add ruff pre-commit hook

esoteric-ephemera · esoteric-ephemera · commit 2762399fce01 · 2024-05-14T09:34:57.000-07:00
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -8,6 +8,13 @@ ci:
   skip: [flake8, autoflake, mypy]
 
 repos:
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.3
+    hooks:
+      - id: ruff
+        args: [--fix, --unsafe-fixes]
+
   - repo: https://github.com/psf/black
     rev: 24.2.0
     hooks:
diff --git a/examples/MP_compliant_job.py b/examples/MP_compliant_job.py
@@ -9,7 +9,6 @@
 
 
 def get_GaAs_structure(a0: float = 5.6) -> Structure:
-
     lattice_vectors = a0 * np.array([[0.0 if i == j else 0.5 for j in range(3)] for i in range(3)])
     return Structure(
         lattice=Lattice(lattice_vectors),
@@ -32,9 +31,11 @@ def assign_meta(flow, metadata: dict, name: str | None = None):
 
 
 def get_MP_compliant_r2SCAN_flow(
-    structure: Structure, user_incar_settings: dict | None = None, metadata: dict | None = None, name: str | None = None
+    structure: Structure,
+    user_incar_settings: dict | None = None,
+    metadata: dict | None = None,
+    name: str | None = None,
 ) -> Flow:
-
     from atomate2.vasp.jobs.mp import MPMetaGGAStaticMaker
     from atomate2.vasp.powerups import update_user_incar_settings
 
@@ -53,7 +54,6 @@ def get_MP_compliant_r2SCAN_flow(
 
 
 def run_job_fully_locally(flow, job_store=None):
-
     from jobflow import run_locally, JobStore
     from maggma.stores import MemoryStore
 
@@ -66,7 +66,6 @@ def run_job_fully_locally(flow, job_store=None):
 
 
 def MP_compliant_calc():
-
     structure = get_GaAs_structure()
     flow = get_MP_compliant_r2SCAN_flow(
         structure=structure,
@@ -84,7 +83,6 @@ def MP_compliant_calc():
 
 
 def MP_non_compliant_calc():
-
     structure = get_GaAs_structure()
     flow = get_MP_compliant_r2SCAN_flow(
         structure=structure,
@@ -103,16 +101,17 @@ def MP_non_compliant_calc():
 
 
 def MP_flows() -> None:
-
     compliant_task_doc = MP_compliant_calc()
     dumpfn(jsanitize(compliant_task_doc), "./MP_compatible_GaAs_r2SCAN_static.json.gz")
 
     non_compliant_task_doc = MP_non_compliant_calc()
-    dumpfn(jsanitize(non_compliant_task_doc), "./MP_incompatible_GaAs_r2SCAN_static.json.gz")
+    dumpfn(
+        jsanitize(non_compliant_task_doc),
+        "./MP_incompatible_GaAs_r2SCAN_static.json.gz",
+    )
 
 
 def generate_task_documents(cdir, task_id: str | None = None, filename: str | None = None) -> TaskDocument:
-
     from atomate.vasp.drones import VaspDrone
     from emmet.core.mpid import MPID
 
@@ -130,5 +129,4 @@ def generate_task_documents(cdir, task_id: str | None = None, filename: str | No
 
 
 if __name__ == "__main__":
-
     MP_flows()
diff --git a/pymatgen/io/validation/check_common_errors.py b/pymatgen/io/validation/check_common_errors.py
@@ -84,7 +84,6 @@ def _check_parse(self) -> None:
             )
 
     def _check_gga_and_metagga(self) -> None:
-
         # Check for cases where both GGA and METAGGA are set. This should *not* be allowed, as it can erroneously change
         # the outputted energy significantly. See https://github.com/materialsproject/atomate2/issues/453#issuecomment-1699605867
         # for more details.
@@ -101,7 +100,6 @@ def _check_electronic_convergence(self) -> None:
         if self.incar.get("ALGO", self.defaults["ALGO"]["value"]).lower() != "chi":
             # Response function calculations are non-self-consistent: only one ionic step, no electronic SCF
             if self.parameters.get("LEPSILON", self.defaults["LEPSILON"]["value"]):
-
                 final_esteps = self.ionic_steps[-1]["electronic_steps"]
                 to_check = {"e_wo_entrp", "e_fr_energy", "e_0_energy"}
 
diff --git a/pymatgen/io/validation/check_for_excess_empty_space.py b/pymatgen/io/validation/check_for_excess_empty_space.py
@@ -25,7 +25,11 @@ def check_for_excess_empty_space(structure):
     lattice_vec_3_diffs = np.diff(lattice_vec_3_frac_coords)
     max_lattice_vec_3_empty_dist = max(lattice_vec_3_diffs) * lattice_vec_lengths[2]
 
