Bump ruff version (#6614)

Most of the changes here are minor import sorting changes (I checked all of them and they all look more correct than before).
The only other change were couple type-comparison (E721) fixes

.github/system_tests/test_daemon.py

@@ -16,16 +16,6 @@
 import tempfile
 import time
 
-from aiida.common import StashMode, exceptions
-from aiida.engine import run, submit
-from aiida.engine.daemon.client import get_daemon_client
-from aiida.engine.persistence import ObjectLoader
-from aiida.engine.processes import CalcJob, Process
-from aiida.manage.caching import enable_caching
-from aiida.orm import CalcJobNode, Dict, Int, List, Str, load_code, load_node
-from aiida.orm.nodes.caching import NodeCaching
-from aiida.plugins import CalculationFactory, WorkflowFactory
-from aiida.workflows.arithmetic.add_multiply import add, add_multiply
 from workchains import (
     ArithmeticAddBaseWorkChain,
     CalcFunctionRunnerWorkChain,
@@ -39,6 +29,16 @@
     WorkFunctionRunnerWorkChain,
 )
 
+from aiida.common import StashMode, exceptions
+from aiida.engine import run, submit
+from aiida.engine.daemon.client import get_daemon_client
+from aiida.engine.persistence import ObjectLoader
+from aiida.engine.processes import CalcJob, Process
+from aiida.manage.caching import enable_caching
+from aiida.orm import CalcJobNode, Dict, Int, List, Str, load_code, load_node
+from aiida.orm.nodes.caching import NodeCaching
+from aiida.plugins import CalculationFactory, WorkflowFactory
+from aiida.workflows.arithmetic.add_multiply import add, add_multiply
 from tests.utils.memory import get_instances
 
 CODENAME_ADD = 'add@localhost'

.molecule/default/files/polish/cli.py

@@ -14,6 +14,7 @@
 import time
 
 import click
+
 from aiida.cmdline.params import options, types
 from aiida.cmdline.utils import decorators
 

.pre-commit-config.yaml

@@ -37,16 +37,10 @@ repos:
     args: [--line-length=120, --fail-on-change]
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.0
+  rev: v0.7.3
   hooks:
   - id: ruff-format
-    exclude: &exclude_ruff >
-      (?x)^(
-        docs/source/topics/processes/include/snippets/functions/parse_docstring_expose_ipython.py|
-        docs/source/topics/processes/include/snippets/functions/signature_plain_python_call_illegal.py|
-      )$
   - id: ruff
-    exclude: *exclude_ruff
     args: [--fix, --exit-non-zero-on-fix, --show-fixes]
 
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks

docs/source/howto/include/scripts/performance_benchmark_base.py

@@ -2,6 +2,7 @@
 """Script to benchmark the performance of the AiiDA workflow engine on a given installation."""
 
 import click
+
 from aiida.cmdline.params import options
 from aiida.cmdline.utils import decorators, echo
 

docs/source/internals/includes/snippets/api.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 import click
+from flask_restful import Resource
+
 from aiida import load_profile
 from aiida.restapi import common
 from aiida.restapi.api import AiidaApi, App
 from aiida.restapi.run_api import run_api
-from flask_restful import Resource
 
 
 class NewResource(Resource):

docs/source/topics/processes/include/snippets/serialize/run_workchain_serialize.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env runaiida
-from aiida.engine import run
 from serialize_workchain import SerializeWorkChain
 
+from aiida.engine import run
+
 if __name__ == '__main__':
     print(run(SerializeWorkChain, a=1, b=1.2, c=True))
     # Result: {'a': 1, 'b': 1.2, 'c': True}

docs/source/topics/workflows/include/snippets/expose_inputs/complex_parent.py

@@ -1,6 +1,7 @@
-from aiida.engine import ToContext, WorkChain
 from child import ChildWorkChain
 
+from aiida.engine import ToContext, WorkChain
+
 
 class ComplexParentWorkChain(WorkChain):
     @classmethod

docs/source/topics/workflows/include/snippets/expose_inputs/run_complex.py

@@ -1,8 +1,9 @@
 #!/usr/bin/env runaiida
 
+from complex_parent import ComplexParentWorkChain
+
 from aiida.engine import run
 from aiida.orm import Bool, Float, Int
-from complex_parent import ComplexParentWorkChain
 
 if __name__ == '__main__':
     result = run(

docs/source/topics/workflows/include/snippets/expose_inputs/run_simple.py

@@ -1,8 +1,9 @@
 #!/usr/bin/env runaiida
 
+from simple_parent import SimpleParentWorkChain
+
 from aiida.engine import run
 from aiida.orm import Bool, Float, Int
-from simple_parent import SimpleParentWorkChain
 
 if __name__ == '__main__':
     result = run(SimpleParentWorkChain, a=Int(1), b=Float(1.2), c=Bool(True))

docs/source/topics/workflows/include/snippets/expose_inputs/simple_parent.py

@@ -1,6 +1,7 @@
-from aiida.engine import ToContext, WorkChain
 from child import ChildWorkChain
 
