More ruff (isort) (#497)

* more ruff

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

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

* Add preferred config

---------

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

pyproject.toml

@@ -27,7 +27,7 @@ extend-exclude = '''
 exclude = ["docs/*"]
 
 [tool.ruff.lint]
-select = ["F401", "I002"] # TODO: eventually, expand to other 'I', 'D', and other 'F' linting
+select = ["F401", "I"] # TODO: eventually, expand to other 'D', and other 'F' linting
 fixable = ["ALL"]
 
 [tool.ruff.lint.per-file-ignores]
@@ -41,6 +41,11 @@ fixable = ["ALL"]
 "src/nwbinspector/version/__init__.py" = ["F401", "I"]
 "src/nwbinspector/register_checks/__init__.py" = ["F401", "I"]
 
+[tool.ruff.lint.isort]
+relative-imports-order = "closest-to-furthest"
+known-first-party = ["nwbinspector"]
+
+
 
 [tool.codespell]
 skip = '.git*,*.pdf,*.css'

setup.py

@@ -1,7 +1,8 @@
-from setuptools import setup, find_packages
 from pathlib import Path
 from shutil import copy
 
+from setuptools import find_packages, setup
+
 root = Path(__file__).parent
 with open(root / "README.md", "r") as f:
     long_description = f.read()

src/nwbinspector/_configuration.py

@@ -1,19 +1,20 @@
 """Primary functions for inspecting NWBFiles."""
 
 import json
-import jsonschema
 from pathlib import Path
-from typing import Optional, List
 from types import FunctionType
+from typing import List, Optional
 
+import jsonschema
 import yaml
 
-from . import available_checks
-from ._registration import Importance
 from nwbinspector.utils._utils import (
     PathType,
 )
 
+from . import available_checks
+from ._registration import Importance
+
 INTERNAL_CONFIGS = dict(dandi=Path(__file__).parent / "internal_configs" / "dandi.inspector_config.yaml")
 
 

src/nwbinspector/_formatting.py

@@ -1,20 +1,20 @@
 """Internally used tools specifically for rendering more human-readable output from collected check results."""
 
-import os
 import json
+import os
 import sys
-from typing import Dict, List, Optional, Union
-from pathlib import Path
-from enum import Enum
+from collections import defaultdict
 from datetime import datetime
+from enum import Enum
+from pathlib import Path
 from platform import platform
-from collections import defaultdict
+from typing import Dict, List, Optional, Union
 
 import numpy as np
 
-from ._types import InspectorMessage, Importance
 from ._organization import organize_messages
-from .utils import get_package_version, FilePathType
+from ._types import Importance, InspectorMessage
+from .utils import FilePathType, get_package_version
 
 
 class InspectorOutputJSONEncoder(json.JSONEncoder):

src/nwbinspector/_inspection.py

@@ -1,29 +1,29 @@
 """Primary functions for inspecting NWBFiles."""
 
-import re
 import importlib
+import re
 import traceback
-from pathlib import Path
-from typing import Union, Optional, List, Iterable
+from collections import defaultdict
 from concurrent.futures import ProcessPoolExecutor, as_completed
+from pathlib import Path
+from typing import Iterable, List, Optional, Union
 from warnings import filterwarnings, warn
-from collections import defaultdict
-from packaging.version import Version
 
 import pynwb
-from tqdm import tqdm
 from natsort import natsorted
+from packaging.version import Version
+from tqdm import tqdm
 
 from . import available_checks, configure_checks
-from ._registration import InspectorMessage, Importance
+from ._registration import Importance, InspectorMessage
 from .tools import get_s3_urls_and_dandi_paths
 from .utils import (
     FilePathType,
-    PathType,
     OptionalListOfStrings,
-    robust_s3_read,
+    PathType,
     calculate_number_of_cpu,
     get_package_version,
+    robust_s3_read,
 )
 
 

src/nwbinspector/_inspection_cli.py

@@ -1,16 +1,24 @@
 """Primary functions for inspecting NWBFiles."""
 
