Avoid using eval, replace manual offset in enumerate and rename s…

…ingle letter variables (#3739)

* `sourcery` tweaks

* replace usage of `eval`

* replace `eval`

* replace usage of `eval`

* document default angle_tolerance=5 degrees in SpacegroupAnalyzer

* rename single-letter variables in many files

* rename variables for readability

* use `start` arg in enumerate to replace manual offset

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

pymatgen/analysis/bond_dissociation.py

@@ -104,8 +104,8 @@ def __init__(
                 " are less reliable! This is a bad idea!"
             )
             self.bond_pairs = []
-            for ii, bond in enumerate(self.ring_bonds):
-                for jj in range(ii + 1, len(self.ring_bonds)):
+            for ii, bond in enumerate(self.ring_bonds, start=1):
+                for jj in range(ii, len(self.ring_bonds)):
                     bond_pair = [bond, self.ring_bonds[jj]]
                     self.bond_pairs += [bond_pair]
             for bond_pair in self.bond_pairs:

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -742,7 +742,11 @@ def elastic_centered_graph(self, start_node=None):
         check_centered_connected_subgraph = nx.MultiGraph()
         check_centered_connected_subgraph.add_nodes_from(centered_connected_subgraph.nodes())
         check_centered_connected_subgraph.add_edges_from(
-            [e for e in centered_connected_subgraph.edges(data=True) if np.allclose(e[2]["delta"], np.zeros(3))]
+            [
+                edge
+                for edge in centered_connected_subgraph.edges(data=True)
+                if np.allclose(edge[2]["delta"], np.zeros(3))
+            ]
         )
         if not is_connected(check_centered_connected_subgraph):
             raise RuntimeError("Could not find a centered graph.")

pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -797,7 +797,7 @@ def faces(self, sites, permutation=None):
         list of its vertices coordinates.
         """
         coords = [site.coords for site in sites] if permutation is None else [sites[ii].coords for ii in permutation]
-        return [[coords[ii] for ii in f] for f in self._faces]
+        return [[coords[ii] for ii in face] for face in self._faces]
 
     def edges(self, sites, permutation=None, input="sites"):
         """
@@ -814,7 +814,7 @@ def edges(self, sites, permutation=None, input="sites"):
         #     coords = [sites[ii].coords for ii in permutation]
         if permutation is not None:
             coords = [coords[ii] for ii in permutation]
-        return [[coords[ii] for ii in e] for e in self._edges]
+        return [[coords[ii] for ii in edge] for edge in self._edges]
 
     def solid_angles(self, permutation=None):
         """
@@ -854,11 +854,11 @@ def get_pmeshes(self, sites, permutation=None):
             elif len(face) == 4:
                 out += "5\n"
             else:
-                for ii, f in enumerate(face):
+                for ii, f in enumerate(face, start=1):
                     out += "4\n"
                     out += f"{len(_vertices) + iface}\n"
                     out += f"{f}\n"
-                    out += f"{face[np.mod(ii + 1, len(face))]}\n"
+                    out += f"{face[np.mod(ii, len(face))]}\n"
                     out += f"{len(_vertices) + iface}\n"
             if len(face) in [3, 4]:
                 for face_vertex in face:

pymatgen/analysis/chemenv/coordination_environments/structure_environments.py

@@ -502,7 +502,7 @@ def init_neighbors_sets(self, isite, additional_conditions=None, valences=None):
                     }
                     site_voronoi_indices = [
                         inb
-                        for inb, voro_nb_dict in enumerate(site_voronoi)
+                        for inb, _voro_nb_dict in enumerate(site_voronoi)
                         if (
                             distance_conditions[idp][inb]
                             and angle_conditions[iap][inb]

