Auto-update pre-commit hooks

Author: BryantLi-BLI

.pre-commit-config.yaml

@@ -3,22 +3,22 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.9.3
+  rev: v0.15.1
   hooks:
   - id: ruff
     args: [--fix]
     exclude: tutorials/grueneisen_workflow.ipynb
   - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  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: 1.19.1
+  rev: 1.20.0
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
@@ -31,22 +31,22 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.14.1
+  rev: v1.19.1
   hooks:
   - id: mypy
     files: ^src/
     additional_dependencies:
     - tokenize-rt==4.1.0
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.4.0
+  rev: v2.4.1
   hooks:
   - id: codespell
     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: 0.8.1
+  rev: 0.9.0
   hooks:
     - id: nbstripout
       args:

docs/user/codes/openmm.md

@@ -85,7 +85,6 @@ for PF6- here, the built in partial charge method fails.
 import numpy as np
 from pymatgen.core.structure import Molecule
 
-
 pf6 = Molecule(
     ["P", "F", "F", "F", "F", "F", "F"],
     [
@@ -142,7 +141,6 @@ from atomate2.openmm.jobs.core import (
 )
 from jobflow import Flow, run_locally
 
-
 production_maker = OpenMMFlowMaker(
     name="production_flow",
     makers=[

docs/user/codes/vasp.md

@@ -300,7 +300,6 @@ A Grüneisen workflow for VASP can be started as follows:
 from atomate2.vasp.flows.gruneisen import GruneisenMaker
 from pymatgen.core.structure import Structure
 
-
 structure = Structure(
     lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
     species=["Mg", "O"],
@@ -324,7 +323,6 @@ The following script allows you to start the default workflow for VASP with some
 from atomate2.vasp.flows.qha import QhaMaker
 from pymatgen.core.structure import Structure
 
-
 structure = Structure(
     lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
     species=["Mg", "O"],
@@ -349,7 +347,6 @@ You can start the workflow as follows:
 from atomate2.vasp.flows.eos import EosMaker
 from pymatgen.core.structure import Structure
 
-
 structure = Structure(
     lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
     species=["Mg", "O"],
@@ -651,13 +648,11 @@ gamma_only_static_maker = StaticMaker(input_set_generator=custom_gamma_only_set)
 For those who are more familiar with manual *k*-point generation, you can use a VASP-style KPOINTS file or string to set the *k*-points as well:
 
 ```py
-kpoints = Kpoints.from_str(
-    """Uniform density Monkhorst-Pack mesh
+kpoints = Kpoints.from_str("""Uniform density Monkhorst-Pack mesh
 0
 Monkhorst-pack
 5 5 5
-"""
-)
+""")
 custom_static_set = StaticSetGenerator(user_kpoints_settings=kpoints)
 ```
 

src/atomate2/abinit/schemas/calculation.py

@@ -6,7 +6,7 @@
 import os
 from datetime import datetime, timezone
 from pathlib import Path
-from typing import Optional, Union
+from typing import Union
 
 from abipy.electrons.gsr import GsrFile
 from abipy.flowtk import events
@@ -82,23 +82,23 @@ class CalculationOutput(BaseModel):
         None, description="The Fermi level from the calculation in eV"
     )
 
-    forces: Optional[list[Vector3D]] = Field(
+    forces: list[Vector3D] | None = Field(
         None, description="Forces acting on each atom"
     )
-    stress: Optional[Matrix3D] = Field(None, description="The stress on the cell")
-    is_metal: Optional[bool] = Field(None, description="Whether the system is metallic")
-    bandgap: Optional[float] = Field(
+    stress: Matrix3D | None = Field(None, description="The stress on the cell")
+    is_metal: bool | None = Field(None, description="Whether the system is metallic")
+    bandgap: float | None = Field(
         None, description="The band gap from the calculation in eV"
     )
-    direct_bandgap: Optional[float] = Field(
+    direct_bandgap: float | None = Field(
         None, description="The direct band gap from the calculation in eV"
     )
-    cbm: Optional[float] = Field(
+    cbm: float | None = Field(
         None,
         description="The conduction band minimum, or LUMO for molecules, in eV "
         "(if system is not metallic)",
     )
-    vbm: Optional[float] = Field(
+    vbm: float | None = Field(
         None,
         description="The valence band maximum, or HOMO for molecules, in eV "
         "(if system is not metallic)",
@@ -194,7 +194,7 @@ class Calculation(BaseModel):
     event_report: events.EventReport = Field(
         None, description="Event report of this abinit job."
     )
-    output_file_paths: Optional[dict[str, str]] = Field(
+    output_file_paths: dict[str, str] | None = Field(
         None,
         description="Paths (relative to dir_name) of the Abinit output files "
         "associated with this calculation",