+import json
 import os
 import re
-import json
 from pathlib import Path
 from typing import Optional
 from warnings import warn
 
 import click
 
-from ._formatting import _get_report_header, InspectorOutputJSONEncoder
-from . import Importance, inspect_all, format_messages, print_to_console, save_report, __version__, load_config
+from . import (
+    Importance,
+    __version__,
+    format_messages,
+    inspect_all,
+    load_config,
+    print_to_console,
+    save_report,
+)
+from ._formatting import InspectorOutputJSONEncoder, _get_report_header
 from .utils import strtobool
 
 

src/nwbinspector/_organization.py

@@ -1,7 +1,7 @@
 """Internally used tools specifically for rendering more human-readable output from collected check results."""
 
-from typing import List, Optional
 from enum import Enum
+from typing import List, Optional
 
 from natsort import natsorted
 

src/nwbinspector/_registration.py

@@ -5,11 +5,10 @@
 
 import h5py
 from pynwb import NWBFile
-from pynwb.file import Subject
 from pynwb.ecephys import Device, ElectrodeGroup
+from pynwb.file import Subject
 
-from ._types import Importance, Severity, InspectorMessage
-
+from ._types import Importance, InspectorMessage, Severity
 
 available_checks = list()
 

src/nwbinspector/_types.py

@@ -1,7 +1,7 @@
 """Primary decorator used on a check function to add it to the registry and automatically parse its output."""
 
-from enum import Enum
 from dataclasses import dataclass
+from enum import Enum
 from typing import Optional
 
 

src/nwbinspector/checks/__init__.py

@@ -1,87 +1,87 @@
+from ._behavior import (
+    check_compass_direction_unit,
+    check_spatial_series_degrees_magnitude,
+    check_spatial_series_dims,
+    check_spatial_series_radians_magnitude,
+)
 from ._ecephys import (
-    check_negative_spike_times,
     check_electrical_series_dims,
     check_electrical_series_reference_electrodes_table,
+    check_negative_spike_times,
     check_spike_times_not_in_unobserved_interval,
 )
 from ._general import (
     check_description,
     check_name_slashes,
 )
+from ._icephys import (
+    check_intracellular_electrode_cell_id_exists,
+)
 from ._image_series import (
     check_image_series_data_size,
     check_image_series_external_file_relative,
     check_image_series_external_file_valid,
 )
 from ._images import (
-    check_order_of_images_unique,
-    check_order_of_images_len,
     check_index_series_points_to_image,
+    check_order_of_images_len,
+    check_order_of_images_unique,
 )
 from ._nwb_containers import (
     check_empty_string_for_optional_attribute,
-    check_small_dataset_compression,
     check_large_dataset_compression,
+    check_small_dataset_compression,
 )
 from ._nwbfile_metadata import (
-    check_keywords,
+    check_doi_publications,
+    check_experiment_description,
+    check_experimenter_exists,
+    check_experimenter_form,
     check_institution,
+    check_keywords,
+    check_processing_module_name,
+    check_session_start_time_future_date,
+    check_session_start_time_old_date,
     check_subject_age,
-    check_subject_sex,
     check_subject_exists,
-    check_doi_publications,
-    check_experimenter_form,
-    check_experimenter_exists,
-    check_experiment_description,
     check_subject_id_exists,
+    check_subject_proper_age_range,
+    check_subject_sex,
     check_subject_species_exists,
     check_subject_species_form,
-    check_subject_proper_age_range,
-    check_session_start_time_future_date,
-    check_processing_module_name,
-    check_session_start_time_old_date,
 )
 from ._ogen import (
     check_optogenetic_stimulus_site_has_optogenetic_series,
 )
 from ._ophys import (
+    check_emission_lambda_in_nm,
     check_excitation_lambda_in_nm,
     check_plane_segmentation_image_mask_shape_against_ref_images,
     check_roi_response_series_dims,
-    check_emission_lambda_in_nm,
     check_roi_response_series_link_to_plane_segmentation,
 )
 from ._tables import (
-    check_single_row,
-    check_ids_unique,
-    check_empty_table,
     check_col_not_nan,
     check_column_binary_capability,
     check_dynamic_table_region_data_validity,
+    check_empty_table,
+    check_ids_unique,
+    check_single_row,
+    check_table_time_columns_are_not_negative,
+    check_table_values_for_dict,
     check_time_interval_time_columns,
     check_time_intervals_stop_after_start,
-    check_table_values_for_dict,
-    check_table_time_columns_are_not_negative,
 )
 from ._time_series import (
-    check_resolution,
+    check_data_orientation,
     check_missing_unit,
+    check_rate_is_not_zero,
     check_regular_timestamps,
+    check_resolution,
+    check_timestamp_of_the_first_sample_is_not_negative,
     check_timestamps_ascending,
-    check_data_orientation,
-    check_timestamps_without_nans,
     check_timestamps_match_first_dimension,
-    check_timestamp_of_the_first_sample_is_not_negative,
-    check_rate_is_not_zero,
-)
-from ._icephys import (
-    check_intracellular_electrode_cell_id_exists,
-)
-from ._behavior import (
-    check_compass_direction_unit,
-    check_spatial_series_radians_magnitude,
-    check_spatial_series_dims,
-    check_spatial_series_degrees_magnitude,
+    check_timestamps_without_nans,
 )
 
