precommit

Author: esoteric-ephemera

pymatgen/io/validation/check_common_errors.py

@@ -6,7 +6,6 @@
 from typing import TYPE_CHECKING
 
 from pymatgen.io.validation.common import SETTINGS, BaseValidator
-from pymatgen.io.validation.settings import IOValidationSettings
 
 if TYPE_CHECKING:
     from numpy.typing import ArrayLike

pymatgen/io/validation/check_incar.py

@@ -15,6 +15,7 @@
 
 # TODO: fix ISIF getting overwritten by MP input set.
 
+
 class CheckIncar(BaseValidator):
     """
     Check calculation parameters related to INCAR input tags.
@@ -35,8 +36,7 @@ class CheckIncar(BaseValidator):
 
     name: str = "Check INCAR tags"
     fft_grid_tolerance: float | None = Field(
-        SETTINGS.VASP_FFT_GRID_TOLERANCE,
-        description="Tolerance for determining sufficient density of FFT grid."
+        SETTINGS.VASP_FFT_GRID_TOLERANCE, description="Tolerance for determining sufficient density of FFT grid."
     )
     bandgap_tol: float = Field(1.0e-4, description="Tolerance for assuming a material has no gap.")
 
@@ -72,7 +72,7 @@ def check(self, vasp_files: VaspFiles, reasons: list[str], warnings: list[str])
             resp = vasp_param.check(user_incar_params[vasp_param.name], valid_incar_params[vasp_param.name])
             msgs[vasp_param.severity].extend(resp.get(vasp_param.severity, []))
 
-    def update_parameters_and_defaults(self, vasp_files: VaspFiles) -> tuple[dict[str,Any], dict[str,Any]]:
+    def update_parameters_and_defaults(self, vasp_files: VaspFiles) -> tuple[dict[str, Any], dict[str, Any]]:
         """Update a set of parameters according to supplied rules and defaults.
 
         While many of the parameters in VASP need only a simple check to determine
@@ -298,10 +298,7 @@ def _update_fft_params(self, user_incar: dict, ref_incar: dict, vasp_files: Vasp
         """Update ENCUT and parameters related to the FFT grid."""
 
         # ensure that ENCUT is appropriately updated
-        user_incar["ENMAX"] = user_incar.get(
-            "ENCUT",
-            getattr(vasp_files.vasprun,"parameters",{}).get("ENMAX")
-        )
+        user_incar["ENMAX"] = user_incar.get("ENCUT", getattr(vasp_files.vasprun, "parameters", {}).get("ENMAX"))
 
         ref_incar["ENMAX"] = vasp_files.valid_input_set.incar.get("ENCUT", self.vasp_defaults["ENMAX"])
 
@@ -513,17 +510,17 @@ def _update_electronic_params(self, user_incar: dict, ref_incar: dict, vasp_file
                 )
             except Exception:
                 self.vasp_defaults["NELECT"] = VaspParam(
-                    name = "NELECT",
-                    value = None,
-                    tag = "electronic",
-                    operation= "auto fail",
+                    name="NELECT",
+                    value=None,
+                    tag="electronic",
+                    operation="auto fail",
                     severity="warning",
-                    alias = "NELECT / POTCAR",
+                    alias="NELECT / POTCAR",
                     comment=(
                         "Issue checking whether NELECT was changed to make "
                         "the structure have a non-zero charge. This is likely due to the "
                         "directory not having a POTCAR file."
-                    )
+                    ),
                 )
 
             # NBANDS.
@@ -549,10 +546,9 @@ def _update_ionic_params(self, user_incar: dict, ref_incar: dict, vasp_files: Va
 
         # IBRION.
         ref_incar["IBRION"] = [-1, 1, 2]
-        if (
-            (inp_set_ibrion := vasp_files.valid_input_set.incar.get("IBRION")) 
-            and inp_set_ibrion not in ref_incar["IBRION"]
-        ):
+        if (inp_set_ibrion := vasp_files.valid_input_set.incar.get("IBRION")) and inp_set_ibrion not in ref_incar[
+            "IBRION"
+        ]:
             ref_incar["IBRION"].append(inp_set_ibrion)
 
         ionic_steps = []

pymatgen/io/validation/check_kpoints_kspacing.py

@@ -70,7 +70,7 @@ def _check_user_shifted_mesh(self, vasp_files: VaspFiles, reasons: list[str], wa
     def _check_explicit_mesh_permitted(self, vasp_files: VaspFiles, reasons: list[str], warnings: list[str]) -> None:
         # Check for explicit kpoint meshes
 
