simplify dict["key"] if "key" in dict else None to dict.get("key") (#3038)

Author: janosh

pymatgen/analysis/chemenv/connectivity/tests/test_connected_components.py

@@ -858,11 +858,11 @@ def test_coordination_sequences(self):
             "structure_environments_files",
             "se_mp-5020.json",
         )
-        with open(BaTiO3_se_fpath) as f:
-            dd = json.load(f)
-        se = StructureEnvironments.from_dict(dd)
+        with open(BaTiO3_se_fpath) as file:
+            dct = json.load(file)
+        struct_envs = StructureEnvironments.from_dict(dct)
         lse = LightStructureEnvironments.from_structure_environments(
-            strategy=SimplestChemenvStrategy(), structure_environments=se
+            strategy=SimplestChemenvStrategy(), structure_environments=struct_envs
         )
         cf = ConnectivityFinder()
         sc = cf.get_structure_connectivity(light_structure_environments=lse)

pymatgen/analysis/chemenv/connectivity/tests/test_structure_connectivity.py

@@ -28,11 +28,11 @@ def test_serialization(self):
             "structure_environments_files",
             "se_mp-5020.json",
         )
-        with open(BaTiO3_se_fpath) as f:
-            dd = json.load(f)
-        se = StructureEnvironments.from_dict(dd)
+        with open(BaTiO3_se_fpath) as file:
+            dd = json.load(file)
+        struct_envs = StructureEnvironments.from_dict(dd)
         lse = LightStructureEnvironments.from_structure_environments(
-            strategy=SimplestChemenvStrategy(), structure_environments=se
+            strategy=SimplestChemenvStrategy(), structure_environments=struct_envs
         )
         cf = ConnectivityFinder()
         sc = cf.get_structure_connectivity(light_structure_environments=lse)

pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -327,7 +327,7 @@ def as_dict(self):
         }
 
     @classmethod
-    def from_dict(cls, dd):
+    def from_dict(cls, dct):
         """
         Reconstructs the SeparationPlane algorithm from its JSON-serializable dict representation.
 
@@ -336,22 +336,18 @@ def from_dict(cls, dd):
 
         Returns: a SeparationPlane algorithm.
         """
-        eop = (
-            [np.array(eo_perm) for eo_perm in dd["explicit_optimized_permutations"]]
-            if ("explicit_optimized_permutations" in dd and dd["explicit_optimized_permutations"] is not None)
-            else None
-        )
+        eop = [np.array(eo_perm) for eo_perm in dct.get("explicit_optimized_permutations", [])] or None
         return cls(
-            plane_points=dd["plane_points"],
-            mirror_plane=dd["mirror_plane"],
-            ordered_plane=dd["ordered_plane"],
-            point_groups=dd["point_groups"],
-            ordered_point_groups=dd["ordered_point_groups"],
-            explicit_permutations=[np.array(eperm) for eperm in dd["explicit_permutations"]],
+            plane_points=dct["plane_points"],
+            mirror_plane=dct["mirror_plane"],
+            ordered_plane=dct["ordered_plane"],
+            point_groups=dct["point_groups"],
+            ordered_point_groups=dct["ordered_point_groups"],
+            explicit_permutations=[np.array(eperm) for eperm in dct["explicit_permutations"]],
             explicit_optimized_permutations=eop,
-            multiplicity=dd["multiplicity"] if "multiplicity" in dd else None,
-            other_plane_points=dd["other_plane_points"] if "other_plane_points" in dd else None,
-            minimum_number_of_points=dd["minimum_number_of_points"],
+            multiplicity=dct.get("multiplicity"),
+            other_plane_points=dct.get("other_plane_points"),
+            minimum_number_of_points=dct["minimum_number_of_points"],
         )
 
     def __str__(self):
@@ -599,50 +595,52 @@ def as_dict(self):
             "IUCr_symbol": self.IUCrsymbol,
             "coordination": self.coordination,
             "central_site": [float(xx) for xx in self.central_site],
-            "points": [[float(xx) for xx in pp] for pp in self.points] if self.points is not None else None,
-            "solid_angles": [float(ang) for ang in self._solid_angles] if self._solid_angles is not None else None,
+            "points": [[float(xx) for xx in pp] for pp in (self.points or [])] or None,
+            "solid_angles": [float(ang) for ang in (self._solid_angles or [])] or None,
             "deactivate": self.deactivate,
             "_faces": self._faces,
             "_edges": self._edges,
-            "_algorithms": [algo.as_dict for algo in self._algorithms] if self._algorithms is not None else None,
+            "_algorithms": [algo.as_dict for algo in (self._algorithms or [])] or None,
             "equivalent_indices": self.equivalent_indices,
             "neighbors_sets_hints": [nbsh.as_dict() for nbsh in self.neighbors_sets_hints]
             if self.neighbors_sets_hints is not None
             else None,
         }
 
     @classmethod
-    def from_dict(cls, dd):
+    def from_dict(cls, dct):
         """
         Reconstructs the CoordinationGeometry from its JSON-serializable dict representation.
 