 __all__ = [

src/nwbinspector/checks/_behavior.py

@@ -1,9 +1,9 @@
 """Checks for types belonging to the pynwb.behavior module."""
 
 import numpy as np
-from pynwb.behavior import SpatialSeries, CompassDirection
+from pynwb.behavior import CompassDirection, SpatialSeries
 
-from .._registration import register_check, Importance, InspectorMessage
+from .._registration import Importance, InspectorMessage, register_check
 
 
 @register_check(importance=Importance.CRITICAL, neurodata_type=SpatialSeries)

src/nwbinspector/checks/_ecephys.py

@@ -1,12 +1,11 @@
 """Check functions specific to extracellular electrophysiology neurodata types."""
 
 import numpy as np
-
-from pynwb.misc import Units
 from pynwb.ecephys import ElectricalSeries
+from pynwb.misc import Units
 
+from .._registration import Importance, InspectorMessage, register_check
 from ..utils import get_data_shape
-from .._registration import register_check, Importance, InspectorMessage
 
 
 @register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=Units)

src/nwbinspector/checks/_general.py

@@ -1,6 +1,6 @@
 """Check functions that examine any general neurodata_type with the available attributes."""
 
-from .._registration import register_check, InspectorMessage, Importance
+from .._registration import Importance, InspectorMessage, register_check
 
 COMMON_DESCRIPTION_PLACEHOLDERS = ["no description", "no desc", "none", "placeholder"]
 

src/nwbinspector/checks/_icephys.py

@@ -2,7 +2,7 @@
 
 from pynwb.icephys import IntracellularElectrode
 
-from .._registration import register_check, Importance, InspectorMessage
+from .._registration import Importance, InspectorMessage, register_check
 
 
 @register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=IntracellularElectrode)

src/nwbinspector/checks/_image_series.py

@@ -6,7 +6,7 @@
 from pynwb.image import ImageSeries
 from pynwb.ophys import TwoPhotonSeries
 
-from .._registration import register_check, Importance, InspectorMessage
+from .._registration import Importance, InspectorMessage, register_check
 from ..tools import get_nwbfile_path_from_internal_object
 
 

src/nwbinspector/checks/_images.py

@@ -1,10 +1,9 @@
 """Checks specific to the Images neurodata type."""
 
 from packaging.version import Version
-
 from pynwb.image import IndexSeries
 
-from .._registration import register_check, Importance, InspectorMessage
+from .._registration import Importance, InspectorMessage, register_check
 from ..utils import get_package_version
 
 # The Images neurodata type was unavailable prior to PyNWB v.2.1.0

src/nwbinspector/checks/_nwb_containers.py

@@ -5,8 +5,7 @@
 import h5py
 from pynwb import NWBContainer
 
-
-from .._registration import register_check, Importance, InspectorMessage, Severity
+from .._registration import Importance, InspectorMessage, Severity, register_check
 
 
 @register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=NWBContainer)