[pre-commit.ci] pre-commit autoupdate (aiidaplugins#106)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0)
- [github.com/astral-sh/ruff-pre-commit: v0.1.7 → v0.4.2](astral-sh/ruff-pre-commit@v0.1.7...v0.4.2)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -8,15 +8,15 @@ exclude: >
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-json
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.4.2
     hooks:
     - id: ruff
       args: [--fix]

docs/source/tutorials/include/scripts/run_raw_basic.py

@@ -5,6 +5,7 @@
 the official benchmarks of LAMMPS. It is a simple MD simulation of a protein. It requires an additional input file in
 the working directory ``data.rhodo``. This example shows how to add such additional input files.
 """
+
 import io
 import textwrap
 

examples/calculations/launch_lammps_md.py

@@ -1,6 +1,7 @@
 """
 Sets up an example for the calculation of bcc Fe using ``aiida-lammps``.
 """
+
 from aiida import orm
 from aiida.common.extendeddicts import AttributeDict
 from aiida.engine import run_get_node

examples/calculations/launch_lammps_minimize.py

@@ -1,6 +1,7 @@
 """
 Sets up an example for the calculation of bcc Fe using ``aiida-lammps``.
 """
+
 from aiida import orm
 from aiida.common.extendeddicts import AttributeDict
 from aiida.engine import run_get_node

examples/launch_lammps_base_restart_file.py

@@ -1,6 +1,7 @@
 """
 Sets up an example for the calculation of bcc Fe using ``aiida-lammps``.
 """
+
 from aiida import orm
 from aiida.common.extendeddicts import AttributeDict
 from aiida.engine import run_get_node

examples/launch_lammps_base_restart_folder.py

@@ -1,6 +1,7 @@
 """
 Sets up an example for the calculation of bcc Fe using ``aiida-lammps``.
 """
+
 from aiida import orm
 from aiida.common.extendeddicts import AttributeDict
 from aiida.engine import run_get_node

examples/launch_lammps_base_script.py

@@ -5,6 +5,7 @@
 script for the ``script`` input of the ``LammpsBaseCalculation``, other inputs, such as ``structure`` and ``potential``
 no longer have to be specified.
 """
+
 import io
 import textwrap
 

examples/launch_lammps_raw_script.py

@@ -4,6 +4,7 @@
 the official benchmarks of LAMMPS. It is a simple MD simulation of a protein. It requires an additional input file in
 the working directory ``data.rhodo``. This example shows how to add such additional input files.
 """
+
 import io
 import textwrap
 

src/aiida_lammps/calculations/base.py

@@ -6,6 +6,7 @@
 is generated depending on the parameters provided, the type of potential,
 the input structure and whether or not a restart file is provided.
 """
+
 import os
 from typing import ClassVar, Union
 

src/aiida_lammps/calculations/raw.py

@@ -1,4 +1,5 @@
 """Plugin with minimal interface to run LAMMPS."""
+
 import shutil
 from typing import Union
 

src/aiida_lammps/data/potential.py

@@ -16,6 +16,7 @@ class written by Sebastiaan Huber.
 `schema <https://openkim.org/doc/schema/kimspec/>`_, as to make them more easy
 to track and as compatible as possible to the KIM schema.
 """
+
 import datetime
 
 # pylint: disable=arguments-differ, too-many-public-methods
@@ -421,7 +422,7 @@ def validate_extra_tags(self, extra_tags: dict):
         :raises ValueError: If the value of the entry does not match the possible values
         """
         for key, value in self._extra_keys.items():
-            _value = extra_tags.get(key, None)
+            _value = extra_tags.get(key)
             _accepted_values = value.get("values", None)
             _validator = value.get("validator", None)
             if _value is not None and _validator is not None:

