Merge pull request #1512 from pyiron/ruff_sorting

Add import sorting to ruff

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: ruff
         name: ruff lint
-        args: ["--fix"]
+        args: ["--select", "I", "--fix"]
         files: ^pyiron_base/
       - id: ruff-format
         name: ruff format

pyiron_base/__init__.py

@@ -2,52 +2,49 @@
 # 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 pyiron_base.state import state
-
 # API of the pyiron_base module - in alphabetical order
 from pyiron_base.interfaces.factory import PyironFactory
-from pyiron_base.storage.flattenedstorage import FlattenedStorage
-from pyiron_base.storage.hdfio import FileHDFio, ProjectHDFio
-from pyiron_base.storage.datacontainer import DataContainer
-from pyiron_base.storage.has_stored_traits import HasStoredTraits
-from pyiron_base.storage.inputlist import InputList
-from pyiron_base.storage.parameters import GenericParameters
-from pyiron_base.jobs.job.extension.executable import Executable
-from pyiron_base.project.external import Notebook, load, dump
+from pyiron_base.interfaces.has_groups import HasGroups
+from pyiron_base.interfaces.has_hdf import HasHDF
+from pyiron_base.interfaces.object import HasDatabase, HasStorage, PyironObject
+from pyiron_base.jobs.datamining import PyironTable, TableJob
 from pyiron_base.jobs.dynamic import warn_dynamic_job_classes
 from pyiron_base.jobs.flex.factory import create_job_factory
-from pyiron_base.jobs.job.extension.server.queuestatus import validate_que_request
-from pyiron_base.jobs.job.generic import GenericJob
-from pyiron_base.jobs.job.interactive import InteractiveBase
+from pyiron_base.jobs.job.extension.executable import Executable
 from pyiron_base.jobs.job.extension.jobstatus import (
     JobStatus,
-    job_status_successful_lst,
     job_status_finished_lst,
     job_status_lst,
+    job_status_successful_lst,
 )
-from pyiron_base.jobs.job.jobtype import JOB_CLASS_DICT, JobType, JobTypeChoice
-from pyiron_base.jobs.job.template import TemplateJob, PythonTemplateJob
+from pyiron_base.jobs.job.extension.server.queuestatus import validate_que_request
 from pyiron_base.jobs.job.factory import JobFactoryCore
+from pyiron_base.jobs.job.generic import GenericJob
+from pyiron_base.jobs.job.interactive import InteractiveBase
+from pyiron_base.jobs.job.jobtype import JOB_CLASS_DICT, JobType, JobTypeChoice
+from pyiron_base.jobs.job.template import PythonTemplateJob, TemplateJob
+from pyiron_base.jobs.job.toolkit import BaseTools, Toolkit
 from pyiron_base.jobs.master.flexible import FlexibleMaster
 from pyiron_base.jobs.master.generic import GenericMaster, get_function_from_string
 from pyiron_base.jobs.master.interactivewrapper import InteractiveWrapper
 from pyiron_base.jobs.master.list import ListMaster
-from pyiron_base.jobs.master.parallel import ParallelMaster, JobGenerator
-from pyiron_base.project.generic import Project, Creator
-from pyiron_base.utils.parser import Logstatus, extract_data_from_file
-from pyiron_base.state.settings import Settings
+from pyiron_base.jobs.master.parallel import JobGenerator, ParallelMaster
+from pyiron_base.project.external import Notebook, dump, load
+from pyiron_base.project.generic import Creator, Project
+from pyiron_base.state import state
 from pyiron_base.state.install import install_dialog
-from pyiron_base.jobs.datamining import PyironTable, TableJob
-from pyiron_base.interfaces.object import HasDatabase, HasStorage, PyironObject
-from pyiron_base.interfaces.has_groups import HasGroups
-from pyiron_base.interfaces.has_hdf import HasHDF
-
-from pyiron_base.jobs.job.toolkit import Toolkit, BaseTools
+from pyiron_base.state.settings import Settings
+from pyiron_base.storage.datacontainer import DataContainer
+from pyiron_base.storage.flattenedstorage import FlattenedStorage
+from pyiron_base.storage.has_stored_traits import HasStoredTraits
+from pyiron_base.storage.hdfio import FileHDFio, ProjectHDFio
+from pyiron_base.storage.inputlist import InputList
+from pyiron_base.storage.parameters import GenericParameters
+from pyiron_base.utils.jedi import fix_ipython_autocomplete
+from pyiron_base.utils.parser import Logstatus, extract_data_from_file
 
 # Internal init
 from ._version import get_versions
-from pyiron_base.utils.jedi import fix_ipython_autocomplete
-
 
 Project.register_tools("base", BaseTools)
 

pyiron_base/_tests.py

@@ -4,17 +4,18 @@
 
 """Classes to help developers avoid code duplication when writing tests for pyiron."""
 
