sty: Manual fixes for remaining checks

effigies · effigies · commit 83da101b9b41 · 2024-11-16T10:05:53.000-05:00
diff --git a/docs/conf.py b/docs/conf.py
@@ -36,7 +36,7 @@
 os.close(tffiledesc)
 templateflow.api.get = mock.MagicMock(return_value=tffilename)
 
-from niworkflows import __copyright__, __packagename__, __version__
+from niworkflows import __copyright__, __packagename__, __version__  # noqa:E402
 
 sys.path.append(os.path.abspath('sphinxext'))
 
diff --git a/niworkflows/__about__.py b/niworkflows/__about__.py
@@ -27,10 +27,8 @@
 as well as for open-source software distribution.
 """
 
-from datetime import datetime
-
 __packagename__ = 'niworkflows'
-__copyright__ = f'Copyright {datetime.now().year}, The NiPreps Developers'
+__copyright__ = 'Copyright, The NiPreps Developers'
 __credits__ = [
     'Oscar Esteban',
     'Ross Blair',
diff --git a/niworkflows/anat/ants.py b/niworkflows/anat/ants.py
@@ -23,7 +23,6 @@
 """Nipype translation of ANTs' workflows."""
 
 # general purpose
-from collections import OrderedDict
 from multiprocessing import cpu_count
 from warnings import warn
 
@@ -55,10 +54,11 @@
 from ..utils.misc import get_template_specs
 
 ATROPOS_MODELS = {
-    'T1w': OrderedDict([('nclasses', 3), ('csf', 1), ('gm', 2), ('wm', 3)]),
-    'T2w': OrderedDict([('nclasses', 3), ('csf', 3), ('gm', 2), ('wm', 1)]),
-    'FLAIR': OrderedDict([('nclasses', 3), ('csf', 1), ('gm', 3), ('wm', 2)]),
+    'T1w': {'nclasses': 3, 'csf': 1, 'gm': 2, 'wm': 3},
+    'T2w': {'nclasses': 3, 'csf': 3, 'gm': 2, 'wm': 1},
+    'FLAIR': {'nclasses': 3, 'csf': 1, 'gm': 3, 'wm': 2},
 }
+T1W_MODEL = tuple(ATROPOS_MODELS['T1w'].values())
 
 
 def init_brain_extraction_wf(
@@ -293,7 +293,8 @@ def init_brain_extraction_wf(
     except ValueError:
         warn(
             "antsAI's option --search-grid was added in ANTS 2.3.0 "
-            f'({init_aff.interface.version} found.)'
+            f'({init_aff.interface.version} found.)',
+            stacklevel=1,
         )
 
     # Set up spatial normalization
@@ -355,6 +356,7 @@ def init_brain_extraction_wf(
             "N4BiasFieldCorrection's --rescale-intensities option was added in ANTS 2.1.0 "
             f'({inu_n4_final.interface.version} found.) Please consider upgrading.',
             UserWarning,
+            stacklevel=1,
         )
 
     # Apply mask
@@ -501,7 +503,7 @@ def init_atropos_wf(
     omp_nthreads=None,
     mem_gb=3.0,
     padding=10,
-    in_segmentation_model=tuple(ATROPOS_MODELS['T1w'].values()),
+    in_segmentation_model=T1W_MODEL,
     bspline_fitting_distance=200,
     wm_prior=False,
 ):
@@ -758,6 +760,7 @@ def init_atropos_wf(
             "N4BiasFieldCorrection's --rescale-intensities option was added in ANTS 2.1.0 "
             f'({inu_n4_final.interface.version} found.) Please consider upgrading.',
             UserWarning,
+            stacklevel=1,
         )
 
     # Apply mask
@@ -987,6 +990,7 @@ def init_n4_only_wf(
             "N4BiasFieldCorrection's --rescale-intensities option was added in ANTS 2.1.0 "
             f'({inu_n4_final.interface.version} found.) Please consider upgrading.',
             UserWarning,
+            stacklevel=1,
         )
 
