized '
+            f"Save coordination geometry {cg.name!r} (symbol {cg_symbol!r}) and new explicit and optimized "
             'permutations ? ("y" to confirm)'
         )
         if test == "y":

dev_scripts/chemenv/test_algos.py

@@ -97,4 +97,4 @@
         print("   => ", algos_results)
         iperm += 1
     t2 = time.clock()
-    print(f'Time to test {nperms} permutations for geometry "{cg.name}" (symbol "{cg_symbol}") : {t2 - t1:.2f} seconds')
+    print(f"Time to test {nperms} permutations for geometry {cg.name!r} (symbol {cg_symbol!r}) : {t2 - t1:.2f} seconds")

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -210,7 +210,7 @@ def __init__(
         environments_data=None,
         links_data=None,
         graph=None,
-    ):
+    ) -> None:
         """
         Constructor for the ConnectedComponent object.
 
@@ -354,7 +354,7 @@ def coordination_sequence(self, source_node, path_size=5, coordination="number",
             elif coordination == "env:number":
                 cseq[0] = {source_node.coordination_environment: 1}
             else:
-                raise ValueError(f'Coordination type "{coordination}" is not valid for coordination_sequence.')
+                raise ValueError(f"Coordination type {coordination!r} is not valid for coordination_sequence.")
         while path_len < path_size:
             new_ends = []
             for current_node_end, current_delta_end in current_ends:
@@ -377,7 +377,7 @@ def coordination_sequence(self, source_node, path_size=5, coordination="number",
                 myenvs = [myend.coordination_environment for myend, _ in current_ends]
                 cseq[path_len] = {myenv: myenvs.count(myenv) for myenv in set(myenvs)}
             else:
-                raise ValueError(f'Coordination type "{coordination}" is not valid for coordination_sequence.')
+                raise ValueError(f"Coordination type {coordination!r} is not valid for coordination_sequence.")
         return cseq
 
     def __len__(self):
@@ -395,7 +395,7 @@ def compute_periodicity(self, algorithm="all_simple_paths"):
         elif algorithm == "cycle_basis":
             self.compute_periodicity_cycle_basis()
         else:
-            raise ValueError(f'Algorithm "{algorithm}" is not allowed to compute periodicity')
+            raise ValueError(f"Algorithm {algorithm!r} is not allowed to compute periodicity")
         self._order_periodicity_vectors()
 
     def compute_periodicity_all_simple_paths_algorithm(self):

pymatgen/analysis/chemenv/connectivity/connectivity_finder.py

@@ -76,6 +76,6 @@ def setup_parameters(self, multiple_environments_choice):
         if multiple_environments_choice is not None:
             if multiple_environments_choice not in ["TAKE_HIGHEST_FRACTION"]:
                 raise ValueError(
-                    f'Option "{multiple_environments_choice}" for multiple_environments_choice is not allowed'
+                    f"Option {multiple_environments_choice!r} for multiple_environments_choice is not allowed"
                 )
         self.multiple_environments_choice = multiple_environments_choice

pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py

@@ -162,7 +162,7 @@ class AdditionalConditionInt(int, StrategyOption):
 
     allowed_values = "Integer amongst :\n"
     for integer, description in AdditionalConditions.CONDITION_DESCRIPTION.items():
-        allowed_values += f' - {integer:d} for "{description}"\n'
+        allowed_values += f" - {integer:d} for {description!r}\n"
 
     def __new__(cls, integer):
         """Special int representing additional conditions."""
@@ -442,7 +442,7 @@ def __eq__(self, other: object) -> bool:
         raise NotImplementedError()
 
     def __str__(self):
-        out = f'  Chemenv Strategy "{type(self).__name__}"\n'
+        out = f"  Chemenv Strategy {type(self).__name__!r}\n"
         out += f"  {'=' * (19 + len(type(self).__name__))}\n\n"
         out += f"  Description :\n  {'-' * 13}\n"
         out += self.STRATEGY_DESCRIPTION
@@ -1335,7 +1335,7 @@ def __init__(self, average_type, aa, bb):
         elif self.average_type == "arithmetic":
             self.eval = self.aweight
         else:
-            raise ValueError(f'Average type is "{average_type}" while it should be "geometric" or "arithmetic"')
+            raise ValueError(f"Average type is {average_type!r} while it should be 'geometric' or 'arithmetic'")
         self.aa = aa
         self.bb = bb
         if self.aa == 0:
@@ -2046,7 +2046,7 @@ def __init__(
             raise NotImplementedError()
             # self.area_weight = self.w_area_has_intersection_smoothstep
         else:
-            raise ValueError(f'Weight type is "{weight_type}" while it should be "has_intersection"')
+            raise ValueError(f'Weight type is {weight_type!r} while it should be "has_intersection"')
         self.surface_definition = surface_definition
         self.nb_sets_from_hints = nb_sets_from_hints
         self.other_nb_sets = other_nb_sets

pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -392,7 +392,7 @@ def __init__(self, hints_type, options):
                     neighbors set could be found from a "cap hint".
             """
             if hints_type not in self.ALLOWED_HINTS_TYPES:
-                raise ValueError(f'Type "{type}" for NeighborsSetsHints is not allowed')
+                raise ValueError(f"Type {type!r} for NeighborsSetsHints is not allowed")
             self.hints_type = hints_type
             self.options = options
 
@@ -1171,7 +1171,7 @@ def get_geometry_from_name(self, name):
         for gg in self.cg_list:
             if gg.name == name or name in gg.alternative_names:
                 return gg
-        raise LookupError(f'No coordination geometry found with name "{name}"')
+        raise LookupError(f"No coordination geometry found with name {name!r}")
 
     def get_geometry_from_IUPAC_symbol(self, IUPAC_symbol):
         """
@@ -1183,7 +1183,7 @@ def get_geometry_from_IUPAC_symbol(self, IUPAC_symbol):
         for gg in self.cg_list:
             if gg.IUPAC_symbol == IUPAC_symbol:
                 return gg
-        raise LookupError(f'No coordination geometry found with IUPAC symbol "{IUPAC_symbol}"')
+        raise LookupError(f"No coordination geometry found with IUPAC symbol {IUPAC_symbol!r}")
 
     def get_geometry_from_IUCr_symbol(self, IUCr_symbol):
         """
@@ -1195,7 +1195,7 @@ def get_geometry_from_IUCr_symbol(self, IUCr_symbol):
         for gg in self.cg_list:
             if gg.IUCr_symbol == IUCr_symbol:
                 return gg
-        raise LookupError(f'No coordination geometry found with IUCr symbol "{IUCr_symbol}"')
+        raise LookupError(f"No coordination geometry found with IUCr symbol {IUCr_symbol!r}")
 
     def get_geometry_from_mp_symbol(self, mp_symbol):
         """
@@ -1207,7 +1207,7 @@ def get_geometry_from_mp_symbol(self, mp_symbol):
         for gg in self.cg_list:
             if gg.mp_symbol == mp_symbol:
                 return gg
-        raise LookupError(f'No coordination geometry found with mp_symbol "{mp_symbol}"')
+        raise LookupError(f"No coordination geometry found with mp_symbol {mp_symbol!r}")
 
     def is_a_valid_coordination_geometry(
         self, mp_symbol=None, IUPAC_symbol=None, IUCr_symbol=None, name=None, cn=None

pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -785,7 +785,7 @@ def compute_structure_environments(
                             # Get possibly missing neighbors sets
                             if cg.neighbors_sets_hints is None:
                                 continue
-                            logging.debug(f'       ... getting hints from cg with mp_symbol "{cg_symbol}" ...')
+                            logging.debug(f"       ... getting hints from cg with mp_symbol {cg_symbol!r} ...")
                             hints_info = {
                                 "csm": cg_dict["symmetry_measure"],
                                 "nb_set": nb_set,

pymatgen/analysis/chemenv/coordination_environments/structure_environments.py

@@ -651,7 +651,7 @@ def get_csm(self, isite, mp_symbol):
             raise ChemenvError(
                 "StructureEnvironments",
                 "get_csm",
-                f'Number of csms for site #{str(isite)} with mp_symbol "{mp_symbol}" = {str(len(csms))}',
+                f"Number of csms for site #{str(isite)} with mp_symbol {mp_symbol!r} = {str(len(csms))}",
             )
         return csms[0]
 
@@ -1968,7 +1968,7 @@ def site_has_clear_environment(self, isite, conditions=None):
                 if ce[target] > condition["maxnumber"]:
                     return False
             else:
-                raise ValueError(f'Target "{target}" for condition of clear environment is not allowed')
+                raise ValueError(f"Target {target!r} for condition of clear environment is not allowed")
         return True
 
     def structure_has_clear_environments(self, conditions=None, skip_none=True, skip_empty=False):
@@ -2294,7 +2294,7 @@ def add_coord_geom(
             raise ChemenvError(
                 self.__class__,
                 "add_coord_geom",
-                f'Coordination geometry with mp_symbol "{mp_symbol}" is not valid',
+                f"Coordination geometry with mp_symbol {mp_symbol!r} is not valid",
             )
         if mp_symbol in list(self.coord_geoms) and not override:
             raise ChemenvError(

pymatgen/analysis/chemenv/coordination_environments/tests/test_coordination_geometries.py

