From 295e1c7e2af5ef4e108ab1a2c3b0ed7774a5be43 Mon Sep 17 00:00:00 2001 From: Talmo Pereira Date: Tue, 27 Feb 2024 16:14:09 +0000 Subject: [PATCH] Black format --- sleap_io/io/nwb.py | 13 +++++++------ sleap_io/io/slp.py | 6 +++--- sleap_io/model/instance.py | 8 +++++--- tests/fixtures/jabs.py | 1 + tests/fixtures/labels.py | 1 + tests/fixtures/labelstudio.py | 1 + tests/fixtures/slp.py | 1 + tests/io/test_jabs.py | 1 + tests/io/test_labelstudio.py | 1 + tests/io/test_main.py | 1 + tests/io/test_slp.py | 1 + tests/io/test_utils.py | 1 + tests/model/test_instance.py | 1 + tests/model/test_labeled_frame.py | 1 + tests/model/test_labels.py | 1 + tests/model/test_skeleton.py | 1 + tests/model/test_video.py | 1 + 17 files changed, 29 insertions(+), 12 deletions(-) diff --git a/sleap_io/io/nwb.py b/sleap_io/io/nwb.py index 6618eb74..317f337d 100644 --- a/sleap_io/io/nwb.py +++ b/sleap_io/io/nwb.py @@ -1,4 +1,5 @@ """Functions to write and read from the neurodata without borders (NWB) format.""" + from copy import deepcopy from typing import List, Optional, Union from pathlib import Path @@ -91,12 +92,12 @@ def read_nwb(path: str) -> Labels: frame_inds = np.searchsorted( timestamps, get_timestamps(pose_estimation_series) ) - tracks_numpy[ - frame_inds, track_idx, node_idx, : - ] = pose_estimation_series.data[:] - confidence[ - frame_inds, track_idx, node_idx - ] = pose_estimation_series.confidence[:] + tracks_numpy[frame_inds, track_idx, node_idx, :] = ( + pose_estimation_series.data[:] + ) + confidence[frame_inds, track_idx, node_idx] = ( + pose_estimation_series.confidence[:] + ) video_tracks[Path(pose_estimation.original_videos[0]).as_posix()] = ( tracks_numpy, diff --git a/sleap_io/io/slp.py b/sleap_io/io/slp.py index 2d329562..65486a3b 100644 --- a/sleap_io/io/slp.py +++ b/sleap_io/io/slp.py @@ -107,9 +107,9 @@ def write_videos(labels_path: str, videos: list[Video]): elif type(video.backend) == HDF5Video: video_json = { "backend": { - "filename": "." - if video.backend.has_embedded_images - else video.filename, + "filename": ( + "." if video.backend.has_embedded_images else video.filename + ), "dataset": video.backend.dataset, "input_format": video.backend.input_format, "convert_range": False, diff --git a/sleap_io/model/instance.py b/sleap_io/model/instance.py index 5d48907e..ceb5ad04 100644 --- a/sleap_io/model/instance.py +++ b/sleap_io/model/instance.py @@ -226,9 +226,11 @@ def _convert_points(self, attr, points): for node in points.keys() ] vals = [ - point - if type(point) == self._POINT_TYPE - else self._make_default_point(*point) + ( + point + if type(point) == self._POINT_TYPE + else self._make_default_point(*point) + ) for point in points.values() ] points = {k: v for k, v in zip(keys, vals)} diff --git a/tests/fixtures/jabs.py b/tests/fixtures/jabs.py index 6aff4f62..40710834 100644 --- a/tests/fixtures/jabs.py +++ b/tests/fixtures/jabs.py @@ -1,4 +1,5 @@ """Fixtures that return paths to jabs .h5 files.""" + import pytest diff --git a/tests/fixtures/labels.py b/tests/fixtures/labels.py index bdc5e7c6..3b977cc8 100644 --- a/tests/fixtures/labels.py +++ b/tests/fixtures/labels.py @@ -1,4 +1,5 @@ """Fixtures that return `Labels` objects.""" + import pytest import sleap_io diff --git a/tests/fixtures/labelstudio.py b/tests/fixtures/labelstudio.py index affd967f..5eed741a 100644 --- a/tests/fixtures/labelstudio.py +++ b/tests/fixtures/labelstudio.py @@ -1,4 +1,5 @@ """Fixtures that return paths to label-studio .json files.""" + import pytest from