     # fmt: off
diff --git a/niworkflows/anat/freesurfer.py b/niworkflows/anat/freesurfer.py
@@ -37,8 +37,10 @@
 )
 from ..interfaces.surf import NormalizeSurf
 
+SUBJECTS_DIR = getenv('SUBJECTS_DIR')
 
-def init_gifti_surface_wf(name='gifti_surface_wf', subjects_dir=getenv('SUBJECTS_DIR', None)):
+
+def init_gifti_surface_wf(name='gifti_surface_wf', subjects_dir=SUBJECTS_DIR):
     """
     Build a Nipype workflow to prepare GIFTI surfaces from FreeSurfer.
 
diff --git a/niworkflows/conftest.py b/niworkflows/conftest.py
@@ -51,7 +51,7 @@ def find_resource_or_skip(resource):
 
 
 @pytest.fixture(autouse=True)
-def add_np(doctest_namespace):
+def _add_np(doctest_namespace):
     from .testing import data_dir, data_dir_canary
     from .utils.bids import collect_data
 
diff --git a/niworkflows/engine/__init__.py b/niworkflows/engine/__init__.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
diff --git a/niworkflows/func/tests/test_util.py b/niworkflows/func/tests/test_util.py
diff --git a/niworkflows/interfaces/bids.py b/niworkflows/interfaces/bids.py
@@ -69,7 +69,7 @@
 if sys.version_info < (3, 10):  # PY39
     builtin_zip = zip
 
-    def zip(*args, strict=False):
+    def zip(*args, strict=False):  # noqa: A001
         if strict and any(len(args[0]) != len(arg) for arg in args):
             raise ValueError('strict_zip() requires all arguments to have the same length')
         return builtin_zip(*args)
@@ -676,7 +676,7 @@ def _run_interface(self, runtime):
                 if data_dtype == 'source':  # match source dtype
                     try:
                         data_dtype = nb.load(self.inputs.source_file[0]).get_data_dtype()
-                    except Exception:
+                    except Exception:  # noqa: BLE001
                         LOGGER.warning(
                             f'Could not get data type of file {self.inputs.source_file[0]}'
                         )
@@ -1193,7 +1193,7 @@ def _run_interface(self, runtime):
                 if data_dtype == 'source':  # match source dtype
                     try:
                         data_dtype = nb.load(self.inputs.source_file[0]).get_data_dtype()
-                    except Exception:
+                    except Exception:  # noqa: BLE001
                         LOGGER.warning(
                             f'Could not get data type of file {self.inputs.source_file[0]}'
                         )
diff --git a/niworkflows/interfaces/cifti.py b/niworkflows/interfaces/cifti.py
@@ -22,8 +22,9 @@
 #
 """Handling connectivity: combines FreeSurfer surfaces with subcortical volumes."""
 
+from __future__ import annotations
+
 import json
-import typing
 import warnings
 from pathlib import Path
 
@@ -252,7 +253,7 @@ def _create_cifti_image(
     bold_surfs: tuple[str, str],
     surface_labels: tuple[str, str],
     tr: float,
-    metadata: typing.Optional[dict] = None,
+    metadata: dict | None = None,
 ):
     """
     Generate CIFTI image in target space.
@@ -280,7 +281,7 @@ def _create_cifti_image(
     bold_img = nb.load(bold_file)
     label_img = nb.load(volume_label)
     if label_img.shape != bold_img.shape[:3]:
-        warnings.warn('Resampling bold volume to match label dimensions')
+        warnings.warn('Resampling bold volume to match label dimensions', stacklevel=1)
         bold_img = resample_to_img(bold_img, label_img)
 