+from aiida.engine import ToContext, WorkChain
+
 
 class SimpleParentWorkChain(WorkChain):
     @classmethod

pyproject.toml

@@ -388,6 +388,10 @@ testpaths = [
 xfail_strict = true
 
 [tool.ruff]
+exclude = [
+  'docs/source/topics/processes/include/snippets/functions/parse_docstring_expose_ipython.py',
+  'docs/source/topics/processes/include/snippets/functions/signature_plain_python_call_illegal.py'
+]
 line-length = 120
 
 [tool.ruff.format]

src/aiida/cmdline/groups/dynamic.py

@@ -177,7 +177,7 @@ def list_options(self, entry_point: str) -> list:
             # ``typing.Union[str, None].__args__`` will return the tuple ``(str, NoneType)``. So to get the real type,
             # we simply remove all ``NoneType`` and the remaining type should be the type of the option.
             if hasattr(field_info.annotation, '__args__'):
-                args = list(filter(lambda e: e != type(None), field_info.annotation.__args__))
+                args = list(filter(lambda e: e is not type(None), field_info.annotation.__args__))
                 # Click parameters only support specifying a single type, so we default to the first one even if the
                 # pydantic model defines multiple.
                 field_type = args[0]

src/aiida/engine/processes/workchains/workchain.py

@@ -208,7 +208,7 @@ def _resolve_nested_context(self, key: str) -> tuple[AttributeDict, str]:
             #   (subclasses of AttributeDict) but after resolution of an Awaitable this will be the value itself
             # * assumption: a resolved value is never a plain AttributeDict, on the other hand if a resolved Awaitable
             #   would be an AttributeDict we can append things to it since the order of tasks is maintained.
-            if type(ctx) != AttributeDict:
+            if type(ctx) is not AttributeDict:
                 raise ValueError(
                     f'Can not update the context for key `{key}`:'
                     f' found instance of `{type(ctx)}` at `{".".join(ctx_path[:index+1])}`, expected AttributeDict'

src/aiida/storage/sqlite_dos/migrations/versions/main_0002_recompute_hash_calc_job_node.py

@@ -18,9 +18,10 @@
 
 from __future__ import annotations
 
-from aiida.common.log import AIIDA_LOGGER
 from alembic import op
 
+from aiida.common.log import AIIDA_LOGGER
+
 LOGGER = AIIDA_LOGGER.getChild(__file__)
 
 revision = 'main_0002'
@@ -39,9 +40,10 @@ def drop_hashes(conn, hash_extra_key: str, entry_point_string: str | None = None
         value should be a complete entry point string, e.g., ``aiida.node:process.calculation.calcjob`` to drop the hash
         of all ``CalcJobNode`` rows.
     """
+    from sqlalchemy.sql import text
+
     from aiida.orm.utils.node import get_type_string_from_class
     from aiida.plugins import load_entry_point_from_string
-    from sqlalchemy.sql import text
 
     if entry_point_string is not None:
         entry_point = load_entry_point_from_string(entry_point_string)

tests/benchmark/test_archive.py

@@ -15,6 +15,7 @@
 from io import StringIO
 
 import pytest
+
 from aiida.common.links import LinkType
 from aiida.engine import ProcessState
 from aiida.orm import CalcFunctionNode, Dict, load_node

tests/benchmark/test_engine.py

@@ -13,6 +13,7 @@
 """
 
 import pytest
+
 from aiida.engine import WorkChain, run_get_node, while_
 from aiida.orm import InstalledCode, Int
 from aiida.plugins.factories import CalculationFactory

tests/benchmark/test_nodes.py

@@ -15,6 +15,7 @@
 from io import StringIO
 
 import pytest
+
 from aiida.common import NotExistent
 from aiida.orm import Data, load_node
 

tests/brokers/test_rabbitmq.py

@@ -13,11 +13,12 @@
 
 import pytest
 import requests
+from kiwipy.rmq import RmqThreadCommunicator
+from packaging.version import parse
+
 from aiida.brokers.rabbitmq import client, utils
 from aiida.engine.processes import ProcessState, control
 from aiida.orm import Int
-from kiwipy.rmq import RmqThreadCommunicator
-from packaging.version import parse
 
 pytestmark = pytest.mark.requires_rmq
 

tests/calculations/arithmetic/test_add.py

@@ -9,6 +9,7 @@
 """Tests for the `ArithmeticAddCalculation` plugin."""
 
