Keep working.

qsiprep/cli/parser.py

@@ -211,9 +211,9 @@ def _bids_filter(value, parser):
         metavar='FILE',
         help='A JSON file describing custom BIDS input filters using PyBIDS. '
         'For further details, please check out '
-        'https://fmriprep.readthedocs.io/en/%s/faq.html#'
+        'https://fmriprep.readthedocs.io/en/'
+        f'{currentv.base_version if is_release else "latest"}/faq.html#'
         'how-do-I-select-only-certain-files-to-be-input-to-fMRIPrep'
-        % (currentv.base_version if is_release else 'latest'),
     )
     g_bids.add_argument(
         '--bids-database-dir',
@@ -710,12 +710,10 @@ def parse_args(args=None, namespace=None):
 
     # Ensure input and output folders are not the same
     if output_dir == bids_dir:
+        rec_path = output_dir / 'derivatives' / f"qsiprep-{version.split('+')[0]}"
         parser.error(
             'The selected output folder is the same as the input BIDS folder. '
-            'Please modify the output path (suggestion: %s).'
-            % bids_dir
-            / 'derivatives'
-            / ('qsiprep-%s' % version.split('+')[0])
+            f'Please modify the output path (suggestion: {rec_path}).'
         )
 
     if bids_dir in work_dir.parents:
@@ -755,7 +753,7 @@ def parse_args(args=None, namespace=None):
     if missing_subjects:
         parser.error(
             'One or more participant labels were not found in the BIDS directory: '
-            '%s.' % ', '.join(missing_subjects)
+            f"{', '.join(missing_subjects)}."
         )
 
     # Determine which sessions to process and group them

qsiprep/cli/run.py

@@ -122,7 +122,7 @@ def main():
 
     config.loggers.workflow.log(
         15,
-        '\n'.join(['QSIPrep config:'] + ['\t\t%s' % s for s in config.dumps().splitlines()]),
+        '\n'.join(['QSIPrep config:'] + [f'\t\t{s}' for s in config.dumps().splitlines()]),
     )
     config.loggers.workflow.log(25, 'QSIPrep started!')
     errno = 1  # Default is error exit unless otherwise set

qsiprep/cli/version.py

@@ -1,13 +1,34 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
 """Version CLI helpers."""
 
-from datetime import datetime
+from contextlib import suppress
+from datetime import datetime, timezone
 from pathlib import Path
 
 import requests
 
-from .. import __version__
+from qsiprep import __version__
 
 RELEASE_EXPIRY_DAYS = 14
 DATE_FMT = '%Y%m%d'
@@ -20,6 +41,7 @@ def check_latest():
     latest = None
     date = None
     outdated = None
+    now = datetime.now(tz=timezone.utc)
     cachefile = Path.home() / '.cache' / 'qsiprep' / 'latest'
     try:
         cachefile.parent.mkdir(parents=True, exist_ok=True)
@@ -29,23 +51,22 @@ def check_latest():
     if cachefile and cachefile.exists():
         try:
             latest, date = cachefile.read_text().split('|')
-        except Exception:
+        except Exception:  # noqa: S110, BLE001
             pass
         else:
             try:
                 latest = Version(latest)
-                date = datetime.strptime(date, DATE_FMT)
+                date = datetime.strptime(date, DATE_FMT).astimezone(timezone.utc)
             except (InvalidVersion, ValueError):
                 latest = None
             else:
-                if abs((datetime.now() - date).days) > RELEASE_EXPIRY_DAYS:
+                if abs((now - date).days) > RELEASE_EXPIRY_DAYS:
                     outdated = True
 
     if latest is None or outdated is True:
-        try:
+        response = None
+        with suppress(Exception):
             response = requests.get(url='https://pypi.org/pypi/qsiprep/json', timeout=1.0)
-        except Exception:
-            response = None
 
         if response and response.status_code == 200:
             versions = [Version(rel) for rel in response.json()['releases'].keys()]
@@ -56,26 +77,23 @@ def check_latest():
             latest = None
 