     # ensure images match HCP orientation (LAS)
diff --git a/niworkflows/interfaces/freesurfer.py b/niworkflows/interfaces/freesurfer.py
@@ -566,7 +566,7 @@ def mri_info(fname, argument):
     import numpy as np
 
     cmd_info = f'mri_info --{argument} {fname}'
-    proc = sp.Popen(cmd_info, stdout=sp.PIPE, shell=True)
+    proc = sp.Popen(cmd_info, stdout=sp.PIPE, shell=True)  # noqa: S602
     data = bytearray(proc.stdout.read())
     mstring = np.fromstring(data.decode('utf-8'), sep='\n')
     result = np.reshape(mstring, (4, -1))
diff --git a/niworkflows/interfaces/images.py b/niworkflows/interfaces/images.py
@@ -133,7 +133,7 @@ def _run_interface(self, runtime):
 
         nii_list = []
         # Remove one-sized extra dimensions
-        for i, f in enumerate(in_files):
+        for f in in_files:
             filenii = nb.load(f)
             filenii = nb.squeeze_image(filenii)
             if len(filenii.shape) == 5:
diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
@@ -760,11 +760,14 @@ def _merge_rois(in_files, newpath=None):
     nonzero = np.any(data, axis=3)
     for roi in in_files[1:]:
         img = nb.load(roi)
-        assert img.shape == data.shape, 'Mismatch in image shape'
-        assert np.allclose(img.affine, affine), 'Mismatch in affine'
+        if not img.shape == data.shape:
+            raise ValueError('Mismatch in image shape')
+        if not np.allclose(img.affine, affine):
+            raise ValueError('Mismatch in affine')
         roi_data = np.asanyarray(img.dataobj)
         roi_nonzero = np.any(roi_data, axis=3)
-        assert not np.any(roi_nonzero & nonzero), 'Overlapping ROIs'
+        if np.any(roi_nonzero & nonzero):
+            raise ValueError('Overlapping ROIs')
         nonzero |= roi_nonzero
         data += roi_data
         del roi_data
diff --git a/niworkflows/interfaces/reportlets/__init__.py b/niworkflows/interfaces/reportlets/__init__.py
@@ -2,4 +2,4 @@
 
 msg = 'Niworkflows will be deprecating reporting in favor of a standalone library "nireports".'
 
-warnings.warn(msg, PendingDeprecationWarning)
+warnings.warn(msg, PendingDeprecationWarning, stacklevel=2)
diff --git a/niworkflows/interfaces/tests/test_bids.py b/niworkflows/interfaces/tests/test_bids.py
@@ -380,7 +380,7 @@ def test_DerivativesDataSink_build_path(
                 # Nibabel 5.3 avoids unnecessary roundtrips for Cifti2Headers
                 # Older versions transformed a `SeriesStep="2"` into `SeriesStep="2.0"`
                 chksum = 'f7b8755c6ad0d8dcdb60676331b52a23ce288b61'
-        assert sha1(Path(out).read_bytes()).hexdigest() == chksum
+        assert sha1(Path(out).read_bytes()).hexdigest() == chksum  # noqa: S324
 
 
 @pytest.mark.parametrize('interface', [bintfs.DerivativesDataSink, bintfs.PrepareDerivative])
@@ -660,7 +660,7 @@ def test_DerivativesDataSink_values(tmp_path, interface, dtype):
     nii = nb.load(out_file)
     assert np.allclose(nii.dataobj, expected)
 
-    checksum = sha1(out_file.read_bytes()).hexdigest()
+    checksum = sha1(out_file.read_bytes()).hexdigest()  # noqa: S324
     out_file.unlink()
 
     # Rerun to ensure determinism with non-zero data
@@ -676,7 +676,7 @@ def test_DerivativesDataSink_values(tmp_path, interface, dtype):
 
     prep_result = prep.run()
 
-    assert sha1(out_file.read_bytes()).hexdigest() == checksum
+    assert sha1(out_file.read_bytes()).hexdigest() == checksum  # noqa: S324
 
