[MAINT] run isort and flake8 on the whole nilearn code base in CI

.flake8

@@ -2,12 +2,14 @@
 exclude =
     .git,
     __pycache__,
-	env,
-	venv,
+	auto_examples,
     build,
     dist,
+	env,
 	nilearn/externals/tempita
+	nilearn/externals/
 	nilearn_cache
+	venv,
 --select = D,E,F,W,C90
 docstring-convention = numpy
 max-line-length = 79

.github/workflows/flake8.yml

@@ -36,21 +36,4 @@ jobs:
 
       - name: "Run Flake8 on whole file"
         shell: bash {0}
-        run: |
-          flake8 --verbose \
-            examples/0[0234567]* \
-            maint_tools \
-            nilearn/_utils \
-            nilearn/connectome \
-            nilearn/datasets \
-            nilearn/de* \
-            nilearn/glm \
-            nilearn/image \
-            nilearn/interfaces \
-            nilearn/input_data \
-            nilearn/maskers \
-            nilearn/mass_univariate \
-            nilearn/regions \
-            nilearn/reporting \
-            nilearn/surface \
-            nilearn/*.py
+        run: flake8 --verbose .

.github/workflows/isort.yml

@@ -29,22 +29,8 @@ jobs:
           python -m pip install --upgrade pip isort
 
       - name: "Run isort"
-        run: |
-          isort --diff --check --settings-path pyproject.toml \
+        run: isort --diff --check --settings-path pyproject.toml \
             examples/0[0234567]* \
             maint_tools \
-            nilearn/_utils \
-            nilearn/connectome \
-            nilearn/datasets \
-            nilearn/de* \
-            nilearn/glm \
-            nilearn/image \
-            nilearn/interfaces \
-            nilearn/input_data \
-            nilearn/maskers \
-            nilearn/mass_univariate \
-            nilearn/plotting \
-            nilearn/regions \
-            nilearn/rerporting \
-            nilearn/surface \
-            nilearn/*.py
+            nilearn \
+            doc

doc/conf.py

@@ -15,6 +15,7 @@
 import sys
 
 import sphinx
+
 from nilearn._utils import _compare_version
 
 # ----------------------------------------------------------------------------

nilearn/_utils/data_gen.py

@@ -11,11 +11,12 @@
 import scipy.linalg
 import scipy.signal
 from nibabel import Nifti1Image
+from scipy.ndimage import binary_dilation
+from sklearn.utils import check_random_state
+
 from nilearn import datasets, image, maskers, masking
 from nilearn._utils import as_ndarray, logger
 from nilearn.interfaces.bids._utils import _bids_entities, _check_bids_label
-from scipy.ndimage import binary_dilation
-from sklearn.utils import check_random_state
 
 
 def generate_mni_space_img(n_scans=1, res=30, random_state=0, mask_dilation=2):

nilearn/_utils/niimg_conversions.py

@@ -7,10 +7,11 @@
 # License: simplified BSD
 import warnings
 
-import nilearn as ni
 import numpy as np
 from joblib import Memory
 
+import nilearn as ni
+
 from .cache_mixin import cache
 from .exceptions import DimensionError
 from .helpers import stringify_path

nilearn/_utils/testing.py

@@ -12,6 +12,7 @@
 
 import pytest
 import sklearn
+
 from nilearn._utils import _compare_version
 
 # we use memory_profiler library for memory consumption checks

nilearn/_utils/tests/test_cache_mixin.py

@@ -3,9 +3,10 @@
 import shutil
 from pathlib import Path
 
-import nilearn
 import pytest
 from joblib import Memory
+
+import nilearn
 from nilearn._utils import CacheMixin, cache_mixin
 
 

nilearn/_utils/tests/test_class_inspect.py

@@ -5,9 +5,10 @@
 which we historically used,
 ignores modules whose name starts with an underscore.
 """
-from nilearn._utils import class_inspect
 from sklearn.base import BaseEstimator
 
