STY: black; adapt flake8 rules

Author: effigies

.flake8

@@ -3,6 +3,7 @@ max-line-length = 99
 doctests = False
 exclude=*build/
 ignore =
+    E203
     W503
 per-file-ignores =
     **/__init__.py : F401

smriprep/__about__.py

@@ -26,9 +26,7 @@
 
 from ._version import __version__
 
-__copyright__ = (
-    "Copyright 2019, Center for Reproducible Neuroscience, Stanford University"
-)
+__copyright__ = "Copyright 2019, Center for Reproducible Neuroscience, Stanford University"
 __credits__ = [
     "Oscar Esteban",
     "Chris Gorgolewski",

smriprep/cli/run.py

@@ -37,10 +37,7 @@ def check_deps(workflow):
     return sorted(
         (node.interface.__class__.__name__, node.interface._cmd)
         for node in workflow._get_all_nodes()
-        if (
-            hasattr(node.interface, "_cmd")
-            and which(node.interface._cmd.split()[0]) is None
-        )
+        if (hasattr(node.interface, "_cmd") and which(node.interface._cmd.split()[0]) is None)
     )
 
 
@@ -85,9 +82,7 @@ def get_parser():
     )
 
     # optional arguments
-    parser.add_argument(
-        "--version", action="version", version=f"smriprep v{__version__}"
-    )
+    parser.add_argument("--version", action="version", version=f"smriprep v{__version__}")
 
     g_bids = parser.add_argument_group("Options for filtering BIDS queries")
     g_bids.add_argument(
@@ -137,18 +132,15 @@ def get_parser():
     g_perfm.add_argument(
         "--low-mem",
         action="store_true",
-        help="attempt to reduce memory usage (will increase disk usage "
-        "in working directory)",
+        help="attempt to reduce memory usage (will increase disk usage " "in working directory)",
     )
     g_perfm.add_argument(
         "--use-plugin",
         action="store",
         default=None,
         help="nipype plugin configuration file",
     )
-    g_perfm.add_argument(
-        "--boilerplate", action="store_true", help="generate boilerplate only"
-    )
+    g_perfm.add_argument("--boilerplate", action="store_true", help="generate boilerplate only")
     g_perfm.add_argument(
         "-v",
         "--verbose",
@@ -276,8 +268,7 @@ def get_parser():
         "--stop-on-first-crash",
         action="store_true",
         default=False,
-        help="Force stopping on first crash, even if a work directory"
-        " was specified.",
+        help="Force stopping on first crash, even if a work directory" " was specified.",
     )
     g_other.add_argument(
         "--notrack",
@@ -395,22 +386,16 @@ def _warn_redirect(message, category, filename, lineno, file=None, line=None):
             from niworkflows.utils.misc import _copy_any
 
             dseg_tsv = str(api.get("fsaverage", suffix="dseg", extension=[".tsv"]))
-            _copy_any(
-                dseg_tsv, str(Path(output_dir) / "smriprep" / "desc-aseg_dseg.tsv")
-            )
-            _copy_any(
-                dseg_tsv, str(Path(output_dir) / "smriprep" / "desc-aparcaseg_dseg.tsv")
-            )
+            _copy_any(dseg_tsv, str(Path(output_dir) / "smriprep" / "desc-aseg_dseg.tsv"))
+            _copy_any(dseg_tsv, str(Path(output_dir) / "smriprep" / "desc-aparcaseg_dseg.tsv"))
         logger.log(25, "sMRIPrep finished without errors")
     finally:
         from niworkflows.reports import generate_reports
         from ..utils.bids import write_derivative_description, write_bidsignore
 
