Merge pull request #139 from DimitriPapadopoulos/ruff

Apply new ruff rules

.maint/update_authors.py

@@ -188,7 +188,7 @@ def zenodo(
     misses = set(miss_creators).intersection(miss_contributors)
     if misses:
         print(
-            "Some people made commits, but are missing in .maint/ " f"files: {', '.join(misses)}",
+            f"Some people made commits, but are missing in .maint/ files: {', '.join(misses)}",
             file=sys.stderr,
         )
 
@@ -268,7 +268,7 @@ def _aslist(value):
 
     if misses:
         print(
-            "Some people made commits, but are missing in .maint/ " f"files: {', '.join(misses)}",
+            f"Some people made commits, but are missing in .maint/ files: {', '.join(misses)}",
             file=sys.stderr,
         )
 

nireports/assembler/misc.py

@@ -144,7 +144,7 @@ def dict2html(indict, table_id):
     if not rows:
         return None
 
-    width = max([len(row) for row in rows])
+    width = max(len(row) for row in rows)
 
     result_str = '<table id="%s" class="table table-sm table-striped">\n' % table_id
     td = "<td{1}>{0}</td>".format

nireports/assembler/report.py

@@ -255,15 +255,11 @@ def __init__(
 
         if bids_filters.get("subject"):
             subject_id = bids_filters["subject"]
-            bids_filters["subject"] = (
-                subject_id[4:] if subject_id.startswith("sub-") else subject_id
-            )
+            bids_filters["subject"] = subject_id.removeprefix("sub-")
 
         if bids_filters.get("session"):
             session_id = bids_filters["session"]
-            bids_filters["session"] = (
-                session_id[4:] if session_id.startswith("ses-") else session_id
-            )
+            bids_filters["session"] = session_id.removeprefix("ses-")
 
         if bids_filters and out_filename == "report.html":
             out_filename = build_path(bids_filters, OUTPUT_NAME_PATTERN)
@@ -493,9 +489,9 @@ def _process_orderings(orderings, hits):
             tuple(bids_file.get_entities().get(k, None) for k in orderings) for bids_file in hits
         }
         # remove the all None member if it exists
-        none_member = tuple([None for k in orderings])
+        none_member = (None,) * len(orderings)
         if none_member in all_value_combos:
-            all_value_combos.remove(tuple([None for k in orderings]))
+            all_value_combos.remove(none_member)
         # see what values exist for each entity
         unique_values = [
             {value[idx] for value in all_value_combos} for idx in range(len(orderings))

nireports/interfaces/__init__.py

@@ -33,9 +33,9 @@
 __all__ = (
     "CompCorVariancePlot",
     "ConfoundsCorrelationPlot",
-    "RaincloudPlot",
     "FMRISummary",
     "PlotContours",
     "PlotMosaic",
     "PlotSpikes",
+    "RaincloudPlot",
 )

nireports/interfaces/nuisance.py

@@ -109,7 +109,7 @@ class _ConfoundsCorrelationPlotInputSpec(BaseInterfaceInputSpec):
     ignore_initial_volumes = traits.Int(
         0,
         usedefault=True,
-        desc="Number of non-steady-state volumes at the beginning of the scan " "to ignore.",
+        desc="Number of non-steady-state volumes at the beginning of the scan to ignore.",
     )
 
 

nireports/interfaces/reporting/masks.py

@@ -59,7 +59,7 @@ def _run_interface(self, runtime):
         if self.generate_report:
             self.inputs.mask = True
 
-        return super(BETRPT, self)._run_interface(runtime)
+        return super()._run_interface(runtime)
 
     def _post_run_hook(self, runtime):
         """generates a report showing slices from each axis of an arbitrary
@@ -76,7 +76,7 @@ def _post_run_hook(self, runtime):
             self._mask_file,
         )
 
-        return super(BETRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _BrainExtractionInputSpecRPT(
@@ -114,7 +114,7 @@ def _post_run_hook(self, runtime):
             self._mask_file,
         )
 
-        return super(BrainExtractionRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _ACompCorInputSpecRPT(nrb._SVGReportCapableInputSpec, confounds.CompCorInputSpec):
@@ -148,7 +148,7 @@ def _post_run_hook(self, runtime):
             self._mask_file,
         )
 
-        return super(ACompCorRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _TCompCorInputSpecRPT(nrb._SVGReportCapableInputSpec, confounds.TCompCorInputSpec):
@@ -184,7 +184,7 @@ def _post_run_hook(self, runtime):
             self.aggregate_outputs(runtime=runtime).high_variance_masks,
         )
 
-        return super(TCompCorRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _SimpleShowMaskInputSpec(nrb._SVGReportCapableInputSpec):
@@ -201,7 +201,7 @@ def _post_run_hook(self, runtime):
         self._seg_files = [self.inputs.mask_file]
         self._masked = True
 
