sty: run ruff

mriqc/cli/parser.py

@@ -479,7 +479,6 @@ def _bids_filter(value):
 
 def parse_args(args=None, namespace=None):
     """Parse args and run further checks on the command line."""
-    from contextlib import suppress
     from json import loads
     from logging import DEBUG, FileHandler
     from pathlib import Path
@@ -555,10 +554,9 @@ def parse_args(args=None, namespace=None):
     if output_dir == bids_dir:
         parser.error(
             'The selected output folder is the same as the input BIDS folder. '
-            'Please modify the output path (suggestion: %s).'
-            % bids_dir
+            f'Please modify the output path (suggestion: {bids_dir}).'
             / 'derivatives'
-            / ('mriqc-%s' % version.split('+')[0])
+            / ('mriqc-{}'.format(version.split('+')[0]))
         )
 
     if bids_dir in work_dir.parents:

mriqc/interfaces/webapi.py

@@ -169,15 +169,17 @@ def _run_interface(self, runtime):
             config.loggers.interface.info(messages.QC_UPLOAD_COMPLETE)
             return runtime
 
-        errmsg = '\n'.join([
-            'Unsuccessful upload.',
-            f'Server response status {response.status_code}:',
-            response.text,
-            '',
-            '',
-            'Payload:',
-            json.dumps(payload, indent=2),
-        ])
+        errmsg = '\n'.join(
+            [
+                'Unsuccessful upload.',
+                f'Server response status {response.status_code}:',
+                response.text,
+                '',
+                '',
+                'Payload:',
+                json.dumps(payload, indent=2),
+            ]
+        )
         config.loggers.interface.warning(errmsg)
         if self.inputs.strict:
             raise RuntimeError(errmsg)
@@ -227,11 +229,7 @@ def upload_qc_metrics(
     data = deepcopy(in_data)
 
     # Check modality
-    modality = (
-        meta.get('modality', None)
-        or meta.get('suffix', None)
-        or modality
-    )
+    modality = meta.get('modality', None) or meta.get('suffix', None) or modality
     if modality not in ('T1w', 'bold', 'T2w'):
         errmsg = (
             'Submitting to MRIQCWebAPI: image modality should be "bold", "T1w", or "T2w", '
@@ -244,9 +242,7 @@ def upload_qc_metrics(
 
     # Check for fields with appended _id
     bids_meta_names = {k: k.replace('_id', '') for k in META_WHITELIST if k.endswith('_id')}
-    data['bids_meta'].update({
-        k: meta[v] for k, v in bids_meta_names.items() if v in meta
-    })
+    data['bids_meta'].update({k: meta[v] for k, v in bids_meta_names.items() if v in meta})
 
     # For compatibility with WebAPI. Should be rolled back to int
     if (run_id := data['bids_meta'].get('run_id', None)) is not None:

mriqc/workflows/anatomical/base.py

@@ -53,6 +53,7 @@
 """
 
 from itertools import chain
+
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
@@ -94,18 +95,24 @@ def anat_qc_workflow(name='anatMRIQC'):
     #     config.workflow.biggest_file_gb['t1w'],
     #     config.workflow.biggest_file_gb['t2w'],
     # )
-    dataset = list(chain(
-        config.workflow.inputs.get('t1w', []),
-        config.workflow.inputs.get('t2w', []),
-    ))
-    metadata = list(chain(
-        config.workflow.inputs_metadata.get('t1w', []),
-        config.workflow.inputs_metadata.get('t2w', []),
-    ))
-    entities = list(chain(
-        config.workflow.inputs_entities.get('t1w', []),
-        config.workflow.inputs_entities.get('t2w', []),
-    ))
+    dataset = list(
+        chain(
+            config.workflow.inputs.get('t1w', []),
+            config.workflow.inputs.get('t2w', []),
+        )
+    )
+    metadata = list(
+        chain(
+            config.workflow.inputs_metadata.get('t1w', []),
+            config.workflow.inputs_metadata.get('t2w', []),
+        )
+    )
+    entities = list(
+        chain(
+            config.workflow.inputs_entities.get('t1w', []),
+            config.workflow.inputs_entities.get('t2w', []),
+        )
+    )
     message = BUILDING_WORKFLOW.format(
         modality='anatomical',
         detail=f'for {len(dataset)} NIfTI files.',
@@ -117,9 +124,12 @@ def anat_qc_workflow(name='anatMRIQC'):
 
     # Define workflow, inputs and outputs
     # 0. Get data
-    inputnode = pe.Node(niu.IdentityInterface(
-        fields=['in_file', 'metadata', 'entities'],
-    ), name='inputnode')
+    inputnode = pe.Node(
+        niu.IdentityInterface(
+            fields=['in_file', 'metadata', 'entities'],
+        ),
+        name='inputnode',
+    )
     inputnode.synchronize = True  # Do not test combinations of iterables
     inputnode.iterables = [
         ('in_file', dataset),

mriqc/workflows/diffusion/base.py

@@ -98,9 +98,12 @@ def dmri_qc_workflow(name='dwiMRIQC'):
     # Define workflow, inputs and outputs
     # 0. Get data, put it in RAS orientation
     workflow = pe.Workflow(name=name)
-    inputnode = pe.Node(niu.IdentityInterface(
-        fields=['in_file', 'metadata', 'entities'],
-    ), name='inputnode')
+    inputnode = pe.Node(
+        niu.IdentityInterface(
+            fields=['in_file', 'metadata', 'entities'],
+        ),
+        name='inputnode',
+    )
     inputnode.synchronize = True  # Do not test combinations of iterables
     inputnode.iterables = [
         ('in_file', dataset),

mriqc/workflows/functional/base.py

@@ -43,7 +43,6 @@
 This workflow is orchestrated by :py:func:`fmri_qc_workflow`.
 """
 
-
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 from niworkflows.utils.connections import pop_file as _pop
@@ -86,9 +85,12 @@ def fmri_qc_workflow(name='funcMRIQC'):
     # Define workflow, inputs and outputs
     # 0. Get data, put it in RAS orientation
     workflow = pe.Workflow(name=name)
-    inputnode = pe.Node(niu.IdentityInterface(
-        fields=['in_file', 'metadata', 'entities'],
-    ), name='inputnode')
+    inputnode = pe.Node(
+        niu.IdentityInterface(
+            fields=['in_file', 'metadata', 'entities'],
+        ),
+        name='inputnode',
+    )
     inputnode.synchronize = True  # Do not test combinations of iterables
     inputnode.iterables = [
         ('in_file', dataset),

mriqc/workflows/functional/output.py

@@ -49,7 +49,7 @@ def init_func_report_wf(name='func_report_wf'):
     # from mriqc.interfaces.reports import IndividualReport
 
     verbose = config.execution.verbose_reports
-    mem_gb = config.workflow.biggest_file_gb["bold"]
+    mem_gb = config.workflow.biggest_file_gb['bold']
     reportlets_dir = config.execution.work_dir / 'reportlets'
 
     workflow = pe.Workflow(name=name)