         logger.log(25, "Writing reports for participants: %s", ", ".join(subject_list))
         # Generate reports phase
-        errno += generate_reports(
-            subject_list, output_dir, run_uuid, packagename="smriprep"
-        )
+        errno += generate_reports(subject_list, output_dir, run_uuid, packagename="smriprep")
         write_derivative_description(bids_dir, str(Path(output_dir) / "smriprep"))
         write_bidsignore(Path(output_dir) / "smriprep")
     sys.exit(int(errno > 0))
@@ -458,13 +443,9 @@ def build_workflow(opts, retval):
     # First check that bids_dir looks like a BIDS folder
     bids_dir = opts.bids_dir.resolve()
     layout = BIDSLayout(str(bids_dir), validate=False)
-    subject_list = collect_participants(
-        layout, participant_label=opts.participant_label
-    )
+    subject_list = collect_participants(layout, participant_label=opts.participant_label)
 
-    bids_filters = (
-        json.loads(opts.bids_filter_file.read_text()) if opts.bids_filter_file else None
-    )
+    bids_filters = json.loads(opts.bids_filter_file.read_text()) if opts.bids_filter_file else None
 
     # Load base plugin_settings from file if --use-plugin
     if opts.use_plugin is not None:
@@ -552,9 +533,7 @@ def build_workflow(opts, retval):
     if opts.reports_only:
         from niworkflows.reports import generate_reports
 
-        logger.log(
-            25, "Running --reports-only on participants %s", ", ".join(subject_list)
-        )
+        logger.log(25, "Running --reports-only on participants %s", ", ".join(subject_list))
         if opts.run_uuid is not None:
             run_uuid = opts.run_uuid
         retval["return_code"] = generate_reports(
@@ -644,9 +623,7 @@ def build_workflow(opts, retval):
     except (FileNotFoundError, CalledProcessError, TimeoutExpired):
         logger.warning("Could not generate CITATION.tex file:\n%s", " ".join(cmd))
     else:
-        copyfile(
-            pkgrf("smriprep", "data/boilerplate.bib"), str(log_dir / "CITATION.bib")
-        )
+        copyfile(pkgrf("smriprep", "data/boilerplate.bib"), str(log_dir / "CITATION.bib"))
     return retval
 
 

smriprep/interfaces/cifti.py

@@ -16,9 +16,7 @@ class _GenerateDScalarInputSpec(TraitedSpec):
         usedefault=True,
         desc="CIFTI surface target space",
     )
-    grayordinates = traits.Enum(
-        "91k", "170k", usedefault=True, desc="Final CIFTI grayordinates"
-    )
+    grayordinates = traits.Enum("91k", "170k", usedefault=True, desc="Final CIFTI grayordinates")
     scalar_surfs = traits.List(
         File(exists=True),
         mandatory=True,
@@ -36,11 +34,11 @@ class GenerateDScalar(SimpleInterface):
     """
     Generate a HCP-style CIFTI-2 image from scalar surface files.
     """
+
     input_spec = _GenerateDScalarInputSpec
     output_spec = _GenerateDScalarOutputSpec
 
     def _run_interface(self, runtime):
-
         surface_labels, metadata = _prepare_cifti(self.inputs.grayordinates)
         self._results["out_file"] = _create_cifti_image(
             self.inputs.scalar_surfs,
@@ -87,14 +85,14 @@ def _prepare_cifti(grayordinates: str) -> ty.Tuple[list, dict]:
             "surface-den": "32k",
             "tf-res": "02",
             "grayords": "91,282",
-            "res-mm": "2mm"
+            "res-mm": "2mm",
         },
         "170k": {
             "surface-den": "59k",
             "tf-res": "06",
             "grayords": "170,494",
-            "res-mm": "1.6mm"
-        }
+            "res-mm": "1.6mm",
+        },
     }
     if grayordinates not in grayord_key:
         raise NotImplementedError(f"Grayordinates {grayordinates} is not supported.")
@@ -129,7 +127,7 @@ def _prepare_cifti(grayordinates: str) -> ty.Tuple[list, dict]:
         "SpatialReference": {
             "CIFTI_STRUCTURE_CORTEX_LEFT": surfaces_url % "L",
             "CIFTI_STRUCTURE_CORTEX_RIGHT": surfaces_url % "R",
-        }
+        },
     }
     return surface_labels, metadata
 

