Fix ruff PLC0206 and PLR6104 (#4035)

* fix ruff PLC0206

* fix/ignore ruff PLR6104

* simplify np.prod(arr.shape) -> arr.size

* add missing args to get_partial_doses doc str

* fix ruff N818 Exception name `SymmetryUndetermined` should be named with an Error suffix

* fix TestGruneisenParameter.test_average_gruneisen

    def test_average_gruneisen(self):
        assert self.gruneisen_obj.average_gruneisen() == approx(1.164231026696211)
>       assert self.gruneisen_obj.average_gruneisen(squared=False) == approx(0.849759667411049)
E       assert 1.3554338835221134 == 0.849759667411049 ± 8.5e-07
E
E         comparison failed
E         Obtained: 1.3554338835221134
E         Expected: 0.849759667411049 ± 8.5e-07

* auto-format .github/workflows/issue-metrics.yml

* rename index variables

.github/workflows/issue-metrics.yml

@@ -2,7 +2,7 @@ name: Monthly issue metrics
 on:
   workflow_dispatch:
   schedule:
-    - cron: '3 2 1 * *'
+    - cron: "3 2 1 * *" # Run at 2:03am on the first of every month
 
 permissions:
   contents: read
@@ -17,28 +17,28 @@ jobs:
       issues: write
       pull-requests: read
     steps:
-    - name: Get dates for last month
-      shell: bash
-      run: |
-        # Calculate the first day of the previous month
-        first_day=$(date -d "last month" +%Y-%m-01)
+      - name: Get dates for last month
+        shell: bash
+        run: |
+          # Calculate the first day of the previous month
+          first_day=$(date -d "last month" +%Y-%m-01)
 
-        # Calculate the last day of the previous month
-        last_day=$(date -d "$first_day +1 month -1 day" +%Y-%m-%d)
+          # Calculate the last day of the previous month
+          last_day=$(date -d "$first_day +1 month -1 day" +%Y-%m-%d)
 
-        #Set an environment variable with the date range
-        echo "$first_day..$last_day"
-        echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
+          #Set an environment variable with the date range
+          echo "$first_day..$last_day"
+          echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
 
-    - name: Run issue-metrics tool
-      uses: github/issue-metrics@v3
-      env:
-        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        SEARCH_QUERY: 'repo:materialsproject/pymatgen is:issue created:${{ env.last_month }} -reason:"not planned"'
+      - name: Run issue-metrics tool
+        uses: github/issue-metrics@v3
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SEARCH_QUERY: 'repo:materialsproject/pymatgen is:issue created:${{ env.last_month }} -reason:"not planned"'
 
-    - name: Create issue
-      uses: peter-evans/create-issue-from-file@v5
-      with:
-        title: Monthly issue metrics report
-        token: ${{ secrets.GITHUB_TOKEN }}
-        content-filepath: ./issue_metrics.md
+      - name: Create issue
+        uses: peter-evans/create-issue-from-file@v5
+        with:
+          title: Monthly issue metrics report
+          token: ${{ secrets.GITHUB_TOKEN }}
+          content-filepath: ./issue_metrics.md

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -65,8 +65,8 @@ def simple_expansion(
             CoordinationEnvironmentMorphing
         """
         morphing_description = [
-            {"ineighbor": i_nb, "site_type": "neighbor", "expansion_origin": "central_site"}
-            for i_nb in neighbors_indices
+            {"ineighbor": nbr_idx, "site_type": "neighbor", "expansion_origin": "central_site"}
+            for nbr_idx in neighbors_indices
         ]
         return cls(
             initial_environment_symbol=initial_environment_symbol,
@@ -158,11 +158,11 @@ def get_structure(self, morphing_factor):
             if morphing["site_type"] != "neighbor":
                 raise ValueError(f"Key \"site_type\" is {morphing['site_type']} while it can only be neighbor")
 
-            i_site = morphing["ineighbor"] + 1
+            site_idx = morphing["ineighbor"] + 1
             if morphing["expansion_origin"] == "central_site":
                 origin = bare_points[0]
-            vector = bare_points[i_site] - origin
-            coords[i_site] += vector * (morphing_factor - 1.0)
+            vector = bare_points[site_idx] - origin
+            coords[site_idx] += vector * (morphing_factor - 1.0)
 
         return Structure(lattice=lattice, species=species, coords=coords, coords_are_cartesian=True)
 

src/pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -142,8 +142,8 @@ def make_supergraph(graph, multiplicity, periodicity_vectors):
     if isinstance(multiplicity, int) or len(multiplicity) == 1:
         mult = multiplicity if isinstance(multiplicity, int) else multiplicity[0]
         nodes = graph.nodes(data=True)
-        inodes = [isite for isite, data in nodes]
-        indices_nodes = {isite: inodes.index(isite) for isite in inodes}
+        node_indices = [idx for idx, data in nodes]
+        indices_nodes = {idx: node_indices.index(idx) for idx in node_indices}
         edges = graph.edges(data=True, keys=True)
         connecting_edges = []
         other_edges = []