pymatgen/analysis/chemenv/coordination_environments/voronoi.py

@@ -146,8 +146,8 @@ def setup_voronoi_list(self, indices, voronoi_cutoff):
             logging.debug("Please consider increasing voronoi_distance_cutoff")
         t1 = time.process_time()
         logging.debug("Setting up Voronoi list :")
-        for jj, isite in enumerate(indices):
-            logging.debug(f"  - Voronoi analysis for site #{isite} ({jj + 1}/{len(indices)})")
+        for jj, isite in enumerate(indices, start=1):
+            logging.debug(f"  - Voronoi analysis for site #{isite} ({jj}/{len(indices)})")
             site = self.structure[isite]
             neighbors1 = [(site, 0.0, isite)]
             neighbors1.extend(struct_neighbors[isite])

pymatgen/analysis/chemenv/utils/chemenv_config.py

@@ -97,7 +97,7 @@ def setup_package_options(self):
         self.package_options = self.DEFAULT_PACKAGE_OPTIONS
         print("Choose between the following strategies : ")
         strategies = list(strategies_class_lookup)
-        for idx, strategy in enumerate(strategies, 1):
+        for idx, strategy in enumerate(strategies, start=1):
             print(f" <{idx}> : {strategy}")
         test = input(" ... ")
         self.package_options["default_strategy"] = {

pymatgen/analysis/chemenv/utils/graph_utils.py

@@ -268,7 +268,7 @@ def from_edges(cls, edges, edges_are_ordered: bool = True) -> Self:
         order in the list.
         """
         if edges_are_ordered:
-            nodes = [e[0] for e in edges]
+            nodes = [edge[0] for edge in edges]
             if not all(e1e2[0][1] == e1e2[1][0] for e1e2 in zip(edges, edges[1:])) or edges[-1][1] != edges[0][0]:
                 raise ValueError("Could not construct a cycle from edges.")
         else:
@@ -490,8 +490,8 @@ def get_all_elementary_cycles(graph):
         edge_idx += 1
     cycles_matrix = np.zeros(shape=(len(cycle_basis), edge_idx), dtype=bool)
     for icycle, cycle in enumerate(cycle_basis):
-        for in1, n1 in enumerate(cycle):
-            n2 = cycle[(in1 + 1) % len(cycle)]
+        for in1, n1 in enumerate(cycle, start=1):
+            n2 = cycle[(in1) % len(cycle)]
             iedge = all_edges_dict[(n1, n2)]
             cycles_matrix[icycle, iedge] = True
 

pymatgen/analysis/diffraction/tem.py

@@ -588,7 +588,7 @@ def get_plot_2d(self, structure: Structure) -> go.Figure:
             ),
         ]
         layout = dict(
-            title="2D Diffraction Pattern<br>Beam Direction: " + "".join(str(e) for e in self.beam_direction),
+            title="2D Diffraction Pattern<br>Beam Direction: " + "".join(map(str, self.beam_direction)),
             font={"size": 14, "color": "#7f7f7f"},
             hovermode="closest",
             xaxis={

pymatgen/analysis/elasticity/elastic.py

@@ -276,7 +276,7 @@ def snyder_ac(self, structure: Structure) -> float:
         n_sites = len(structure)
         n_atoms = structure.composition.num_atoms
         site_density = 1e30 * n_sites / structure.volume
-        tot_mass = sum(e.atomic_mass for e in structure.species)
+        tot_mass = sum(spec.atomic_mass for spec in structure.species)
         avg_mass = 1.6605e-27 * tot_mass / n_atoms
         return (
             0.38483
@@ -330,7 +330,7 @@ def clarke_thermalcond(self, structure: Structure) -> float:
             float: Clarke's thermal conductivity (in SI units)
         """
         n_sites = len(structure)
-        tot_mass = sum(e.atomic_mass for e in structure.species)
+        tot_mass = sum(spec.atomic_mass for spec in structure.species)
         n_atoms = structure.composition.num_atoms
         weight = float(structure.composition.weight)
         avg_mass = 1.6605e-27 * tot_mass / n_atoms
@@ -761,8 +761,8 @@ def get_strain_from_stress(self, stress):
         """
         compl_exp = self.get_compliance_expansion()
         strain = 0
-        for n, compl in enumerate(compl_exp):
-            strain += compl.einsum_sequence([stress] * (n + 1)) / factorial(n + 1)
+        for n, compl in enumerate(compl_exp, start=1):
+            strain += compl.einsum_sequence([stress] * (n)) / factorial(n)
         return strain
 
