Fix ruff PERF401: manual-list-comprehension (#4449)

* unignore PERF401 rule

* fix core

* fix dev_scripts

* fix ext

* fix entries

* fix symmetry

* fix transformations

* fix alchemy

* fix apps

* fix command line

* fix phonon

* fix lobster

* fix vasp

* fix io

* fix electronic structure

* fix analysis

* fix typo

* fix some mypy error

* add test

Author: DanielYang59

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -131,9 +131,7 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                 continue
     n_cols = 5
     n_lines = int(np.ceil(float(len(sep_plane_cgs)) / n_cols))
-    sep_plane_cgs_grid = []
-    for _ in range(n_lines):
-        sep_plane_cgs_grid.append([""] * n_cols)
+    sep_plane_cgs_grid = [[""] * n_cols for _ in range(n_lines)]
     for line_idx in range(n_lines):
         for col_idx in range(n_cols):
             ii = line_idx * n_cols + col_idx

dev_scripts/update_spacegroup_data.py

@@ -58,10 +58,7 @@ def remove_identity_from_full_hermann_mauguin(symbol: str) -> str:
     blickrichtungen = symbol.split(" ")
     if blickrichtungen[1].startswith("3"):
         return symbol
-    blickrichtungen_new = []
-    for br in blickrichtungen:
-        if br != "1":
-            blickrichtungen_new.append(br + " ")
+    blickrichtungen_new = [br + " " for br in blickrichtungen if br != "1"]
     return "".join(blickrichtungen_new)
 
 

pyproject.toml

@@ -213,7 +213,6 @@ ignore = [
     "FBT002", # Boolean default positional argument in function
     "PD011", # (A lot of false positive on non-Pandas objects)
     "PERF203", # Use of try-except in for/while loop
-    "PERF401", # Replace "for" loops with list comprehension
     "PLR0911", # Too many return statements
     "PLR0912", # Too many branches
     "PLR0913", # Too many arguments

src/pymatgen/alchemy/transmuters.py

@@ -80,8 +80,7 @@ def __len__(self):
 
     def __str__(self):
         output = ["Current structures", "------------"]
-        for ts in self.transformed_structures:
-            output.append(str(ts.final_structure))
+        output.extend(str(ts.final_structure) for ts in self.transformed_structures)
         return "\n".join(output)
 
     def undo_last_change(self) -> None:

src/pymatgen/analysis/adsorption.py

@@ -454,20 +454,17 @@ def generate_adsorption_structures(
             xrep = np.ceil(min_lw / np.linalg.norm(self.slab.lattice.matrix[0]))
             yrep = np.ceil(min_lw / np.linalg.norm(self.slab.lattice.matrix[1]))
             repeat = [xrep, yrep, 1]
-        structs = []
 
-        find_args = find_args or {}
-        for coords in self.find_adsorption_sites(**find_args)["all"]:
-            structs.append(
-                self.add_adsorbate(
-                    molecule,
-                    coords,
-                    repeat=repeat,
-                    translate=translate,
-                    reorient=reorient,
-                )
+        return [
+            self.add_adsorbate(
+                molecule,
+                coords,
+                repeat=repeat,
+                translate=translate,
+                reorient=reorient,
             )
-        return structs
+            for coords in self.find_adsorption_sites(**(find_args or {}))["all"]
+        ]
 
     def adsorb_both_surfaces(
         self,

src/pymatgen/analysis/bond_dissociation.py

@@ -150,12 +150,12 @@ def fragment_and_process(self, bonds):
                         # Since a ring opening still yields a single molecule, it should have the same charge as the
                         # principle:
                         if frag["initial_molecule"]["charge"] == self.molecule_entry["final_molecule"]["charge"]:
-                            good_entries.append(frag)
+                            good_entries.append(frag)  # noqa: PERF401
                     # If we didn't find any good entries, let's also look at those that exhibit structural changes:
                     if len(good_entries) == 0:
                         for frag in opened_entries[1]:  # 1 -> YES structural change
                             if frag["initial_molecule"]["charge"] == self.molecule_entry["final_molecule"]["charge"]:
-                                good_entries.append(frag)
+                                good_entries.append(frag)  # noqa: PERF401
                     # If we still have no good entries, something must have gone wrong with the calculations:
                     if len(good_entries) == 0:
                         bb = BabelMolAdaptor.from_molecule_graph(RO_frag)

src/pymatgen/analysis/bond_valence.py

@@ -414,9 +414,7 @@ def _recurse(assigned=None):
 
                 return [int(assigned[site]) for site in structure]
             assigned = {}
-            new_best_vset = []
-            for _ in equi_sites:
-                new_best_vset.append([])
+            new_best_vset = [[] for _ in equi_sites]
             for ival, val in enumerate(self._best_vset):
                 new_best_vset[attrib[ival]].append(val)
             for val, sites in zip(new_best_vset, equi_sites, strict=True):

