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[pre-commit.ci] pre-commit autoupdate (#430)
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* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 23.12.1 → 24.1.1](psf/black@23.12.1...24.1.1)

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

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

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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pre-commit-ci[bot] authored Jan 29, 2024
1 parent 6e8e8c4 commit 8f741eb
Showing 22 changed files with 22 additions and 1 deletion.
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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@@ -6,6 +6,6 @@ repos:
- id: end-of-file-fixer
- id: trailing-whitespace
- repo: https://github.com/psf/black
rev: 23.12.1
rev: 24.1.1
hooks:
- id: black
1 change: 1 addition & 0 deletions src/nwbinspector/checks/behavior.py
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@@ -1,4 +1,5 @@
"""Checks for types belonging to the pynwb.behavior module."""

import numpy as np
from pynwb.behavior import SpatialSeries, CompassDirection

1 change: 1 addition & 0 deletions src/nwbinspector/checks/ecephys.py
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@@ -1,4 +1,5 @@
"""Check functions specific to extracellular electrophysiology neurodata types."""

import numpy as np

from pynwb.misc import Units
1 change: 1 addition & 0 deletions src/nwbinspector/checks/general.py
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@@ -1,4 +1,5 @@
"""Check functions that examine any general neurodata_type with the available attributes."""

from ..register_checks import register_check, InspectorMessage, Importance

COMMON_DESCRIPTION_PLACEHOLDERS = ["no description", "no desc", "none", "placeholder"]
1 change: 1 addition & 0 deletions src/nwbinspector/checks/icephys.py
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@@ -1,4 +1,5 @@
"""Checks specific to intracellular electrophysiology neurodata types."""

from pynwb.icephys import IntracellularElectrode

from ..register_checks import register_check, Importance, InspectorMessage
1 change: 1 addition & 0 deletions src/nwbinspector/checks/image_series.py
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@@ -1,4 +1,5 @@
"""Check functions specific to ImageSeries."""

import ntpath
from pathlib import Path

1 change: 1 addition & 0 deletions src/nwbinspector/checks/images.py
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@@ -1,4 +1,5 @@
"""Checks specific to the Images neurodata type."""

from packaging.version import Version

from pynwb.image import IndexSeries
1 change: 1 addition & 0 deletions src/nwbinspector/checks/nwb_containers.py
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@@ -1,4 +1,5 @@
"""Check functions that can apply to any object inside an NWBContainer."""

import os

import h5py
1 change: 1 addition & 0 deletions src/nwbinspector/checks/nwbfile_metadata.py
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@@ -1,4 +1,5 @@
"""Check functions that examine general NWBFile metadata."""

import re
from datetime import datetime

1 change: 1 addition & 0 deletions src/nwbinspector/checks/ophys.py
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@@ -1,4 +1,5 @@
"""Check functions specific to optical electrophysiology neurodata types."""

from pynwb.ophys import (
RoiResponseSeries,
PlaneSegmentation,
1 change: 1 addition & 0 deletions src/nwbinspector/checks/tables.py
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@@ -1,4 +1,5 @@
"""Check functions that can apply to any descendant of DynamicTable."""

from numbers import Real
from typing import List, Optional

1 change: 1 addition & 0 deletions src/nwbinspector/checks/time_series.py
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@@ -1,4 +1,5 @@
"""Check functions that can apply to any descendant of TimeSeries."""

import numpy as np

from pynwb import TimeSeries
1 change: 1 addition & 0 deletions src/nwbinspector/inspector_tools.py
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@@ -1,4 +1,5 @@
"""Internally used tools specifically for rendering more human-readable output from collected check results."""

import os
import sys
from typing import Dict, List, Optional, Union
1 change: 1 addition & 0 deletions src/nwbinspector/nwbinspector.py
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@@ -1,4 +1,5 @@
"""Primary functions for inspecting NWBFiles."""

import os
import re
import importlib
1 change: 1 addition & 0 deletions src/nwbinspector/register_checks.py
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@@ -1,4 +1,5 @@
"""Primary decorator used on a check function to add it to the registry and automatically parse its output."""

from collections.abc import Iterable
from functools import wraps
from enum import Enum
1 change: 1 addition & 0 deletions src/nwbinspector/testing.py
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@@ -1,4 +1,5 @@
"""Helper functions for internal use across the testing suite."""

import os
import json
from uuid import uuid4
1 change: 1 addition & 0 deletions src/nwbinspector/tools/_read_nwbfile.py
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@@ -1,4 +1,5 @@
"""Temporary module for thorough testing and evaluation of the proposed `read_nwbfile` helper function."""

from pathlib import Path
from warnings import filterwarnings
from typing import Optional, Literal, Union
1 change: 1 addition & 0 deletions src/nwbinspector/tools/dandi.py
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@@ -1,4 +1,5 @@
"""Helper functions related to DANDI for internal use that rely on external dependencies (i.e., dandi)."""

import re
from typing import Optional, Dict
from concurrent.futures import ProcessPoolExecutor, as_completed
1 change: 1 addition & 0 deletions src/nwbinspector/tools/nwb.py
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@@ -1,4 +1,5 @@
"""Helper functions related to NWB for internal use that rely on external dependencies (i.e., pynwb)."""

from pynwb import NWBFile


1 change: 1 addition & 0 deletions src/nwbinspector/utils.py
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@@ -1,4 +1,5 @@
"""Commonly reused logic for evaluating conditions; must not have external dependencies."""

import os
import re
import json
1 change: 1 addition & 0 deletions tests/read_nwbfile_tests.py
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@@ -1,4 +1,5 @@
"""Temporary tests for thorough testing and evaluation of the proposed `read_nwbfile` helper function."""

from pathlib import Path

import pytest
1 change: 1 addition & 0 deletions tests/streaming_tests.py
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@@ -1,4 +1,5 @@
"""All tests that specifically require streaming to be enabled (i.e., ROS3 version of h5py, fsspec, etc.)."""

import os
import pytest
from shutil import rmtree

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