     def get_effective_ecs(self, strain, order=2):

pymatgen/analysis/graphs.py

@@ -2156,8 +2156,8 @@ def build_unique_fragments(self):
             unique_frags = []
             for frag in fragments:
                 found = False
-                for f in unique_frags:
-                    if _isomorphic(frag, f):
+                for fragment in unique_frags:
+                    if _isomorphic(frag, fragment):
                         found = True
                         break
                 if not found:
@@ -2438,8 +2438,8 @@ def find_rings(self, including=None) -> list[list[tuple[int, int]]]:
 
         for cycle in cycles_nodes:
             edges = []
-            for idx, itm in enumerate(cycle):
-                edges.append((cycle[idx - 1], itm))
+            for idx, itm in enumerate(cycle, start=-1):
+                edges.append((cycle[idx], itm))
             cycles_edges.append(edges)
 
         return cycles_edges

pymatgen/analysis/local_env.py

@@ -3337,8 +3337,8 @@ def get_order_parameters(
         if self._geomops2:
             # Compute all (unique) angles and sort the resulting list.
             aij = []
-            for ir, r in enumerate(rij_norm):
-                for j in range(ir + 1, len(rij_norm)):
+            for ir, r in enumerate(rij_norm, start=1):
+                for j in range(ir, len(rij_norm)):
                     aij.append(acos(max(-1.0, min(np.inner(r, rij_norm[j]), 1.0))))
             aijs = sorted(aij)
 

pymatgen/analysis/magnetism/heisenberg.py

@@ -187,9 +187,9 @@ def _get_nn_dict(self):
         # Keep only up to NNNN and call dists equal if they are within tol
         all_dists = sorted(set(all_dists))
         rm_list = []
-        for idx, d in enumerate(all_dists[:-1]):
-            if abs(d - all_dists[idx + 1]) < tol:
-                rm_list.append(idx + 1)
+        for idx, d in enumerate(all_dists[:-1], start=1):
+            if abs(d - all_dists[idx]) < tol:
+                rm_list.append(idx)
 
         all_dists = [d for idx, d in enumerate(all_dists) if idx not in rm_list]
 
@@ -567,11 +567,10 @@ def get_interaction_graph(self, filename=None):
 
         # Save to a json file if desired
         if filename:
-            if filename.endswith(".json"):
-                dumpfn(igraph, filename)
-            else:
+            if not filename.endswith(".json"):
                 filename += ".json"
-                dumpfn(igraph, filename)
+
+            dumpfn(igraph, filename)
 
         return igraph
 
@@ -729,8 +728,9 @@ def _do_cleanup(structures, energies):
         # Check for duplicate / degenerate states (sometimes different initial
         # configs relax to the same state)
         remove_list = []
+        e_tol = 6  # 10^-6 eV/atom tol on energies
+
         for idx, energy in enumerate(energies):
-            e_tol = 6  # 10^-6 eV/atom tol on energies
             energy = round(energy, e_tol)
             if idx not in remove_list:
                 for i_check, e_check in enumerate(energies):
@@ -746,7 +746,7 @@ def _do_cleanup(structures, energies):
         #         remove_list.append(idx)
 
         # Remove duplicates
-        if len(remove_list) > 0:
+        if remove_list:
             ordered_structures = [struct for idx, struct in enumerate(ordered_structures) if idx not in remove_list]
             energies = [energy for idx, energy in enumerate(energies) if idx not in remove_list]
 
@@ -923,7 +923,7 @@ def from_dict(cls, dct: dict) -> Self:
 
         # Reconstitute the exchange matrix DataFrame
         try:
-            ex_mat = eval(dct["ex_mat"])
+            ex_mat = literal_eval(dct["ex_mat"])
             ex_mat = pd.DataFrame.from_dict(ex_mat)
         except SyntaxError:  # if ex_mat is empty
             ex_mat = pd.DataFrame(columns=["E", "E0"])