smriprep/interfaces/freesurfer.py

@@ -263,6 +263,7 @@ class MRIsConvertData(fs.utils.MRIsConvert):
     Wraps mris_convert to automatically select the correct ?h.white surface if
     passed a file from the subject's surf/ directory
     """
+
     input_spec = _MRIsConvertDataInputSpec
 
     def _gen_filename(self, name):

smriprep/interfaces/templateflow.py

@@ -39,12 +39,8 @@
 class _TemplateFlowSelectInputSpec(BaseInterfaceInputSpec):
     template = traits.Str("MNI152NLin2009cAsym", mandatory=True, desc="Template ID")
     atlas = InputMultiObject(traits.Str, desc="Specify an atlas")
-    cohort = InputMultiObject(
-        traits.Either(traits.Str, traits.Int), desc="Specify a cohort"
-    )
-    resolution = InputMultiObject(
-        traits.Int, desc="Specify a template resolution index"
-    )
+    cohort = InputMultiObject(traits.Either(traits.Str, traits.Int), desc="Specify a cohort")
+    resolution = InputMultiObject(traits.Int, desc="Specify a template resolution index")
     template_spec = traits.DictStrAny(
         {"atlas": None, "cohort": None}, usedefault=True, desc="Template specifications"
     )
@@ -135,10 +131,9 @@ def _run_interface(self, runtime):
 
         self._results["t1w_file"] = tf.get(name[0], desc=None, suffix="T1w", **specs)
 
-        self._results["brain_mask"] = (
-            tf.get(name[0], desc="brain", suffix="mask", **specs)
-            or tf.get(name[0], label="brain", suffix="mask", **specs)
-        )
+        self._results["brain_mask"] = tf.get(
+            name[0], desc="brain", suffix="mask", **specs
+        ) or tf.get(name[0], label="brain", suffix="mask", **specs)
         return runtime
 
 

smriprep/utils/bids.py

@@ -101,9 +101,7 @@ def _normalize_q(query, space=None):
             query["to"] = output_spaces
         return query
 
-    queries = [
-        _normalize_q(q, space=None) for q in spec["queries"]["baseline"].values()
-    ]
+    queries = [_normalize_q(q, space=None) for q in spec["queries"]["baseline"].values()]
 
     queries += [
         _normalize_q(q, space=s)

smriprep/workflows/anatomical.py

@@ -232,9 +232,7 @@ def init_anat_preproc_wf(
     )
 
     inputnode = pe.Node(
-        niu.IdentityInterface(
-            fields=["t1w", "t2w", "roi", "flair", "subjects_dir", "subject_id"]
-        ),
+        niu.IdentityInterface(fields=["t1w", "t2w", "roi", "flair", "subjects_dir", "subject_id"]),
         name="inputnode",
     )
 
@@ -263,27 +261,22 @@ def init_anat_preproc_wf(
     if existing_derivatives is not None:
         LOGGER.log(
             25,
-            "Anatomical workflow will reuse prior derivatives found in the "
-            "output folder (%s).",
+            "Anatomical workflow will reuse prior derivatives found in the output folder (%s).",
             output_dir,
         )
         desc += """
 Anatomical preprocessing was reused from previously existing derivative objects.\n"""
         workflow.__desc__ = desc
 
         templates = existing_derivatives.pop("template")
-        templatesource = pe.Node(
-            niu.IdentityInterface(fields=["template"]), name="templatesource"
-        )
+        templatesource = pe.Node(niu.IdentityInterface(fields=["template"]), name="templatesource")
         templatesource.iterables = [("template", templates)]
         outputnode.inputs.template = templates
 
         for field, value in existing_derivatives.items():
             setattr(outputnode.inputs, field, value)
 