src/aiida_lammps/data/trajectory.py

@@ -4,6 +4,7 @@
 The idea is that each of the steps of the simulation are stored as ZIP files
 which can then be easily accessed by the user.
 """
+
 # pylint: disable=too-many-ancestors
 import io
 import tempfile
@@ -195,14 +196,18 @@ def get_step_string(self, step_idx):
         """Return the content string, for a specific trajectory step."""
         step_idx = list(range(self.number_steps))[step_idx]
         zip_name = f'{self.base.attributes.get("zip_prefix")}{step_idx}'
-        with self.base.repository.open(
-            self.base.attributes.get("trajectory_filename"),
-            mode="rb",
-        ) as handle, ZipFile(
-            handle,
-            "r",
-            self.base.attributes.get("compression_method"),
-        ) as zip_file, zip_file.open(zip_name, "r") as step_file:
+        with (
+            self.base.repository.open(
+                self.base.attributes.get("trajectory_filename"),
+                mode="rb",
+            ) as handle,
+            ZipFile(
+                handle,
+                "r",
+                self.base.attributes.get("compression_method"),
+            ) as zip_file,
+            zip_file.open(zip_name, "r") as step_file,
+        ):
             content = step_file.read()
         return content.decode("utf8")
 
@@ -218,14 +223,17 @@ def iter_step_strings(self, steps=None):
         elif isinstance(steps, int):
             steps = range(0, self.number_steps, steps)
 
-        with self.base.repository.open(
-            self.base.attributes.get("trajectory_filename"),
-            mode="rb",
-        ) as handle, ZipFile(
-            handle,
-            "r",
-            self.base.attributes.get("compression_method"),
-        ) as zip_file:
+        with (
+            self.base.repository.open(
+                self.base.attributes.get("trajectory_filename"),
+                mode="rb",
+            ) as handle,
+            ZipFile(
+                handle,
+                "r",
+                self.base.attributes.get("compression_method"),
+            ) as zip_file,
+        ):
             for step_idx in steps:
                 zip_name = f'{self.base.attributes.get("zip_prefix")}{step_idx}'
                 with zip_file.open(zip_name) as step_file:

src/aiida_lammps/parsers/base.py

@@ -4,6 +4,7 @@
 It takes care of parsing the lammps.out file, the trajectory file and the
 yaml file with the final value of the variables printed in the ``thermo_style``.
 """
+
 import glob
 import os
 import time

src/aiida_lammps/parsers/inputfile.py

@@ -833,7 +833,7 @@ def write_thermo_block(
                         )
                     )
 
-    computes_printing = parameters_thermo.get("thermo_printing", None)
+    computes_printing = parameters_thermo.get("thermo_printing")
 
     if computes_printing is None or not computes_printing:
         fixed_thermo = ["step", "temp", "epair", "emol", "etotal", "press"]
@@ -879,7 +879,7 @@ def write_restart_block(
 
     restart_block = {"final": "", "intermediate": ""}
 
-    if "print_final" in parameters_restart and parameters_restart["print_final"]:
+    if parameters_restart.get("print_final"):
         restart_block["final"] += generate_header(
             "Start of the write restart information"
         )
@@ -888,16 +888,13 @@ def write_restart_block(
             "End of the write restart information"
         )
 
-    if (
-        "print_intermediate" in parameters_restart
-        and parameters_restart["print_intermediate"]
-    ):
+    if parameters_restart.get("print_intermediate"):
         restart_block["intermediate"] += generate_header(
             "Start of the intermediate write restart information"
         )
-        restart_block[
-            "intermediate"
-        ] += f"restart {parameters_restart.get('num_steps', int(max_number_steps/10))} {restart_filename}\n"
+        restart_block["intermediate"] += (
+            f"restart {parameters_restart.get('num_steps', int(max_number_steps/10))} {restart_filename}\n"
+        )
         restart_block["intermediate"] += generate_header(
             "End of the intermediate write restart information"
         )

src/aiida_lammps/parsers/parse_raw/lammps_output.py

@@ -1,4 +1,5 @@
 """Set of functions to parse the unformatted output file from LAMMPS"""
+
 # pylint: disable=fixme
 import ast
 import re
@@ -96,9 +97,9 @@ def parse_outputfile(
                 line.strip().split("=")[-1].strip()
             )
         if "Energy initial, next-to-last, final" in line:
-            global_parsed_data["minimization"][
-                "energy_relative_difference"
-            ] = _calculate_energy_tolerance(data[index + 1])
+            global_parsed_data["minimization"]["energy_relative_difference"] = (
+                _calculate_energy_tolerance(data[index + 1])
+            )
         if "Force two-norm initial, final" in line:
             global_parsed_data["minimization"]["force_two_norm"] = float(
                 line.strip().split("=")[-1].split()[-1].strip()