         Args:
-            dd: a JSON-serializable dict representation of a CoordinationGeometry.
+            dct: a JSON-serializable dict representation of a CoordinationGeometry.
 
         Returns: a CoordinationGeometry.
         """
         dec = MontyDecoder()
         return cls(
-            mp_symbol=dd["mp_symbol"],
-            name=dd["name"],
-            alternative_names=dd["alternative_names"],
-            IUPAC_symbol=dd["IUPAC_symbol"],
-            IUCr_symbol=dd["IUCr_symbol"],
-            coordination=dd["coordination"],
-            central_site=dd["central_site"],
-            points=dd["points"],
+            mp_symbol=dct["mp_symbol"],
+            name=dct["name"],
+            alternative_names=dct["alternative_names"],
+            IUPAC_symbol=dct["IUPAC_symbol"],
+            IUCr_symbol=dct["IUCr_symbol"],
+            coordination=dct["coordination"],
+            central_site=dct["central_site"],
+            points=dct["points"],
             solid_angles=(
-                dd["solid_angles"] if "solid_angles" in dd else [4.0 * np.pi / dd["coordination"]] * dd["coordination"]
+                dct["solid_angles"]
+                if "solid_angles" in dct
+                else [4.0 * np.pi / dct["coordination"]] * dct["coordination"]
             ),
-            deactivate=dd["deactivate"],
-            faces=dd["_faces"],
-            edges=dd["_edges"],
-            algorithms=[dec.process_decoded(algo_d) for algo_d in dd["_algorithms"]]
-            if dd["_algorithms"] is not None
+            deactivate=dct["deactivate"],
+            faces=dct["_faces"],
+            edges=dct["_edges"],
+            algorithms=[dec.process_decoded(algo_d) for algo_d in dct["_algorithms"]]
+            if dct["_algorithms"] is not None
             else None,
-            equivalent_indices=dd["equivalent_indices"] if "equivalent_indices" in dd else None,
-            neighbors_sets_hints=[cls.NeighborsSetsHints.from_dict(nbshd) for nbshd in dd["neighbors_sets_hints"]]
-            if ("neighbors_sets_hints" in dd and dd["neighbors_sets_hints"] is not None)
+            equivalent_indices=dct.get("equivalent_indices"),
+            neighbors_sets_hints=[cls.NeighborsSetsHints.from_dict(nbshd) for nbshd in dct["neighbors_sets_hints"]]
+            if ("neighbors_sets_hints" in dct and dct["neighbors_sets_hints"] is not None)
             else None,
         )
 

pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -683,17 +683,17 @@ def compute_structure_environments(
 
         # Initialize the StructureEnvironments object (either from initial_structure_environments or from scratch)
         if initial_structure_environments is not None:
-            se = initial_structure_environments
-            if se.structure != self.structure:
+            struct_envs = initial_structure_environments
+            if struct_envs.structure != self.structure:
                 raise ValueError("Structure is not the same in initial_structure_environments")
-            if se.voronoi != self.detailed_voronoi:
-                if self.detailed_voronoi.is_close_to(se.voronoi):
-                    self.detailed_voronoi = se.voronoi
+            if struct_envs.voronoi != self.detailed_voronoi:
+                if self.detailed_voronoi.is_close_to(struct_envs.voronoi):
+                    self.detailed_voronoi = struct_envs.voronoi
                 else:
                     raise ValueError("Detailed Voronoi is not the same in initial_structure_environments")
-            se.info = info
+            struct_envs.info = info
         else:
-            se = StructureEnvironments(
+            struct_envs = StructureEnvironments(
                 voronoi=self.detailed_voronoi,
                 valences=self.valences,
                 sites_map=self.sites_map,
@@ -740,7 +740,7 @@ def compute_structure_environments(
             if optimization > 0:
                 self.detailed_voronoi.local_planes[isite] = {}
                 self.detailed_voronoi.separations[isite] = {}
-            se.init_neighbors_sets(
+            struct_envs.init_neighbors_sets(
                 isite=isite,
                 additional_conditions=additional_conditions,
                 valences=valences,
@@ -749,14 +749,14 @@ def compute_structure_environments(
             to_add_from_hints = []
             nb_sets_info = {}
 