@@ -296,21 +296,21 @@ def test_coordination_geometry(self):
         assert allcg.get_geometry_from_name("Octahedron").mp_symbol == cg_oct.mp_symbol
         with pytest.raises(LookupError) as exc_info:
             allcg.get_geometry_from_name("Octahedran")
-        assert str(exc_info.value) == 'No coordination geometry found with name "Octahedran"'
+        assert str(exc_info.value) == "No coordination geometry found with name 'Octahedran'"
 
         assert allcg.get_geometry_from_IUPAC_symbol("OC-6").mp_symbol == cg_oct.mp_symbol
         with pytest.raises(LookupError) as exc_info:
             allcg.get_geometry_from_IUPAC_symbol("OC-7")
-        assert str(exc_info.value) == 'No coordination geometry found with IUPAC symbol "OC-7"'
+        assert str(exc_info.value) == "No coordination geometry found with IUPAC symbol 'OC-7'"
 
         assert allcg.get_geometry_from_IUCr_symbol("[6o]").mp_symbol == cg_oct.mp_symbol
         with pytest.raises(LookupError) as exc_info:
             allcg.get_geometry_from_IUCr_symbol("[6oct]")
-        assert str(exc_info.value) == 'No coordination geometry found with IUCr symbol "[6oct]"'
+        assert str(exc_info.value) == "No coordination geometry found with IUCr symbol '[6oct]'"
 
         with pytest.raises(LookupError) as exc_info:
             allcg.get_geometry_from_mp_symbol("O:7")
-        assert str(exc_info.value) == 'No coordination geometry found with mp_symbol "O:7"'
+        assert str(exc_info.value) == "No coordination geometry found with mp_symbol 'O:7'"
 
         assert (
             allcg.pretty_print(maxcn=4)

pymatgen/analysis/chemenv/coordination_environments/tests/test_weights.py

@@ -131,7 +131,7 @@ def test_normalized_angle_distance_weight(self):
         with pytest.raises(ValueError, match="Both exponents are 0."):
             NormalizedAngleDistanceNbSetWeight(average_type="arithmetic", aa=0, bb=0)
         with pytest.raises(
-            ValueError, match='Average type is "arithmetix" ' 'while it should be "geometric" or "arithmetic"'
+            ValueError, match="Average type is 'arithmetix' while it should be 'geometric' or 'arithmetic'"
         ):
             NormalizedAngleDistanceNbSetWeight(average_type="arithmetix", aa=1, bb=1)
 

pymatgen/analysis/chemenv/coordination_environments/voronoi.py

@@ -475,7 +475,7 @@ def neighbors_surfaces_bounded(self, isite, surface_calculation_options=None):
             }
         else:
             raise ValueError(
-                f'Type "{surface_calculation_options["type"]}" for the surface calculation in DetailedVoronoiContainer '
+                f'Type {surface_calculation_options["type"]!r} for the surface calculation in DetailedVoronoiContainer '
                 "is invalid"
             )
         max_dist = surface_calculation_options["distance_bounds"]["upper"] + 0.1
@@ -705,7 +705,7 @@ def voronoi_parameters_bounds_and_limits(self, isite, plot_type, max_dist):
             dist_limits = [0.0, 1.0]
         else:
             raise NotImplementedError(
-                f"Plotting type \"{plot_type['distance_parameter']}\" for the distance is not implemented"
+                f"Plotting type {plot_type['distance_parameter']!r} for the distance is not implemented"
             )
         if plot_type["angle_parameter"][0] == "initial_normalized":
             aa = [0.0]
@@ -718,7 +718,7 @@ def voronoi_parameters_bounds_and_limits(self, isite, plot_type, max_dist):
             angle_bounds = np.array(aa)
         else:
             raise NotImplementedError(
-                f"Plotting type \"{plot_type['angle_parameter']}\" for the angle is not implemented"
+                f"Plotting type {plot_type['angle_parameter']!r} for the angle is not implemented"
             )
         ang_limits = [0.0, 1.0]
         return {
@@ -854,7 +854,7 @@ def dp_func(dp):
             for idist, dist in enumerate(mydists):
                 yy += mydcns[idist] * normal_cdf_step(xx, mean=dist, scale=scale)
         else:
-            raise ValueError(f"Step function of type \"{step_function['type']}\" is not allowed")
+            raise ValueError(f"Step function of type {step_function['type']!r} is not allowed")
         subplot.plot(xx, yy)
 