-from contextlib import redirect_stdout
 import doctest
-from io import StringIO
-import unittest
 import os
-from pyiron_base import PythonTemplateJob, state
-from pyiron_base.project.generic import Project
+import unittest
 from abc import ABC
+from contextlib import redirect_stdout
 from inspect import getfile
+from io import StringIO
+
 import numpy as np
 
+from pyiron_base import PythonTemplateJob, state
+from pyiron_base.project.generic import Project
 
 __author__ = "Liam Huber"
 __copyright__ = (

pyiron_base/_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_base/cli/control.py

@@ -8,7 +8,7 @@
 import os
 import warnings
 
-from pyiron_base.cli import cp, ls, mv, rm, install, reloadfile, wrapper
+from pyiron_base.cli import cp, install, ls, mv, reloadfile, rm, wrapper
 
 __author__ = "Marvin Poul"
 __copyright__ = (

pyiron_base/cli/ls.py

@@ -8,7 +8,9 @@
 import datetime
 import re
 import sys
+
 import pandas as pd
+
 import pyiron_base.jobs.job.extension.jobstatus
 from pyiron_base import Project
 

pyiron_base/cli/reloadfile.py

@@ -2,8 +2,10 @@
 # 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 os
-from h5io_browser.base import _open_hdf
 import shutil
+
+from h5io_browser.base import _open_hdf
+
 from pyiron_base import Project
 from pyiron_base.state import state
 

pyiron_base/cli/rm.py

@@ -5,6 +5,7 @@
 """
 
 import os
+
 from pyiron_base.project.generic import Project
 
 __author__ = "Marvin Poul"

pyiron_base/database/filetable.py

@@ -6,14 +6,16 @@
 """
 
 import datetime
+import os
 from abc import ABCMeta
 from collections.abc import Iterable
+
 import numpy as np
-import os
 import pandas
+from h5io_browser.base import _read_hdf, _write_hdf
 from pyfileindex import PyFileIndex
+
 from pyiron_base.database.interface import IsDatabase
-from h5io_browser.base import _read_hdf, _write_hdf
 
 __author__ = "Jan Janssen"
 __copyright__ = (

pyiron_base/database/generic.py

@@ -5,30 +5,33 @@
 DatabaseAccess class deals with accessing the database
 """
 
-import numpy as np
-import re
 import os
+import re
 from datetime import datetime
+from queue import Empty as QueueEmpty
+from queue import SimpleQueue
+from threading import Lock, Thread
+
+import numpy as np
 import pandas
 from pyiron_snippets.deprecate import deprecate
 from pyiron_snippets.logger import logger
+from pyiron_snippets.retry import retry
 from sqlalchemy import (
-    create_engine,
     MetaData,
     Table,
-    text,
     and_,
+    create_engine,
     or_,
+    text,
 )
+from sqlalchemy.exc import DatabaseError, OperationalError
 from sqlalchemy.pool import NullPool
 from sqlalchemy.sql import select
-from sqlalchemy.exc import OperationalError, DatabaseError
-from threading import Thread, Lock
-from queue import SimpleQueue, Empty as QueueEmpty
-from pyiron_snippets.retry import retry
-from pyiron_base.database.tables import get_historical_table
+
 from pyiron_base.database.interface import IsDatabase
 from pyiron_base.database.sqlcolumnlength import CHEMICALFORMULA_STR_LENGTH
+from pyiron_base.database.tables import get_historical_table
 
 __author__ = "Murat Han Celik"
 __copyright__ = (

pyiron_base/database/interface.py

@@ -5,16 +5,17 @@
 DatabaseAccess class deals with accessing the database
 """
 
+import fnmatch
+import re
+import typing
+import warnings
 from abc import ABC, abstractmethod
 from collections.abc import Iterable
-import warnings
+
 import numpy as np
-import re
 import pandas
 from pyiron_snippets.deprecate import deprecate
 from pyiron_snippets.logger import logger
-import typing
-import fnmatch
 
 __author__ = "Murat Han Celik"
 __copyright__ = (

pyiron_base/database/jobtable.py

@@ -6,6 +6,7 @@
 """
 
 import numpy as np
+
 from pyiron_base.database.filetable import FileTable
 
 __author__ = "Jan Janssen"

pyiron_base/database/manager.py

@@ -5,11 +5,13 @@
 A class for mediating connections to SQL databases.
 """
 