     if cachefile is not None and latest is not None:
-        try:
-            cachefile.write_text('|'.join(('%s' % latest, datetime.now().strftime(DATE_FMT))))
-        except Exception:
-            pass
+        with suppress(OSError):
+            cachefile.write_text(f'{latest}|{now.strftime(DATE_FMT)}')
 
     return latest
 
 
 def is_flagged():
     """Check whether current version is flagged."""
     # https://raw.githubusercontent.com/pennlinc/qsiprep/master/.versions.json
-    flagged = tuple()
-    try:
+    flagged = ()
+    response = None
+    with suppress(Exception):
         response = requests.get(
             url="""\
 https://raw.githubusercontent.com/pennlinc/qsiprep/master/.versions.json""",
             timeout=1.0,
         )
-    except Exception:
-        response = None
 
     if response and response.status_code == 200:
         flagged = response.json().get('flagged', {}) or {}

qsiprep/cli/workflow.py

@@ -144,7 +144,7 @@ def build_boilerplate(config_file, workflow):
     logs_path = config.execution.output_dir / 'logs'
     boilerplate = workflow.visit_desc()
     citation_files = {
-        ext: logs_path / ('CITATION.%s' % ext) for ext in ('bib', 'tex', 'md', 'html')
+        ext: logs_path / f'CITATION.{ext}' for ext in ('bib', 'tex', 'md', 'html')
     }
 
     if boilerplate:

qsiprep/interfaces/ants.py

@@ -120,14 +120,14 @@ def _list_outputs(self):
             if isinstance(input_image, list):
                 input_image = input_image[0]
             path, fname, ext = split_filename(input_image)
-            affine = '%s/%s%s%d0GenericAffine.mat' % (cwd, prefix, fname, num)
-            warp = '%s/%s%s%d1Warp.nii.gz' % (cwd, prefix, fname, num)
-            inv_warp = '%s/%s%s%d1InverseWarp.nii.gz' % (cwd, prefix, fname, num)
+            affine = f'{cwd}/{prefix}{fname}{num}0GenericAffine.mat'
+            warp = f'{cwd}/{prefix}{fname}{num}1Warp.nii.gz'
+            inv_warp = f'{cwd}/{prefix}{fname}{num}1InverseWarp.nii.gz'
             forward_transforms.append([affine, warp])
             reverse_transforms.append([inv_warp, affine])
 
         templates = [
-            '%s/%stemplate%s.nii.gz' % (cwd, prefix, tnum)
+            f'{cwd}/{prefix}template{tnum}.nii.gz'
             for tnum in range(self.inputs.num_modalities)
         ]
         outputs = self.output_spec().get()

qsiprep/tests/utils.py

@@ -94,10 +94,10 @@ def check_generated_files(output_dir, output_list_file, optional_output_list_fil
     found_files = [os.path.relpath(f, output_dir) for f in found_files]
 
     # Ignore figures
-    found_files = sorted(list(set([f for f in found_files if 'figures' not in f])))
+    found_files = sorted(set([f for f in found_files if 'figures' not in f]))
 
     # Ignore logs
-    found_files = sorted(list(set([f for f in found_files if 'log' not in f.split(os.path.sep)])))
+    found_files = sorted(set([f for f in found_files if 'log' not in f.split(os.path.sep)]))
 
     with open(output_list_file) as fo:
         expected_files = fo.readlines()
@@ -110,8 +110,8 @@ def check_generated_files(output_dir, output_list_file, optional_output_list_fil
             optional_files = [f.rstrip() for f in optional_files]
 
     if sorted(found_files) != sorted(expected_files):
-        expected_not_found = sorted(list(set(expected_files) - set(found_files)))
-        found_not_expected = sorted(list(set(found_files) - set(expected_files)))
+        expected_not_found = sorted(set(expected_files) - set(found_files))
+        found_not_expected = sorted(set(found_files) - set(expected_files))
 
         msg = ''
         if expected_not_found:
@@ -143,7 +143,7 @@ def reorder_expected_outputs():
         with open(expected_output_file) as fo:
             file_contents = fo.readlines()
 