 
 @needs_data_dir
@@ -710,7 +710,7 @@ def test_ReadSidecarJSON_connection(testdata_dir, field):
     ('derivatives', 'subjects_dir'),
     [
         (os.getenv('FREESURFER_HOME'), 'subjects'),
-        ('/tmp', os.path.join(os.getenv('FREESURFER_HOME'), 'subjects')),
+        ('/tmp', os.path.join(os.getenv('FREESURFER_HOME'), 'subjects')),  # noqa: S108
     ],
 )
 def test_fsdir_noaction(derivatives, subjects_dir):
diff --git a/niworkflows/interfaces/tests/test_nibabel.py b/niworkflows/interfaces/tests/test_nibabel.py
@@ -108,7 +108,7 @@ def test_merge_rois(tmpdir, create_roi, affine, data, roi_index, error, err_mess
         merge.run()
         return
     # otherwise check expected exceptions
-    with pytest.raises(AssertionError) as err:
+    with pytest.raises(ValueError, match=r'Mismatch|Overlapping') as err:
         merge.run()
     assert err_message in str(err.value)
 
@@ -167,13 +167,13 @@ def test_ApplyMask(tmp_path):
 
     # Test errors
     nb.Nifti1Image(mask, 2 * np.eye(4), None).to_filename(str(in_mask))
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError, match=r'affines are not similar'):
         ApplyMask(in_file=str(in_file), in_mask=str(in_mask), threshold=0.4).run()
 
     nb.Nifti1Image(mask[:-1, ...], np.eye(4), None).to_filename(str(in_mask))
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError, match=r'sizes do not match'):
         ApplyMask(in_file=str(in_file), in_mask=str(in_mask), threshold=0.4).run()
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError, match=r'sizes do not match'):
         ApplyMask(in_file=str(in_file4d), in_mask=str(in_mask), threshold=0.4).run()
 
 
@@ -207,7 +207,7 @@ def test_SplitSeries(tmp_path, shape, exp_n):
         n = int(isinstance(split.outputs.out_files, str)) or len(split.outputs.out_files)
         assert n == exp_n
     else:
-        with pytest.raises(ValueError):
+        with pytest.raises(ValueError, match=r'Invalid shape'):
             _interface.run()
 
 
@@ -227,7 +227,7 @@ def test_MergeSeries(tmp_path):
     merge = MergeSeries(in_files=[str(in_file)] + [str(in_4D)]).run()
     assert nb.load(merge.outputs.out_file).dataobj.shape == (20, 20, 20, 5)
 
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError, match=r'incorrect number of dimensions'):
         MergeSeries(in_files=[str(in_file)] + [str(in_4D)], allow_4D=False).run()
 
 
@@ -243,7 +243,7 @@ def test_MergeSeries_affines(tmp_path):
     nb.Nifti1Image(data, aff, None).to_filename(files[1])
 
     # affine mismatch will cause this to fail
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError, match=r'does not match affine'):
         MergeSeries(in_files=files).run()
     # but works if we set a tolerance
     MergeSeries(in_files=files, affine_tolerance=1e-04).run()
diff --git a/niworkflows/interfaces/tests/test_utility.py b/niworkflows/interfaces/tests/test_utility.py
@@ -31,10 +31,10 @@
 
 def test_KeySelect():
     """Test KeySelect."""
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError, match=r'duplicated entries'):
         KeySelect(fields='field1', keys=['a', 'b', 'c', 'a'])
 
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError, match=r'list or .* must be provided'):
         KeySelect(fields=[])
 
 
diff --git a/niworkflows/interfaces/utility.py b/niworkflows/interfaces/utility.py
@@ -553,10 +553,10 @@ def less_breakable(a_string):
         tsv_data.set_index(index_column, drop=True, inplace=True)
     if enforce_case:
         tsv_data.index = [
-            re.sub(re_to_snake, snake, less_breakable(i), 0).lower() for i in tsv_data.index
+            re.sub(re_to_snake, snake, less_breakable(i), count=0).lower() for i in tsv_data.index
         ]
         tsv_data.columns = [
-            re.sub(re_to_camel, camel, less_breakable(i).title(), 0).replace('Csf', 'CSF')
+            re.sub(re_to_camel, camel, less_breakable(i).title(), count=0).replace('Csf', 'CSF')
             for i in tsv_data.columns
         ]
     json_data = tsv_data.to_json(orient='index')
diff --git a/niworkflows/reports/core.py b/niworkflows/reports/core.py
@@ -290,8 +290,9 @@ def __init__(
 
