Merge pull request #1496 from pyiron/ruff

ruff fixes

.ci_support/pyironconfig.py

@@ -3,17 +3,21 @@
 
 def main():
     current_path = os.path.abspath(os.path.curdir)
-    top_level_path = current_path.replace('\\', '/')
-    resource_path = os.path.join(current_path, "tests", "static").replace('\\', '/')
-    pyiron_config = os.path.expanduser('~/.pyiron').replace('\\', '/')
+    top_level_path = current_path.replace("\\", "/")
+    resource_path = os.path.join(current_path, "tests", "static").replace("\\", "/")
+    pyiron_config = os.path.expanduser("~/.pyiron").replace("\\", "/")
     if not os.path.exists(pyiron_config):
-        with open(pyiron_config, 'w') as f:
-            f.writelines(['[DEFAULT]\n',
-                          'TOP_LEVEL_DIRS = ' + top_level_path + '\n',
-                          'RESOURCE_PATHS = ' + resource_path + '\n'])
+        with open(pyiron_config, "w") as f:
+            f.writelines(
+                [
+                    "[DEFAULT]\n",
+                    "TOP_LEVEL_DIRS = " + top_level_path + "\n",
+                    "RESOURCE_PATHS = " + resource_path + "\n",
+                ]
+            )
     else:
-        print('config exists')
+        print("config exists")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

.ci_support/release.py

@@ -4,12 +4,19 @@
 def get_setup_version_and_pattern(setup_content):
     depend_lst, version_lst = [], []
     for l in setup_content:
-        if '==' in l:
-            lst = l.split('[')[-1].split(']')[0].replace(' ', '').replace('"', '').replace("'", '').split(',')
+        if "==" in l:
+            lst = (
+                l.split("[")[-1]
+                .split("]")[0]
+                .replace(" ", "")
+                .replace('"', "")
+                .replace("'", "")
+                .split(",")
+            )
             for dep in lst:
-                if dep != '\n':
-                    version_lst.append(dep.split('==')[1])
-                    depend_lst.append(dep.split('==')[0])
+                if dep != "\n":
+                    version_lst.append(dep.split("==")[1])
+                    depend_lst.append(dep.split("==")[0])
 
     version_high_dict = {d: v for d, v in zip(depend_lst, version_lst)}
     return version_high_dict
@@ -19,10 +26,10 @@ def get_env_version(env_content):
     read_flag = False
     depend_lst, version_lst = [], []
     for l in env_content:
-        if 'dependencies:' in l:
+        if "dependencies:" in l:
             read_flag = True
         elif read_flag:
-            lst = l.replace('- ', '').replace(' ', '').replace('\n', '').split("=")
+            lst = l.replace("- ", "").replace(" ", "").replace("\n", "").split("=")
             if len(lst) == 2:
                 depend_lst.append(lst[0])
                 version_lst.append(lst[1])
@@ -43,7 +50,7 @@ def update_dependencies(setup_content, version_low_dict, version_high_dict):
         for k, v in pattern_dict.items():
             if v in l:
                 l = l.replace(v, version_combo_dict[k])
-        setup_content_new +=l
+        setup_content_new += l
     return setup_content_new
 
 
@@ -55,13 +62,13 @@ def convert_key(key, convert_dict):
 
 
 if __name__ == "__main__":
-    with open('.ci_support/pypi_vs_conda_names.json', 'r') as f:
+    with open(".ci_support/pypi_vs_conda_names.json", "r") as f:
         name_conversion_dict = {v: k for k, v in json.load(f).items()}
 
-    with open('pyproject.toml', "r") as f:
+    with open("pyproject.toml", "r") as f:
         setup_content = f.readlines()
 
-    with open('environment.yml', "r") as f:
+    with open("environment.yml", "r") as f:
         env_content = f.readlines()
 
     env_version_dict = {
@@ -72,8 +79,10 @@ def convert_key(key, convert_dict):
     setup_content_new = update_dependencies(
         setup_content=setup_content[2:],
         version_low_dict=env_version_dict,
-        version_high_dict=get_setup_version_and_pattern(setup_content=setup_content[2:]),
+        version_high_dict=get_setup_version_and_pattern(
+            setup_content=setup_content[2:]
+        ),
     )
 
-    with open('pyproject.toml', "w") as f:
-        f.writelines("".join(setup_content[:2]) + setup_content_new)
+    with open("pyproject.toml", "w") as f:
+        f.writelines("".join(setup_content[:2]) + setup_content_new)

.ci_support/update_environment.py

@@ -8,8 +8,8 @@
 
 import yaml
 
-environment_file = '.ci_support/environment.yml'
-name_mapping_file = '.ci_support/pypi_vs_conda_names.json'
+environment_file = ".ci_support/environment.yml"
+name_mapping_file = ".ci_support/pypi_vs_conda_names.json"
 
 
 class EnvironmentUpdater:
@@ -24,10 +24,10 @@ def __init__(self, package_name, from_version, to_version):
         """
         self.from_version = from_version
         self.to_version = to_version
-        with open(name_mapping_file, 'r') as f:
+        with open(name_mapping_file, "r") as f:
             self._name_conversion_dict = json.load(f)
 