+import os
 from urllib.parse import quote_plus
+
 from pyiron_snippets.logger import logger
 from pyiron_snippets.singleton import Singleton
+
 from pyiron_base.state.settings import settings as s
-import os
 
 __author__ = "Jan Janssen, Liam Huber"
 __copyright__ = (

pyiron_base/database/performance.py

@@ -5,15 +5,16 @@
 
 import pandas as pd
 from sqlalchemy import (
-    create_engine,
-    select,
-    distinct,
     MetaData,
     Table,
+    create_engine,
+    distinct,
+    false,
     func,
     or_,
-    false,
+    select,
 )
+
 from pyiron_base.state import state
 
 __author__ = "Muhammad Hassani"

pyiron_base/database/tables.py

@@ -13,17 +13,18 @@
     String,
     Table,
 )
+
 from pyiron_base.database.sqlcolumnlength import (
-    PROJECT_PATH_STR_LENGTH,
-    PROJECT_STR_LENGTH,
-    JOB_STR_LENGTH,
-    SUBJOB_STR_LENGTH,
     CHEMICALFORMULA_STR_LENGTH,
-    STATUS_STR_LENGTH,
+    COMPUTER_STR_LENGTH,
     HAMILTON_STR_LENGTH,
     HAMVERSION_STR_LENGTH,
+    JOB_STR_LENGTH,
+    PROJECT_PATH_STR_LENGTH,
+    PROJECT_STR_LENGTH,
+    STATUS_STR_LENGTH,
+    SUBJOB_STR_LENGTH,
     USERNAME_STR_LENGTH,
-    COMPUTER_STR_LENGTH,
 )
 
 __author__ = "Murat Han Celik, Liam Huber"

pyiron_base/interfaces/has_hdf.py

@@ -3,10 +3,10 @@
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 """Interface for classes to serialize to HDF5."""
 
-from pyiron_base.storage.hdfio import ProjectHDFio
-
 from abc import ABC, abstractmethod
 
+from pyiron_base.storage.hdfio import ProjectHDFio
+
 __author__ = "Marvin Poul"
 __copyright__ = (
     "Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "

pyiron_base/interfaces/lockable.py

@@ -15,10 +15,10 @@
 sibling classes may bring in.
 """
 
+import warnings
 from contextlib import nullcontext
-from typing import Optional, Literal
 from functools import wraps
-import warnings
+from typing import Literal, Optional
 
 from pyiron_base.interfaces.has_groups import HasGroups
 

pyiron_base/interfaces/object.py

@@ -7,10 +7,11 @@
 """
 
 from abc import ABC
-from pyiron_base.storage.datacontainer import DataContainer
+
 from pyiron_base.interfaces.has_hdf import HasHDF
-from pyiron_base.storage.hdfio import ProjectHDFio
 from pyiron_base.state import state
+from pyiron_base.storage.datacontainer import DataContainer
+from pyiron_base.storage.hdfio import ProjectHDFio
 
 __author__ = "Liam Huber"
 __copyright__ = (

pyiron_base/jobs/datamining.py

@@ -4,23 +4,23 @@
 
 import codecs
 import concurrent.futures
+import json
+import os
+import types
 from datetime import datetime
+from typing import List, Tuple
+
 import cloudpickle
-import json
 import numpy as np
-import os
 import pandas
 from pandas.errors import EmptyDataError
 from pyiron_snippets.deprecate import deprecate
 from tqdm.auto import tqdm
-import types
-from typing import List, Tuple
 
-from pyiron_base.jobs.job.generic import GenericJob
 from pyiron_base.jobs.job.extension import jobstatus
+from pyiron_base.jobs.job.generic import GenericJob
 from pyiron_base.storage.hdfio import FileHDFio
 
-
 __author__ = "Uday Gajera, Jan Janssen, Joerg Neugebauer"
 __copyright__ = (
     "Copyright 2020, Max-Planck-Institut für Eisenforschung GmbH - "

pyiron_base/jobs/flex/executablecontainer.py

@@ -1,8 +1,8 @@
 import cloudpickle
 import numpy as np
 
-from pyiron_base.jobs.job.template import TemplateJob
 from pyiron_base.jobs.job.runfunction import CalculateFunctionCaller
+from pyiron_base.jobs.job.template import TemplateJob
 
 
 class ExecutableContainerJob(TemplateJob):