[STY] use isort (#191)

* use isort

* [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

@@ -31,11 +31,11 @@ repos:
     hooks:
     -   id: flynt
 
--   repo: https://github.com/asottile/reorder-python-imports
-    rev: v3.12.0
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
     hooks:
-    -   id: reorder-python-imports
-        args: [--py37-plus, --add-import, from __future__ import annotations]
+    -   id: isort
+        args: [--profile, black]
 
 -   repo: https://github.com/psf/black
     rev: 24.1.1

bidsmreye/bids_utils.py

@@ -8,15 +8,16 @@
 from bids import BIDSLayout  # type: ignore
 
 from bidsmreye._version import __version__
-from bidsmreye.configuration import Config
-from bidsmreye.configuration import config_to_dict
-from bidsmreye.configuration import get_bids_filter_config
-from bidsmreye.configuration import get_bidsname_config
-from bidsmreye.configuration import get_pybids_config
+from bidsmreye.configuration import (
+    Config,
+    config_to_dict,
+    get_bids_filter_config,
+    get_bidsname_config,
+    get_pybids_config,
+)
 from bidsmreye.logging import bidsmreye_log
 from bidsmreye.methods import methods
-from bidsmreye.utils import copy_license
-from bidsmreye.utils import create_dir_if_absent
+from bidsmreye.utils import copy_license, create_dir_if_absent
 
 log = bidsmreye_log("bidsmreye")
 

bidsmreye/bidsmreye.py

@@ -6,18 +6,19 @@
 import json
 import sys
 from pathlib import Path
-from typing import Any
-from typing import IO
+from typing import IO, Any
 
 import rich
 
 from bidsmreye._version import __version__
 from bidsmreye.configuration import Config
-from bidsmreye.defaults import allowed_actions
-from bidsmreye.defaults import available_models
-from bidsmreye.defaults import default_log_level
-from bidsmreye.defaults import default_model
-from bidsmreye.defaults import log_levels
+from bidsmreye.defaults import (
+    allowed_actions,
+    available_models,
+    default_log_level,
+    default_model,
+    log_levels,
+)
 from bidsmreye.download import download
 from bidsmreye.generalize import generalize
 from bidsmreye.logging import bidsmreye_log

bidsmreye/configuration.py

@@ -6,10 +6,7 @@
 from pathlib import Path
 from typing import Any
 
-from attrs import asdict
-from attrs import converters
-from attrs import define
-from attrs import field
+from attrs import asdict, converters, define, field
 from bids import BIDSLayout  # type: ignore
 
 from bidsmreye.logging import bidsmreye_log

bidsmreye/download.py

@@ -6,15 +6,13 @@
 import sys
 import warnings
 from pathlib import Path
-from typing import Any
-from typing import IO
+from typing import IO, Any
 
 import pkg_resources
 import pooch
 import rich
 
-from bidsmreye.defaults import available_models
-from bidsmreye.defaults import default_model
+from bidsmreye.defaults import available_models, default_model
 from bidsmreye.logging import bidsmreye_log
 
 log = bidsmreye_log(name="bidsmreye")

bidsmreye/generalize.py

@@ -11,24 +11,26 @@
 import numpy as np
 import pandas as pd
 from bids import BIDSLayout  # type: ignore
-from deepmreye import analyse
-from deepmreye import train
-from deepmreye.util import data_generator
-from deepmreye.util import model_opts
+from deepmreye import analyse, train
+from deepmreye.util import data_generator, model_opts
 from rich import print
 
-from bidsmreye.bids_utils import check_layout
-from bidsmreye.bids_utils import create_bidsname
-from bidsmreye.bids_utils import get_dataset_layout
-from bidsmreye.bids_utils import list_subjects
+from bidsmreye.bids_utils import (
+    check_layout,
+    create_bidsname,
+    get_dataset_layout,
+    list_subjects,
+)
 from bidsmreye.configuration import Config
 from bidsmreye.logging import bidsmreye_log
 from bidsmreye.quality_control import quality_control_output
-from bidsmreye.utils import add_sidecar_in_root
-from bidsmreye.utils import check_if_file_found
-from bidsmreye.utils import create_dir_for_file
-from bidsmreye.utils import move_file
-from bidsmreye.utils import set_this_filter
+from bidsmreye.utils import (
+    add_sidecar_in_root,
+    check_if_file_found,
+    create_dir_for_file,
+    move_file,
+    set_this_filter,
+)
 
 log = bidsmreye_log(name="bidsmreye")
 

bidsmreye/methods.py

@@ -9,8 +9,7 @@
 import chevron
 
 from bidsmreye._version import __version__
-from bidsmreye.defaults import available_models
-from bidsmreye.defaults import default_model
+from bidsmreye.defaults import available_models, default_model
 from bidsmreye.utils import create_dir_for_file
 