+from nilearn._utils import class_inspect
+
 ##############################################################################
 # Helpers for the tests
 

nilearn/_utils/tests/test_data_gen.py

@@ -5,6 +5,7 @@
 
 import numpy as np
 import pytest
+
 from nilearn._utils.data_gen import (
     _add_metadata_to_bids_dataset,
     create_fake_bids_dataset,

nilearn/_utils/tests/test_extmath.py

@@ -1,8 +1,9 @@
 """Test the _utils.extmath module."""
 import numpy as np
-from nilearn._utils.extmath import fast_abs_percentile, is_spd
 from sklearn.utils import check_random_state
 
+from nilearn._utils.extmath import fast_abs_percentile, is_spd
+
 
 def test_fast_abs_percentile():
     rng = check_random_state(1)

nilearn/_utils/tests/test_helpers.py

@@ -1,6 +1,7 @@
 import warnings
 
 import pytest
+
 from nilearn._utils import helpers
 
 

nilearn/_utils/tests/test_logger.py

@@ -6,9 +6,10 @@
 """
 import contextlib
 
-from nilearn._utils.logger import log
 from sklearn.base import BaseEstimator
 
+from nilearn._utils.logger import log
+
 
 @contextlib.contextmanager
 def capture_output():

nilearn/_utils/tests/test_ndimage.py

@@ -6,6 +6,7 @@
 """
 import numpy as np
 import pytest
+
 from nilearn._utils import data_gen
 from nilearn._utils.ndimage import _peak_local_max, largest_connected_component
 

nilearn/_utils/tests/test_niimg.py

@@ -6,6 +6,7 @@
 import pytest
 from nibabel import Nifti1Header, Nifti1Image
 from nibabel.tmpdirs import InTemporaryDirectory
+
 from nilearn._utils import load_niimg, niimg, testing
 from nilearn.image import get_data, new_img_like
 

nilearn/_utils/tests/test_niimg_conversions.py

@@ -14,10 +14,12 @@
 from pathlib import Path
 
 import nibabel
-import nilearn as ni
 import numpy as np
 import pytest
 from nibabel import Nifti1Image
+from numpy.testing import assert_array_almost_equal, assert_array_equal
+
+import nilearn as ni
 from nilearn import _utils, image
 from nilearn._utils import niimg_conversions, testing
 from nilearn._utils.exceptions import DimensionError
@@ -27,7 +29,6 @@
     with_memory_profiler,
 )
 from nilearn.image import get_data
-from numpy.testing import assert_array_almost_equal, assert_array_equal
 
 
 class PhonyNiimage(nibabel.spatialimages.SpatialImage):

nilearn/_utils/tests/test_numpy_conversions.py

@@ -10,6 +10,7 @@
 
 import numpy as np
 import pytest
+
 from nilearn._utils.numpy_conversions import as_ndarray, csv_to_array
 
 

nilearn/_utils/tests/test_param_validation.py

@@ -6,14 +6,15 @@
 import nibabel
 import numpy as np
 import pytest
+from sklearn.base import BaseEstimator
+
 from nilearn._utils.extmath import fast_abs_percentile
 from nilearn._utils.param_validation import (
     MNI152_BRAIN_VOLUME,
     _get_mask_volume,
     check_feature_screening,
     check_threshold,
 )
-from sklearn.base import BaseEstimator
 
 mni152_brain_mask = (
     "/usr/share/fsl/data/standard/MNI152_T1_1mm_brain_mask.nii.gz"

nilearn/_utils/tests/test_segmentation.py

@@ -6,6 +6,7 @@
 
 import numpy as np
 import pytest
+
 from nilearn._utils.segmentation import _random_walker
 
 

nilearn/_utils/tests/test_testing.py

@@ -1,6 +1,7 @@
 import nibabel
 import numpy as np
 import pytest
+
 from nilearn._utils.testing import (
     assert_memory_less_than,
     with_memory_profiler,

nilearn/conftest.py

@@ -3,6 +3,7 @@
 import numpy as np
 import pytest
 from nibabel import Nifti1Image
+
 from nilearn import image
 