-            for cn, nb_sets in se.neighbors_sets[isite].items():
+            for cn, nb_sets in struct_envs.neighbors_sets[isite].items():
                 if cn not in all_cns:
                     continue
                 for inb_set, nb_set in enumerate(nb_sets):
                     logging.debug(f"    ... getting environments for nb_set ({cn:d}, {inb_set:d})")
                     t_nbset1 = time.process_time()
                     ce = self.update_nb_set_environments(
-                        se=se,
+                        se=struct_envs,
                         isite=isite,
                         cn=cn,
                         inb_set=inb_set,
@@ -784,10 +784,10 @@ def compute_structure_environments(
                                 suggested_nb_set_voronoi_indices = nb_sets_hints.hints(hints_info)
                                 for idx_new, new_nb_set_voronoi_indices in enumerate(suggested_nb_set_voronoi_indices):
                                     logging.debug(f"           hint # {idx_new:d}")
-                                    new_nb_set = se.NeighborsSet(
-                                        structure=se.structure,
+                                    new_nb_set = struct_envs.NeighborsSet(
+                                        structure=struct_envs.structure,
                                         isite=isite,
-                                        detailed_voronoi=se.voronoi,
+                                        detailed_voronoi=struct_envs.voronoi,
                                         site_voronoi_indices=new_nb_set_voronoi_indices,
                                         sources={
                                             "origin": "nb_set_hints",
@@ -804,10 +804,10 @@ def compute_structure_environments(
                                         continue
                                     if new_nb_set in [ta["new_nb_set"] for ta in to_add_from_hints]:
                                         has_nb_set = True
-                                    elif cn_new_nb_set not in se.neighbors_sets[isite]:
+                                    elif cn_new_nb_set not in struct_envs.neighbors_sets[isite]:
                                         has_nb_set = False
                                     else:
-                                        has_nb_set = new_nb_set in se.neighbors_sets[isite][cn_new_nb_set]
+                                        has_nb_set = new_nb_set in struct_envs.neighbors_sets[isite][cn_new_nb_set]
                                     if not has_nb_set:
                                         to_add_from_hints.append(
                                             {
@@ -821,16 +821,16 @@ def compute_structure_environments(
                                         logging.debug("              => already present")
             logging.debug("    ... getting environments for nb_sets added from hints")
             for missing_nb_set_to_add in to_add_from_hints:
-                se.add_neighbors_set(isite=isite, nb_set=missing_nb_set_to_add["new_nb_set"])
+                struct_envs.add_neighbors_set(isite=isite, nb_set=missing_nb_set_to_add["new_nb_set"])
             for missing_nb_set_to_add in to_add_from_hints:
                 isite_new_nb_set = missing_nb_set_to_add["isite"]
                 cn_new_nb_set = missing_nb_set_to_add["cn_new_nb_set"]
                 new_nb_set = missing_nb_set_to_add["new_nb_set"]
-                inew_nb_set = se.neighbors_sets[isite_new_nb_set][cn_new_nb_set].index(new_nb_set)
+                inew_nb_set = struct_envs.neighbors_sets[isite_new_nb_set][cn_new_nb_set].index(new_nb_set)
                 logging.debug(f"    ... getting environments for nb_set ({cn_new_nb_set}, {inew_nb_set}) - from hints")
                 t_nbset1 = time.process_time()
                 self.update_nb_set_environments(
-                    se=se,
+                    se=struct_envs,
                     isite=isite_new_nb_set,
                     cn=cn_new_nb_set,
                     inb_set=inew_nb_set,
@@ -842,7 +842,7 @@ def compute_structure_environments(
                     nb_sets_info[cn] = {}
                 nb_sets_info[cn][inew_nb_set] = {"time": t_nbset2 - t_nbset1}
             t2 = time.process_time()
-            se.update_site_info(isite=isite, info_dict={"time": t2 - t1, "nb_sets_info": nb_sets_info})
+            struct_envs.update_site_info(isite=isite, info_dict={"time": t2 - t1, "nb_sets_info": nb_sets_info})
             if timelimit is not None:
                 time_elapsed = t2 - time_init
                 time_left = timelimit - time_elapsed
@@ -852,7 +852,7 @@ def compute_structure_environments(
             logging.debug(f"    ... computed in {t2 - t1:.2f} seconds")
         time_end = time.process_time()
         logging.debug(f"    ... compute_structure_environments ended in {time_end - time_init:.2f} seconds")
-        return se
+        return struct_envs
 
     def update_nb_set_environments(self, se, isite, cn, inb_set, nb_set, recompute=False, optimization=None):
         """

pymatgen/analysis/chemenv/coordination_environments/structure_environments.py

@@ -1343,7 +1343,7 @@ def from_dict(cls, d):
         neighbors_sets = [
             {
                 int(cn): [
-                    cls.NeighborsSet.from_dict(dd=nb_set_dict, structure=structure, detailed_voronoi=voronoi)
+                    cls.NeighborsSet.from_dict(nb_set_dict, structure=structure, detailed_voronoi=voronoi)
                     for nb_set_dict in nb_sets
                 ]
                 for cn, nb_sets in site_nbs_sets_dict.items()
@@ -2127,7 +2127,7 @@ def from_dict(cls, d):
             all_nbs_sites.append({"site": site, "index": nb_site["index"], "image_cell": image_cell})
         neighbors_sets = [
             [
-                cls.NeighborsSet.from_dict(dd=nb_set, structure=structure, all_nbs_sites=all_nbs_sites)
+                cls.NeighborsSet.from_dict(nb_set, structure=structure, all_nbs_sites=all_nbs_sites)
                 for nb_set in site_nb_sets
             ]
             if site_nb_sets is not None

