From 8f741eb021eea3d2318993ee38819e066794fb4f Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 29 Jan 2024 13:52:21 -0500 Subject: [PATCH] [pre-commit.ci] pre-commit autoupdate (#430) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 23.12.1 → 24.1.1](https://github.com/psf/black/compare/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> --- .pre-commit-config.yaml | 2 +- src/nwbinspector/checks/behavior.py | 1 + src/nwbinspector/checks/ecephys.py | 1 + src/nwbinspector/checks/general.py | 1 + src/nwbinspector/checks/icephys.py | 1 + src/nwbinspector/checks/image_series.py | 1 + src/nwbinspector/checks/images.py | 1 + src/nwbinspector/checks/nwb_containers.py | 1 + src/nwbinspector/checks/nwbfile_metadata.py | 1 + src/nwbinspector/checks/ophys.py | 1 + src/nwbinspector/checks/tables.py | 1 + src/nwbinspector/checks/time_series.py | 1 + src/nwbinspector/inspector_tools.py | 1 + src/nwbinspector/nwbinspector.py | 1 + src/nwbinspector/register_checks.py | 1 + src/nwbinspector/testing.py | 1 + src/nwbinspector/tools/_read_nwbfile.py | 1 + src/nwbinspector/tools/dandi.py | 1 + src/nwbinspector/tools/nwb.py | 1 + src/nwbinspector/utils.py | 1 + tests/read_nwbfile_tests.py | 1 + tests/streaming_tests.py | 1 + 22 files changed, 22 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6dedbc032..4775f9179 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -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 diff --git a/src/nwbinspector/checks/behavior.py b/src/nwbinspector/checks/behavior.py index 1ecb9c683..972e07ab3 100644 --- a/src/nwbinspector/checks/behavior.py +++ b/src/nwbinspector/checks/behavior.py @@ -1,4 +1,5 @@ """Checks for types belonging to the pynwb.behavior module.""" + import numpy as np from pynwb.behavior import SpatialSeries, CompassDirection diff --git a/src/nwbinspector/checks/ecephys.py b/src/nwbinspector/checks/ecephys.py index 5044bd8d1..ae8dea384 100644 --- a/src/nwbinspector/checks/ecephys.py +++ b/src/nwbinspector/checks/ecephys.py @@ -1,4 +1,5 @@ """Check functions specific to extracellular electrophysiology neurodata types.""" + import numpy as np from pynwb.misc import Units diff --git a/src/nwbinspector/checks/general.py b/src/nwbinspector/checks/general.py index fd700ceb8..08b72244c 100644 --- a/src/nwbinspector/checks/general.py +++ b/src/nwbinspector/checks/general.py @@ -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"] diff --git a/src/nwbinspector/checks/icephys.py b/src/nwbinspector/checks/icephys.py index a2d2e959d..e926b8f2c 100644 --- a/src/nwbinspector/checks/icephys.py +++ b/src/nwbinspector/checks/icephys.py @@ -1,4 +1,5 @@ """Checks specific to intracellular electrophysiology neurodata types.""" + from pynwb.icephys import IntracellularElectrode from ..register_checks import register_check, Importance, InspectorMessage diff --git a/src/nwbinspector/checks/image_series.py b/src/nwbinspector/checks/image_series.py index 07203f3e4..0d2d76108 100644 --- a/src/nwbinspector/checks/image_series.py +++ b/src/nwbinspector/checks/image_series.py @@ -1,4 +1,5 @@ """Check functions specific to ImageSeries.""" + import ntpath from pathlib import Path diff --git a/src/nwbinspector/checks/images.py b/src/nwbinspector/checks/images.py index 1ee77c9bb..e91db0546 100644 --- a/src/nwbinspector/checks/images.py +++ b/src/nwbinspector/checks/images.py @@ -1,4 +1,5 @@ """Checks specific to the Images neurodata type.""" + from packaging.version import Version from pynwb.image import IndexSeries diff --git a/src/nwbinspector/checks/nwb_containers.py b/src/nwbinspector/checks/nwb_containers.py index d6e8af64b..1bee852e7 100644 --- a/src/nwbinspector/checks/nwb_containers.py +++ b/src/nwbinspector/checks/nwb_containers.py @@ -1,4 +1,5 @@ """Check functions that can apply to any object inside an NWBContainer.""" + import os import h5py diff --git a/src/nwbinspector/checks/nwbfile_metadata.py b/src/nwbinspector/checks/nwbfile_metadata.py index d6e32b276..09b30b138 100644 --- a/src/nwbinspector/checks/nwbfile_metadata.py +++ b/src/nwbinspector/checks/nwbfile_metadata.py @@ -1,4 +1,5 @@ """Check functions that examine general NWBFile metadata.""" + import re from datetime import datetime diff --git a/src/nwbinspector/checks/ophys.py b/src/nwbinspector/checks/ophys.py index 8b5834624..a455a38f0 100644 --- a/src/nwbinspector/checks/ophys.py +++ b/src/nwbinspector/checks/ophys.py @@ -1,4 +1,5 @@ """Check functions specific to optical electrophysiology neurodata types.""" + from pynwb.ophys import ( RoiResponseSeries, PlaneSegmentation, diff --git a/src/nwbinspector/checks/tables.py b/src/nwbinspector/checks/tables.py index a7ccaf8d7..ef13a8b9f 100644 --- a/src/nwbinspector/checks/tables.py +++ b/src/nwbinspector/checks/tables.py @@ -1,4 +1,5 @@ """Check functions that can apply to any descendant of DynamicTable.""" + from numbers import Real from typing import List, Optional diff --git a/src/nwbinspector/checks/time_series.py b/src/nwbinspector/checks/time_series.py index 05b958c18..adab06594 100644 --- a/src/nwbinspector/checks/time_series.py +++ b/src/nwbinspector/checks/time_series.py @@ -1,4 +1,5 @@ """Check functions that can apply to any descendant of TimeSeries.""" + import numpy as np from pynwb import TimeSeries diff --git a/src/nwbinspector/inspector_tools.py b/src/nwbinspector/inspector_tools.py index 265bbf424..ee4703806 100644 --- a/src/nwbinspector/inspector_tools.py +++ b/src/nwbinspector/inspector_tools.py @@ -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 diff --git a/src/nwbinspector/nwbinspector.py b/src/nwbinspector/nwbinspector.py index 010040ccd..748f6fe7a 100644 --- a/src/nwbinspector/nwbinspector.py +++ b/src/nwbinspector/nwbinspector.py @@ -1,4 +1,5 @@ """Primary functions for inspecting NWBFiles.""" + import os import re import importlib diff --git a/src/nwbinspector/register_checks.py b/src/nwbinspector/register_checks.py index 764ce4a12..d8e8ba277 100644 --- a/src/nwbinspector/register_checks.py +++ b/src/nwbinspector/register_checks.py @@ -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 diff --git a/src/nwbinspector/testing.py b/src/nwbinspector/testing.py index 2bb2ec7cc..a2ece3ce6 100644 --- a/src/nwbinspector/testing.py +++ b/src/nwbinspector/testing.py @@ -1,4 +1,5 @@ """Helper functions for internal use across the testing suite.""" + import os import json from uuid import uuid4 diff --git a/src/nwbinspector/tools/_read_nwbfile.py b/src/nwbinspector/tools/_read_nwbfile.py index 2a5e12e20..fff903cff 100644 --- a/src/nwbinspector/tools/_read_nwbfile.py +++ b/src/nwbinspector/tools/_read_nwbfile.py @@ -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 diff --git a/src/nwbinspector/tools/dandi.py b/src/nwbinspector/tools/dandi.py index b3dd890b1..ac0d5625d 100644 --- a/src/nwbinspector/tools/dandi.py +++ b/src/nwbinspector/tools/dandi.py @@ -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 diff --git a/src/nwbinspector/tools/nwb.py b/src/nwbinspector/tools/nwb.py index 86f7bc130..24676220d 100644 --- a/src/nwbinspector/tools/nwb.py +++ b/src/nwbinspector/tools/nwb.py @@ -1,4 +1,5 @@ """Helper functions related to NWB for internal use that rely on external dependencies (i.e., pynwb).""" + from pynwb import NWBFile diff --git a/src/nwbinspector/utils.py b/src/nwbinspector/utils.py index 5a0095c75..75ba6c8c9 100644 --- a/src/nwbinspector/utils.py +++ b/src/nwbinspector/utils.py @@ -1,4 +1,5 @@ """Commonly reused logic for evaluating conditions; must not have external dependencies.""" + import os import re import json diff --git a/tests/read_nwbfile_tests.py b/tests/read_nwbfile_tests.py index 28fca9c3b..c0f687328 100644 --- a/tests/read_nwbfile_tests.py +++ b/tests/read_nwbfile_tests.py @@ -1,4 +1,5 @@ """Temporary tests for thorough testing and evaluation of the proposed `read_nwbfile` helper function.""" + from pathlib import Path import pytest diff --git a/tests/streaming_tests.py b/tests/streaming_tests.py index 9f5bce0b3..78bec8324 100644 --- a/tests/streaming_tests.py +++ b/tests/streaming_tests.py @@ -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