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

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src/aiida/cmdline/commands/cmd_process.py

@@ -608,25 +608,25 @@ def process_dump(
     from aiida.tools.archive.exceptions import ExportValidationError
     from aiida.tools.dumping.data import DataDumper
     from aiida.tools.dumping.processes import ProcessDumper
-    from aiida.tools.dumping.data import DataDumper
+
     # from aiida.tools.dumping.utils import validate_rich_options
     from aiida.tools.dumping.rich import rich_from_cli
 
     processdumper_kwargs = {
-        "include_inputs": include_inputs,
-        "include_outputs": include_outputs,
-        "include_attributes": include_attributes,
-        "include_extras": include_extras,
-        "flat": flat,
+        'include_inputs': include_inputs,
+        'include_outputs': include_outputs,
+        'include_attributes': include_attributes,
+        'include_extras': include_extras,
+        'flat': flat,
     }
 
     rich_kwargs = {
-        "rich_dump_all": rich_dump_all,
+        'rich_dump_all': rich_dump_all,
     }
 
     datadumper_kwargs = {
-        "also_raw": also_raw,
-        "also_rich": also_rich,
+        'also_raw': also_raw,
+        'also_rich': also_rich,
     }
 
     # if also_rich:
@@ -644,7 +644,7 @@ def process_dump(
 
     data_dumper = DataDumper(
         overwrite=overwrite,
-        rich_spec_dict = rich_spec_dict,
+        rich_spec_dict=rich_spec_dict,
         **datadumper_kwargs,
         **rich_kwargs,
     )

src/aiida/cmdline/commands/cmd_storage.py

@@ -20,7 +20,6 @@
 from aiida.cmdline.utils import decorators, echo
 from aiida.common import exceptions
 from aiida.tools.dumping import CollectionDumper, DataDumper, ProcessDumper
-from aiida.tools.dumping.utils import dumper_pretty_print
 
 
 @verdi.group('storage')
@@ -306,12 +305,9 @@ def storage_dump(
     groups,
 ):
     """Dump all data in an AiiDA profile's storage to disk."""
-    from rich.pretty import pprint
+
 
     from aiida import orm
-    import time
-    import json
-    from aiida.tools.dumping.collection import DEFAULT_ENTITIES_TO_DUMP
     from aiida.tools.dumping.parser import DumpConfigParser
     from aiida.tools.dumping.rich import (
         DEFAULT_CORE_EXPORT_MAPPING,
@@ -320,8 +316,7 @@ def storage_dump(
     )
     from aiida.tools.dumping.utils import validate_make_dump_path
 
-
-    profile = ctx.obj["profile"]
+    profile = ctx.obj['profile']
     profile_name = profile.name
 
     # from aiida.manage.manager import get_manager
@@ -353,37 +348,36 @@ def storage_dump(
     #     echo.echo_critical('`all_entries` and `groups` specified. Set only one.')
 
     if dump_config_file is None:
-
         general_kwargs = {
-            "path": path,
-            "overwrite": overwrite,
-            "incremental": incremental,
-            "dry_run": dry_run,
+            'path': path,
+            'overwrite': overwrite,
+            'incremental': incremental,
+            'dry_run': dry_run,
         }
 
         processdumper_kwargs = {
-            "include_inputs": include_inputs,
-            "include_outputs": include_outputs,
-            "include_attributes": include_attributes,
-            "include_extras": include_extras,
-            "flat": flat,
+            'include_inputs': include_inputs,
+            'include_outputs': include_outputs,
+            'include_attributes': include_attributes,
+            'include_extras': include_extras,
+            'flat': flat,
             # "calculations_hidden": calculations_hidden
         }
 
         datadumper_kwargs = {
-            "also_raw": also_raw,
-            "also_rich": also_rich,
-            "data_hidden": data_hidden,
+            'also_raw': also_raw,
+            'also_rich': also_rich,
+            'data_hidden': data_hidden,
         }
 
         collection_kwargs = {
-            "should_dump_processes": dump_processes,
-            "should_dump_data": dump_data,
-            "only_top_level_workflows": only_top_level_workflows,
+            'should_dump_processes': dump_processes,
+            'should_dump_data': dump_data,
+            'only_top_level_workflows': only_top_level_workflows,
         }
 
         rich_kwargs = {
-            "rich_dump_all": rich_dump_all,
+            'rich_dump_all': rich_dump_all,
         }
 
         if rich_spec is not None:
@@ -396,47 +390,38 @@ def storage_dump(
     else:
         kwarg_dicts_from_config = DumpConfigParser.parse_config_file(dump_config_file)
 
