Revert "New ruff fixes."

This reverts commit ea8c3c5.

src/pymatgen/analysis/graphs.py

@@ -2419,8 +2419,8 @@ def find_rings(self, including=None) -> list[list[tuple[int, int]]]:
 
         for cycle in cycles_nodes:
             edges = []
-            for _idx, itm in enumerate(cycle, start=-1):
-                edges.append((itm, itm))
+            for idx, itm in enumerate(cycle, start=-1):
+                edges.append((cycle[idx], itm))
             cycles_edges.append(edges)
 
         return cycles_edges

src/pymatgen/core/structure.py

@@ -3465,20 +3465,20 @@ def find_nn_pos_before_site(site_idx: int):
             elif idx == 1:
                 nn = find_nn_pos_before_site(idx)
                 bond_length = self.get_distance(idx, nn[0])
-                output.append(f"{site.specie} {nn[0] + 1} B{idx}")
+                output.append(f"{self[idx].specie} {nn[0] + 1} B{idx}")
                 output_var.append(f"B{idx}={bond_length:.6f}")
             elif idx == 2:
                 nn = find_nn_pos_before_site(idx)
                 bond_length = self.get_distance(idx, nn[0])
                 angle = self.get_angle(idx, nn[0], nn[1])
-                output.append(f"{site.specie} {nn[0] + 1} B{idx} {nn[1] + 1} A{idx}")
+                output.append(f"{self[idx].specie} {nn[0] + 1} B{idx} {nn[1] + 1} A{idx}")
                 output_var.extend((f"B{idx}={bond_length:.6f}", f"A{idx}={angle:.6f}"))
             else:
                 nn = find_nn_pos_before_site(idx)
                 bond_length = self.get_distance(idx, nn[0])
                 angle = self.get_angle(idx, nn[0], nn[1])
                 dih = self.get_dihedral(idx, nn[0], nn[1], nn[2])
-                output.append(f"{site.specie} {nn[0] + 1} B{idx} {nn[1] + 1} A{idx} {nn[2] + 1} D{idx}")
+                output.append(f"{self[idx].specie} {nn[0] + 1} B{idx} {nn[1] + 1} A{idx} {nn[2] + 1} D{idx}")
                 output_var.extend((f"B{idx}={bond_length:.6f}", f"A{idx}={angle:.6f}", f"D{idx}={dih:.6f}"))
         return "\n".join(output) + "\n\n" + "\n".join(output_var)
 

src/pymatgen/io/abinit/netcdf.py

@@ -1,3 +1,5 @@
+#
+
 """Wrapper for netCDF readers."""
 
 from __future__ import annotations

src/pymatgen/io/abinit/pseudos.py

@@ -1095,7 +1095,7 @@ def read_ppdesc(self, filename):
 
                 if pspcod == 7:
                     # PAW -> need to know the format pspfmt
-                    tokens = line.split()
+                    tokens = lines[lineno].split()
                     pspfmt, _creatorID = tokens[:2]
 
                     ppdesc = ppdesc._replace(format=pspfmt)

src/pymatgen/io/adf.py

@@ -192,8 +192,8 @@ def remove_subkey(self, subkey):
         """
         if len(self.subkeys) > 0:
             key = subkey if isinstance(subkey, str) else subkey.key
-            for idx, sk in enumerate(self.subkeys):
-                if sk.key == key:
+            for idx, subkey in enumerate(self.subkeys):
+                if subkey.key == key:
                     self.subkeys.pop(idx)
                     break
 

src/pymatgen/io/cp2k/inputs.py

@@ -2531,7 +2531,7 @@ def from_str(cls, string: str) -> Self:
         if "GTH" in string:
             data["potential_type"] = "GTH"
         for idx, char in enumerate(string, start=1):
-            if char == "Q" and char.isnumeric():
+            if char == "Q" and string[idx].isnumeric():
                 data["electrons"] = int("".join(_ for _ in string[idx:] if _.isnumeric()))
 
         for x in ("LDA", "PADA", "MGGA", "GGA", "HF", "PBE0", "PBE", "BP", "BLYP", "B3LYP", "SCAN"):