-        with open(environment_file, 'r') as f:
+        with open(environment_file, "r") as f:
             self.environment = yaml.safe_load(f)
 
         self.package_name = self._convert_package_name(package_name)
@@ -42,17 +42,19 @@ def _convert_package_name(self, name):
     def _update_dependencies(self):
         updated_dependencies = []
 
-        for dep in self.environment['dependencies']:
-            updated_dependencies.append(re.sub(
-                r'(' + self.package_name + '.*)' + self.from_version,
-                r'\g<1>' + self.to_version,
-                dep
-            ))
+        for dep in self.environment["dependencies"]:
+            updated_dependencies.append(
+                re.sub(
+                    r"(" + self.package_name + ".*)" + self.from_version,
+                    r"\g<1>" + self.to_version,
+                    dep,
+                )
+            )
 
-        self.environment['dependencies'] = updated_dependencies
+        self.environment["dependencies"] = updated_dependencies
 
     def _write(self):
-        with open(environment_file, 'w') as f:
+        with open(environment_file, "w") as f:
             yaml.safe_dump(self.environment, f)
 
     def update_dependencies(self):
@@ -61,9 +63,13 @@ def update_dependencies(self):
         self._write()
 
 
-if len(sys.argv) != 7 or not (sys.argv[1] == 'Bump' and sys.argv[3] == 'from' and sys.argv[5] == 'to'):
-    raise ValueError(f"Title of a dependabot PR 'Bump <package> from <version> to <version>' expected, "
-                     f"but got {' '.join(sys.argv[1:])}")
+if len(sys.argv) != 7 or not (
+    sys.argv[1] == "Bump" and sys.argv[3] == "from" and sys.argv[5] == "to"
+):
+    raise ValueError(
+        f"Title of a dependabot PR 'Bump <package> from <version> to <version>' expected, "
+        f"but got {' '.join(sys.argv[1:])}"
+    )
 package_to_update = sys.argv[2]
 from_version = sys.argv[4]
 to_version = sys.argv[6]

.github/workflows/unittests.yml

@@ -67,9 +67,3 @@ jobs:
       - name: Coveralls
         if: matrix.label == 'linux-64-py-3-12'
         uses: coverallsapp/github-action@v2
-      - name: Codacy
-        if:  matrix.label == 'linux-64-py-3-12' && github.event_name != 'push'
-        continue-on-error: True
-        shell: bash -l {0}
-        run: |
-          python-codacy-coverage -r coverage.xml

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.2
+    hooks:
+      - id: ruff
+        name: ruff lint
+        args: ["--select", "I", "--fix"]
+        files: ^pyiron_atomistics/
+      - id: ruff-format
+        name: ruff format

pyiron_atomistics/__init__.py

@@ -1,13 +1,13 @@
-from pyiron_atomistics.project import Project
-from pyiron_atomistics.toolkit import AtomisticsTools
+from pyiron_base import JOB_CLASS_DICT, Notebook, install_dialog
+from pyiron_base import Project as ProjectBase
+
 from pyiron_atomistics.atomistics.structure.atoms import (
+    Atoms,
     ase_to_pyiron,
     pyiron_to_ase,
-    Atoms,
 )
-from pyiron_base import Notebook, install_dialog, JOB_CLASS_DICT
-
-from pyiron_base import Project as ProjectBase
+from pyiron_atomistics.project import Project
+from pyiron_atomistics.toolkit import AtomisticsTools
 
 ProjectBase.register_tools("atomistics", AtomisticsTools)
 

pyiron_atomistics/_tests.py

@@ -12,11 +12,12 @@
 """
 
 import unittest
-from os.path import split, join
-from os import remove
-from pyiron_atomistics.project import Project
 from abc import ABC
 from inspect import getfile
+from os import remove
+from os.path import join, split
+
+from pyiron_atomistics.project import Project
 
 __author__ = "Liam Huber"
 __copyright__ = (

pyiron_atomistics/_version.py

@@ -11,12 +11,12 @@
 """Git implementation of _version.py."""
 
 import errno
+import functools
 import os
 import re
 import subprocess
 import sys
 from typing import Any, Callable, Dict, List, Optional, Tuple
-import functools
 
 
 def get_keywords() -> Dict[str, str]:

pyiron_atomistics/atomistics/generic/object_type.py

@@ -3,6 +3,7 @@
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
 from __future__ import print_function
+
 import importlib
 
 __author__ = "Joerg Neugebauer, Jan Janssen"

pyiron_atomistics/atomistics/job/atomistic.py

@@ -3,26 +3,29 @@
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
 import copy
-import warnings
-import numpy as np
 import numbers
 import os
-from typing import Callable, Union, Tuple
-from ase.io import write as ase_write
 import posixpath
+import warnings
 from functools import wraps
+from typing import Callable, Tuple, Union
 