 

bidsmreye/prepare_data.py

@@ -10,18 +10,22 @@
 from bids import BIDSLayout  # type: ignore
 from deepmreye import preprocess
 
-from bidsmreye.bids_utils import check_layout
-from bidsmreye.bids_utils import create_bidsname
-from bidsmreye.bids_utils import get_dataset_layout
-from bidsmreye.bids_utils import init_dataset
-from bidsmreye.bids_utils import list_subjects
-from bidsmreye.bids_utils import save_sampling_frequency_to_json
+from bidsmreye.bids_utils import (
+    check_layout,
+    create_bidsname,
+    get_dataset_layout,
+    init_dataset,
+    list_subjects,
+    save_sampling_frequency_to_json,
+)
 from bidsmreye.configuration import Config
 from bidsmreye.logging import bidsmreye_log
-from bidsmreye.utils import check_if_file_found
-from bidsmreye.utils import get_deepmreye_filename
-from bidsmreye.utils import move_file
-from bidsmreye.utils import set_this_filter
+from bidsmreye.utils import (
+    check_if_file_found,
+    get_deepmreye_filename,
+    move_file,
+    set_this_filter,
+)
 
 log = bidsmreye_log(name="bidsmreye")
 

bidsmreye/quality_control.py

@@ -12,16 +12,16 @@
 from bids import BIDSLayout  # type: ignore
 from scipy.stats.distributions import chi2
 
-from bidsmreye.bids_utils import check_layout
-from bidsmreye.bids_utils import create_bidsname
-from bidsmreye.bids_utils import get_dataset_layout
-from bidsmreye.bids_utils import init_dataset
-from bidsmreye.bids_utils import list_subjects
+from bidsmreye.bids_utils import (
+    check_layout,
+    create_bidsname,
+    get_dataset_layout,
+    init_dataset,
+    list_subjects,
+)
 from bidsmreye.configuration import Config
 from bidsmreye.logging import bidsmreye_log
-from bidsmreye.utils import check_if_file_found
-from bidsmreye.utils import create_dir_for_file
-from bidsmreye.utils import set_this_filter
+from bidsmreye.utils import check_if_file_found, create_dir_for_file, set_this_filter
 from bidsmreye.visualize import visualize_eye_gaze_data
 
 log = bidsmreye_log("bidsmreye")

bidsmreye/visualize.py

@@ -11,13 +11,10 @@
 from plotly.subplots import make_subplots
 
 from bidsmreye._version import __version__
-from bidsmreye.bids_utils import get_dataset_layout
-from bidsmreye.bids_utils import list_subjects
+from bidsmreye.bids_utils import get_dataset_layout, list_subjects
 from bidsmreye.configuration import Config
 from bidsmreye.logging import bidsmreye_log
-from bidsmreye.utils import check_if_file_found
-from bidsmreye.utils import set_this_filter
-
+from bidsmreye.utils import check_if_file_found, set_this_filter
 
 LINE_WIDTH = 3
 FONT_SIZE = dict(size=14)

tests/test_bids_utils.py

@@ -4,16 +4,19 @@
 import shutil
 from pathlib import Path
 
-from .utils import pybids_test_dataset
-from bidsmreye.bids_utils import check_layout
-from bidsmreye.bids_utils import create_bidsname
-from bidsmreye.bids_utils import get_dataset_layout
-from bidsmreye.bids_utils import init_dataset
-from bidsmreye.bids_utils import list_subjects
+from bidsmreye.bids_utils import (
+    check_layout,
+    create_bidsname,
+    get_dataset_layout,
+    init_dataset,
+    list_subjects,
+)
 from bidsmreye.configuration import Config
 from bidsmreye.prepare_data import save_sampling_frequency_to_json
 from bidsmreye.utils import set_this_filter
 