-        general_kwargs = kwarg_dicts_from_config["general_kwargs"]
-        processdumper_kwargs = kwarg_dicts_from_config["processdumper_kwargs"]
-        datadumper_kwargs = kwarg_dicts_from_config["datadumper_kwargs"]
-        collection_kwargs = kwarg_dicts_from_config["collection_kwargs"]
-        rich_kwargs = kwarg_dicts_from_config["rich_kwargs"]
+        general_kwargs = kwarg_dicts_from_config['general_kwargs']
+        processdumper_kwargs = kwarg_dicts_from_config['processdumper_kwargs']
+        datadumper_kwargs = kwarg_dicts_from_config['datadumper_kwargs']
+        collection_kwargs = kwarg_dicts_from_config['collection_kwargs']
+        rich_kwargs = kwarg_dicts_from_config['rich_kwargs']
 
-        rich_spec_dict = rich_from_config(
-            kwarg_dicts_from_config["rich_spec"], **rich_kwargs
-        )
+        rich_spec_dict = rich_from_config(kwarg_dicts_from_config['rich_spec'], **rich_kwargs)
 
     # Obtain these specifically for easy access and modifications
-    path = general_kwargs["path"]
-    overwrite = general_kwargs["overwrite"]
-    dry_run = general_kwargs["dry_run"]
-    incremental = general_kwargs["incremental"]
+    path = general_kwargs['path']
+    overwrite = general_kwargs['overwrite']
+    dry_run = general_kwargs['dry_run']
+    incremental = general_kwargs['incremental']
 
     if not overwrite and incremental:
-        echo.echo_report(
-            "Overwrite set to false, but incremental dumping selected. Will keep existing directories."
-        )
+        echo.echo_report('Overwrite set to false, but incremental dumping selected. Will keep existing directories.')
 
     if not str(path).endswith(profile.name):
         path /= profile.name
 
     # TODO: Implement proper dry-run feature
-    dry_run_message = (
-        f"Dry run for dumping of profile `{profile.name}`'s data at path: `{path}`.\n"
-    )
-    dry_run_message += "Only directories will be created."
+    dry_run_message = f"Dry run for dumping of profile `{profile.name}`'s data at path: `{path}`.\n"
+    dry_run_message += 'Only directories will be created.'
 
-    if dry_run or (
-        not collection_kwargs["should_dump_processes"]
-        and not collection_kwargs["should_dump_data"]
-    ):
+    if dry_run or (not collection_kwargs['should_dump_processes'] and not collection_kwargs['should_dump_data']):
         echo.echo_report(dry_run_message)
         return
 
     else:
         echo.echo_report(f"Dumping of profile `{profile.name}`'s data at path: `{path}`.")
 
-    SAFEGUARD_FILE = ".verdi_storage_dump"  # noqa: N806
+    SAFEGUARD_FILE = '.verdi_storage_dump'  # noqa: N806
 
     try:
         validate_make_dump_path(
@@ -470,6 +455,7 @@ def storage_dump(
     # dumper_pretty_print(process_dumper)
 
     from aiida.tools.dumping.incremental import DumpNodeCollector
+
     dumpnodecollector = DumpNodeCollector(dump_parent_path=path)
 
     dumpnodecollector.update_uuids_before_dump()
@@ -494,22 +480,18 @@ def storage_dump(
             **rich_kwargs,
             data_dumper=data_dumper,
             process_dumper=process_dumper,
-            deduplicate=deduplicate
+            deduplicate=deduplicate,
         )
         collection_dumper.create_entity_counter()
         # dumper_pretty_print(collection_dumper, include_private_and_dunder=False)
 
         if dump_processes and collection_dumper._should_dump_processes():
-            echo.echo_report(
-                f"Dumping processes not in any group for profile `{profile.name}`..."
-            )
+            echo.echo_report(f'Dumping processes not in any group for profile `{profile.name}`...')
             collection_dumper.dump_processes()
         if dump_data:
             if not also_rich and not also_raw:
-                echo.echo_critical(
-                    "`--dump-data was given, but neither --also-raw or --also-rich specified."
-                )
-            echo.echo_report(f"Dumping data not in any group for profile {profile.name}...")
+                echo.echo_critical('`--dump-data was given, but neither --also-raw or --also-rich specified.')
+            echo.echo_report(f'Dumping data not in any group for profile {profile.name}...')
 
             collection_dumper.dump_data_rich()
         # collection_dumper.dump_plugin_data()
@@ -518,14 +500,14 @@ def storage_dump(
     # TODO: Invert default behavior here, as I typically want to dump all entries
     # TODO: Possibly define a new click option instead
     # all_entries = not all_entries
-    if not groups: # and all_entries:
+    if not groups:  # and all_entries:
         groups = orm.QueryBuilder().append(orm.Group).all(flat=True)
 
     if groups is not None and not nodes:
         for group in groups:
             if organize_by_groups:
-                group_subdir = Path(*group.type_string.split("."))
-                group_path = path / "groups" / group_subdir / group.label
+                group_subdir = Path(*group.type_string.split('.'))
+                group_path = path / 'groups' / group_subdir / group.label
             else:
                 group_path = path
 