-    max_empty_distance = max(max_lattice_vec_1_empty_dist, max_lattice_vec_2_empty_dist, max_lattice_vec_3_empty_dist)
+    max_empty_distance = max(
+        max_lattice_vec_1_empty_dist,
+        max_lattice_vec_2_empty_dist,
+        max_lattice_vec_3_empty_dist,
+    )
 
     # Check 2: get max voronoi polyhedra volume in structure
     def get_max_voronoi_polyhedra_volume(structure):
diff --git a/pymatgen/io/validation/check_incar.py b/pymatgen/io/validation/check_incar.py
@@ -109,7 +109,6 @@ def check(self) -> None:
         # Validate each parameter in the set of working parameters
         simple_validator = BasicValidator()
         for key in working_params.defaults:
-
             if self.fast and len(self.reasons) > 0:
                 # fast check: stop checking whenever a single check fails
                 break
@@ -326,7 +325,10 @@ def update_precision_params(self) -> None:
         self.parameters["LREAL"] = str(self._incar.get("LREAL", self.defaults["LREAL"]["value"])).upper()
         # PREC.
         self.parameters["PREC"] = self.parameters["PREC"].upper()
-        if self.input_set.incar.get("PREC", self.defaults["PREC"]["value"]).upper() in ["ACCURATE", "HIGH"]:
+        if self.input_set.incar.get("PREC", self.defaults["PREC"]["value"]).upper() in [
+            "ACCURATE",
+            "HIGH",
+        ]:
             self.valid_values["PREC"] = ["ACCURATE", "ACCURA", "HIGH"]
         else:
             raise ValueError("Validation code check for PREC tag needs to be updated to account for a new input set!")
@@ -374,7 +376,10 @@ def update_misc_special_params(self) -> None:
         if self._incar.get("IWAVPR"):
             self.parameters["IWAVPR"] = self._incar["IWAVPR"] if self._incar["IWAVPR"] is not None else 0
             self.defaults["IWAVPR"].update(
-                {"operation": "==", "comment": "VASP discourages users from setting the IWAVPR tag (as of July 2023)."}
+                {
+                    "operation": "==",
+                    "comment": "VASP discourages users from setting the IWAVPR tag (as of July 2023).",
+                }
             )
 
         # LCORR.
@@ -451,8 +456,16 @@ def update_fft_params(self) -> None:
             self.valid_values["ENMAX"] = max(self.parameters["ENMAX"], self.valid_values["ENMAX"])
 
             (
-                [self.valid_values["NGX"], self.valid_values["NGY"], self.valid_values["NGZ"]],
-                [self.valid_values["NGXF"], self.valid_values["NGYF"], self.valid_values["NGZF"]],
+                [
+                    self.valid_values["NGX"],
+                    self.valid_values["NGY"],
+                    self.valid_values["NGZ"],
+                ],
+                [
+                    self.valid_values["NGXF"],
+                    self.valid_values["NGYF"],
+                    self.valid_values["NGZF"],
+                ],
             ) = self.input_set.calculate_ng(custom_encut=self.valid_values["ENMAX"])
 
             for key in grid_keys:
@@ -566,7 +579,8 @@ def update_smearing_params(self, bandgap_tol=1.0e-4) -> None:
         for ionic_step in self._ionic_steps:
             if eentropy := ionic_step["electronic_steps"][-1].get("eentropy"):
                 self.parameters["ELECTRONIC ENTROPY"] = max(
-                    self.parameters["ELECTRONIC ENTROPY"], abs(eentropy / self.structure.num_sites)
+                    self.parameters["ELECTRONIC ENTROPY"],
+                    abs(eentropy / self.structure.num_sites),
                 )
 