src/pymatgen/analysis/chemenv/connectivity/connectivity_finder.py

@@ -46,24 +46,24 @@ def get_structure_connectivity(self, light_structure_environments):
         logging.info("Setup of structure connectivity graph")
         structure_connectivity = StructureConnectivity(light_structure_environments)
         structure_connectivity.add_sites()
-        for isite, _site in enumerate(light_structure_environments.structure):
-            site_neighbors_sets = light_structure_environments.neighbors_sets[isite]
+        for site_idx, _site in enumerate(light_structure_environments.structure):
+            site_neighbors_sets = light_structure_environments.neighbors_sets[site_idx]
             if site_neighbors_sets is None:
                 continue
             if len(site_neighbors_sets) > 1:
                 if self.multiple_environments_choice is None:
-                    raise ValueError(f"Local environment of site {isite} is a mix and nothing is asked about it")
+                    raise ValueError(f"Local environment of site {site_idx} is a mix and nothing is asked about it")
                 if self.multiple_environments_choice == "TAKE_HIGHEST_FRACTION":
-                    imax = np.argmax(
-                        [ee["ce_fraction"] for ee in light_structure_environments.coordination_environments[isite]]
+                    idx_max = np.argmax(
+                        [ee["ce_fraction"] for ee in light_structure_environments.coordination_environments[site_idx]]
                     )
-                    print(f"IMAX {imax}")
-                    site_neighbors_set = site_neighbors_sets[imax]
+                    print(f"IMAX {idx_max}")
+                    site_neighbors_set = site_neighbors_sets[idx_max]
                 else:
                     raise RuntimeError("Should not be here")
             else:
                 site_neighbors_set = site_neighbors_sets[0]
-            structure_connectivity.add_bonds(isite, site_neighbors_set)
+            structure_connectivity.add_bonds(site_idx, site_neighbors_set)
         return structure_connectivity
 
     def setup_parameters(self, multiple_environments_choice):

src/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py

@@ -114,8 +114,8 @@ def add_bonds(self, isite, site_neighbors_set):
                         exists = True
                         break
             elif isite == nb_index_unitcell:
-                for isite1, ineighb1, data1 in existing_edges:
-                    if isite1 == ineighb1 and (
+                for site_idx1, ineighb1, data1 in existing_edges:
+                    if site_idx1 == ineighb1 and (
                         np.allclose(data1["delta"], nb_image_cell) or np.allclose(data1["delta"], -nb_image_cell)
                     ):
                         exists = True
@@ -164,7 +164,7 @@ def setup_environment_subgraph(self, environments_symbols, only_atoms=None):
         # Initialize graph for a subset of environments
         self._environment_subgraph = nx.MultiGraph()
         # Add the sites with the required environment(s)
-        for isite, ce_this_site_all in enumerate(self.light_structure_environments.coordination_environments):
+        for site_idx, ce_this_site_all in enumerate(self.light_structure_environments.coordination_environments):
             if ce_this_site_all is None:
                 continue
             if len(ce_this_site_all) == 0:
@@ -173,30 +173,30 @@ def setup_environment_subgraph(self, environments_symbols, only_atoms=None):
             if ce_this_site in environments_symbols:
                 if only_atoms is None:
                     env_node = get_environment_node(
-                        self.light_structure_environments.structure[isite],
-                        isite,
+                        self.light_structure_environments.structure[site_idx],
+                        site_idx,
                         ce_this_site,
                     )
                     self._environment_subgraph.add_node(env_node)
                 elif self.light_structure_environments.structure.is_ordered:
-                    if self.light_structure_environments.structure[isite].specie.symbol in only_atoms:
+                    if self.light_structure_environments.structure[site_idx].specie.symbol in only_atoms:
                         env_node = get_environment_node(
-                            self.light_structure_environments.structure[isite],
-                            isite,
+                            self.light_structure_environments.structure[site_idx],
+                            site_idx,
                             ce_this_site,
                         )
                         self._environment_subgraph.add_node(env_node)
                 else:
                     # TODO add the possibility of a "constraint" on the minimum percentage
                     # of the atoms on the site
                     this_site_elements = [
-                        sp.symbol for sp in self.light_structure_environments.structure[isite].species_and_occu
+                        sp.symbol for sp in self.light_structure_environments.structure[site_idx].species_and_occu
                     ]
                     for elem_symbol in this_site_elements:
                         if elem_symbol in only_atoms:
                             env_node = get_environment_node(
-                                self.light_structure_environments.structure[isite],
-                                isite,
+                                self.light_structure_environments.structure[site_idx],
+                                site_idx,
                                 ce_this_site,
                             )
                             self._environment_subgraph.add_node(env_node)

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

@@ -262,9 +262,9 @@ def equivalent_site_index_and_transform(self, psite):
                 uc_psite = psite.to_unit_cell()
                 site_idx = self.structure_environments.structure.index(uc_psite)
             except ValueError:
-                for isite2, site2 in enumerate(self.structure_environments.structure):
+                for site_idx2, site2 in enumerate(self.structure_environments.structure):
                     if psite.is_periodic_image(site2):
-                        site_idx = isite2
+                        site_idx = site_idx2
                         break
         # Get the translation between psite and its corresponding site in the unit cell (Translation I)
         this_site = self.structure_environments.structure[site_idx]