sleap_io import Skeleton, Node, Edge diff --git a/tests/fixtures/slp.py b/tests/fixtures/slp.py index 98421657..1b82a32e 100644 --- a/tests/fixtures/slp.py +++ b/tests/fixtures/slp.py @@ -1,4 +1,5 @@ """Fixtures that return paths to .slp files.""" + import pytest diff --git a/tests/io/test_jabs.py b/tests/io/test_jabs.py index 60e369ff..d2535390 100644 --- a/tests/io/test_jabs.py +++ b/tests/io/test_jabs.py @@ -1,4 +1,5 @@ """Tests for functions in the sleap_io.io.jabs file.""" + import numpy as np import h5py diff --git a/tests/io/test_labelstudio.py b/tests/io/test_labelstudio.py index 84aed221..71f360bc 100644 --- a/tests/io/test_labelstudio.py +++ b/tests/io/test_labelstudio.py @@ -1,4 +1,5 @@ """Tests for functions in the sleap_io.io.labelstudio file.""" + from sleap_io import Labels from sleap_io.io.labelstudio import parse_tasks, read_labels, convert_labels from sleap_io.io.slp import read_labels as slp_read_labels diff --git a/tests/io/test_main.py b/tests/io/test_main.py index 2cdf2963..f70fbacd 100644 --- a/tests/io/test_main.py +++ b/tests/io/test_main.py @@ -1,4 +1,5 @@ """Tests for functions in the sleap_io.io.main file.""" + from sleap_io import Labels from sleap_io.io.main import ( load_slp, diff --git a/tests/io/test_slp.py b/tests/io/test_slp.py index 7ef02d48..17001dbc 100644 --- a/tests/io/test_slp.py +++ b/tests/io/test_slp.py @@ -1,4 +1,5 @@ """Tests for functions in the sleap_io.io.slp file.""" + from sleap_io import ( Video, Skeleton, diff --git a/tests/io/test_utils.py b/tests/io/test_utils.py index 45d63092..de47763f 100644 --- a/tests/io/test_utils.py +++ b/tests/io/test_utils.py @@ -1,4 +1,5 @@ """Tests for the sleap_io.io.test_utils file.""" + import pytest import h5py import numpy as np diff --git a/tests/model/test_instance.py b/tests/model/test_instance.py index 204636e6..1381bad1 100644 --- a/tests/model/test_instance.py +++ b/tests/model/test_instance.py @@ -1,4 +1,5 @@ """Tests for methods in the sleap_io.model.instance file.""" + from pickletools import pyset import numpy as np from numpy.testing import assert_equal diff --git a/tests/model/test_labeled_frame.py b/tests/model/test_labeled_frame.py index b2a21878..f8093ced 100644 --- a/tests/model/test_labeled_frame.py +++ b/tests/model/test_labeled_frame.py @@ -1,4 +1,5 @@ """Tests for methods in sleap_io.model.labeled_frame file.""" + from numpy.testing import assert_equal from sleap_io import Video, Skeleton, Instance, PredictedInstance from sleap_io.model.labeled_frame import LabeledFrame diff --git a/tests/model/test_labels.py b/tests/model/test_labels.py index 4112f395..e52a8103 100644 --- a/tests/model/test_labels.py +++ b/tests/model/test_labels.py @@ -1,4 +1,5 @@ """Test methods and functions in the sleap_io.model.labels file.""" + from numpy.testing import assert_equal import pytest from sleap_io import ( diff --git a/tests/model/test_skeleton.py b/tests/model/test_skeleton.py index 399e4017..27a61c2c 100644 --- a/tests/model/test_skeleton.py +++ b/tests/model/test_skeleton.py @@ -1,4 +1,5 @@ """Tests for methods in the sleap_io.model.skeleton file.""" + import pytest from sleap_io.model.skeleton import Node, Edge, Symmetry, Skeleton diff --git a/tests/model/test_video.py b/tests/model/test_video.py index 65ee8c38..53c9baf0 100644 --- a/tests/model/test_video.py +++ b/tests/model/test_video.py @@ -1,4 +1,5 @@ """Tests for methods in the sleap_io.model.video file.""" + from sleap_io import Video from sleap_io.io.video import MediaVideo import numpy as np