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

@@ -88,10 +88,10 @@ def test_structure_environments_neighbors_sets(self):
         with open(f"{se_files_dir}/se_mp-7000.json") as f:
             dd = json.load(f)
 
-        se = StructureEnvironments.from_dict(dd)
+        struct_envs = StructureEnvironments.from_dict(dd)
 
         isite = 6
-        nb_set = se.neighbors_sets[isite][4][0]
+        nb_set = struct_envs.neighbors_sets[isite][4][0]
 
         nb_set_surface_points = [
             [1.0017922780870239, 0.99301365328679292],

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

@@ -37,14 +37,14 @@ def test_structure_environments(self):
             with open(f"{struct_env_files_dir}/se_mp-7000.json") as f:
                 dd = json.load(f)
 
-            se = StructureEnvironments.from_dict(dd)
+            struct_envs = StructureEnvironments.from_dict(dd)
             isite = 6
-            csm_and_maps_fig, csm_and_maps_subplot = se.get_csm_and_maps(isite=isite)
+            csm_and_maps_fig, csm_and_maps_subplot = struct_envs.get_csm_and_maps(isite=isite)
             assert_array_almost_equal(csm_and_maps_subplot.lines[0].get_xydata().flatten(), [0.0, 0.53499332])
             assert_array_almost_equal(csm_and_maps_subplot.lines[1].get_xydata().flatten(), [1.0, 0.47026441])
             assert_array_almost_equal(csm_and_maps_subplot.lines[2].get_xydata().flatten(), [2.0, 0.00988778])
 
-            environments_figure, environments_subplot = se.get_environments_figure(isite=isite)
+            environments_figure, environments_subplot = struct_envs.get_environments_figure(isite=isite)
             assert_array_almost_equal(
                 np.array(environments_subplot.patches[0].get_xy()),
                 [
@@ -98,14 +98,14 @@ def test_structure_environments(self):
                 ],
             )
 
-            se.save_environments_figure(isite=isite, imagename="image.png")
+            struct_envs.save_environments_figure(isite=isite, imagename="image.png")
             assert os.path.exists("image.png")
 
-            assert len(se.differences_wrt(se)) == 0
+            assert len(struct_envs.differences_wrt(struct_envs)) == 0
 
-            assert se == se
+            assert struct_envs == struct_envs
 
-            ce = se.ce_list[isite][4][0]
+            ce = struct_envs.ce_list[isite][4][0]
 
             assert len(ce), 4
 
@@ -140,7 +140,7 @@ def test_structure_environments(self):
             min_geoms = ce.minimum_geometries(n=3)
             assert len(min_geoms) == 3
 
-            ce2 = se.ce_list[7][4][0]
+            ce2 = struct_envs.ce_list[7][4][0]
 
             assert ce.is_close_to(ce2, rtol=0.01, atol=1e-4)
             assert not ce.is_close_to(ce2, rtol=0.0, atol=1e-8)
@@ -153,11 +153,11 @@ def test_light_structure_environments(self):
             with open(f"{struct_env_files_dir}/se_mp-7000.json") as f:
                 dd = json.load(f)
 
-            se = StructureEnvironments.from_dict(dd)
+            struct_envs = StructureEnvironments.from_dict(dd)
 
             strategy = SimplestChemenvStrategy()
             lse = LightStructureEnvironments.from_structure_environments(
-                structure_environments=se, strategy=strategy, valences="undefined"
+                structure_environments=struct_envs, strategy=strategy, valences="undefined"
             )
             isite = 6
             nb_set = lse.neighbors_sets[isite][0]
@@ -241,7 +241,7 @@ def test_light_structure_environments(self):
             multi_strategy = MultiWeightsChemenvStrategy.stats_article_weights_parameters()
 
             lse_multi = LightStructureEnvironments.from_structure_environments(
-                strategy=multi_strategy, structure_environments=se, valences="undefined"
+                strategy=multi_strategy, structure_environments=struct_envs, valences="undefined"
             )
             assert lse_multi.coordination_environments[isite][0]["csm"] == pytest.approx(0.009887784240541068)
             assert lse_multi.coordination_environments[isite][0]["ce_fraction"] == pytest.approx(1.0)