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

@@ -677,7 +677,7 @@ def compute_structure_environments(
             ]
 
         if only_indices is not None:
-            sites_indices = [isite for isite in indices if isite in only_indices]
+            sites_indices = [*set(indices) & set(only_indices)]
 
         # Get the VoronoiContainer for the sites defined by their indices (sites_indices)
         logging.debug("Getting DetailedVoronoiContainer")
@@ -749,22 +749,22 @@ def compute_structure_environments(
             self.detailed_voronoi.separations = [None] * len(self.structure)
 
         # Loop on all the sites
-        for isite, site in enumerate(self.structure):
-            if isite not in sites_indices:
-                logging.debug(f" ... in site #{isite}/{len(self.structure)} ({site.species_string}) : skipped")
+        for site_idx, site in enumerate(self.structure):
+            if site_idx not in sites_indices:
+                logging.debug(f" ... in site #{site_idx}/{len(self.structure)} ({site.species_string}) : skipped")
                 continue
             if break_it:
                 logging.debug(
-                    f" ... in site #{isite}/{len(self.structure)} ({site.species_string}) : skipped (timelimit)"
+                    f" ... in site #{site_idx}/{len(self.structure)} ({site.species_string}) : skipped (timelimit)"
                 )
                 continue
-            logging.debug(f" ... in site #{isite}/{len(self.structure)} ({site.species_string})")
+            logging.debug(f" ... in site #{site_idx}/{len(self.structure)} ({site.species_string})")
             t1 = time.process_time()
             if optimization > 0:
-                self.detailed_voronoi.local_planes[isite] = {}
-                self.detailed_voronoi.separations[isite] = {}
+                self.detailed_voronoi.local_planes[site_idx] = {}
+                self.detailed_voronoi.separations[site_idx] = {}
             struct_envs.init_neighbors_sets(
-                isite=isite,
+                isite=site_idx,
                 additional_conditions=additional_conditions,
                 valences=valences,
             )
@@ -773,15 +773,15 @@ def compute_structure_environments(
             nb_sets_info = {}
             cn = 0
 
-            for cn, nb_sets in struct_envs.neighbors_sets[isite].items():
+            for cn, nb_sets in struct_envs.neighbors_sets[site_idx].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}, {inb_set})")
                     t_nbset1 = time.process_time()
                     ce = self.update_nb_set_environments(
                         se=struct_envs,
-                        isite=isite,
+                        isite=site_idx,
                         cn=cn,
                         inb_set=inb_set,
                         nb_set=nb_set,
@@ -809,7 +809,7 @@ def compute_structure_environments(
                                     logging.debug(f"           hint # {idx_new}")
                                     new_nb_set = struct_envs.NeighborsSet(
                                         structure=struct_envs.structure,
-                                        isite=isite,
+                                        isite=site_idx,
                                         detailed_voronoi=struct_envs.voronoi,
                                         site_voronoi_indices=new_nb_set_voronoi_indices,
                                         sources={
@@ -827,14 +827,14 @@ 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 struct_envs.neighbors_sets[isite]:
+                                    elif cn_new_nb_set not in struct_envs.neighbors_sets[site_idx]:
                                         has_nb_set = False
                                     else:
-                                        has_nb_set = new_nb_set in struct_envs.neighbors_sets[isite][cn_new_nb_set]
+                                        has_nb_set = new_nb_set in struct_envs.neighbors_sets[site_idx][cn_new_nb_set]
                                     if not has_nb_set:
                                         to_add_from_hints.append(
                                             {
-                                                "isite": isite,
+                                                "isite": site_idx,
                                                 "new_nb_set": new_nb_set,
                                                 "cn_new_nb_set": cn_new_nb_set,
                                             }
@@ -844,7 +844,7 @@ 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:
-                struct_envs.add_neighbors_set(isite=isite, nb_set=missing_nb_set_to_add["new_nb_set"])
+                struct_envs.add_neighbors_set(isite=site_idx, 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"]
@@ -865,7 +865,7 @@ def compute_structure_environments(
                     nb_sets_info[cn] = {}
                 nb_sets_info[cn][inew_nb_set] = {"time": t_nbset2 - t_nbset1}
             t2 = time.process_time()
-            struct_envs.update_site_info(isite=isite, info_dict={"time": t2 - t1, "nb_sets_info": nb_sets_info})
+            struct_envs.update_site_info(isite=site_idx, 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
@@ -1029,7 +1029,7 @@ def setup_test_perfect_environment(
         # Rotating the test environment
         if random_rotation == "RANDOM":
             uu = rng.random(3) + 0.1
-            uu = uu / norm(uu)
+            uu /= norm(uu)
             theta = np.pi * rng.random()
             cos_theta = np.cos(theta)
             sin_theta = np.sin(theta)