src/aiida_lammps/parsers/parse_raw/trajectory.py

@@ -1,5 +1,5 @@
-"""Set of functions to parse the LAMMPS dump output.
-"""
+"""Set of functions to parse the LAMMPS dump output."""
+
 # pylint: disable=fixme
 from collections import namedtuple
 import re

src/aiida_lammps/parsers/raw.py

@@ -1,4 +1,5 @@
 """Base parser for LAMMPS output."""
+
 import time
 
 from aiida import orm

src/aiida_lammps/utils.py

@@ -1,4 +1,5 @@
 """General utility functions for aiida-lammps"""
+
 import enum
 
 from aiida import __version__ as aiida_version_

src/aiida_lammps/validation/__init__.py

@@ -1,2 +1,3 @@
 """Package for validating JSON objects against schemas."""
+
 from aiida_lammps.validation.utils import validate_against_schema  # noqa: F401

src/aiida_lammps/validation/utils.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 """Utility functions for validating JSON objects against schemas."""
+
 import json
 import os
 from typing import Union

src/aiida_lammps/workflows/base.py

@@ -1,4 +1,5 @@
 """Workchain to run a LAMMPS calculation with automated error handling and restarts."""
+
 import re
 
 from aiida import orm

src/aiida_lammps/workflows/md.py

@@ -1,4 +1,5 @@
 """Workflow for a molecular dynamics simulation in LAMMPS."""
+
 import os
 from typing import Union
 

src/aiida_lammps/workflows/relax.py

@@ -1,4 +1,5 @@
 """Workflow for the relaxation of a structure using the minimization procedure in LAMMPS."""
+
 from itertools import groupby
 import os
 from typing import Union

tests/__init__.py

@@ -1,2 +1 @@
-""" tests for the plugin that does not pollute your profiles/databases.
-"""
+"""tests for the plugin that does not pollute your profiles/databases."""

tests/calculations/test_raw.py

@@ -1,4 +1,5 @@
 """Test the `LammpsRawCalculation`"""
+
 import io
 import textwrap
 

tests/parsers/test_raw.py

@@ -1,4 +1,5 @@
 """Tests for the :mod:`aiida_lammps.parsers.raw` module."""
+
 # pylint: disable=redefined-outer-name
 from aiida.plugins import ParserFactory
 

tests/test_calculations.py

@@ -1,4 +1,5 @@
 """Test the aiida-lammps calculations."""
+
 import copy
 
 from aiida import orm

tests/test_generate_structure.py

@@ -1,4 +1,5 @@
 """Test the structure generation in aiida-lammps"""
+
 from aiida_lammps.parsers.utils import generate_lammps_structure
 import pytest
 

tests/test_parsers.py

@@ -1,6 +1,7 @@
 """
 Tests to aiida-lammps parsers.
 """
+
 import os
 
 from aiida.plugins import ParserFactory

tests/test_potential_data.py

@@ -1,4 +1,5 @@
 """Test the functionality of the lammps potential data object"""
+
 import os
 
 from aiida_lammps.data.potential import LammpsPotentialData

tests/test_trajectory.py

@@ -1,4 +1,5 @@
 """Tests for the aiida-lammps trajectory data type"""
+
 import os
 
 from aiida_lammps.data.trajectory import LammpsTrajectory

tests/test_workflows.py

@@ -1,4 +1,5 @@
 """Tests for the workflows in aiida-lammps"""
+
 # pylint: disable=redefined-outer-name
 from aiida import orm
 from aiida.common import AttributeDict, LinkType

tests/utils.py

@@ -1,4 +1,5 @@
 """Set of functions to test the aiida-lammps functionality."""
+
 from collections.abc import Mapping
 from contextlib import contextmanager
 import distutils.spawn