src/atomate2/abinit/schemas/task.py

@@ -5,7 +5,7 @@
 import logging
 from collections.abc import Sequence
 from pathlib import Path
-from typing import Any, Optional, Union
+from typing import Any, Union
 
 from abipy.abio.inputs import AbinitInput
 from abipy.flowtk import events
@@ -89,7 +89,7 @@ class OutputDoc(BaseModel):
     """
 
     structure: Union[Structure] = Field(None, description="The output structure object")
-    trajectory: Optional[Sequence[Union[Structure]]] = Field(
+    trajectory: Sequence[Union[Structure]] | None = Field(
         None, description="The trajectory of output structures"
     )
     energy: float = Field(
@@ -98,15 +98,15 @@ class OutputDoc(BaseModel):
     energy_per_atom: float = Field(
         None, description="The final DFT energy per atom for the last calculation"
     )
-    bandgap: Optional[float] = Field(
+    bandgap: float | None = Field(
         None, description="The DFT bandgap for the last calculation"
     )
-    cbm: Optional[float] = Field(None, description="CBM for this calculation")
-    vbm: Optional[float] = Field(None, description="VBM for this calculation")
-    forces: Optional[list[Vector3D]] = Field(
+    cbm: float | None = Field(None, description="CBM for this calculation")
+    vbm: float | None = Field(None, description="VBM for this calculation")
+    forces: list[Vector3D] | None = Field(
         None, description="Forces on atoms from the last calculation"
     )
-    stress: Optional[Matrix3D] = Field(
+    stress: Matrix3D | None = Field(
         None, description="Stress on the unit cell from the last calculation"
     )
 
@@ -179,49 +179,47 @@ class AbinitTaskDoc(StructureMetadata):
         Additional json loaded from the calculation directory
     """
 
-    dir_name: Optional[str] = Field(
-        None, description="The directory for this Abinit task"
-    )
-    last_updated: Optional[str] = Field(
+    dir_name: str | None = Field(None, description="The directory for this Abinit task")
+    last_updated: str | None = Field(
         default_factory=datetime_str,
         description="Timestamp for when this task document was last updated",
     )
-    completed_at: Optional[str] = Field(
+    completed_at: str | None = Field(
         None, description="Timestamp for when this task was completed"
     )
-    input: Optional[InputDoc] = Field(
+    input: InputDoc | None = Field(
         None, description="The input to the first calculation"
     )
-    output: Optional[OutputDoc] = Field(
+    output: OutputDoc | None = Field(
         None, description="The output of the final calculation"
     )
     structure: Union[Structure] = Field(
         None, description="Final output atoms from the task"
     )
-    state: Optional[TaskState] = Field(None, description="State of this task")
-    event_report: Optional[events.EventReport] = Field(
+    state: TaskState | None = Field(None, description="State of this task")
+    event_report: events.EventReport | None = Field(
         None, description="Event report of this abinit job."
     )
-    included_objects: Optional[list[AbinitObject]] = Field(
+    included_objects: list[AbinitObject] | None = Field(
         None, description="List of Abinit objects included with this task document"
     )
-    abinit_objects: Optional[dict[AbinitObject, Any]] = Field(
+    abinit_objects: dict[AbinitObject, Any] | None = Field(
         None, description="Abinit objects associated with this task"
     )
-    task_label: Optional[str] = Field(None, description="A description of the task")
-    tags: Optional[list[str]] = Field(
+    task_label: str | None = Field(None, description="A description of the task")
+    tags: list[str] | None = Field(
         None, description="Metadata tags for this task document"
     )
-    author: Optional[str] = Field(
+    author: str | None = Field(
         None, description="Author extracted from transformations"
     )
-    icsd_id: Optional[str] = Field(
+    icsd_id: str | None = Field(
         None, description="International crystal structure database id of the structure"
     )
-    calcs_reversed: Optional[list[Calculation]] = Field(
+    calcs_reversed: list[Calculation] | None = Field(
         None, description="The inputs and outputs for all Abinit runs in this task."
     )
-    transformations: Optional[dict[str, Any]] = Field(
+    transformations: dict[str, Any] | None = Field(
         None,
         description="Information on the structural transformations, parsed from a "
         "transformations.json file",
@@ -231,7 +229,7 @@ class AbinitTaskDoc(StructureMetadata):
         description="Information on the custodian settings used to run this "
         "calculation, parsed from a custodian.json file",
     )
-    additional_json: Optional[dict[str, Any]] = Field(
+    additional_json: dict[str, Any] | None = Field(
         None, description="Additional json loaded from the calculation directory"
     )
 

