Auto-update pre-commit hooks

Author: Zhuoying

.pre-commit-config.yaml

@@ -3,21 +3,21 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.6.1
+  rev: v0.14.3
   hooks:
   - id: ruff
     args: [--fix]
   - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v6.0.0
   hooks:
   - id: check-yaml
   - id: fix-encoding-pragma
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/asottile/blacken-docs
-  rev: 1.18.0
+  rev: 1.20.0
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
@@ -30,22 +30,22 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.11.1
+  rev: v1.18.2
   hooks:
   - id: mypy
     files: ^src/
     additional_dependencies:
     - tokenize-rt==4.1.0
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.3.0
+  rev: v2.4.1
   hooks:
   - id: codespell
-    stages: [commit, commit-msg]
+    stages: [pre-commit, commit-msg]
     args: [--ignore-words-list, 'titel,statics,ba,nd,te,atomate']
     types_or: [python, rst, markdown]
 - repo: https://github.com/kynan/nbstripout
-  rev: 0.7.1
+  rev: 0.8.1
   hooks:
     - id: nbstripout
       args:

src/atomate2/abinit/jobs/base.py

@@ -54,8 +54,7 @@ def setup_job(
 
     if structure is None and prev_outputs is None and restart_from is None:
         raise RuntimeError(
-            "At least one of structure, prev_outputs or "
-            "restart_from should be defined."
+            "At least one of structure, prev_outputs or restart_from should be defined."
         )
 
     if history is None:

src/atomate2/cli/dev.py

@@ -560,9 +560,9 @@ def test_run_{test_name}(self, mock_abinit, abinit_test_dir, clean_dir):
         from atomate2.abinit.schemas.core import AbinitTaskDocument
 
         # load the initial structure, the maker and the ref_paths from the test_dir
-        test_dir = abinit_test_dir / {" / ".join(
-        [f'"{part}"' for part in test_dir.parts[index_part:]]
-    )}
+        test_dir = abinit_test_dir / {
+        " / ".join([f'"{part}"' for part in test_dir.parts[index_part:]])
+    }
         structure = Structure.from_file(test_dir / "initial_structure.json.gz")
         maker_info = loadfn(test_dir / "maker.json.gz")
         maker = maker_info["maker"]
@@ -602,13 +602,13 @@ def save_abinit_maker(maker: Maker) -> None:
     author_mail = None
     if git:
         name = subprocess.run(
-            "git config user.name".split(),
+            ["git", "config", "user.name"],
             capture_output=True,
             encoding="utf-8",
             check=True,
         )
         mail = subprocess.run(
-            "git config user.email".split(),
+            ["git", "config", "user.email"],
             capture_output=True,
             encoding="utf-8",
             check=True,

src/atomate2/common/schemas/defects.py

@@ -2,7 +2,6 @@
 
 import logging
 from collections.abc import Sequence
-from itertools import starmap
 from typing import Any, Callable, Optional, Union
 
 import numpy as np
@@ -246,14 +245,10 @@ def get_cs_entry(
             return ComputedStructureEntry(structure=struct, energy=energy, data=data)
 
         entries1 = list(
-            starmap(
-                get_cs_entry, zip(structures1, energies1, static_dirs1, static_uuids1)
-            )
+            map(get_cs_entry, structures1, energies1, static_dirs1, static_uuids1)
         )
         entries2 = list(
-            starmap(
-                get_cs_entry, zip(structures2, energies2, static_dirs2, static_uuids2)
-            )
+            map(get_cs_entry, structures2, energies2, static_dirs2, static_uuids2)
         )
 
         return cls.from_entries(entries1, entries2, relaxed_uuid1, relaxed_uuid2)