 import pytest
+
 from aiida import orm
 from aiida.calculations.arithmetic.add import ArithmeticAddCalculation
 from aiida.common import datastructures

tests/calculations/test_templatereplacer.py

@@ -11,6 +11,7 @@
 import io
 
 import pytest
+
 from aiida import orm
 from aiida.common import datastructures
 

tests/calculations/test_transfer.py

@@ -11,6 +11,7 @@
 import os
 
 import pytest
+
 from aiida import orm
 from aiida.common import datastructures
 

tests/cmdline/commands/test_archive_create.py

@@ -13,11 +13,11 @@
 import zipfile
 
 import pytest
+
 from aiida.cmdline.commands import cmd_archive
 from aiida.orm import Computer, Dict, Group, InstalledCode
 from aiida.storage.sqlite_zip.migrator import list_versions
 from aiida.tools.archive import ArchiveFormatSqlZip
-
 from tests.utils.archives import get_archive_file
 
 pytest.mark.usefixtures('chdir_tmp_path')

tests/cmdline/commands/test_archive_import.py

@@ -9,11 +9,11 @@
 """Tests for `verdi archive import`."""
 
 import pytest
+
 from aiida.cmdline.commands import cmd_archive
 from aiida.orm import Group
 from aiida.storage.sqlite_zip.migrator import list_versions
 from aiida.tools.archive import ArchiveFormatSqlZip
-
 from tests.utils.archives import get_archive_file
 
 ARCHIVE_PATH = 'export/migrate'

tests/cmdline/commands/test_calcjob.py

@@ -11,6 +11,8 @@
 import io
 
 import pytest
+from click.testing import CliRunner
+
 from aiida import orm
 from aiida.cmdline.commands import cmd_calcjob as command
 from aiida.common.datastructures import CalcJobState
@@ -19,8 +21,6 @@
 from aiida.orm.nodes.data.remote.base import RemoteData
 from aiida.plugins import CalculationFactory
 from aiida.plugins.entry_point import get_entry_point_string_from_class
-from click.testing import CliRunner
-
 from tests.utils.archives import import_test_archive
 
 

tests/cmdline/commands/test_code.py

@@ -17,6 +17,7 @@
 
 import click
 import pytest
+
 from aiida.cmdline.commands import cmd_code
 from aiida.cmdline.params.options.commands.code import validate_label_uniqueness
 from aiida.common.exceptions import MultipleObjectsError, NotExistent

tests/cmdline/commands/test_computer.py

@@ -16,6 +16,7 @@
 
 import pytest
 import yaml
+
 from aiida import orm
 from aiida.cmdline.commands.cmd_computer import (
     computer_configure,

tests/cmdline/commands/test_config.py

@@ -9,6 +9,7 @@
 """Tests for ``verdi config``."""
 
 import pytest
+
 from aiida import get_profile
 from aiida.cmdline.commands import cmd_verdi
 

tests/cmdline/commands/test_daemon.py

@@ -12,6 +12,7 @@
 from unittest.mock import patch
 
 import pytest
+
 from aiida import get_profile
 from aiida.cmdline.commands import cmd_daemon
 from aiida.engine.daemon.client import DaemonClient

tests/cmdline/commands/test_data.py

@@ -16,6 +16,7 @@
 
 import numpy as np
 import pytest
+
 from aiida import orm
 from aiida.cmdline.commands import cmd_group
 from aiida.cmdline.commands.cmd_data import (
@@ -33,7 +34,6 @@
 from aiida.engine import calcfunction
 from aiida.orm import ArrayData, BandsData, CifData, Dict, Group, KpointsData, RemoteData, StructureData, TrajectoryData
 from aiida.orm.nodes.data.cif import has_pycifrw
-
 from tests.static import STATIC_DIR
 
 

tests/cmdline/commands/test_devel.py

@@ -11,6 +11,7 @@
 import re
 
 import pytest
+
 from aiida.cmdline.commands import cmd_devel
 from aiida.orm import Node, ProcessNode, QueryBuilder, WorkChainNode
 

tests/cmdline/commands/test_group.py

@@ -9,6 +9,7 @@
 """Tests for the `verdi group` command."""
 
 import pytest
+
 from aiida import orm
 from aiida.cmdline.commands import cmd_group
 from aiida.cmdline.utils.echo import ExitCode

tests/cmdline/commands/test_group_ls.py

@@ -11,9 +11,10 @@
 from textwrap import dedent
 
 import pytest
+from click.testing import CliRunner
+
 from aiida import orm
 from aiida.cmdline.commands.cmd_group import group_path_ls
-from click.testing import CliRunner
 
 
 @pytest.fixture

tests/cmdline/commands/test_node.py

@@ -16,6 +16,7 @@
 import warnings
 
 import pytest
+
 from aiida import orm
 from aiida.cmdline.commands import cmd_node
 from aiida.cmdline.utils.echo import ExitCode

tests/cmdline/commands/test_plugin.py

@@ -9,6 +9,7 @@
 """Tests for the `verdi plugin list` command."""
 
 import pytest
+
 from aiida.cmdline.commands import cmd_plugin
 from aiida.parsers import Parser
 from aiida.plugins import BaseFactory

tests/cmdline/commands/test_presto.py

@@ -3,6 +3,7 @@
 import textwrap
 
 import pytest
+
 from aiida.cmdline.commands.cmd_presto import get_default_presto_profile_name, verdi_presto
 from aiida.manage.configuration import profile_context
 from aiida.manage.configuration.config import Config