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

@@ -451,8 +451,7 @@ def compute_periodicity_all_simple_paths_algorithm(self):
                         this_path_deltas_new = []
                         for edge_data in self._connected_subgraph[node1][node2].values():
                             delta = get_delta(node1, node2, edge_data)
-                            for current_delta in this_path_deltas:
-                                this_path_deltas_new.append(current_delta + delta)
+                            this_path_deltas_new.extend(current_delta + delta for current_delta in this_path_deltas)
                         this_path_deltas = this_path_deltas_new
                     this_node_cell_img_vectors.extend(this_path_deltas)
                     this_node_cell_img_vectors = get_linearly_independent_vectors(this_node_cell_img_vectors)
@@ -487,8 +486,7 @@ def compute_periodicity_cycle_basis(self) -> None:
                 this_cycle_deltas_new = []
                 for edge_data in self._connected_subgraph[node1][node2].values():
                     delta = get_delta(node1, node2, edge_data)
-                    for current_delta in this_cycle_deltas:
-                        this_cycle_deltas_new.append(current_delta + delta)
+                    this_cycle_deltas_new.extend(current_delta + delta for current_delta in this_cycle_deltas)
                 this_cycle_deltas = this_cycle_deltas_new
             all_deltas.extend(this_cycle_deltas)
             all_deltas = get_linearly_independent_vectors(all_deltas)

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

@@ -2729,11 +2729,10 @@ def get_site_coordination_environments_fractions(
         site_nb_sets = self.structure_environments.neighbors_sets[isite]
         if site_nb_sets is None:
             return None
-        cn_maps = []
-        for cn, nb_sets in site_nb_sets.items():
-            for inb_set in range(len(nb_sets)):
-                # CHECK THE ADDITIONAL CONDITION HERE ?
-                cn_maps.append((cn, inb_set))
+
+        # CHECK THE ADDITIONAL CONDITION HERE ?
+        cn_maps = [(cn, inb_set) for cn, nb_sets in site_nb_sets.items() for inb_set in range(len(nb_sets))]
+
         weights_additional_info = {"weights": {isite: {}}}
         for wdict in self.ordered_weights:
             cn_maps_new = []

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

@@ -632,8 +632,7 @@ def __str__(self):
             outs.append("... not yet implemented")
         else:
             outs.append("  - list of points :")
-            for pp in self.points:
-                outs.append(f"    - {pp}")
+            outs.extend(f"    - {pp}" for pp in self.points)
         outs.extend(("------------------------------------------------------------", ""))
 
         return "\n".join(outs)
@@ -754,9 +753,7 @@ def ref_permutation(self, permutation):
         Returns:
             Permutation: Reference permutation of the perfect CoordinationGeometry.
         """
-        perms = []
-        for eqv_indices in self.equivalent_indices:
-            perms.append(tuple(permutation[ii] for ii in eqv_indices))
+        perms = [tuple(permutation[ii] for ii in eqv_indices) for eqv_indices in self.equivalent_indices]
         perms.sort()
         return perms[0]
 
@@ -925,8 +922,8 @@ def __repr__(self):
             "#=================================#",
             "",
         ]
-        for cg in self.cg_list:
-            outs.append(repr(cg))
+
+        outs.extend(repr(cg) for cg in self.cg_list)
 
         return "\n".join(outs)
 
@@ -939,9 +936,8 @@ def __str__(self):
             "#=======================================================#",
             "",
         ]
-        for cg in self.cg_list:
-            if cg.is_implemented():
-                outs.append(str(cg))
+
+        outs.extend(str(cg) for cg in self.cg_list if cg.is_implemented())
 
         return "\n".join(outs)