         return fig
@@ -913,7 +913,7 @@ def ap_func(ap):
             for iang, ang in enumerate(myangs):
                 yy += mydcns[iang] * normal_cdf_step(xx, mean=ang, scale=scale)
         else:
-            raise ValueError(f"Step function of type \"{step_function['type']}\" is not allowed")
+            raise ValueError(f"Step function of type {step_function['type']!r} is not allowed")
         subplot.plot(xx, yy)
 
         return fig

pymatgen/analysis/chemenv/utils/chemenv_config.py

@@ -89,7 +89,7 @@ def setup(self):
                 print(" ... wrong key, try again ...")
             print()
         if test == "S":
-            print(f'Configuration has been saved to file "{config_file}"')
+            print(f"Configuration has been saved to file {config_file!r}")
 
     @property
     def has_materials_project_access(self):
@@ -117,7 +117,7 @@ def setup_package_options(self):
         if len(strategy_class.STRATEGY_OPTIONS) > 0:
             for option, option_dict in strategy_class.STRATEGY_OPTIONS.items():
                 while True:
-                    print(f"  => Enter value for option '{option}' (<ENTER> for default = {option_dict['default']})\n")
+                    print(f"  => Enter value for option {option!r} (<ENTER> for default = {option_dict['default']})\n")
                     print("     Valid options are :\n")
                     print(f"       {option_dict['type'].allowed_values}")
                     test = input("     Your choice : ")
@@ -184,6 +184,6 @@ def auto_load(cls, root_dir=None):
             return ChemEnvConfig(package_options=config_dict["package_options"])
 
         except OSError:
-            print(f'Unable to load configuration from file "{config_file}" ...')
+            print(f"Unable to load configuration from file {config_file!r} ...")
             print(" ... loading default configuration")
             return ChemEnvConfig()

pymatgen/analysis/chemenv/utils/func_utils.py

@@ -40,7 +40,7 @@ def __init__(self, function, options_dict=None):
         :param options_dict: Dictionary containing the parameters for the ratio function.
         """
         if function not in self.ALLOWED_FUNCTIONS:
-            raise ValueError(f'Function "{function}" is not allowed in RatioFunction of type "{type(self).__name__}"')
+            raise ValueError(f'Function {function!r} is not allowed in RatioFunction of type "{type(self).__name__}"')
         self.eval = object.__getattribute__(self, function)
         self.function = function
         self.setup_parameters(options_dict=options_dict)
@@ -67,26 +67,26 @@ def setup_parameters(self, options_dict):
                 if len(function_options) == 1:
                     opts = f'Option "{function_options[0]}"'
                 else:
-                    opts1 = ", ".join(f'"{op}"' for op in function_options[:-1])
+                    opts1 = ", ".join(f"{op!r}" for op in function_options[:-1])
                     opts = f'Options {opts1} and "{function_options[-1]}"'
                 if options_dict is None or len(options_dict) == 0:
                     missing = "no option was provided."
                 else:
                     optgiven = list(options_dict)
                     if len(options_dict) == 1:
-                        missing = f'only "{optgiven[0]}" was provided.'
+                        missing = f"only {optgiven[0]!r} was provided."
                     else:
-                        missing1 = ", ".join(f'"{miss}"' for miss in optgiven[:-1])
-                        missing = f'only {missing1} and "{optgiven[-1]}" were provided.'
+                        missing1 = ", ".join(f"{miss!r}" for miss in optgiven[:-1])
+                        missing = f"only {missing1} and {optgiven[-1]!r} were provided."
                 raise ValueError(
-                    f'{opts} should be provided for function "{self.function}" in RatioFunction of '
-                    f'type "{type(self).__name__}" while {missing}'
+                    f"{opts} should be provided for function {self.function!r} in RatioFunction of "
+                    f"type {type(self).__name__!r} while {missing}"
                 )
             # Setup the options and raise an error if a wrong option is provided
             for key, val in options_dict.items():
                 if key not in function_options:
                     raise ValueError(
-                        f'Option "{key}" not allowed for function "{self.function}" in RatioFunction of '
+                        f"Option {key!r} not allowed for function {self.function!r} in RatioFunction of "
                         f'type "{type(self).__name__}"'
                     )
                 setattr(self, key, val)