-        return super(SimpleShowMaskRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _ROIsPlotInputSpecRPT(nrb._SVGReportCapableInputSpec):

nireports/interfaces/reporting/registration.py

@@ -67,7 +67,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(ApplyTOPUPRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _FUGUEInputSpecRPT(nrb._SVGReportCapableInputSpec, fsl.preprocess.FUGUEInputSpec):
@@ -94,7 +94,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(FUGUERPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _FLIRTInputSpecRPT(nrb._SVGReportCapableInputSpec, fsl.preprocess.FLIRTInputSpec):
@@ -119,7 +119,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(FLIRTRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _ApplyXFMInputSpecRPT(nrb._SVGReportCapableInputSpec, fsl.preprocess.ApplyXFMInputSpec):
@@ -183,7 +183,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(BBRegisterRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _MRICoregInputSpecRPT(nrb._SVGReportCapableInputSpec, fs.registration.MRICoregInputSpec):
@@ -230,7 +230,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(MRICoregRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _SimpleBeforeAfterInputSpecRPT(nrb._SVGReportCapableInputSpec):
@@ -259,7 +259,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(SimpleBeforeAfterRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _ResampleBeforeAfterInputSpecRPT(_SimpleBeforeAfterInputSpecRPT):
@@ -291,7 +291,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        runtime = super(ResampleBeforeAfterRPT, self)._post_run_hook(runtime)
+        runtime = super()._post_run_hook(runtime)
         _LOGGER.info("Successfully created report (%s)", self._out_report)
         os.unlink(fname)
 

nireports/interfaces/reporting/segmentation.py

@@ -50,7 +50,7 @@ def _run_interface(self, runtime):
         if self.generate_report:
             self.inputs.segments = True
 
-        return super(FASTRPT, self)._run_interface(runtime)
+        return super()._run_interface(runtime)
 
     def _post_run_hook(self, runtime):
         """generates a report showing nine slices, three per axis, of an
@@ -72,7 +72,7 @@ def _post_run_hook(self, runtime):
             outputs.tissue_class_files,
         )
 
-        return super(FASTRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _ReconAllInputSpecRPT(
@@ -104,14 +104,14 @@ def _post_run_hook(self, runtime):
 
         _LOGGER.info("Generating report for ReconAll (subject %s)", outputs.subject_id)
 
-        return super(ReconAllRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _MELODICInputSpecRPT(nrb._SVGReportCapableInputSpec, fsl.model.MELODICInputSpec):
     out_report = File(
         "melodic_reportlet.svg",
         usedefault=True,
-        desc="Filename for the visual" " report generated " "by Nipype.",
+        desc="Filename for the visual report generated by Nipype.",
     )
     report_mask = File(
         desc="Mask used to draw the outline on the reportlet. "
@@ -129,12 +129,12 @@ class MELODICRPT(fsl.MELODIC):
     _out_report = None
 
     def __init__(self, generate_report=False, **kwargs):
-        super(MELODICRPT, self).__init__(**kwargs)
+        super().__init__(**kwargs)
         self.generate_report = generate_report
 
     def _post_run_hook(self, runtime):
         # Run _post_run_hook of super class
-        runtime = super(MELODICRPT, self)._post_run_hook(runtime)
+        runtime = super()._post_run_hook(runtime)
         # leave early if there's nothing to do
         if not self.generate_report:
             return runtime
@@ -163,7 +163,7 @@ def _post_run_hook(self, runtime):
 
     def _list_outputs(self):
         try:
-            outputs = super(MELODICRPT, self)._list_outputs()
+            outputs = super()._list_outputs()
         except NotImplementedError:
             outputs = {}
         if self._out_report is not None:
@@ -187,7 +187,7 @@ class _ICA_AROMAInputSpecRPT(nrb._SVGReportCapableInputSpec, fsl.aroma.ICA_AROMA
     out_report = File(
         "ica_aroma_reportlet.svg",
         usedefault=True,
-        desc="Filename for the visual" " report generated " "by Nipype.",
+        desc="Filename for the visual report generated by Nipype.",
     )
     report_mask = File(
         desc="Mask used to draw the outline on the reportlet. "
@@ -221,4 +221,4 @@ def _post_run_hook(self, runtime):
 
         _LOGGER.info("Generating report for ICA AROMA")
 
-        return super(ICA_AROMARPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)

nireports/reportlets/modality/func.py

@@ -36,14 +36,14 @@ class fMRIPlot:
     """Generates the fMRI Summary Plot."""
 
     __slots__ = (
-        "timeseries",
-        "segments",
-        "tr",
         "confounds",
-        "spikes",
         "nskip",
-        "sort_carpet",
         "paired_carpet",
+        "segments",
+        "sort_carpet",
+        "spikes",
+        "timeseries",
+        "tr",
     )
 
     def __init__(

nireports/reportlets/xca.py

@@ -105,9 +105,7 @@ def plot_melodic_components(
     else:
         mask_img = nb.load(report_mask)
 
-    mask_sl = []
-    for j in range(3):
-        mask_sl.append(transform_to_2d(mask_img.get_fdata(), j))
+    mask_sl = [transform_to_2d(mask_img.get_fdata(), j) for j in range(3)]
 
     timeseries = np.loadtxt(os.path.join(melodic_dir, "melodic_mix"))
     power = np.loadtxt(os.path.join(melodic_dir, "melodic_FTmix"))

nireports/tools/timeseries.py

@@ -73,7 +73,7 @@ def cifti_timeseries(dataset):
     }
     seg = {label: [] for label in list(labels.values()) + ["Other"]}
     for bm in matrix.get_index_map(1).brain_models:
-        label = "Other" if bm.brain_structure not in labels else labels[bm.brain_structure]
+        label = labels.get(bm.brain_structure, "Other")
         seg[label] += list(range(bm.index_offset, bm.index_offset + bm.index_count))
 
     return dataset.get_fdata(dtype="float32").T, seg