         convert_eV_to_meV = 1000
@@ -702,7 +716,8 @@ def update_ionic_params(self):
                 cur_ionic_step_energies = [ionic_step["e_fr_energy"] for ionic_step in self._ionic_steps]
                 cur_ionic_step_energy_gradient = np.diff(cur_ionic_step_energies)
                 self.parameters["MAX ENERGY GRADIENT"] = round(
-                    max(np.abs(cur_ionic_step_energy_gradient)) / self.structure.num_sites, 3
+                    max(np.abs(cur_ionic_step_energy_gradient)) / self.structure.num_sites,
+                    3,
                 )
                 self.valid_values["MAX ENERGY GRADIENT"] = 1
                 self.defaults["MAX ENERGY GRADIENT"] = {
@@ -736,7 +751,8 @@ def update_ionic_params(self):
 
         elif self.valid_values["EDIFFG"] < 0.0:
             self.parameters["EDIFFG"] = round(
-                max([np.linalg.norm(force_on_atom) for force_on_atom in self.task_doc["output"]["forces"]]), 3
+                max([np.linalg.norm(force_on_atom) for force_on_atom in self.task_doc["output"]["forces"]]),
+                3,
             )
 
             self.valid_values["EDIFFG"] = abs(self.valid_values["EDIFFG"])
@@ -788,7 +804,17 @@ class BasicValidator:
     """
 
     # avoiding dunder methods because these raise too many NotImplemented's
-    operations: set[str | None] = {"==", ">", ">=", "<", "<=", "in", "approx", "auto fail", None}
+    operations: set[str | None] = {
+        "==",
+        ">",
+        ">=",
+        "<",
+        "<=",
+        "in",
+        "approx",
+        "auto fail",
+        None,
+    }
 
     def __init__(self, global_tolerance=1.0e-4) -> None:
         """Set math.isclose tolerance"""
diff --git a/pymatgen/io/validation/check_kpoints_kspacing.py b/pymatgen/io/validation/check_kpoints_kspacing.py
@@ -109,7 +109,9 @@ def _check_kpoint_density(self) -> None:
             self.kpoints = self.kpoints.as_dict()
 
         cur_num_kpts = max(
-            self.kpoints.get("nkpoints", 0), np.prod(self.kpoints.get("kpoints")), len(self.kpoints.get("kpoints"))
+            self.kpoints.get("nkpoints", 0),
+            np.prod(self.kpoints.get("kpoints")),
+            len(self.kpoints.get("kpoints")),
         )
         if cur_num_kpts < valid_num_kpts:
             self.reasons.append(
diff --git a/pymatgen/io/validation/check_package_versions.py b/pymatgen/io/validation/check_package_versions.py
@@ -1,4 +1,4 @@
-""" Optionally check whether package versions are up to date. """
+"""Optionally check whether package versions are up to date."""
 
 from __future__ import annotations
 from importlib.metadata import version
diff --git a/pymatgen/io/validation/check_potcar.py b/pymatgen/io/validation/check_potcar.py
@@ -110,9 +110,13 @@ def _check_potcar_spec(self):
                 # format error string
                 incorrect_potcars = [potcar.split("_")[0] for potcar in incorrect_potcars]
                 if len(incorrect_potcars) == 2:
-                    incorrect_potcars = ", ".join(incorrect_potcars[:-1]) + f" and {incorrect_potcars[-1]}"  # type: ignore
+                    incorrect_potcars = (
+                        ", ".join(incorrect_potcars[:-1]) + f" and {incorrect_potcars[-1]}"
+                    )  # type: ignore
                 elif len(incorrect_potcars) >= 3:
-                    incorrect_potcars = ", ".join(incorrect_potcars[:-1]) + "," + f" and {incorrect_potcars[-1]}"  # type: ignore
+                    incorrect_potcars = (
+                        ", ".join(incorrect_potcars[:-1]) + "," + f" and {incorrect_potcars[-1]}"
+                    )  # type: ignore
 