src/atomate2/aims/schemas/calculation.py

@@ -7,7 +7,7 @@
 from collections.abc import Sequence
 from datetime import datetime, timezone
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Optional
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 from ase.spectrum.band_structure import BandStructure
@@ -98,32 +98,32 @@ class CalculationOutput(BaseModel):
         None, description="The final structure from the calculation"
     )
 
-    efermi: Optional[float] = Field(
+    efermi: float | None = Field(
         None, description="The Fermi level from the calculation in eV"
     )
 
-    forces: Optional[list[Vector3D]] = Field(
+    forces: list[Vector3D] | None = Field(
         None, description="Forces acting on each atom"
     )
-    all_forces: Optional[list[list[Vector3D]]] = Field(
+    all_forces: list[list[Vector3D]] | None = Field(
         None,
         description="Forces acting on each atom for each structure in the output file",
     )
-    stress: Optional[Matrix3D] = Field(None, description="The stress on the cell")
-    stresses: Optional[list[Matrix3D]] = Field(
+    stress: Matrix3D | None = Field(None, description="The stress on the cell")
+    stresses: list[Matrix3D] | None = Field(
         None, description="The atomic virial stresses"
     )
 
-    is_metal: Optional[bool] = Field(None, description="Whether the system is metallic")
-    bandgap: Optional[float] = Field(
+    is_metal: bool | None = Field(None, description="Whether the system is metallic")
+    bandgap: float | None = Field(
         None, description="The band gap from the calculation in eV"
     )
     cbm: float = Field(
         None,
         description="The conduction band minimum, or LUMO for molecules, in eV "
         "(if system is not metallic)",
     )
-    vbm: Optional[float] = Field(
+    vbm: float | None = Field(
         None,
         description="The valence band maximum, or HOMO for molecules, in eV "
         "(if system is not metallic)",
@@ -264,7 +264,7 @@ def from_aims_files(
         parse_dos: str | bool = False,
         parse_bandstructure: str | bool = False,
         store_trajectory: bool = False,
-        store_volumetric_data: Optional[Sequence[str]] = STORE_VOLUMETRIC_DATA,
+        store_volumetric_data: Sequence[str] | None = STORE_VOLUMETRIC_DATA,
     ) -> tuple[Self, dict[AimsObject, dict]]:
         """Create an FHI-aims calculation document from a directory and file paths.
 
@@ -393,7 +393,7 @@ def _get_output_file_paths(volumetric_files: list[str]) -> dict[AimsObject, str]
 def _get_volumetric_data(
     dir_name: Path,
     output_file_paths: dict[AimsObject, str],
-    store_volumetric_data: Optional[Sequence[str]],
+    store_volumetric_data: Sequence[str] | None,
 ) -> dict[AimsObject, VolumetricData]:
     """
     Load volumetric data files from a directory.
@@ -430,7 +430,7 @@ def _get_volumetric_data(
     return volumetric_data
 
 
-def _parse_dos(parse_dos: str | bool, aims_output: AimsOutput) -> Optional[Dos]:
+def _parse_dos(parse_dos: str | bool, aims_output: AimsOutput) -> Dos | None:
     """Parse DOS outputs from FHI-aims calculation.
 
     Parameters
@@ -458,7 +458,7 @@ def _parse_dos(parse_dos: str | bool, aims_output: AimsOutput) -> Optional[Dos]:
 
 def _parse_bandstructure(
     parse_bandstructure: str | bool, aims_output: AimsOutput
-) -> Optional[BandStructure]:
+) -> BandStructure | None:
     """
     Get the band structure.
 
@@ -478,7 +478,7 @@ def _parse_bandstructure(
     return None
 
 
-def _parse_trajectory(aims_output: AimsOutput) -> Optional[Trajectory]:
+def _parse_trajectory(aims_output: AimsOutput) -> Trajectory | None:
     """Grab a Trajectory object given an FHI-aims output object.
 
     Parameters