-        if isinstance(self.allow_explicit_kpoint_mesh,bool):
+        if isinstance(self.allow_explicit_kpoint_mesh, bool):
             allow_explicit = self.allow_explicit_kpoint_mesh
         elif self.allow_explicit_kpoint_mesh == "auto":
             allow_explicit = vasp_files.run_type == "nonscf"

pymatgen/io/validation/common.py

@@ -6,7 +6,7 @@
 from importlib import import_module
 import os
 from pathlib import Path
-from pydantic import BaseModel, Field, computed_field, model_serializer, PrivateAttr
+from pydantic import BaseModel, Field, model_serializer, PrivateAttr
 from typing import TYPE_CHECKING, Any
 
 from pymatgen.core import Structure
@@ -21,6 +21,7 @@
 
 SETTINGS = IOValidationSettings()
 
+
 class ValidationError(Exception):
     """Define custom exception during validation."""
 
@@ -35,11 +36,9 @@ class _PotcarSummaryStatsKeywords(BaseModel):
         data: set[str] = Field(description="The keywords in the POTCAR body.")
 
         @model_serializer
-        def set_to_list(self) -> dict[str,list[str]]:
+        def set_to_list(self) -> dict[str, list[str]]:
             """Ensure JSON compliance of set fields."""
-            return {
-                k : list(getattr(self,k)) for k in ("header","data")
-            }
+            return {k: list(getattr(self, k)) for k in ("header", "data")}
 
     class _PotcarSummaryStatsStats(BaseModel):
         """Schematize `PotcarSingle._summary_stats["stats"]` field."""
@@ -88,7 +87,10 @@ class LightVasprun(BaseModel):
     kpoints: Kpoints = Field(description="The actual k-points used in the calculation.")
     parameters: dict[str, Any] = Field(description="The default-padded input parameters interpreted by VASP.")
     bandgap: float = Field(description="The bandgap - note that this field is derived from the Vasprun object.")
-    potcar_symbols : list[str] | None = Field(None, description="Optional: if a POTCAR is unavailable, this is used to determine the functional used in the calculation.")
+    potcar_symbols: list[str] | None = Field(
+        None,
+        description="Optional: if a POTCAR is unavailable, this is used to determine the functional used in the calculation.",
+    )
 
     @classmethod
     def from_vasprun(cls, vasprun: Vasprun) -> Self:
@@ -105,7 +107,7 @@ class VaspInputSafe(BaseModel):
     structure: Structure = Field(description="The structure associated with the calculation.")
     kpoints: Kpoints | None = Field(None, description="The optional KPOINTS or IBZKPT file used in the calculation.")
     potcar: list[PotcarSummaryStats] | None = Field(None, description="The optional POTCAR used in the calculation.")
-    _pmg_vis : VaspInputSet | None = PrivateAttr(None)
+    _pmg_vis: VaspInputSet | None = PrivateAttr(None)
 
     @model_serializer
     def deserialize_objects(self) -> dict[str, Any]:
@@ -136,7 +138,6 @@ def from_vasp_input_set(cls, vis: VaspInputSet) -> Self:
         new_vis._pmg_vis = vis
         return new_vis
 
-    
     def _calculate_ng(self, **kwargs) -> tuple[list[int], list[int]] | None:
         """Interface to pymatgen vasp input set as needed."""
         if self._pmg_vis:
@@ -147,7 +148,7 @@ def _calculate_ng(self, **kwargs) -> tuple[list[int], list[int]] | None:
 class VaspFiles(BaseModel):
     """Define required and optional files for validation."""
 