@@ -546,12 +528,9 @@ def storage_dump(
                 # "Dumping processes for group `SSSP/1.3/PBE/efficiency`" is printed for groups that
                 # don't contain processes
                 if collection_dumper._should_dump_processes():
-                    echo.echo_report(f"Dumping processes for group `{group.label}`...")
+                    echo.echo_report(f'Dumping processes for group `{group.label}`...')
                     collection_dumper.dump_processes()
             if dump_data:
-                echo.echo_report(f"Dumping data for group `{group.label}`...")
+                echo.echo_report(f'Dumping data for group `{group.label}`...')
                 collection_dumper.dump_data_rich()
                 # collection_dumper.dump_plugin_data()
-
-
-

src/aiida/cmdline/params/options/main.py

@@ -62,8 +62,9 @@
     'DICT_FORMAT',
     'DICT_KEYS',
     'DRY_RUN',
-    'DUMP_PROCESSES',
+    'DUMP_CONFIG_FILE',
     'DUMP_DATA',
+    'DUMP_PROCESSES',
     'EXIT_STATUS',
     'EXPORT_FORMAT',
     'FAILED',
@@ -76,11 +77,11 @@
     'GROUP_CLEAR',
     'HOSTNAME',
     'IDENTIFIER',
-    'INCREMENTAL',
-    'INCLUDE_INPUTS',
-    'INCLUDE_OUTPUTS',
     'INCLUDE_ATTRIBUTES',
     'INCLUDE_EXTRAS',
+    'INCLUDE_INPUTS',
+    'INCLUDE_OUTPUTS',
+    'INCREMENTAL',
     'INCREMENTAL',
     'INPUT_FORMAT',
     'INPUT_PLUGIN',
@@ -90,8 +91,8 @@
     'NODE',
     'NODES',
     'NON_INTERACTIVE',
-    'ONLY_TOP_LEVEL_WORKFLOWS',
     'OLDER_THAN',
+    'ONLY_TOP_LEVEL_WORKFLOWS',
     'ORDER_BY',
     'ORDER_DIRECTION',
     'ORGANIZE_BY_GROUPS',
@@ -110,9 +111,8 @@
     'PROJECT',
     'RAW',
     'REPOSITORY_PATH',
-    'RICH_SPEC',
-    'DUMP_CONFIG_FILE',
     'RICH_DUMP_ALL',
+    'RICH_SPEC',
     'SCHEDULER',
     'SILENT',
     'SORT',
@@ -870,7 +870,7 @@ def set_log_level(ctx, _param, value):
     is_flag=True,
     type=bool,
     show_default=True,
-    help='If a rich specification is provided, this triggers if all other Data nodes should also be dumped or not.'
+    help='If a rich specification is provided, this triggers if all other Data nodes should also be dumped or not.',
 )
 
 ORGANIZE_BY_GROUPS = OverridableOption(

src/aiida/tools/dumping/__init__.py

@@ -12,4 +12,4 @@
 from .data import DataDumper
 from .processes import ProcessDumper
 
-__all__ = ('ProcessDumper', 'DataDumper', 'CollectionDumper')
+__all__ = ('CollectionDumper', 'DataDumper', 'ProcessDumper')

src/aiida/tools/dumping/incremental.py

@@ -1,10 +1,7 @@
-from aiida import orm
-from aiida.manage import get_manager
-from pathlib import Path
 import json
-import itertools as it
-from rich.pretty import pprint
-from typing import Any
+from pathlib import Path
+
+from aiida import orm
 
 # TODO: flat list using UUIDs, or sorted by type?
 # TODO: individual lists, ids, uuids, etc., or sorted: by data, or more fine-grained

src/aiida/tools/dumping/rich.py

@@ -1,7 +1,6 @@
-
 from aiida.cmdline.commands.cmd_data.cmd_export import data_export
 
-__all__ = ('rich_from_cli', 'rich_from_config', 'DEFAULT_CORE_EXPORT_MAPPING')
+__all__ = ('DEFAULT_CORE_EXPORT_MAPPING', 'rich_from_cli', 'rich_from_config')
 
 DEFAULT_CORE_EXPORT_MAPPING = {
     'core.array': {'exporter': data_export, 'export_format': 'json'},

src/aiida/tools/dumping/utils.py

@@ -79,8 +79,6 @@ def prepare_dump_path(
     (path_to_validate / safeguard_file).touch()
 
 
-
-
 def get_nodes_from_db(qb_instance, qb_filters: t.List | None = None, flat=False):
     # Computers cannot be associated via `with_group`
     # for qb_filter in qb_filters:

tests/conftest.py

@@ -956,8 +956,10 @@ def cat_path() -> Path:
 @pytest.fixture
 def generate_calculation_node_io(generate_calculation_node, tmp_path):
     def _generate_calculation_node_io(entry_point: str | None = None, attach_outputs: bool = True):
-        import numpy as np
         import io
+
+        import numpy as np
+
         from aiida.orm import ArrayData, FolderData, SinglefileData
 
         filename = 'file.txt'