 # we need to import these fixtures even if not used in this module

nilearn/connectome/tests/test_connectivity_matrices.py

@@ -4,6 +4,12 @@
 
 import numpy as np
 import pytest
+from numpy.testing import assert_array_almost_equal, assert_array_equal
+from pandas import DataFrame
+from scipy import linalg
+from sklearn.covariance import EmpiricalCovariance, LedoitWolf
+from sklearn.utils import check_random_state
+
 from nilearn._utils.extmath import is_spd
 from nilearn.connectome.connectivity_matrices import (
     ConnectivityMeasure,
@@ -17,11 +23,6 @@
     vec_to_sym_matrix,
 )
 from nilearn.tests.test_signal import generate_signals
-from numpy.testing import assert_array_almost_equal, assert_array_equal
-from pandas import DataFrame
-from scipy import linalg
-from sklearn.covariance import EmpiricalCovariance, LedoitWolf
-from sklearn.utils import check_random_state
 
 CONNECTIVITY_KINDS = (
     "covariance",

nilearn/connectome/tests/test_group_sparse_cov.py

@@ -1,5 +1,6 @@
 import numpy as np
 import pytest
+
 from nilearn._utils.data_gen import generate_group_sparse_gaussian_graphs
 from nilearn.connectome import GroupSparseCovariance, GroupSparseCovarianceCV
 from nilearn.connectome.group_sparse_cov import (

nilearn/datasets/_testing.py

@@ -39,9 +39,10 @@
 from unittest.mock import MagicMock
 
 import pytest
-from nilearn._utils.testing import serialize_niimg
 from requests.exceptions import HTTPError
 
+from nilearn._utils.testing import serialize_niimg
+
 
 @pytest.fixture(autouse=True)
 def temp_nilearn_data_dir(tmp_path_factory, monkeypatch):

nilearn/datasets/data/convert_templates.py

@@ -21,6 +21,7 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
+
 from nilearn.image import get_data, load_img, new_img_like
 from nilearn.masking import apply_mask, unmask
 from nilearn.plotting import plot_img

nilearn/datasets/func.py

@@ -20,9 +20,10 @@
 except ImportError:  # SciPy < 1.8
     from scipy.io.matlab.miobase import MatReadError
 
-from nilearn.image import get_data
 from sklearn.utils import Bunch
 
+from nilearn.image import get_data
+
 from .._utils import check_niimg, fill_doc
 from .._utils.numpy_conversions import csv_to_array
 from .utils import (

nilearn/datasets/tests/test_atlas.py

@@ -13,12 +13,13 @@
 import numpy as np
 import pandas as pd
 import pytest
+from numpy.testing import assert_array_equal
+
 from nilearn._utils import data_gen
 from nilearn._utils.testing import serialize_niimg
 from nilearn.datasets import atlas, utils
 from nilearn.datasets._testing import dict_to_archive
 from nilearn.image import get_data
-from numpy.testing import assert_array_equal
 
 
 def test_get_dataset_dir(tmp_path):

nilearn/datasets/tests/test_func.py

@@ -17,10 +17,11 @@
 import numpy as np
 import pandas as pd
 import pytest
+from sklearn.utils import check_random_state
+
 from nilearn.datasets import func
 from nilearn.datasets._testing import dict_to_archive, list_to_archive
 from nilearn.datasets.utils import _get_dataset_dir
-from sklearn.utils import check_random_state
 
 
 def _load_localizer_index():

nilearn/datasets/tests/test_neurovault.py

@@ -15,6 +15,7 @@
 import pandas as pd
 import pytest
 import requests
+
 from nilearn._utils.data_gen import generate_fake_fmri
 from nilearn.datasets import neurovault
 from nilearn.image import load_img

nilearn/datasets/tests/test_struct.py

@@ -11,6 +11,7 @@
 import numpy as np
 import pandas as pd
 import pytest
+
 from nilearn.datasets import struct, utils
 from nilearn.datasets._testing import dict_to_archive, list_to_archive
 

nilearn/datasets/tests/test_testing.py

@@ -5,6 +5,7 @@
 
 import pytest
 import requests
+
 from nilearn import image
 from nilearn._utils.data_gen import generate_fake_fmri
 from nilearn.datasets import _testing

nilearn/datasets/tests/test_utils.py

@@ -16,6 +16,7 @@
 import numpy as np
 import pytest
 import requests
+
 from nilearn import datasets
 from nilearn.datasets import utils
 from nilearn.datasets.utils import _get_dataset_descr