src/pymatgen/io/lmto.py

@@ -197,7 +197,7 @@ def from_str(cls, data: str, sigfigs: int = 8) -> Self:
                         pass
                 elif token in ["PLAT", "POS"]:
                     try:
-                        arr = np.array([round(float(i), sigfigs) for i in field.split()])
+                        arr = np.array([round(float(i), sigfigs) for i in fields[idx].split()])
                     except ValueError:
                         arr = np.array([round(float(i), sigfigs) for i in fields[idx].split()[:-1]])
                     if token == "PLAT":

src/pymatgen/io/vasp/outputs.py

@@ -137,10 +137,10 @@ def _parse_vasp_array(elem) -> list[list[float]]:
 def _parse_from_incar(filename: PathLike, key: str) -> Any:
     """Helper function to parse a parameter from the INCAR."""
     dirname = os.path.dirname(filename)
-    for fn in os.listdir(dirname):
-        if re.search("INCAR", fn):
+    for filename in os.listdir(dirname):
+        if re.search("INCAR", filename):
             warnings.warn(f"INCAR found. Using {key} from INCAR.")
-            incar = Incar.from_file(os.path.join(dirname, fn))
+            incar = Incar.from_file(os.path.join(dirname, filename))
             return incar.get(key, None)
     return None
 

src/pymatgen/io/xtb/inputs.py

@@ -84,7 +84,7 @@ def constrains_template(molecule, reference_fnm, constraints) -> str:
             if val + 1 not in atoms_for_mtd:
                 interval_list.append(val)
                 if idx != len(atoms_for_mtd):
-                    interval_list.append(val)
+                    interval_list.append(atoms_for_mtd[idx])
         allowed_mtd_string = ",".join(
             [f"{interval_list[i]}-{interval_list[i + 1]}" for i in range(len(interval_list)) if i % 2 == 0]
         )

src/pymatgen/io/xtb/outputs.py

@@ -74,8 +74,8 @@ def _parse_crest_output(self):
             value = None
             if entry and "-" in entry:
                 option = entry[1:]
-                if i < len(split_cmd) and "-" not in entry:
-                    value = entry
+                if i < len(split_cmd) and "-" not in split_cmd[i]:
+                    value = split_cmd[i]
                 self.cmd_options[option] = value
         # Get input charge for decorating parsed molecules
         chg = 0

src/pymatgen/phonon/thermal_displacements.py

@@ -332,6 +332,7 @@ def visualize_directionality_quality_criterion(
             raise ValueError("Illegal which_structure value.")
 
         with open(filename, mode="w", encoding="utf-8") as file:
+            #
             file.write("#VESTA_FORMAT_VERSION 3.5.4\n \n \n")
             file.write("CRYSTAL\n\n")
             file.write("TITLE\n")

src/pymatgen/symmetry/kpath.py

@@ -1482,13 +1482,13 @@ def _get_key_lines(key_points, bz_as_key_point_inds):
             face_center_ind = facet_as_key_point_inds[-1]
             for j, ind in enumerate(facet_as_key_point_inds_bndy, start=-1):
                 if (
-                    min(ind, ind),
-                    max(ind, ind),
+                    min(ind, facet_as_key_point_inds_bndy[j]),
+                    max(ind, facet_as_key_point_inds_bndy[j]),
                 ) not in key_lines:
                     key_lines.append(
                         (
-                            min(ind, ind),
-                            max(ind, ind),
+                            min(ind, facet_as_key_point_inds_bndy[j]),
+                            max(ind, facet_as_key_point_inds_bndy[j]),
                         )
                     )
                 k = j + 2 if j != len(facet_as_key_point_inds_bndy) - 2 else 0

tests/io/abinit/test_inputs.py

@@ -184,8 +184,8 @@ def test_api(self):
         assert len(multi) == 1
         assert multi.ndtset == 1
         assert multi.isnc
-        for _i, inp in enumerate(multi):
-            assert list(inp) == list(inp)
+        for i, inp in enumerate(multi):
+            assert list(inp) == list(multi[i])
 
         multi.addnew_from(0)
         assert multi.ndtset == 2