-        anat_reports_wf.inputs.inputnode.source_file = [
-            existing_derivatives["t1w_preproc"]
-        ]
+        anat_reports_wf.inputs.inputnode.source_file = [existing_derivatives["t1w_preproc"]]
 
         stdselect = pe.Node(
             KeySelect(fields=["std_preproc", "std_mask"], keys=templates),
@@ -322,11 +315,7 @@ def init_anat_preproc_wf(
     desc += """\
 with `N4BiasFieldCorrection` [@n4], distributed with ANTs {ants_ver} \
 [@ants, RRID:SCR_004757]"""
-    desc += (
-        ".\n"
-        if num_t1w > 1
-        else ", and used as T1w-reference throughout the workflow.\n"
-    )
+    desc += ".\n" if num_t1w > 1 else ", and used as T1w-reference throughout the workflow.\n"
 
     desc += """\
 The T1w-reference was then skull-stripped with a *Nipype* implementation of
@@ -357,9 +346,7 @@ def init_anat_preproc_wf(
         contrast="T1w",
     )
 
-    anat_validate = pe.Node(
-        ValidateImage(), name="anat_validate", run_without_submitting=True
-    )
+    anat_validate = pe.Node(ValidateImage(), name="anat_validate", run_without_submitting=True)
 
     # 2. Brain-extraction and INU (bias field) correction.
     if skull_strip_mode == "auto":

smriprep/workflows/base.py

@@ -193,9 +193,7 @@ def init_smriprep_wf(
         for node in single_subject_wf._get_all_nodes():
             node.config = deepcopy(single_subject_wf.config)
         if freesurfer:
-            smriprep_wf.connect(
-                fsdir, "subjects_dir", single_subject_wf, "inputnode.subjects_dir"
-            )
+            smriprep_wf.connect(fsdir, "subjects_dir", single_subject_wf, "inputnode.subjects_dir")
         else:
             smriprep_wf.add_nodes([single_subject_wf])
 
@@ -360,13 +358,9 @@ def init_single_subject_wf(
             Path(output_dir) / "smriprep", subject_id, std_spaces, freesurfer
         )
 
-    inputnode = pe.Node(
-        niu.IdentityInterface(fields=["subjects_dir"]), name="inputnode"
-    )
+    inputnode = pe.Node(niu.IdentityInterface(fields=["subjects_dir"]), name="inputnode")
 
-    bidssrc = pe.Node(
-        BIDSDataGrabber(subject_data=subject_data, anat_only=True), name="bidssrc"
-    )
+    bidssrc = pe.Node(BIDSDataGrabber(subject_data=subject_data, anat_only=True), name="bidssrc")
 
     bids_info = pe.Node(
         BIDSInfo(bids_dir=layout.root), name="bids_info", run_without_submitting=True

smriprep/workflows/norm.py

@@ -137,9 +137,7 @@ def init_anat_norm_wf(
             ants_ver=ANTsInfo.version() or "(version unknown)",
             targets="%s standard space%s"
             % (
-                defaultdict(
-                    "several".format, {1: "one", 2: "two", 3: "three", 4: "four"}
-                )[ntpls],
+                defaultdict("several".format, {1: "one", 2: "two", 3: "three", 4: "four"})[ntpls],
                 "s" * (ntpls != 1),
             ),
             targets_id=", ".join(templates),
@@ -230,9 +228,7 @@ def init_anat_norm_wf(
     std_dseg = pe.Node(ApplyTransforms(interpolation="MultiLabel"), name="std_dseg")
 
     std_tpms = pe.MapNode(
-        ApplyTransforms(
-            dimension=3, default_value=0, float=True, interpolation="Gaussian"
-        ),
+        ApplyTransforms(dimension=3, default_value=0, float=True, interpolation="Gaussian"),
         iterfield=["input_image"],
         name="std_tpms",
     )