-        file_contents = sorted(list(set(file_contents)))
+        file_contents = sorted(set(file_contents))
 
         with open(expected_output_file, 'w') as fo:
             fo.writelines(file_contents)

qsiprep/viz/utils.py

@@ -93,7 +93,7 @@ def plot_denoise(
         # Find and replace the figure_1 id.
         xml_data = etree.fromstring(svg)
         find_text = etree.ETXPath("//{%s}g[@id='figure_1']" % SVGNS)
-        find_text(xml_data)[0].set('id', '%s-%s-%s' % (div_id, mode, uuid4()))
+        find_text(xml_data)[0].set('id', f'{div_id}-{mode}-{uuid4()}')
 
         svg_fig = SVGFigure()
         svg_fig.root = xml_data
@@ -144,7 +144,7 @@ def plot_acpc(
         # Find and replace the figure_1 id.
         xml_data = etree.fromstring(svg)
         find_text = etree.ETXPath("//{%s}g[@id='figure_1']" % SVGNS)
-        find_text(xml_data)[0].set('id', '%s-%s-%s' % (div_id, mode, uuid4()))
+        find_text(xml_data)[0].set('id', f'{div_id}-{mode}-{uuid4()}')
 
         svg_fig = SVGFigure()
         svg_fig.root = xml_data

qsiprep/workflows/anatomical/__init__.py

@@ -1 +1,3 @@
 from .volume import init_anat_preproc_wf, init_synthseg_wf, init_synthstrip_wf
+
+__all__ = ['init_anat_preproc_wf', 'init_synthseg_wf', 'init_synthstrip_wf']

qsiprep/workflows/fieldmap/__init__.py

@@ -46,3 +46,12 @@
 from .pepolar import init_pepolar_unwarp_wf
 from .syn import init_syn_sdc_wf
 from .unwarp import init_fmap_unwarp_report_wf, init_sdc_unwarp_wf
+
+__all__ = [
+    'init_sdc_wf',
+    'init_drbuddi_wf',
+    'init_pepolar_unwarp_wf',
+    'init_syn_sdc_wf',
+    'init_fmap_unwarp_report_wf',
+    'init_sdc_unwarp_wf',
+]

qsiprep/workflows/fieldmap/base.py

@@ -166,7 +166,7 @@ def init_sdc_wf(fieldmap_info, dwi_meta):
     # PEPOLAR path
     if fieldmap_info['suffix'] in ('epi', 'rpe_series', 'dwi'):
         outputnode.inputs.method = (
-            'PEB/PEPOLAR (phase-encoding based / PE-POLARity): %s' % fieldmap_info['suffix']
+            f'PEB/PEPOLAR (phase-encoding based / PE-POLARity): {fieldmap_info["suffix"]}'
         )
 
         epi_fmaps = fieldmap_info[fieldmap_info['suffix']]
@@ -189,7 +189,7 @@ def init_sdc_wf(fieldmap_info, dwi_meta):
 
     # FIELDMAP path
     if fieldmap_info['suffix'] == 'fieldmap' or fieldmap_info['suffix'].startswith('phase'):
-        outputnode.inputs.method = 'FMB (%s-based)' % fieldmap_info['suffix']
+        outputnode.inputs.method = f'FMB ({fieldmap_info["suffix"]}-based)'
         # Import specific workflows here, so we don't break everything with one
         # unused workflow.
         if fieldmap_info['suffix'] == 'fieldmap':

qsiprep/workflows/fieldmap/drbuddi.py

@@ -152,7 +152,7 @@ def init_drbuddi_wf(
     )
 
     outputnode.inputs.method = (
-        'PEB/PEPOLAR (phase-encoding based / PE-POLARity): %s' % fieldmap_info['suffix']
+        f'PEB/PEPOLAR (phase-encoding based / PE-POLARity): {fieldmap_info["suffix"]}'
     )
 
     gather_drbuddi_inputs = pe.Node(