+from .utils import pybids_test_dataset
+
 
 def test_create_bidsname(tmp_path):
     output_dir = tmp_path / "derivatives"

tests/test_configuration.py

@@ -4,12 +4,15 @@
 
 import pytest
 
+from bidsmreye.configuration import (
+    Config,
+    config_to_dict,
+    get_bidsname_config,
+    get_config,
+    get_pybids_config,
+)
+
 from .utils import pybids_test_dataset
-from bidsmreye.configuration import Config
-from bidsmreye.configuration import config_to_dict
-from bidsmreye.configuration import get_bidsname_config
-from bidsmreye.configuration import get_config
-from bidsmreye.configuration import get_pybids_config
 
 
 def test_Config():

tests/test_download.py

@@ -5,8 +5,7 @@
 
 import pytest
 
-from bidsmreye.download import download
-from bidsmreye.download import download_parser
+from bidsmreye.download import download, download_parser
 
 
 def test_download_parser():

tests/test_quality_control.py

@@ -6,21 +6,25 @@
 import pandas as pd
 import pytest
 
-from .utils import create_basic_data
-from .utils import create_basic_json
-from .utils import create_confounds_tsv
-from .utils import return_bidsmreye_eyetrack_tsv
-from .utils import rm_dir
-from bidsmreye.bids_utils import create_bidsname
-from bidsmreye.bids_utils import get_dataset_layout
+from bidsmreye.bids_utils import create_bidsname, get_dataset_layout
 from bidsmreye.configuration import Config
-from bidsmreye.quality_control import add_qc_to_sidecar
-from bidsmreye.quality_control import compute_displacement_and_outliers
-from bidsmreye.quality_control import compute_robust_outliers
-from bidsmreye.quality_control import get_sampling_frequency
-from bidsmreye.quality_control import perform_quality_control
-from bidsmreye.quality_control import quality_control_input
-from bidsmreye.quality_control import quality_control_output
+from bidsmreye.quality_control import (
+    add_qc_to_sidecar,
+    compute_displacement_and_outliers,
+    compute_robust_outliers,
+    get_sampling_frequency,
+    perform_quality_control,
+    quality_control_input,
+    quality_control_output,
+)
+
+from .utils import (
+    create_basic_data,
+    create_basic_json,
+    create_confounds_tsv,
+    return_bidsmreye_eyetrack_tsv,
+    rm_dir,
+)
 
 
 def time_series():

tests/test_utils.py

@@ -3,14 +3,17 @@
 import shutil
 from pathlib import Path
 
-from .utils import pybids_test_dataset
 from bidsmreye.bids_utils import get_dataset_layout
 from bidsmreye.configuration import Config
-from bidsmreye.utils import copy_license
-from bidsmreye.utils import get_deepmreye_filename
-from bidsmreye.utils import return_deepmreye_output_filename
-from bidsmreye.utils import return_regex
-from bidsmreye.utils import set_this_filter
+from bidsmreye.utils import (
+    copy_license,
+    get_deepmreye_filename,
+    return_deepmreye_output_filename,
+    return_regex,
+    set_this_filter,
+)
+
+from .utils import pybids_test_dataset
 
 
 def test_copy_license(tmp_path):

tests/test_visualize.py

@@ -4,12 +4,11 @@
 
 import pandas as pd
 
-from .utils import create_confounds_tsv
-from .utils import return_bidsmreye_eyetrack_tsv
 from bidsmreye.bidsmreye import bidsmreye
 from bidsmreye.configuration import Config
-from bidsmreye.visualize import group_report
-from bidsmreye.visualize import visualize_eye_gaze_data
+from bidsmreye.visualize import group_report, visualize_eye_gaze_data
+
+from .utils import create_confounds_tsv, return_bidsmreye_eyetrack_tsv
 
 
 def test_visualize_eye_gaze_data():

tests/utils.py

@@ -8,8 +8,7 @@
 import pandas as pd
 from bids.tests import get_test_data_path
 
-from bidsmreye.quality_control import compute_displacement
-from bidsmreye.quality_control import compute_robust_outliers
+from bidsmreye.quality_control import compute_displacement, compute_robust_outliers
 
 
 def create_basic_data():