-from pyiron_atomistics.atomistics.structure.atoms import Atoms
-from pyiron_atomistics.atomistics.structure.neighbors import NeighborsTrajectory
-from pyiron_atomistics.atomistics.structure.has_structure import HasStructure
+import numpy as np
+from ase.io import write as ase_write
 from pyiron_base import (
-    GenericParameters,
-    GenericMaster,
     GenericJob as GenericJobCore,
 )
+from pyiron_base import (
+    GenericMaster,
+    GenericParameters,
+)
 from pyiron_snippets.deprecate import deprecate
 from pyiron_snippets.logger import logger
 
+from pyiron_atomistics.atomistics.structure.atoms import Atoms
+from pyiron_atomistics.atomistics.structure.has_structure import HasStructure
+from pyiron_atomistics.atomistics.structure.neighbors import NeighborsTrajectory
+
 try:
     from pyiron_base import ProjectGUI
 except (ImportError, TypeError, AttributeError):

pyiron_atomistics/atomistics/job/interactive.py

@@ -2,14 +2,16 @@
 # Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
+from collections import defaultdict
+
 import numpy as np
-from pyiron_base import state, InteractiveBase
-from pyiron_atomistics.atomistics.structure.periodic_table import PeriodicTable
+from pyiron_base import InteractiveBase, state
+
 from pyiron_atomistics.atomistics.job.atomistic import (
     AtomisticGenericJob,
     GenericOutput,
 )
-from collections import defaultdict
+from pyiron_atomistics.atomistics.structure.periodic_table import PeriodicTable
 
 __author__ = "Osamu Waseda, Jan Janssen"
 __copyright__ = (

pyiron_atomistics/atomistics/job/interactivewrapper.py

@@ -4,8 +4,9 @@
 
 from pyiron_base import InteractiveWrapper as InteractiveWrapperBase
 from pyiron_snippets.deprecate import deprecate
-from pyiron_atomistics.atomistics.structure.atoms import ase_to_pyiron
+
 from pyiron_atomistics.atomistics.structure.atoms import Atoms as PAtoms
+from pyiron_atomistics.atomistics.structure.atoms import ase_to_pyiron
 
 __author__ = "Osamu Waseda, Jan Janssen"
 __copyright__ = (

pyiron_atomistics/atomistics/job/potentials.py

@@ -6,8 +6,10 @@
 An abstract Potential class to provide an easy access for the available potentials. Currently implemented for the
 OpenKim https://openkim.org database.
 """
-import pandas
+
 import os
+
+import pandas
 from pyiron_base import state
 
 __author__ = "Martin Boeckmann, Jan Janssen"

pyiron_atomistics/atomistics/job/sqs.py

@@ -2,20 +2,21 @@
 # Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
+import itertools
 import random
 import warnings
-import itertools
+
+import numpy as np
+from pyiron_base import DataContainer, GenericParameters, state
+from pyiron_snippets.import_alarm import ImportAlarm
 from structuretoolkit.build import sqs_structures
+
 from pyiron_atomistics.atomistics.job.atomistic import AtomisticGenericJob
-from pyiron_base import state, DataContainer, GenericParameters
-from pyiron_snippets.import_alarm import ImportAlarm
 from pyiron_atomistics.atomistics.structure.atoms import Atoms, ase_to_pyiron
-import numpy as np
-
 
 try:
+    from sqsgenerator import IterationMode, process_settings, sqs_optimize
     from sqsgenerator.settings import BadSettings
-    from sqsgenerator import sqs_optimize, process_settings, IterationMode
 
     import_alarm = ImportAlarm()
 except ImportError:

pyiron_atomistics/atomistics/job/structurecontainer.py

@@ -15,6 +15,7 @@
 
 from pyiron_base import DataContainer, GenericJob
 from pyiron_snippets.deprecate import deprecate
+
 from pyiron_atomistics.atomistics.job.atomistic import AtomisticGenericJob
 from pyiron_atomistics.atomistics.structure.atoms import Atoms
 from pyiron_atomistics.atomistics.structure.has_structure import HasStructure

pyiron_atomistics/atomistics/master/elasticmatrix.py

@@ -5,16 +5,17 @@
 from collections import OrderedDict
 
 import numpy as np
-import spglib
 import scipy.constants
+import spglib
+from atomistics.workflows.elastic.elastic_moduli import ElasticProperties
 from atomistics.workflows.elastic.helper import (
-    generate_structures_helper,
     analyse_structures_helper,
+    generate_structures_helper,
 )
-from atomistics.workflows.elastic.elastic_moduli import ElasticProperties
-from pyiron_atomistics.atomistics.master.parallel import AtomisticParallelMaster
 from pyiron_base import JobGenerator
 
+from pyiron_atomistics.atomistics.master.parallel import AtomisticParallelMaster
+
 __author__ = "Yury Lysogorskiy"
 __copyright__ = "Copyright 2020, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department"
 __version__ = "1.0"