fix ruff PLC0206 Extracting value from dict without calling .items() (#…

…1009)

.pre-commit-config.yaml

@@ -3,13 +3,13 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.6.7
+  rev: v0.6.9
   hooks:
   - id: ruff
     args: [--fix]
   - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: check-yaml
   - id: fix-encoding-pragma

src/atomate2/ase/utils.py

@@ -278,11 +278,11 @@ def as_dict(self) -> dict:
         if self._store_md_outputs:
             traj_dict.update(velocities=self.velocities, temperature=self.temperatures)
         # sanitize dict
-        for key in traj_dict:
-            if all(isinstance(val, np.ndarray) for val in traj_dict[key]):
-                traj_dict[key] = [val.tolist() for val in traj_dict[key]]
-            elif isinstance(traj_dict[key], np.ndarray):
-                traj_dict[key] = traj_dict[key].tolist()
+        for key, value in traj_dict.items():
+            if all(isinstance(val, np.ndarray) for val in value):
+                traj_dict[key] = [val.tolist() for val in value]
+            elif isinstance(value, np.ndarray):
+                traj_dict[key] = value.tolist()
         return traj_dict
 
 

src/atomate2/common/flows/eos.py

@@ -188,7 +188,7 @@ def make(self, structure: Structure, prev_dir: str | Path = None) -> Flow:
             jobs["utility"] += [post_process]
 
         job_list = []
-        for key in jobs:
-            job_list += jobs[key]
+        for val in jobs.values():
+            job_list += val
 
         return Flow(jobs=job_list, output=flow_output, name=self.name)

src/atomate2/common/jobs/gruneisen.py

@@ -77,20 +77,20 @@ def run_phonon_jobs(
     Phonon Jobs or Symmetry of the optimized structures.
     """
     symmetry = []
-    for st in opt_struct:
-        sga = SpacegroupAnalyzer(opt_struct[st], symprec=symprec)
+    for struct in opt_struct.values():
+        sga = SpacegroupAnalyzer(struct, symprec=symprec)
         symmetry.append(int(sga.get_space_group_number()))
     set_symmetry = list(set(symmetry))
     if len(set_symmetry) == 1:
         jobs = []
         phonon_yaml_dirs = dict.fromkeys(("ground", "plus", "minus"), None)
         phonon_imaginary_modes = dict.fromkeys(("ground", "plus", "minus"), None)
-        for st in opt_struct:
+        for st, struct in opt_struct.items():
             # phonon run for all 3 optimized structures (ground state, expanded, shrunk)
             phonon_kwargs = {}
             if prev_calc_dir_argname is not None:
                 phonon_kwargs[prev_calc_dir_argname] = prev_dir_dict[st]
-            phonon_job = phonon_maker.make(structure=opt_struct[st], **phonon_kwargs)
+            phonon_job = phonon_maker.make(structure=struct, **phonon_kwargs)
             phonon_job.append_name(f" {st}")
             # change default phonopy.yaml file name to ensure workflow can be
             # run without having to create folders, thus

src/atomate2/common/schemas/phonons.py

@@ -407,7 +407,7 @@ def from_forces_born(
             force_gamma=True,
         )
         phonon.run_mesh(kpoint.kpts[0])
-        phonon_dos_sigma = kwargs.get("phonon_dos_sigma", None)
+        phonon_dos_sigma = kwargs.get("phonon_dos_sigma")
         dos_use_tetrahedron_method = kwargs.get("dos_use_tetrahedron_method", True)
         phonon.run_total_dos(
             sigma=phonon_dos_sigma, use_tetrahedron_method=dos_use_tetrahedron_method

src/atomate2/cp2k/schemas/calculation.py

@@ -89,8 +89,8 @@ class CalculationInput(BaseModel):
     @classmethod
     def remove_unnecessary(cls, atomic_kind_info: dict) -> dict:
         """Remove unnecessary entry from atomic_kind_info."""
-        for key in atomic_kind_info:
-            if "total_pseudopotential_energy" in atomic_kind_info[key]:
+        for key, value in atomic_kind_info.items():
+            if "total_pseudopotential_energy" in value:
                 del atomic_kind_info[key]["total_pseudopotential_energy"]
         return atomic_kind_info
 
@@ -524,9 +524,9 @@ def _get_volumetric_data(
         except Exception as err:
             raise ValueError(f"Failed to parse {file_type} at {file}.") from err
 
-    for file_type in volumetric_data:
+    for file_type, data in volumetric_data.items():
         if file_type.name in __is_stored_in_Ha__:
-            volumetric_data[file_type].scale(Ha_to_eV)
+            data.scale(Ha_to_eV)
 
     return volumetric_data