         # Default template from niworkflows
         self.template_path = load_resource('reports') / 'report.tpl'
+        if not self.template_path.exists():
+            raise RuntimeError('Could not find report template. Corrupted installation.')
         self._load_config(Path(config or load_resource('reports') / 'default.yml'))
-        assert self.template_path.exists()
 
     def _load_config(self, config):
         from yaml import safe_load as load
@@ -415,7 +416,7 @@ def generate_report(self):
             loader=jinja2.FileSystemLoader(searchpath=str(self.template_path.parent)),
             trim_blocks=True,
             lstrip_blocks=True,
-            autoescape=False,
+            autoescape=False,  # noqa: S701  XXX Investigate if this is a problem in nireports.
         )
         report_tpl = env.get_template(self.template_path.name)
         report_render = report_tpl.render(
diff --git a/niworkflows/utils/bids.py b/niworkflows/utils/bids.py
@@ -154,7 +154,7 @@ def collect_participants(bids_dir, participant_label=None, strict=False, bids_va
         )
         if strict:
             raise exc
-        warnings.warn(exc.msg, BIDSWarning)
+        warnings.warn(exc.msg, BIDSWarning, stacklevel=2)
 
     return found_label
 
diff --git a/niworkflows/utils/debug.py b/niworkflows/utils/debug.py
@@ -57,13 +57,13 @@ def setup_exceptionhook(ipython=False):
     pdb.post_mortem; if not interactive, then invokes default handler.
     """
 
-    def _pdb_excepthook(type, value, tb):
+    def _pdb_excepthook(tp, value, tb):
         import traceback
 
-        traceback.print_exception(type, value, tb)
+        traceback.print_exception(tp, value, tb)
         print()
         if is_interactive():
-            import pdb
+            import pdb  # noqa: T100
 
             pdb.post_mortem(tb)
 
diff --git a/niworkflows/utils/misc.py b/niworkflows/utils/misc.py
diff --git a/niworkflows/utils/testing.py b/niworkflows/utils/testing.py
diff --git a/niworkflows/utils/tests/test_images.py b/niworkflows/utils/tests/test_images.py
diff --git a/niworkflows/utils/tests/test_utils.py b/niworkflows/utils/tests/test_utils.py
diff --git a/niworkflows/viz/__init__.py b/niworkflows/viz/__init__.py
diff --git a/niworkflows/viz/plots.py b/niworkflows/viz/plots.py
diff --git a/niworkflows/viz/utils.py b/niworkflows/viz/utils.py
diff --git a/pyproject.toml b/pyproject.toml

Original file line number	Diff line number	Diff line change
`@@ -37,8 +37,10 @@`
`37`	`37`	`)`
`38`	`38`	`from ..interfaces.surf import NormalizeSurf`
`39`	`39`
	`40`	`+SUBJECTS_DIR = getenv('SUBJECTS_DIR')`
`40`	`41`
`41`		`-def init_gifti_surface_wf(name='gifti_surface_wf', subjects_dir=getenv('SUBJECTS_DIR', None)):`
	`42`	`+`
	`43`	`+def init_gifti_surface_wf(name='gifti_surface_wf', subjects_dir=SUBJECTS_DIR):`
`42`	`44`	`"""`
`43`	`45`	`Build a Nipype workflow to prepare GIFTI surfaces from FreeSurfer.`
`44`	`46`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-#!/usr/bin/env python`
`2`	`1`	`# emacs: -- mode: python; py-indent-offset: 4; indent-tabs-mode: nil --`
`3`	`2`	`# vi: set ft=python sts=4 ts=4 sw=4 et:`
`4`	`3`	`"""`