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/common/schemas/qha.py

@@ -42,16 +42,15 @@ class PhononQHADoc(StructureMetadata, extra="allow"):  # type: ignore[call-arg]
     )
     volume_temperature: Optional[list[float]] = Field(
         None,
-        description="Volumes in Angstrom^3 at temperatures." "Shape: (temperatures, )",
+        description="Volumes in Angstrom^3 at temperatures.Shape: (temperatures, )",
     )
     gibbs_temperature: Optional[list[float]] = Field(
         None,
-        description="Gibbs free energies in eV at temperatures."
-        "Shape: (temperatures, )",
+        description="Gibbs free energies in eV at temperatures.Shape: (temperatures, )",
     )
     bulk_modulus_temperature: Optional[list[float]] = Field(
         None,
-        description="Bulk modulus in GPa  at temperature." "Shape: (temperatures, )",
+        description="Bulk modulus in GPa  at temperature.Shape: (temperatures, )",
     )
     heat_capacity_p_numerical: Optional[list[float]] = Field(
         None,
@@ -60,7 +59,7 @@ class PhononQHADoc(StructureMetadata, extra="allow"):  # type: ignore[call-arg]
     )
     gruneisen_temperature: Optional[list[float]] = Field(
         None,
-        description="Gruneisen parameters at temperatures." "Shape: (temperatures, )",
+        description="Gruneisen parameters at temperatures.Shape: (temperatures, )",
     )
     pressure: Optional[float] = Field(
         None, description="Pressure in GPA at which Gibb's energy was computed"
@@ -147,33 +146,33 @@ def from_phonon_runs(
         # create some plots here
         # add kwargs to change the names and file types
         qha.plot_helmholtz_volume().savefig(
-            f"{kwargs.get('helmholtz_volume_filename','helmholtz_volume')}"
-            f".{kwargs.get('plot_type','pdf')}"
+            f"{kwargs.get('helmholtz_volume_filename', 'helmholtz_volume')}"
+            f".{kwargs.get('plot_type', 'pdf')}"
         )
         qha.plot_volume_temperature().savefig(
-            f"{kwargs.get('volume_temperature_plot','volume_temperature')}"
-            f".{kwargs.get('plot_type','pdf')}"
+            f"{kwargs.get('volume_temperature_plot', 'volume_temperature')}"
+            f".{kwargs.get('plot_type', 'pdf')}"
         )
         qha.plot_thermal_expansion().savefig(
-            f"{kwargs.get('thermal_expansion_plot','thermal_expansion')}"
-            f".{kwargs.get('plot_type','pdf')}"
+            f"{kwargs.get('thermal_expansion_plot', 'thermal_expansion')}"
+            f".{kwargs.get('plot_type', 'pdf')}"
         )
         qha.plot_gibbs_temperature().savefig(
             f"{kwargs.get('gibbs_temperature_plot', 'gibbs_temperature')}"
-            f".{kwargs.get('plot_type','pdf')}"
+            f".{kwargs.get('plot_type', 'pdf')}"
         )
         qha.plot_bulk_modulus_temperature().savefig(
             f"{kwargs.get('bulk_modulus_plot', 'bulk_modulus_temperature')}"
-            f".{kwargs.get('plot_type','pdf')}"
+            f".{kwargs.get('plot_type', 'pdf')}"
         )
         qha.plot_heat_capacity_P_numerical().savefig(
             f"{kwargs.get('heat_capacity_plot', 'heat_capacity_P_numerical')}"
-            f".{kwargs.get('plot_type','pdf')}"
+            f".{kwargs.get('plot_type', 'pdf')}"
         )
         # qha.plot_heat_capacity_P_polyfit().savefig("heat_capacity_P_polyfit.eps")
         qha.plot_gruneisen_temperature().savefig(
             f"{kwargs.get('gruneisen_temperature_plot', 'gruneisen_temperature')}"
-            f".{kwargs.get('plot_type','pdf')}"
+            f".{kwargs.get('plot_type', 'pdf')}"
         )
 
         qha.write_helmholtz_volume(

src/atomate2/forcefields/schemas.py

@@ -148,8 +148,7 @@ class ForceFieldTaskDocument(StructureMetadata):
     is_force_converged: Optional[bool] = Field(
         None,
         description=(
-            "Whether the calculation is converged with respect "
-            "to interatomic forces."
+            "Whether the calculation is converged with respect to interatomic forces."
         ),
     )
 

src/atomate2/lobster/schemas.py

@@ -412,8 +412,7 @@ def from_directory(
                 with open(f"{filename}.json", "w") as fp:
                     json.dump(analyse.condensed_bonding_analysis, fp)
                 with open(f"{filename}.txt", "w") as fp:
-                    for line in describe.text:
-                        fp.write(f"{line}\n")
+                    fp.writelines(f"{line}\n" for line in describe.text)
 
             # Read in strongest icohp values
             sb = _identify_strongest_bonds(