                 self.reasons.append(
                     f"PSEUDOPOTENTIALS --> Incorrect POTCAR files were used for {incorrect_potcars}. "
@@ -157,7 +161,9 @@ def compare_potcar_stats(self, potcar_stats_1: dict, potcar_stats_2: dict) -> bo
         data_match = False
         if key_match:
             data_diff = [
-                abs(potcar_stats_1["stats"].get(key, {}).get(stat) - potcar_stats_2["stats"].get(key, {}).get(stat))  # type: ignore
+                abs(
+                    potcar_stats_1["stats"].get(key, {}).get(stat) - potcar_stats_2["stats"].get(key, {}).get(stat)
+                )  # type: ignore
                 for stat in ["MEAN", "ABSMEAN", "VAR", "MIN", "MAX"]
                 for key in ["header", "data"]
             ]
diff --git a/pymatgen/io/validation/common.py b/pymatgen/io/validation/common.py
@@ -1,4 +1,4 @@
-""" Common class constructor for validation checks. """
+"""Common class constructor for validation checks."""
 
 from dataclasses import dataclass
 
@@ -47,7 +47,6 @@ def check(self) -> None:
 
         checklist = {attr for attr in dir(self) if attr.startswith("_check_")}
         for attr in checklist:
-
             if self.fast and len(self.reasons) > 0:
                 # fast check: stop checking whenever a single check fails
                 break
diff --git a/pymatgen/io/validation/compare_to_MP_ehull.py b/pymatgen/io/validation/compare_to_MP_ehull.py
@@ -24,7 +24,10 @@ def compare_to_MP_ehull(mp_api_key=None, task_doc=None):
         entries = mpr.get_entries_in_chemsys(
             elements=elements,
             compatible_only=True,
-            additional_criteria={"thermo_types": ["GGA_GGA+U", "R2SCAN"], "is_stable": True},
+            additional_criteria={
+                "thermo_types": ["GGA_GGA+U", "R2SCAN"],
+                "is_stable": True,
+            },
         )
 
         entries.append(cur_structure_entry)
diff --git a/pymatgen/io/validation/settings.py b/pymatgen/io/validation/settings.py
@@ -3,6 +3,7 @@
 """
 Settings for pymatgen-io-validation. Used to be part of EmmetSettings.
 """
+
 from importlib.resources import files as import_resource_files
 import json
 from pathlib import Path
diff --git a/pymatgen/io/validation/validation.py b/pymatgen/io/validation/validation.py
@@ -190,7 +190,12 @@ def from_dict(
 
         try:
             valid_input_set = _get_input_set(
-                cls_kwargs["run_type"], cls_kwargs["task_type"], cls_kwargs["calc_type"], structure, input_sets, bandgap
+                cls_kwargs["run_type"],
+                cls_kwargs["task_type"],
+                cls_kwargs["calc_type"],
+                structure,
+                input_sets,
+                bandgap,
             )
         except Exception as e:
             cls_kwargs["reasons"].append(
@@ -200,7 +205,6 @@ def from_dict(
             print(f"Error while finding MP input set: {e}.")
 
         if valid_input_set:
-
             # Tests ordered by expected computational burden - help optimize `fast` check
             # Intuitively, more important checks (INCAR, KPOINTS, and POTCAR settings) would come first
             # But to optimize speed in fast mode (relevant for validating a large batch of calculations)
diff --git a/setup.py b/setup.py
@@ -15,7 +15,12 @@
     name="pymatgen-io-validation",
     packages=find_namespace_packages(include=["pymatgen.io.*"]),
     version="0.0.3",
-    install_requires=["pymatgen>=2024.5.1", "emmet-core>=0.83.6", "pydantic>=2.4.2", "requests>=2.28.1"],
+    install_requires=[
+        "pymatgen>=2024.5.1",
+        "emmet-core>=0.83.6",
+        "pydantic>=2.4.2",
+        "requests>=2.28.1",
+    ],
     extras_require={},
     package_data={"pymatgen.io.validation": ["*.yaml"]},
     author="Matthew Kuner, Janosh Riebesell, Jason Munro, Aaron Kaplan",
diff --git a/tests/test_validation.py b/tests/test_validation.py

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-""" Optionally check whether package versions are up to date. """`
	`1`	`+"""Optionally check whether package versions are up to date."""`
`2`	`2`
`3`	`3`	`from __future__ import annotations`
`4`	`4`	`from importlib.metadata import version`