-    user_input : VaspInputSafe = Field(description="The VASP input set used in the calculation.")
+    user_input: VaspInputSafe = Field(description="The VASP input set used in the calculation.")
     outcar: LightOutcar | None = None
     vasprun: LightVasprun | None = None
 
@@ -194,7 +195,7 @@ def from_paths(
             if (path := _vars.get(file_name)) and Path(path).exists():
                 if file_name == "poscar":
                     config["user_input"]["structure"] = file_cls.from_file(path).structure
-                elif hasattr(file_cls,"from_file"):
+                elif hasattr(file_cls, "from_file"):
                     config["user_input"][file_name] = file_cls.from_file(path)
                 else:
                     config[file_name] = file_cls(path)
@@ -204,7 +205,8 @@ def from_paths(
 
         if config.get("outcar"):
             config["outcar"] = LightOutcar(
-                drift = config["outcar"].drift, magnetization=config["outcar"].magnetization,
+                drift=config["outcar"].drift,
+                magnetization=config["outcar"].magnetization,
             )
         if config.get("vasprun"):
             config["vasprun"] = LightVasprun.from_vasprun(config["vasprun"])

pymatgen/io/validation/emmet_validation.py

@@ -42,9 +42,9 @@ class ValidationDoc(EmmetBaseModel):
     warnings: list[str] = Field([], description="List of potential warnings about this calculation")
 
     @staticmethod
-    def task_doc_to_vasp_files(task_doc : TaskDoc | TaskDocument) -> VaspFiles:
+    def task_doc_to_vasp_files(task_doc: TaskDoc | TaskDocument) -> VaspFiles:
         """Convert an emmet.core TaskDoc or legacy TaskDocument to VaspFiles."""
-        
+
         if isinstance(task_doc, TaskDocument):
             final_calc = Calculation(**task_doc.calcs_reversed[0])
         else:
@@ -66,12 +66,12 @@ def task_doc_to_vasp_files(task_doc : TaskDoc | TaskDocument) -> VaspFiles:
         return VaspFiles(
             user_input=VaspInputSafe(
                 incar=Incar(final_calc.input.incar),
-                kpoints = final_calc.input.kpoints,
+                kpoints=final_calc.input.kpoints,
                 structure=final_calc.input.structure,
                 potcar=potcar_stats,
             ),
-            outcar = LightOutcar(**{k: final_calc.output.outcar.get(k) for k in ("drift", "magnetization")}),
-            vasprun = LightVasprun(
+            outcar=LightOutcar(**{k: final_calc.output.outcar.get(k) for k in ("drift", "magnetization")}),
+            vasprun=LightVasprun(
                 vasp_version=final_calc.vasp_version,
                 ionic_steps=[ionic_step.model_dump() for ionic_step in final_calc.output.ionic_steps],
                 final_energy=task_doc.output.energy,
@@ -91,6 +91,6 @@ def from_task_doc(cls, task_doc: TaskDoc | TaskDocument, **kwargs) -> Self:
             valid=validator.is_valid,
             reasons=validator.reasons,
             warnings=validator.warnings,
-            task_id = task_doc.task_id,
+            task_id=task_doc.task_id,
             **kwargs,
         )

pymatgen/io/validation/validation.py

@@ -39,7 +39,7 @@ def from_vasp_input(
         vasp_file_paths: dict[str, os.PathLike[str]] | None = None,
         vasp_files: VaspFiles | None = None,
         fast: bool = False,
-        check_potcar : bool = True,
+        check_potcar: bool = True,
     ):
 
         if not vasp_files and vasp_file_paths:

tests/conftest.py

@@ -11,11 +11,13 @@
 def test_dir():
     return _test_dir
 
-vasp_calc_data : dict[str,VaspFiles] = {
-    k : VaspFiles(**loadfn(_test_dir / "vasp" / f"{k}.json.gz"))
-    for k in ("Si_uniform","Si_static","Si_old_double_relax")
+
+vasp_calc_data: dict[str, VaspFiles] = {
+    k: VaspFiles(**loadfn(_test_dir / "vasp" / f"{k}.json.gz"))
+    for k in ("Si_uniform", "Si_static", "Si_old_double_relax")
 }
 
+
 def incar_check_list():
     """Pre-defined list of pass/fail tests."""
-    return loadfn(_test_dir / "vasp" / "scf_incar_check_list.yaml")
+    return loadfn(_test_dir / "vasp" / "scf_incar_check_list.yaml")